AI-powered ‘sonar’ on smartglasses tracks gaze, facial expressions

CORNELL UNIVERSITY

ITHACA, N.Y. – Cornell University researchers have developed two technologies that track a person’s gaze and facial expressions through sonar-like sensing. The technology is small enough to fit on commercial smartglasses or virtual reality or augmented reality headsets, yet consumes significantly less power than similar tools using cameras.

Both use speakers and microphones mounted on an eyeglass frame to bounce inaudible soundwaves off the face and pick up reflected signals caused by face and eye movements. One device, GazeTrak, is the first eye-tracking system that relies on acoustic signals. The second, EyeEcho, is the first eyeglass-based system to continuously and accurately detect facial expressions and recreate them through an avatar in real time.

The devices can last for several hours on a smartglass battery and more than a day on a VR headset.

“It’s small, it’s cheap and super low-powered, so you can wear it on smartglasses everyday – it won’t kill your battery,” said Cheng Zhang, assistant professor of information science. Zhang directs the Smart Computer Interfaces for Future Interactions (SciFi) Lab that created the new devices.

“In a VR environment, you want to recreate detailed facial expressions and gaze movements so that you can have better interactions with other users,” said Ke Li, a doctoral student who led the GazeTrak and EyeEcho development.

For GazeTrak, researchers positioned one speaker and four microphones around the inside of each eye frame of a pair of glasses, to bounce and pick up soundwaves from the eyeball and the area around the eyes. The resulting sound signals are fed into a customized deep learning pipeline that uses artificial intelligence to continuously infer the direction of the person’s gaze.

For EyeEcho, one speaker and one microphone is located next to the glasses’ hinges, pointing down to catch skin movement as facial expressions change. The reflected signals are also interpreted using AI.

With this technology, users can have hands-free video calls through an avatar, even in a noisy café or on the street. While some smartglasses have the ability to recognize faces or distinguish between a few specific expressions, currently, none track expressions continuously like EyeEcho.

These two advances have applications beyond enhancing a person’s VR experience. GazeTrak could be used with screen readers to read out portions of text for people with low vision as they peruse a website.

GazeTrak and EyeEcho could also potentially help diagnose or monitor neurodegenerative diseases, like Alzheimer’s and Parkinsons. With these conditions, patients often have abnormal eye movements and less expressive faces, and this type of technology could track the progression of the disease from the comfort of a patient’s home.

Li will present GazeTrak at the Annual International Conference on Mobile Computing and Networking in the fall and EyeEcho at the Association of Computing Machinery CHI conference on Human Factors in Computing Systems in May.

For additional information, see this Cornell Chronicle story.

Media note: Pictures can be viewed and downloaded here: https://cornell.box.com/v/sonarsmartglasses.

-30-

A faster, better way to prevent an AI chatbot from giving toxic responses

Researchers create a curious machine-learning model that finds a wider variety of prompts for training a chatbot to avoid hateful or harmful output

MASSACHUSETTS INSTITUTE OF TECHNOLOGY

CAMBRIDGE, MA – A user could ask ChatGPT to write a computer program or summarize an article, and the AI chatbot would likely be able to generate useful code or write a cogent synopsis. However, someone could also ask for instructions to build a bomb, and the chatbot might be able to provide those, too.

To prevent this and other safety issues, companies that build large language models typically safeguard them using a process called red-teaming. Teams of human testers write prompts aimed at triggering unsafe or toxic text from the model being tested. These prompts are used to teach the chatbot to avoid such responses.

But this only works effectively if engineers know which toxic prompts to use. If human testers miss some prompts, which is likely given the number of possibilities, a chatbot regarded as safe might still be capable of generating unsafe answers.

Researchers from Improbable AI Lab at MIT and the MIT-IBM Watson AI Lab used machine learning to improve red-teaming. They developed a technique to train a red-team large language model to automatically generate diverse prompts that trigger a wider range of undesirable responses from the chatbot being tested.

They do this by teaching the red-team model to be curious when it writes prompts, and to focus on novel prompts that evoke toxic responses from the target model.

The technique outperformed human testers and other machine-learning approaches by generating more distinct prompts that elicited increasingly toxic responses. Not only does their method significantly improve the coverage of inputs being tested compared to other automated methods, but it can also draw out toxic responses from a chatbot that had safeguards built into it by human experts.

“Right now, every large language model has to undergo a very lengthy period of red-teaming to ensure its safety. That is not going to be sustainable if we want to update these models in rapidly changing environments. Our method provides a faster and more effective way to do this quality assurance,” says Zhang-Wei Hong, an electrical engineering and computer science (EECS) graduate student in the Improbable AI lab and lead author of a paper on this red-teaming approach.

Hong’s co-authors include EECS graduate students Idan Shenfield, Tsun-Hsuan Wang, and Yung-Sung Chuang; Aldo Pareja and Akash Srivastava, research scientists at the MIT-IBM Watson AI Lab; James Glass, senior research scientist and head of the Spoken Language Systems Group in the Computer Science and Artificial Intelligence Laboratory (CSAIL); and senior author Pulkit Agrawal, director of Improbable AI Lab and an assistant professor in CSAIL. The research will be presented at the International Conference on Learning Representations.

 

Automated red-teaming

Large language models, like those that power AI chatbots, are often trained by showing them enormous amounts of text from billions of public websites. So, not only can they learn to generate toxic words or describe illegal activities, the models could also leak personal information they may have picked up.

The tedious and costly nature of human red-teaming, which is often ineffective at generating a wide enough variety of prompts to fully safeguard a model, has encouraged researchers to automate the process using machine learning.

Such techniques often train a red-team model using reinforcement learning. This trial-and-error process rewards the red-team model for generating prompts that trigger toxic responses from the chatbot being tested.

But due to the way reinforcement learning works, the red-team model will often keep generating a few similar prompts that are highly toxic to maximize its reward.

For their reinforcement learning approach, the MIT researchers utilized a technique called curiosity-driven exploration. The red-team model is incentivized to be curious about the consequences of each prompt it generates, so it will try prompts with different words, sentence patterns, or meanings.

“If the red-team model has already seen a specific prompt, then reproducing it will not generate any curiosity in the red-team model, so it will be pushed to create new prompts,” Hong says.

During its training process, the red-team model generates a prompt and interacts with the chatbot. The chatbot responds, and a safety classifier rates the toxicity of its response, rewarding the red-team model based on that rating.

 

Rewarding curiosity

The red-team model’s objective is to maximize its reward by eliciting an even more toxic response with a novel prompt. The researchers enable curiosity in the red-team model by modifying the reward signal in the reinforcement learning set up.

First, in addition to maximizing toxicity, they include an entropy bonus that encourages the red-team model to be more random as it explores different prompts. Second, to make the agent curious they include two novelty rewards. One rewards the model based on the similarity of words in its prompts, and the other rewards the model based on semantic similarity. (Less similarity yields a higher reward.)

To prevent the red-team model from generating random, nonsensical text, which can trick the classifier into awarding a high toxicity score, the researchers also added a naturalistic language bonus to the training objective.

With these additions in place, the researchers compared the toxicity and diversity of responses their red-team model generated with other automated techniques. Their model outperformed the baselines on both metrics.

They also used their red-team model to test a chatbot that had been fine-tuned with human feedback so it would not give toxic replies. Their curiosity-driven approach was able to quickly produce 196 prompts that elicited toxic responses from this “safe” chatbot.

“We are seeing a surge of models, which is only expected to rise. Imagine thousands of models or even more and companies/labs pushing model updates frequently. These models are going to be an integral part of our lives and it’s important that they are verified before released for public consumption. Manual verification of models is simply not scalable, and our work is an attempt to reduce the human effort to ensure a safer and trustworthy AI future,” says Agrawal. 

In the future, the researchers want to enable the red-team model to generate prompts about a wider variety of topics. They also want to explore the use of a large language model as the toxicity classifier. In this way, a user could train the toxicity classifier using a company policy document, for instance, so a red-team model could test a chatbot for company policy violations.

“If you are releasing a new AI model and are concerned about whether it will behave as expected, consider using curiosity-driven red-teaming,” says Agrawal.

###

This research is funded, in part, by Hyundai Motor Company, Quanta Computer Inc., the MIT-IBM Watson AI Lab, an Amazon Web Services MLRA research grant, the U.S. Army Research Office, the U.S. Defense Advanced Research Projects Agency Machine Common Sense Program, the U.S. Office of Naval Research, the U.S. Air Force Research Laboratory, and the U.S. Air Force Artificial Intelligence Accelerator.

---

DOI

10.48550/arXiv.2402.19464 

 

Filling in genomic blanks for disease studies works better for some groups than others

A new USC study finds an apparent disparity in the effectiveness of genome-wide association studies concerning a technique that is reliable for those with European or African ancestry as well as for Latinos but serves other populations less well.

KECK SCHOOL OF MEDICINE OF USC

Understanding how genetics affect health is an essential first step toward treating and preventing a host of diseases. New knowledge often comes from genome-wide association studies identifying variations in the genetic code linked with conditions such as cancer and autoimmune disease. The more people’s DNA and health histories that are examined in such research, the more likely genetic and biological insights can be garnered.

However, cost can be a major barrier: Comprehensively sequencing one person’s genome costs about $500 to $1000, a price point often infeasible when applied to several tens of thousands of study participants. So instead, researchers generally focus on key spots where the genetic code tends to vary among different individuals — through genotyping, which costs about $100 per participant. A statistical method called genotype imputation then helps them fill in the genetic blanks based on existing reference panels of fully sequenced genomes.

A new Keck School of Medicine of USC study, supported by the National Institutes of Health and appearing in the American Journal of Human Genetics, identifies a disparity in how well imputation works for different populations. The researchers found that the technique holds up nicely for well-represented groups with European ancestry, as well as for African Americans and Latinos, who have been the subject of recent, concerted efforts to increase representation in sequencing reference panels. However, the researchers found that imputation is far less reliable for other groups, generally doing worse for populations farther away from Europe, except for Africa and Latin America. 

“These global populations are not being imputed as well, meaning that we have a lot more error in filling in missing parts of the genome,” said corresponding author Charleston Chiang, PhD, associate professor of population and public health sciences and associate director at the Keck School of Medicine’s Center for Genetic Epidemiology. “That means the analysis using these imputed data doesn’t work as well. And because researchers filter based on the reliability of imputation, we end up having data for diverse populations with more errors and more holes, leading to less effective study designs.”

Reaching outside of a health science field to examine inequities

Chiang notes that the uniqueness of this study lies in the breadth of the study, where the team evaluated over a hundred global populations for issues with imputation. This has not been previously demonstrated because of the general lack of diversity of available cohorts as well as in reference panels of fully sequenced genomes. This presented a hurdle for understanding how well diverse groups fare with imputation in genetic epidemiology studies. So the research team took a unique approach, borrowing genetic datasets from population genetics, a related field focused on understanding the history and evolution of a wide variety of populations, with less of a focus on disease. 

In all, the scientists combined genomic sequencing data from 23 studies including more than 43,000 people from 123 distinct global populations. They matched each population with a control group of European ancestry and used a standard metric that doesn’t require full genomic sequences — which is normally the case in genome-wide association studies — to compare the reliability of imputation.  

Imputation for populations based in places such as Papua New Guinea, Thailand, Vietnam and Saudi Arabia was substantially less accurate than for populations of European descent. Chiang and his colleagues also plotted the relative reliability of imputation for different groups on a world map that is available online. Imputation for populations based in Asia, Australia, New Zealand and the Pacific Islands generally showed less accuracy.

The team also compared the main metric for the reliability of imputation used to arrive at these findings with a better metric that only works when full sequencing data is available. They found that the main metric is biased so that it overestimates the accuracy of imputation for populations other than people of European ancestry. This suggests that the flaws in imputation are more serious still than indicated by the researchers’ results.

Potential steps to make genome-wide association studies more equitable

The solution for the disparity highlighted in the study is straightforward, yet far from simple to achieve.

“We need to sequence more, and be more inclusive in the individuals who participate in studies,” said Chiang, who also holds an appointment in quantitative and computational biology at USC Dornsife College and is a member of USC Norris Comprehensive Cancer Center. 

One promising sign is that genomic sequencing has become more affordable in recent years and is expected to continue to do so. But cost isn’t the only concern that needs to be addressed. Efforts are needed to earn the trust from diverse communities so they are not hesitant to participate. In some cases, more diversity can complicate genome-wide association studies, particularly in smaller studies, even confounding their findings if the diversity is not properly accounted for or characterized. This creates pressure for scientists to exclude a smaller subset of populations in their data and choose from groups with more members. 

Chiang advocates for a sort of balance.

“As the studies get bigger and bigger, the way that scientists view and analyze these data needs to evolve toward looking at genetic ancestry as more of a continuum,” he said. “If we can start to view everyone as related and branching off the same genetic tree at different places, according to their history, we can incorporate more people and more diversity. 

“Of course, there are valuable reasons to study discrete populations,” he continued. “Group identity can be useful to maintain, for example when studying the social determinants of health that affect what people experience in their daily lives. We need to continue studying particular populations in isolation, but in the long term, we need to be able to reconcile between the two approaches.”

The study’s first author, USC undergraduate Jordan Cahoon, hopes that by beginning to quantify disparities baked into genome-wide association studies, the team’s work will influence future solutions.

“It’s important to understand the weaknesses in the field in terms of equity and fairness,” said Cahoon, a graduating senior majoring in computer science at the USC Viterbi School of Engineering. “I’m hoping that this study will be a good resource for scientists, so they can see how well the populations they’re sequencing are doing in comparison to others.”

About this study

Other co-authors are Xinyue Rui, Echo Tang, Christopher Simons, Jalen Langie, Minhui Chen and Ying-Chu Lo, all of USC.

The study received support from the National Institutes of Health (R35GM14278), a USC Viterbi Merit Fellowship and a USC Provost’s Undergrad Research Fellowship.

---

JOURNAL

American Journal of Human Genetics

DOI

10.1016/j.ajhg.2024.03.011 

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Imputation accuracy across global human populations

ARTICLE PUBLICATION DATE

10-Apr-2024

 

Aboriginal people made pottery, sailed to distant islands thousands of years before Europeans arrived

by Sean Ulm, Ian J. McNiven and Kenneth McLean, The Conversation

Ceramic sherd selection. Photographs: Steve Morton. Credit: Quaternary Science Reviews 

(2024). DOI: 10.1016/j.quascirev.2024.108624

Pottery was largely unknown in Australia before the recent past, despite well-known pottery traditions in nearby Papua New Guinea and the islands of the western Pacific. The absence of ancient Indigenous pottery in Australia has long puzzled researchers.

Over the past 400 years, pottery from southeast Asia appeared across northern Australia, associated with the activities of Makassan people from Sulawesi (this activity was mainly trepanging, or collecting sea cucumbers). Older pottery in Australia is only known from the Torres Strait adjacent to the Papua New Guinea coast, where a few dozen pottery fragments have been reported, mostly dating to around 1700 years ago.

Why has no evidence been found of early pottery use by Aboriginal people? Various explanations have been proposed, including suggesting that archaeologists simply weren't looking hard enough. Well now, we've found some.

In new research published in Quaternary Science Reviews, we report the oldest securely dated ceramics found in Australia from archaeological excavations on Jiigurru (in the Lizard Island group) on the northern Great Barrier Reef located 600km south of Torres Strait. Our analysis shows the pottery was made locally more than 1,800 years ago.

Finding pottery at Jiigurru

Back in 2006, several pieces of pottery were found in Blue Lagoon on Jiigurru, 33km off mainland Cape York Peninsula.

Finding pottery at Jiigurru raised some big questions. How old was it? Was it made by local Aboriginal communities? Or was it traded in from elsewhere? If so, where did it come from? Was it from a European shipwreck? Or was it made by the famous Lapita people who colonized the islands of the southwest Pacific?

Our team excavated several more pieces of pottery from Blue Lagoon in 2009, 2010 and 2012.

Preliminary analyses showed most of the pottery was made from local materials. However, despite a lot of work, our efforts to determine the age of this pottery were inconclusive and we were no closer to working out how old it is, or who made it.

In 2013 we went back to Jiigurru to excavate a shell midden on a headland near where the Blue Lagoon pottery was found. A shell midden represents a place where people lived, containing food remains (shells, bones), charcoal from campfires, and stone tools left behind.

Radiocarbon dating showed people started camping at this place some 4,000 years ago, making it the oldest site then known at Jiigurru. But no pottery was found.

A broader search

By 2016 the team had reached a dead end in investigating the few pieces of pottery we had. Instead, working in partnership with Traditional Owners, we turned the research program to the extraordinary Indigenous history of the whole of Jiigurru and began surveying all the islands.

In 2017 we began excavating a large shell midden at Jiigurru located during the surveys.

To our amazement, around 40cm below the surface we began to find pieces of pottery among the shells in the excavation. We knew this was a big deal. We carefully bagged each piece of pottery and mapped where each sherd came from, and kept digging.

The pottery stopped at about 80cm depth, with 82 pieces of pottery in total. Most are very small, with an average length of just 18 millimeters. The pottery assemblage includes rim and neck pieces and some of the pottery is decorated with pigment and incised lines.

The oldest pottery

But we had another surprise waiting for us.

The deepest cultural material was found nearly two meters below the surface, in levels we radiocarbon dated to around 6,500 years ago. This is the earliest evidence for offshore island use on the northern Great Barrier Reef.

The reef shells eaten and discarded in these lowest levels had been buried so quickly that they still have color on their surfaces. Archaeological sites of this depth and age are uncommon anywhere around the Australian coast.

Radiocarbon dating of charcoal and shells found close to the pottery shows that it is between 2,950 and 1,815 years old, making it the earliest securely dated pottery ever found in Australia. Analysis of the clays and tempers shows that all of the pottery was likely made on Jiigurru.

What does it tell us that we didn't already know?

The findings are clear evidence that Aboriginal people made and used pottery thousands of years ago.

The archaeological evidence does not point to outsiders bringing pottery directly to Jiigurru. Instead, the evidence shows that Cape York First Nations communities were intimately engaged in ancient maritime networks, connecting them with peoples, knowledges and technologies across the Coral Sea region, including the knowledge of how to make pottery.

They were not isolated or geographically constrained, as once conceived.

The results also demonstrate that Aboriginal communities had sophisticated watercraft and navigational skills in using their Sea Country estates more than 6,000 years ago.

What else don't we know?

The Jiigurru pottery gives us new insight into Australia's history and the international reach of First Nations communities thousands of years before British invasion in 1788.

Very little research has been conducted anywhere on eastern Cape York Peninsula. We think it is very unlikely that Jiigurru holds the only secrets to our country's peopled past. What other cultural and historical surprises await to be found?

More information: Sean Ulm et al, Early Aboriginal pottery production and offshore island occupation on Jiigurru (Lizard Island group), Great Barrier Reef, Australia, Quaternary Science Reviews (2024). DOI: 10.1016/j.quascirev.2024.108624

Journal information: Quaternary Science Reviews 

Provided by The Conversation 

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Discovery of pottery rewrites Aboriginal history

 

Switch to green wastewater infrastructure could reduce emissions and provide huge savings, new research finds

by Colorado State University

The Big Thompson River in Rocky Mountain National Park. Credit: The Big Thompson River in Rocky Mountain National Park / Colorado State University.

University researchers have shown that a transition to green wastewater-treatment approaches in the U.S. that leverages the potential of carbon-financing could save a staggering $15.6 billion and just under 30 million metric tons of CO2-equivalent emissions over 40 years.

The comprehensive findings from Colorado State University were highlighted in Nature Communications Earth & Environment in a first-of-its-kind study. The work from the Walter Scott, Jr. College of Engineering explores the potential economic tradeoffs of switching to green infrastructure and technology solutions that go beyond existing gray-water treatment practices.

Built off data collected at over 22,000 facilities, the report provides comprehensive baseline metrics and explores the relationship among emissions, costs and treatment capabilities for utility operators and decision-makers.

Braden Limb is the first author on the paper and a Ph.D. student in the Department of Systems Engineering. He also serves as a research associate in the Department of Mechanical Engineering. He said the findings are a key initial step to categorize and understand potential green solutions for wastewater.

"These findings draw a line in the sand that shows what the potential for adopting green approaches in this space is—both in terms of money saved and total emissions reduced," he said. "It is a starting point to understand what routes are available to us now and how financing strategies can elevate water treatment from a somewhat local issue into something that is addressed globally through market incentives."

The research was completed in partnership with the University of Colorado Boulder and Brigham Young University. Findings center around both point-source water treatment and non-point sources of water pollution.

Traditional point-source water treatment facilities such as sewage plants remove problem nutrients like nitrogen and phosphorus before releasing water back into circulation. This gray-infrastructure system—as it is known—is monitored by the Environmental Protection Agency.

However, regulation standards may tighten in the future, and facilities would need more power, and in turn more emissions, to reach newly allowable thresholds. Existing facilities already account for 2% of all energy use in the U.S. and 45 million metric tons of CO2 emissions, said Limb.

Another significant source of freshwater contamination in the U.S. comes from non-point source activity such as fertilizer runoff from agriculture entering rivers. Other non-point sources of pollution can come from wildfires—aided by climate change—or urban development, for example.

Limb said that rather than building more gray-infrastructure treatment facilities to address those increasing sources, the paper explores green approaches financed through carbon markets that can tackle both types simultaneously.

"There could be a switch to nature-based solutions such as constructing wetlands or reforestation instead of building yet another treatment facility," he said. "Those options could sequester over 4.2 million carbon dioxide emissions per year over a 40-year time horizon and have other complementary benefits we should be aiming for, such as cheaper overall costs."

Carbon financing is a mechanism aimed at mitigating climate change by incentivizing activities that reduce emissions or sequester them from the atmosphere. Companies voluntarily buy "credits" on an open market that represent a reduction or removal of carbon from the atmosphere that can be accomplished in a variety of ways. That credit offsets the institution's emissions from operations as it aims to reach sustainability goals.

These trades incentivize development of sustainable activities and can also provide a source of fresh money to further develop or scale up new approaches.

While there are similar financing markets for water, the problem is initially more localized than it is for air quality and carbon. That dynamic has limited the value of water market trades in the past. The paper suggests that these existing markets could be improved, and that the carbon markets could also be leveraged to change some of the financial incentives farmers have around water treatment and impacts from their activity.

The researchers found that using the markets could generate $679 million annually in revenue, representing an opportunity to further motivate green infrastructure solutions within water quality trading programs to meet regulated standards.

Mechanical Engineering Professor Jason Quinn is a co-author on the study. He said the findings have some limitations, but that this was an important first step to model both the problem and opportunity available now. He said the results in the paper have supported new research at CSU with the National Science Foundation to further develop the needed carbon credit methodology with stakeholders.

"This is the first time we are considering air and water quality simultaneously—water is local and carbon is global," he said. "But by bringing these market mechanisms together we can capitalize on a window of opportunity to accelerate the improvement of America's rivers as we transition to a renewable energy and restored watershed future."

More information: Braden Limb et al, The potential of carbon markets to accelerate green infrastructure based water quality trading, Nature Communications Earth & Environment (2024). DOI: 10.1038/s43247-024-01359-x. www.nature.com/articles/s43247-024-01359-x

Journal information: Nature Communications Earth & Environment 

Provided by Colorado State University Why water must be at the heart of climate action

 

Evolution's recipe book: How 'copy paste' errors led to insect flight, octopus camouflage and human cognition

by Center for Genomic Regulation

The mayfly, one of the 20 species studied in the paper. Credit: Isabel Almudi

Seven hundred million years ago, a remarkable creature emerged for the first time. Though it may not have been much to look at by today's standards, the animal had a front and a back, a top and a bottom. This was a groundbreaking adaptation at the time, and one which laid down the basic body plan which most complex animals, including humans, would eventually inherit.

The inconspicuous animal resided in the ancient seas of Earth, likely crawling along the seafloor. This was the last common ancestor of bilaterians, a vast supergroup of animals including vertebrates (fish, amphibians, reptiles, birds, and mammals), and invertebrates (insects, arthropods, mollusks, worms, echinoderms and many more).

To this day, more than 7,000 groups of genes can be traced back to the last common ancestor of bilaterians, according to a study of 20 different bilaterian species including humans, sharks, mayflies, centipedes and octopuses. The findings were made by researchers at the Centre for Genomic Regulation (CRG) in Barcelona and are published today in the journal Nature Ecology & Evolution.

Remarkably, the study found that around half of these ancestral genes have since been repurposed by animals for use in specific parts of the body, particularly in the brain and reproductive tissues. The findings are surprising because ancient, conserved genes usually have fundamental, important jobs that are needed in many parts of the body.

When the researchers took a closer look, they found a series of serendipitous "copy paste" errors during bilaterian evolution were to blame. For example, there was a significant moment early in the history of vertebrates. A bunch of tissue-specific genes first appeared coinciding with two whole genome duplication events.

Animals could keep one copy for fundamental functions, while the second copy could be used as raw material for evolutionary innovation. Events like these, at varying degrees of scale, occurred constantly throughout the bilaterian evolutionary tree.

"Our genes are like a vast library of recipes that can be cooked up differently to create or change tissues and organs. Imagine you end up with two copies of a recipe for paella by accident. You can keep and enjoy the original recipe while evolution tweaks the extra copy so that it makes risotto instead.

"Now imagine the entire recipe book is copied—twice—and the possibilities it opens for evolution. The legacy of these events, which took place hundreds of millions of years ago, lives on in most complex animals today," explains Federica Mantica, author of the paper and researcher at the Centre for Genomic Regulation (CRG) in Barcelona.

The authors of the study found many examples of new, tissue-specific functions made possible by the specialization of these ancestral genes. For example, the TESMIN and tomb genes, which originated from the same ancestor, ended up independently playing a specialized role in the testis both in vertebrates and insects. Their importance is highlighted by the fact that problems with these genes can disrupt sperm production, affecting fertility in both mice and fruit flies.

The specialization of ancestral genes also laid some foundations for the development of complex nervous systems. For example, in vertebrates, the researchers found genes critical for the formation of myelin sheaths around nerve cells, which are essential for fast nerve signal transmission. In humans they also identified FGF17, which is thought to play an important role in maintaining cognitive functions into old age.

In insects, specific genes became specialized in muscles and in the epidermis for cuticle formation, contributing to their ability to fly. In the skin of octopuses, other genes became specialized to perceive light stimuli, contributing to their ability to change color, camouflage and communicate with other octopuses.

By studying the evolution of species at the tissue level, the study demonstrates that changes in the way genes are used in different parts of the body have played a big role in creating new and unique features in animals. In other words, when genes start acting in specific tissues, it can lead to the development of new physical traits or abilities, which ultimately contributes to animal evolution.

"Our work makes us rethink the roles and functions that genes play. It shows us that genes that are crucial for survival and have been preserved through millions of years can also very easily acquire new functions in evolution.

"It reflects evolution's balancing act between preserving vital roles and exploring new paths," concludes ICREA Research Professor Manuel Irimia, co-author of the paper and researcher at the Centre for Genomic Regulation.

More information: Evolution of tissue-specific expression of ancestral genes across vertebrates and insects, Nature Ecology & Evolution (2024). DOI: 10.1038/s41559-024-02398-5

Journal information: Nature Ecology & Evolution 

Provided by Center for Genomic Regulation

Researchers explore the hagfish genome, reconstruct the early genomic history of vertebrates

The evolving attitudes of Gen X toward evolution

UNIVERSITY OF MICHIGAN

As the centennial of the Scopes Monkey Trial of 1925 approaches, a new study illustrates that the attitudes of Americans in Generation X toward evolution shifted as they aged.

 

The study, led by Jon D. Miller, research scientist emeritus in the Institute for Social Research at the University of Michigan, found that while students in middle and high school tended to express uncertain attitudes toward evolution, those attitudes solidified as they graduated high school, went to college and entered the workforce. 

 

"Some may challenge whether the evolution issue is still of relevance and consider it to be a harmless curiosity," Miller said. "U.S. science and technology continue to prosper, although a substantial minority of American adults reject the idea that humans developed from earlier species of animals. 

 

"However, we believe that there are numerous examples of public policy over recent decades when an understanding of basic biological constructs would have helped inform public and political debate on those issues."

 

The study, published in the journal Public Understanding of Science, used data collected from about 5,000 participants born in the center of Generation X, 1971-1974, over the course of 33 years, from middle school to midlife.

 

"Research on attitudes toward science typically uses a single survey or a series of surveys of different participants," Miller said. "Using the three-decade record from the Longitudinal Study of American Life enables our study to investigate how attitudes develop and shift over formative decades in the same individuals."

 

Middle school and high school students displayed a good deal of uncertainty about evolution, with a third having no attitude about evolution and 44% saying that the statement "human beings as we know them developed from earlier species of animals" was probably true or probably false, reflecting a degree of uncertainty about the issue. 

 

During the 15 years after high school, 28% of these Generation X young adults concluded that evolution was definitely true and 27% thought that evolution was definitely false, according to co-author Mark Ackerman, a professor at Michigan Engineering, the U-M School of Information and Michigan Medicine.

 

"These results demonstrate the impact of postsecondary education, initial career experiences and the polarization of the political system in the United States," Ackerman said.

 

During the next 15 years (from their early 30s to their late 40s), these Generation X LSAL participants reported a small increase in the proportion of individuals seeing evolution as definitely true (30% in 2020) and a small decrease in the proportion seeing evolution as definitely false (23% in 2020). These results reflect the stabilization of the lives of LSAL respondents, with substantial numbers entering a career of their choice, starting a family and becoming more engaged with their community.

 

The study investigated the factors that were associated with the participants' attitudes toward evolution at three points during the study. As in a previous study by the same researchers, factors involving education tended to be strong predictors of the acceptance of evolution, while factors involving fundamentalist religious beliefs tended to be strong predictors of the rejection of evolution. 

 

The experience of college-level science courses, the completion of baccalaureate or more advanced degrees, and the development of civic scientific literacy were strong predictors of increased acceptance of evolution.

 

"Our analysis of a unique longitudinal dataset allowed us to explore the development of attitudes toward a scientific topic in unprecedented detail," Miller said. "And understanding the public's attitudes toward evolution is of particular importance, since evolution is going to continue to be central to biological literacy and—scientific literacy—in the 21st century."

Besides Miller and Ackerman of the University of Michigan, authors included Belén Laspra and Carmelo Polino of the University of Oviedo (Spain), Glenn Branch of the National Center for Science Education, and Robert Pennock of Michigan State University.

 

Study: The acceptance of evolution: A developmental view of Generation X in the United States (DOI: 10.1177/09636625241234815)

 

---

JOURNAL

Public Understanding of Science

DOI

10.1177/09636625241234815 

 

Tropical forests can't recover naturally without fruit eating birds, carbon recovery study shows

by ETH Zurich

The Collared Araçari (Pteroglossus torquatus) is among the few birds that can disperse 

plants with large seeds and play a key role in dispersal in forests in Central and South

 America. It is especially important for young forests growing on abandoned land, as they

 bring in seeds of many different species that will help the forest regenerate a diverse tree 

community. Credit: ETH Zurich / Christian Ziegler

New research from the Crowther Lab at ETH Zurich illustrates a critical barrier to natural regeneration of tropical forests. Their models—from ground-based data gathered in the Atlantic Forest of Brazil—show that when wild tropical birds move freely across forest landscapes, they can increase the carbon storage of regenerating tropical forests by up to 38%.

Fruit eating birds such as the Red-Legged Honeycreeper, Palm Tanager, or the Rufous-Bellied Thrush play a vital role in forest ecosystems by consuming, excreting, and spreading seeds as they move throughout a forested landscape.

Between 70% to 90% of the tree species in tropical forests are dependent on animal seed dispersal. This initial process is essential for allowing forests to grow and function. While earlier studies have established that birds are important for forest biodiversity, researchers at the Crowther Lab now have a quantitative understanding of how they contribute to forest restoration.

The new study, published in the journal Nature Climate Change provides evidence of the important contribution of wild birds (frugivores) in forest regeneration. Researchers compared the carbon storage potential that could be recovered in landscapes with limited fragmentation, with that of highly fragmented landscapes. Their data shows that highly fragmented landscapes restrict the movement of birds, thereby reducing the potential of carbon recovery by up to 38%.

Across the Atlantic Forest region in Brazil, the researchers found that it is critical to maintain a minimum of 40% forest cover. They also find that a distance of 133 meters (approximately 435 feet) or less between forested areas ensures that birds can continue to move throughout the landscape and facilitate ecological recovery.

Wild tropical birds play a key role in tropical forest ecosystems by eating fruits and 

dispersing seeds. Credit: ETH Zurich / Christian Ziegler

The study also found that different bird species have different impacts in terms of seed dispersal. Smaller birds disperse more seeds, but they can only spread small seeds from trees with lower carbon storage potential. In contrast, larger birds such as the Toco toucan or the Curl-crested jay disperse the seeds of trees with a higher carbon storage potential. The problem is that the larger birds are less likely to move across highly fragmented landscapes.

"This crucial information enables us to pinpoint active restoration efforts—like tree planting—in landscapes falling below this forest cover threshold, where assisted restoration is most urgent and effective," Daisy Dent, a Lead Scientist in the Crowther Lab at ETH Zurich.

Restoring functioning ecosystem services

"Allowing larger frugivores to move freely across forest landscapes is critical for healthy tropical forest recovery," says Carolina Bello, a post-doctoral researcher also in the Crowther Lab at ETH Zurich and lead author of the study. "This study demonstrates that especially in tropical ecosystems seed dispersal mediated by birds, plays a fundamental role in determining the species that can regenerate."

A Blue-gray Tanager (Thraupis episcopus) disperses Miconia seeds. Credit: ETH Zurich / Christian Ziegler

Based on current data, this study advances the research from previous ground studies conducted by the authors in the Atlantic Forest in Brazil. The forest is one of the most biologically diverse regions in the world, but it is also one of the most fragmented with only 12% of the original forest remaining and in small areas.

The forest is also one of the most important regions on the planet for large-scale ecological restoration, with 12 million hectares of land targeted for restoration and natural recovery under the Atlantic Forest Restoration Pact. The research shows that increasing forest cover beyond 40% may be critical not only to maintain species diversity, as previously evidenced, but also to maintain and restore the functioning of ecosystem services, such as seed dispersal and carbon storage, to maximize the success of the massive-scale restoration initiative in this region.

"We have always known that birds are essential, but it is remarkable to discover the scale of those effects," says Thomas Crowther, Professor of Ecology at ETH Zurich, and the senior co-author of the study. "If we can recover the complexity of life within these forests, their carbon storage potential would increase significantly."

Strategies for recovering tropical forests

Earlier research suggests that recovering forests could capture more than 2.3 billion metric tons of carbon in the Atlantic Forest region, and that natural regeneration is likely to be more cost-effective—as much as 77% less in implementation costs—than active planting.

The Keel-billed Toucan (Ramphastos sulfuratus) is among the few birds that can disperse

 plants with large seeds and play a key role in dispersal in forests in Central and South 

America. It is especially important for young forests growing on abandoned land, as they

 bring in seeds of many different species that will help the forest regenerate a diverse tree

 community. Credit: ETH Zurich / Christian Ziegler

Researchers note that a range of strategies, such as planting fruit trees and preventing poaching, could enhance animal movement in tropical areas where passive restoration is more likely. Active restoration is necessary in highly fragmented landscapes.

"By identifying the thresholds of forest cover in the surrounding landscape that allow seed dispersal, we can identify areas where natural regeneration is possible, as well as areas where we need to actively plant trees, allowing us to maximize the cost-effectiveness of forest restoration," says Danielle Ramos, a co-author of the paper affiliated with the University of Exeter, UK and Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.

More information: Frugivores enhance potential carbon recovery in fragmented landscapes, Nature Climate Change (2024). DOI: 10.1038/s41558-024-01989-1

Journal information: Nature Climate Change 

Provided by ETH Zurich Rainforest's next generation of trees threatened 30 years after logging