Tuesday, November 05, 2024

 

Breakthrough study shows coral reefs will transform but can persist, if carbon is curbed



University of Hawaii at Manoa
Hawaiian coral reef 

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Hawaiian coral reefs are teeming with life. 

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Credit: Andre Seale.




In a breakthrough study published this week in Proceedings of the National Academy of Sciences, researchers in the Hawaiʻi Institute of Marine Biology (HIMB) at the University of Hawai‘i (UH) at Mānoa have shown that, contrary to most projections, coral reefs are not inevitably doomed, but have the potential to persist and adapt over time, if carbon emissions are curbed and local stressors are addressed. This work was conducted by the Toonen-Bowen “ToBo” Lab, with partners across UH Mānoa and The Ohio State University.

In an island-based laboratory adjacent to the coral reefs they study, HIMB researchers created 40 experimental systems known as “mesocosms,” which mimic the diversity and environment of a coral reef in the wild. The mesocosms included eight of the most common Hawaiian coral species, reef sand, rubble, and a menagerie of creatures which helped represent one of the most diverse ecosystems on the planet. For two years, the team exposed the mesocosms to different scenarios of higher temperature, higher acidity, or a combination of both ocean stressors to see how the reef communities would react to future climate scenarios.

“We included the eight most common coral species in Hawai‘i, which constitute about 95% of the coral cover on Hawaiian reefs, and many of the most common coral types across the Pacific and Indian Oceans,” explains HIMB post-doctoral researcher and lead author of the study, Christopher Jury. “By understanding how these species respond to climate change, we should have a better understanding of how Hawaiian reefs and other Indo-Pacific reefs will change over time, and how to better allocate resources as well as plan for the future.”

Reef structures form over time through a process known as “calcification” where individual coral organisms—or polyps—build their own skeletons by secreting a salt known as calcium carbonate, which becomes limestone. Coral reefs are naturally eroded by a variety of species, and if the balance between reef producers and reef eroders shifts, coral reefs could disappear, and the huge diversity of species which live on coral reefs would have nowhere to live.

As the ToBo lab research team controlled levels of temperature and acidity in the mesocosms, they measured the calcification responses of the eight species of coral, the reef communities, and the biodiversity of these systems. Their findings were entirely unexpected.

“These experimental reef communities persisted as new reef communities rather than collapsing,” shares Jury. “This was a very surprising result, since almost all projections of reef futures suggest that the corals should have almost entirely died, the reef communities should have experienced net carbonate dissolution, and reef biodiversity should have collapsed. None of those things happened in this study.”

Their results are unique, and so is the ToBo lab’s approach to how they study their subject.

“Rather than focusing on just one or two species in isolation, we included the entire complement of reef species from microbes, to algae, invertebrates, and fish, under realistic conditions they would experience in nature,” notes Rob Toonen, co-director of the UH Marine Biology Graduate Program, HIMB Professor and Ruth Gates Endowed Chair, and co-senior author of the study. “These more realistic mesocosm experiments help us to understand how coral reefs will change over time.”

These findings suggest that coral conservation in a changing world is possible, but urgent action is essential for these unique ecosystems to persist.

“Reefs are not inevitably doomed,” emphasizes Jury. “The recognition that coral reefs are not doomed if we take appropriate action on climate change and local stressors reinforces the need to accomplish these goals. Under potential future ocean warming and acidification, coral reef communities will change substantially, but are unlikely to collapse if global change is limited to Paris Climate Agreement targets and local stressors are adequately addressed.”

Coral reefs are among the most diverse ecosystems on the planet, and they support hundreds of millions of people around the world. As our planet rapidly changes in unprecedented ways, coral reefs are under severe threat due to ocean warming and acidification. This study shows that with effective and timely climate change mitigation measures in place, coral reefs will continue to change, but global reef collapse may still be avoidable.


Hawai‘i Institute of Marine Biology (HIMB) is located on Moku o Lo‘e, a storied islet in Kāne‘ohe Bay on the Hawaiian island of O‘ahu. HIMB’s unique location provides researchers with unparalleled, immediate access to their research subject. In this image, a research diver encounters Porites evermanni


  

Caption

A mesocosm system at the Hawai‘i Institute of Marine Biology enables researchers to carefully control and study the impact of ocean warming and acidification while preserving realistic conditions, like those on nearby reefs. 

Credit

Mariana Rocha De Souza

Deep-sea corals are home to previously unknown bacteria with extremely small genomes



Microbes lack ability to break down carbohydrates – species belong to new family of marine bacteria.



Peer-Reviewed Publication

University of Oldenburg

Callogorgia delta 

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The deep-sea coral Callogorgia delta is often found in the Gulf of Mexico near cold seeps. The pink-coloured brittle stars are probably useful for the corals. The photo was taken at a depth of 439 metres.

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Credit: ECOGIG consortium




A German-American research team led by Professor Iliana Baums from the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB) and Dr Samuel Vohsen from Lehigh University in the US has discovered two highly unusual bacterial species in the tissue of two deep-sea corals from the Gulf of Mexico. These previously unknown coral symbionts have an extremely reduced genome and lack the ability to obtain energy from carbohydrates, the team reports in an article published in the scientific journal Nature Communications. “These species are impressive examples of how few genes are needed for a functional organism,” says Baums, who co-authored the paper.

The research team studied several colonies of two soft coral species, Callogorgia delta and Callogorgia Americana, which are found in the Gulf of Mexico at depths ranging from 300 to 900 metres, where it is completely dark. The researchers discovered two previously unknown, closely related species from the mollicutes class of bacteria. Mollicutes often live as parasites either on or in the cells of plants, animals and humans, and in some cases cause diseases. On the basis of their genetic analyses, the researchers propose a new family called Oceanoplasmataceae, to which the two bacteria are to be assigned.

Further investigations revealed that the bacteria are the dominant symbionts of these corals and live in a gelatinous layer of tissue that forms part of their immune defence system and transports nutrients. One of the species (Oceanoplasma callogorgiae) contains only 359 genes which encode proteins for various metabolic functions. The other (Thalassoplasma callogorgiae) has 385 protein-coding genes. By comparison, the intestinal bacterium Escherichia coli contains more than 4,000 such genes, while humans have around 21,000 of them.

Amino acid is their only source of energy

The question of how the metabolism of the two newly discovered microbes can function with such a reduced genome remains a mystery to the researchers: “These bacteria don’t even carry genes for normal carbohydrate metabolism, in other words, for obtaining energy from carbohydrates – something that basically every living organism has,” Baums explains. According to the research to date, their only source of energy is the amino acid arginine, which is provided by the host coral. “But the breakdown of this amino acid provides only tiny amounts of energy. It is astonishing that the bacteria can survive on so little,” says Vohsen. The bacteria also obtain other essential nutrients from their host.

It remains unclear whether the microbes are purely parasites, or whether the corals benefit in some way from their symbionts. According to the scientists’ genetic analysis, the two bacterial species use various defence mechanisms called CRISPR/Cas systems to remove foreign DNA. These systems are also used in biotechnology to edit genes. The researchers hypothesise that these mechanisms may also be useful to the host corals, helping them to fend off pathogens. Another possibility is that the bacteria provide nitrogen to their host when they break down arginine.

For Baums, whose research focuses on both the ecology and evolution of corals, the symbionts offer an opportunity to gain further insights into the history of this diverse group of animals. “I always find it amazing that corals can colonise so many different habitats despite being very simple animals in terms of their genetic blueprint,” says the researcher. Symbionts are crucial for the ability of corals to adapt to different environmental conditions, she explains: “They provide metabolic functions that the corals themselves lack.” For example, tropical corals, which live in shallow, light-flooded waters, rely on photosynthetic algae to provide them with food and energy. Cold-water corals, many of which live in the dark and nutrient-poor deep sea, are thought to rely on bacteria to convert nutrients or obtain energy from chemical compounds.

Baums, an evolutionary ecologist and coral expert, conducts research at the Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB) and holds a joint professorship at the University of Oldenburg and the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research in Bremerhaven. In addition to Professor Baums and Dr Vohsen, scientists from the Max Planck Institute for Marine Microbiology in Bremen, Kiel University and Pennsylvania State University in the US were also involved in the current study.

This deep-sea community was discovered in 2016 at a depth of 624 metres in the Mississippi Canyon, Gulf of Mexico. The coral Callogorgia delta is accompanied by tubeworms and a clam.

Credit

ECOGIG Consortium

 

National Science Foundation supports Hoda Eldardiry's research to enhance AI ethics education



Eldardiry and her team will develop practical competencies that enable students to translate ethical principles into concrete decision-making in artificial intellingence system design.



Virginia Tech

Hoda Eldardiry. 

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Hoda Eldardiry.

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Credit: Photo by Peter Means for Virginia Tech.





As artificial intelligence (AI) increasingly affects peoples’ everyday lives, Hoda Eldardiry, associate professor in the Department of Computer Science and core faculty at the Sanghani Center for Artificial Intelligence and Data Analytics, is conducting research in engineering and computing education that will help students in majors such as computer science, computer engineering, and data science bridge the gap between the classroom and the job site.

Recently, she received a $349,360 grant from the National Science Foundation’s (NSF) Engineering Education program to support her work. 

“We want to ensure that every student is adequately prepared to not only confront but act on the challenges that new AI technologies pose to humans and society,” said Eldardiry. 

Her team for the estimated three-year project includes co-principal investigators Qin Zhu, associate professor, and Dayoung Kim, assistant professor, both in the Department of Engineering Education; James Weichert, a master’s degree student in computer science advised by Eldardiry; and two Ph.D. students in engineering education, Yixiang Sun advised by Zhu and Emad Ali advised by Kim. 

Eldardiry said their research — which includes AI ethics issues related to autonomous vehicles, privacy, and bias — differs from theoretical AI ethics research because their approach is to improve AI ethics education from the perspective of industry professionals currently working in AI and AI policy. 

They have already interviewed a group of these professionals to get a better sense of how they view the AI policy landscape and more crucially, what skills they need to apply their technical backgrounds to real-world problems involving the ethical use of AI. With this project, they aim to engage practicing AI engineers to better understand how they translate AI ethics principles into practical applications when designing AI systems.

“We call these skills ‘translational competencies,’ and this is really the heart of our research,” Eldardiry said. “A curriculum shaped by this research can help cultivate the competencies needed for students to apply often vague ethical principles to concrete decision-making in the development and use of AI systems."

In reviewing current curricula, Eldardiry said, one ethical concern that arises with more and more powerful AI tools and vast amounts of data is the privacy of user data. This is especially important when AI technologies can leverage that user data to find connections or identify users in a way that humans cannot. The social media platform TikTok is a good example of this because it collects so much data about what videos you are watching and is, therefore, really good at triangulating what your interests are and perhaps more personal things like your political ideology or sexual orientation.  

“When we talk about privacy in a computer science ethics class, it is brought up as a fundamental ethical principle, but then the conversation normally stops there. Our current curriculum does not go further into depth about what specific kind of privacy we want to guarantee or the technical details required to build a system that does actually preserve user privacy,” she said. “This is seen as an ‘advanced topic’ that is outside the scope of an undergraduate or even graduate ethics course, but the reality is that these details might be key when a student graduates and is in charge of using or developing an AI system.” 

Another example is self-driving cars and how they should be programmed to prioritize human life. While it is easy to say that the car should avoid any harm to humans all the time, there are inevitably situations where that is not possible and the car must make a split-second decision. So what should the car be programmed to do in that case? Perhaps there is no single “correct” answer, but this is also not an unrealistic scenario to be talking about in an ethics class, Eldardiry said.

“Ultimately, we would like to see a paradigm shift in AI ethics education away from a hands-off approach where students are not engaging with the course material to a very hands-on approach where students are taught and expected to apply the ethical principles they learn or develop to their engineering work,” said Eldardiry. “These translational skills are something that future AI engineers will undoubtedly need in their toolkit and will form a growing part of their job expectations as even the development of AI programs becomes more automated."

Despite its impressive output, generative AI doesn’t have a coherent understanding of the world



Researchers show that even the best-performing large language models don’t form a true model of the world and its rules, and can thus fail unexpectedly on similar tasks.


Massachusetts Institute of Technology





CAMBRIDGE, MA – Large language models can do impressive things, like write poetry or generate viable computer programs, even though these models are trained to predict words that come next in a piece of text.

Such surprising capabilities can make it seem like the models are implicitly learning some general truths about the world.

But that isn’t necessarily the case, according to a new study. The researchers found that a popular type of generative AI model can provide turn-by-turn driving directions in New York City with near-perfect accuracy — without having formed an accurate internal map of the city.

Despite the model’s uncanny ability to navigate effectively, when the researchers closed some streets and added detours, its performance plummeted.

When they dug deeper, the researchers found that the New York maps the model implicitly generated had many nonexistent streets curving between the grid and connecting far away intersections.

This could have serious implications for generative AI models deployed in the real world, since a model that seems to be performing well in one context might break down if the task or environment slightly changes.

“One hope is that, because LLMs can accomplish all these amazing things in language, maybe we could use these same tools in other parts of science, as well. But the question of whether LLMs are learning coherent world models is very important if we want to use these techniques to make new discoveries,” says senior author Ashesh Rambachan, assistant professor of economics and a principal investigator in the MIT Laboratory for Information and Decision Systems (LIDS).

Rambachan is joined on a paper about the work by lead author Keyon Vafa, a postdoc at Harvard University; Justin Y. Chen, an electrical engineering and computer science (EECS) graduate student at MIT; Jon Kleinberg, Tisch University Professor of Computer Science and Information Science at Cornell University; and Sendhil Mullainathan, an MIT professor in the departments of EECS and of Economics, and a member of LIDS. The research will be presented at the Conference on Neural Information Processing Systems.

New metrics

The researchers focused on a type of generative AI model known as a transformer, which forms the backbone of LLMs like GPT-4. Transformers are trained on a massive amount of language-based data to predict the next token in a sequence, such as the next word in a sentence.

But if scientists want to determine whether an LLM has formed an accurate model of the world, measuring the accuracy of its predictions doesn’t go far enough, the researchers say.

For example, they found that a transformer can predict valid moves in a game of Connect 4 nearly every time without understanding any of the rules.

So, the team developed two new metrics that can test a transformer’s world model. The researchers focused their evaluations on a class of problems called deterministic finite automations, or DFAs.  

A DFA is a problem with a sequence of states, like intersections one must traverse to reach a destination, and a concrete way of describing the rules one must follow along the way.

They chose two problems to formulate as DFAs: navigating on streets in New York City and playing the board game Othello.

“We needed test beds where we know what the world model is. Now, we can rigorously think about what it means to recover that world model,” Vafa explains.

The first metric they developed, called sequence distinction, says a model has formed a coherent world model it if sees two different states, like two different Othello boards, and recognizes how they are different. Sequences, that is, ordered lists of data points, are what transformers use to generate outputs.

The second metric, called sequence compression, says a transformer with a coherent world model should know that two identical states, like two identical Othello boards, have the same sequence of possible next steps.

They used these metrics to test two common classes of transformers, one which is trained on data generated from randomly produced sequences and the other on data generated by following strategies.

Incoherent world models

Surprisingly, the researchers found that transformers which made choices randomly formed more accurate world models, perhaps because they saw a wider variety of potential next steps during training.  

“In Othello, if you see two random computers playing rather than championship players, in theory you’d see the full set of possible moves, even the bad moves championship players wouldn’t make,” Vafa explains.

Even though the transformers generated accurate directions and valid Othello moves in nearly every instance, the two metrics revealed that only one generated a coherent world model for Othello moves, and none performed well at forming coherent world models in the wayfinding example.

The researchers demonstrated the implications of this by adding detours to the map of New York City, which caused all the navigation models to fail.

“I was surprised by how quickly the performance deteriorated as soon as we added a detour. If we close just 1 percent of the possible streets, accuracy immediately plummets from nearly 100 percent to just 67 percent,” Vafa says.

When they recovered the city maps the models generated, they looked like an imagined New York City with hundreds of streets crisscrossing overlaid on top of the grid. The maps often contained random flyovers above other streets or multiple streets with impossible orientations.

These results show that transformers can perform surprisingly well at certain tasks without understanding the rules. If scientists want to build LLMs that can capture accurate world models, they need to take a different approach, the researchers say.

“Often, we see these models do impressive things and think they must have understood something about the world. I hope we can convince people that this is a question to think very carefully about, and we don’t have to rely on our own intuitions to answer it,” says Rambachan.

In the future, the researchers want to tackle a more diverse set of problems, such as those where some rules are only partially known. They also want to apply their evaluation metrics to real-world, scientific problems.

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This work is funded, in part, by the Harvard Data Science Initiative, a National Science Foundation Graduate Research Fellowship, a Vannevar Bush Faculty Fellowship, a Simons Collaboration grant, and a grant from the MacArthur Foundation.

 

 



 PALEONTOLOGY

Archaic dolphin could hear high frequency sounds




Staatliche Naturwissenschaftliche Sammlungen Bayerns
Fossil dolphin Romaleodelphis pollerspoecki 

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Fossil dolphin Romaleodelphis pollerspoecki

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Credit: M. Schellenberger, SNSB-BSPG





The shallow inland sea in which the newly described dolphin lived some 22 million years ago together with many other organisms, including a variety of microorganisms, algae, snails, mussels, relatives of squid, and fishes, stretched north of the just emerging Alps. The only fossil known of this dolphin to date comes from a site near Linz in Upper Austria. It was assigned to a new, previously unknown species and genus, and scientifically named Romaleodelphis pollerspoecki by researchers from the Bavarian State Collection of Palaeontology and Geology (SNSB-BSPG) and the Ludwig-Maximilians-University in Munich, as well as the Senckenberg Research Institute and Natural History Museum Frankfurt.

"All that remains of Romaleodelphis pollerspoecki is its fragmented and incomplete skull with an elongated snout and 102 uniform teeth" reports first author Catalina Sánchez Posada who examined the fossil as part of her master's thesis. The animal belongs to the toothed whales, but differs significantly from all previously known prehistoric representatives of this lineage. Comparisons and a complex computer-based analysis of the relationships to other fossil dolphins revealed that Romaleodelphis was probably related to the already extinct, very archaic dolphins of the so-called Chilcacetus clade. "All previously known fossils of this dolphin lineage come from the north-eastern Pacific and the coasts of South America. The discovery of Romaleodelphis pollerspoecki, a putative European relative of this lineage, could therefore provide important new insights into the origin and evolution of the lineage in the earliest Miocene," says PD Dr. Gertrud Rößner, curator of fossil mammals from the Bavarian State Collection of Palaeontology and Geology, senior author of the study.

The fossil of the skull is severely compressed and distorted, which made the examination of the skull anatomy particularly challenging. Computed tomography images taken at the Department of Radiology at the Ludwig Maximilians University Hospital in Munich made it possible to examine and reconstruct internal features.

The anatomical reconstruction of the fossil's inner ear using micro-computed tomography images also yielded astonishing results. "The shape of the well-preserved bony labyrinth in the skull indicates that Romaleodelphis pollerspoecki was able to hear high-frequency signals," explains co-author Dr. Rachel Racicot from Senckenberg Research Institute and Natural History Museum. This makes this dolphin one of the oldest known toothed whales that already had a similarly developed sense of hearing as modern porpoises, for example. These animals are able to communicate in frequency ranges that are beyond the hearing range of their predators. There may also be a connection in the development with the ability of orientation through echolocation, which is typical for dolphins.

The dolphin fossil was unearthed in 1980 by the private collector Jürgen Pollerspöck, who later gave it to the Bavarian State Collection of Palaeontology and Geology for restoration and proper storage. The study has now been published in the Journal of Vertebrate Paleontology.


Childhood overweight is associated with socio-economic vulnerability



Uppsala University
Approximately 85 percent of all Swedish four-year-olds in 2018, 2020 and 2022 were included in the study, which in total comprises over 300,000 individuals. 

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Approximately 85 percent of all Swedish four-year-olds in 2018, 2020 and 2022 were included in the study, which in total comprises over 300,000 individuals.

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Credit: Region Sörmland





More children have overweight in regions with high rates of single parenthood, low education levels, low income and high child poverty. The pandemic may also have reinforced this trend. This is shown by a study conducted by researchers at Uppsala University and Region Sörmland in collaboration with Region Skåne.

“During and after the pandemic, we see a greater difference between regions in terms of children's weight. It even looks like it has exacerbated health inequalities,” explains Charlotte Nylander, a researcher at Uppsala University and the Centre for Clinical Research in Region Sörmland, where she is also a Senior Consultant in Child Health Care.

Approximately 85 percent of all Swedish four-year-olds in 2018, 2020 and 2022 were included in the study, which in total comprises over 300,000 individuals. The researchers compiled the regions’ data on overweight in childhood and then linked it to variables available from Statistics Sweden. The regions of Halland and Örebro are not included in the study due to a lack of aggregated data for 2022.

The results show that the prevalence of overweight or obesity has now fallen to the same levels as before the COVID-19 pandemic, i.e. 11.4%. During the pandemic, the prevalence was 13.3 per cent. However, in several regions, including Västernorrland, Gävleborg and Värmland, the figures are significantly higher than the national average (see attached figure).

“We were worried when we saw the peak during the pandemic and wondered what will happen next. But it is good news that it is back to pre-pandemic levels – we are happy about that. However, overweight in childhood is clearly still a concern that we need to work on,” adds Nylander.

She and her research colleagues are concerned that there was such a significant link to socio-economic disadvantage at the regional level. There were more overweight children in regions with many single parents, low education levels, low income and high child poverty.

“Child healthcare is an important public health arena. It is a matter of highlighting socio-economically disadvantaged children in healthcare and providing early advice on lifestyle habits that can help. But we also need to shift responsibility from the individual to society, where major efforts are needed to improve the situation,” notes researcher Mariette Derwig, a Senior Consultant in Child Health Care in Region Skåne.