Friday, November 18, 2022

Emory students promote youth power at U.N. conference

Eri Saikawa, associate professor of environmental studies (bottom, right) led a delegation of students to the U.N. Framework Convention on Climate Change in Egypt. Click here to see bios of the delegation members.

By Carol Clark

Emory students helped raise the profiles of youth activists during this year’s United Nations Framework Convention on Climate Change, better known as COP, continuing through Nov. 18 in Sharm El-Sheikh, Egypt. 

A delegation of five Emory undergraduates and four graduate students, led by Eri Saikawa, associate professor of environmental sciences, attended the first week of COP as official U.N. observers. They sat in on negotiations and co-hosted a side event with the Climate Justice Program entitled “Youth: From Resistance to Power.” The event featured a panel discussion by four young activists — from Pakistan, Kenya, Mexico and the Philippines — followed by an interactive networking event moderated by the Emory students. 

“It’s inspiring and energizing seeing so many youth raising their voices and pushing for climate action,” says Saikawa. 

Saikawa began leading students from her Climate Change and Society class to the annual global climate talks in 2015, when COP was held in Paris. That year, nearly 200 member countries hammered out the Paris Agreement, aiming to keep the global mean rise in temperature to no more than 2 degrees Celsius above preindustrial levels. 

Student delegates will share what they learned during this year’s COP at a campus event entitled “Climate Conversations: Advancing Towards Global Justice” on Thursday, Nov. 17 at 6 pm in the Emory Student Center, multi-purpose rooms 5 and 6. Attendees can join in activities geared to the topics of environmental justice, climate and business, urban planning, conservation and more. 

The students will also produce podcasts on different aspects of COP for the Emory Climate Talks AmpliFIRE series. 

Following are brief summaries of the experiences and views of four of the Emory undergraduates who traveled to Egypt for COP. 

"Right after we touched down in Sharm El-Sheikh we grabbed our badges and headed to the conference," says Gabriela Rucker, right, shown with fellow senior Clare McCarthy.

“It was exciting to be immersed among 45,000 people working to generate solutions to the climate crisis," says Gabriela Rucker, a senior majoring in environmental sciences on the social science and policy track. 

Her interest in sustainable agriculture took her to the food-systems pavilion. She learned about programs to compensate farmers for preserving ecosystems and the increasing use of seaweed as a nutrient. “That was cool, right off the bat, to hear about those food solutions.” 

Rucker is a member of the Plastic-Free Emory task force and appreciated insights from Eric Njuguna, an activist from Kenya, during the “Youth: From Resistance to Power” event. 

“The United States exports a significant amount of plastics and other recycling abroad, where it ends up in landfills and becomes another country’s problem,” she says. “Eric Njuguna talked about his experiences dealing with trash from the United States. It’s important that people in the United States understand where our trash goes when we throw it away.” 

The connections she made during COP were a highlight for Rucker. “I met a lot of youth with passion and drive,” she says. “We have our careers in front of us so connecting with fellow youth about where they want to go and what they want to work on was invaluable.” 

Rucker is currently an intern at a solar-power development company. “My dream job would involve building solar plants to provide clean electricity for the United States,” she says. “During the next 20 years we need to build out a significant amount of renewable energy infrastructure.” 

Ultimately, COP further fueled her optimism. “I generally have a lot of hope for the progress of humanity,” Rucker says. “I’ve witnessed throughout my life people’s work toward a cleaner and more equitable society. My hope stems from the people who are doing the work to make that vision happen.”

Senior Jack Miklaucic is grateful for the anonymous donor who funds the trips by Emory students to COP. "It's a tribute to Dr. Saikawa's work that a donor is willing to do this for her students year after year," he says.

“The best part of COP for me was attending events led by civic groups doing energy-justice advocacy, which is the kind of work that I want to do,” says Jack Miklaucic, a senior majoring in environmental sciences and philosophy, politics and law. “They were led by really cool people who are fearless about calling out the fossil fuel companies and speaking truth to power. Hopefully, their examples will make me a more effective activist going forward.” 

Miklaucic plans to attend law school and hopes for a career involved with ensuring that utility companies and other energy providers are better regulated. “I want my work to have a direct, positive impact on society,” he says. 

“Enhancing energy efficiency is a big win for everybody,” Miklaucic adds. “It will improve people’s lives on the economic, climate and health levels. We’re already seeing movement toward more energy efficiency so that provides incentive to keep working towards more.” 

He is optimistic regarding climate solutions. “We were looking at a 3-to-4-degree Celsius rise in the global temperature average a few years ago and that’s no longer likely,” he points out. ”It’s important to stay focused on what kind of impact we can make because every tenth of a degree matters for what kind of world we’re going to live in.” 

Miklaucic appreciated the international perspective he gained from COP. “It was interesting to learn how climate activism is different around the world,” he says. “In some places they are persecuted and outright killed for doing what they do. It drove home to me that while it can be frustrating at times working for energy justice in the United States, it’s also a much safer place to be doing it.” 

"Every single person will be affected," says senior Clare McCarthy of climate change.

Clare McCarthy is a senior majoring in environmental sciences on the community building and social change track. She is also pursuing the 4+1 BS/MPH in environmental health at Rollins School of Public Health. 

She began learning about how the climate crisis is a social justice issue while she was in high school. It made her feel guilty to realize how people in the Global South tend to disproportionately suffer the greatest impacts of climate change as opposed to more privileged people in her hometown, where climate change felt distant. 

“That guilt paralyzed me,” she recalls, “until I came to Emory, when I decided to take action.” McCarthy is involved in efforts to hold the Emory administration accountable to stronger climate action through the Emory Climate Coalition and Emory Climate Reality Project. 

COP helped solidify her interest in loss and damage, or the harmful impacts of climate change, as well as efforts by local communities to adapt. She learned more about these issues first-hand by talking to leaders of nongovernment organizations, such as the International Center for Climate Change and Development, based in Bangladesh. 

“Loss and damage and how to address it became a headline issue for the first time at this year’s COP,” McCarthy says. “While it’s great to see this, it cannot be celebrated as a final victory because it’s way overdue and much more work is needed.” 

Countries in the Global South are asking countries in the Global North to set up a mechanism for financing recovery from both economic and health impacts due to climate events. “They want the money to be payments and not in the form of loans because then they will be in debt,” McCarthy says.

She envisions a career working internationally or within the United States to help communities build their capacity to respond to climate change. 

“It makes me feel hopeful to meet so many impressive people working on solutions,” McCarthy says. “The passion and dedication of my fellow activists, here at Emory and in communities around the world, keeps me going.” 

"Climate change is the greatest challenge that my generation faces," says senior Jackson Pentz, second from right. While in Egypt he visited the Great Sphinx of Giza along with his fellow undergraduates, (from left) Clare McCarthy, Gabriela Rucker, Jack Miklaucic and Nick Chang. 

“A lot of people associate environmental science with governmental policy but I’ve always been interested in business as a way of creating social change,” says Jackson Pentz, a senior majoring in Economics and Environmental Science on the Social Science and Policy Track. Pentz is also a member of the Goizueta Business School’s Environmental Management program. 

At COP he was impressed to learn that companies that compete for market share are actually collaborating on sustainability. “Many businesses are finding that in order to address sustainability issues they need to pool their research-and-development funding and share their knowledge,” he says. “The private sector is taking sustainability seriously and can come together more quickly and effectively than governments.”

Pentz already has a job lined up after he graduates in May. He’ll be working as a business consultant at McKinsey and Company specializing in sustainability and natural resources. 

Thinking about the climate crisis at the global, or even the national, level can make you feel helpless, he says. “But if you zoom in on individuals or organizations at the smaller scale, you start to see lots of positive action that can be replicated to make a bigger impact,” he adds. 

At the “Youth: Resistance to Power” event Pentz was buoyed by the remarks of Ayisha Saddiqa, a young climate justice activist who grew up in Pakistan as the member of an Indigenous community.

“She told us that young people shouldn’t feel responsible for saving the world. That’s obviously too big of a burden,” Pentz says. “But she personally feels responsible for working to help her community. If everybody does something manageable to help those around them, that’s how you start a social movement and collective action to improve things on a global scale.”


Youth views on climate take the world stage

Peachtree to Paris: Emory delegation headed to climate talks

Thursday, November 17, 2022

New chemistry toolkit speeds analyses of molecules in solution

"We've freed the researchers from most of the tedious, manual tasks of data input," says Emory theoretical chemist Fang Liu, center. Her team members who developed the toolkit include Emory graduate student Ariel Gale, left, and postdoctoral fellow Eugen Husk, right. Not shown is Xiao Huang, who worked on the project as an undergraduate.

By Carol Clark

A new open-source toolkit automates the process of computing molecular properties in the solution phase, clearing new pathways for artificial-intelligence design and discovery in chemistry and beyond. The Journal of Chemical Physics published the free, open-source toolkit developed by theoretical chemists at Emory University. 

Known as AutoSolvate, the toolkit can speed the creation of large, high-quality datasets needed to make advances in everything from renewable energy to human health. “By using our automated workflow, researchers can quickly generate 10, or even 100 times, more data compared to the traditional approach,” says Fang Liu, Emory assistant professor of chemistry and corresponding author of the paper. “We hope that many researchers will access our toolkit to perform high-throughput simulation and data curation for molecules in solution.” 

Such datasets, Liu adds, will provide a foundation for applying state-of-the-art machine-learning techniques to drive innovation in a broad range of scientific endeavors. 

First author of the paper is Eugen Hruska, a postdoctoral fellow in the Liu lab. Co-authors include Emory PhD candidate Ariel Gale and Xiao Huang, who worked on the paper as an Emory undergraduate and is now a graduate student of chemistry at Duke University. 

Exploring the quantum world 

A theoretical chemist, Liu leads a team specializing in computational quantum chemistry, including modeling and deciphering molecular properties and reactions in the solution phase. 

The world becomes much more complex as it shrinks down to the scale of atoms and small molecules, where quantum mechanics describes the wave-particle duality of energy and matter. 

Theoretical chemists use supercomputers to simulate the structures of molecules and the vast array of interactions that can occur during a reaction so that they can make predictions about how a molecule will behave under certain conditions. Understanding these dynamics is key to identifying promising molecules for various applications and for driving reactions efficiently. 

Researchers have already generated datasets for the properties of many molecules in the gas phase. Molecular properties in the solution phase, however, remain relatively unexplored in the context of big data and machine learning, despite the fact that most reactions occur in solution. 

The problem is that studying a molecule in solution requires much more time and effort. 

A complicated process 

“In the gas phase, molecules are far from each other,” Liu explains, “so when we study a molecule of interest, we don’t have to consider its neighbors.” 

In the solution phase, however, a molecule is closely immersed with many other molecules, making the system much larger. “Imagine a solvent molecule surrounded by layers and layers of water molecules,” Liu says. “Depending on its size and structure, a molecule may be covered by tens, or even up to hundreds, of water molecules. In systems of such large size, the computation will be slow and may not even be feasible.” 

Before running a quantum chemistry program for a molecule in the solution phase it’s necessary to first determine the geometry of the molecule and the location and orientation of the surrounding solvent molecules. 

“This process is difficult to do,” Liu says. “It takes so much time and effort, and it’s so complicated, that a researcher can only perform this calculation for a few systems that they care about in one paper,” Liu says. 

Technical issues can also arise during each step in the process, she adds, leading to errors in the results.

A streamlined solution 

Liu and her colleagues replaced the complicated steps required to perform these calculations with their automated system AutoSolvate. 

Previously, a computational chemist might have to type hundreds of lines of code into a supercomputer to run a simulation. The command-line interface for AutoSolvate, however, requires just a few lines of code to conduct hundreds of calculations automatically. 

“The time for running the simulations may be long, but that’s a job for the computer,” Liu says. “We’ve freed the researchers from most of the tedious, manual tasks of data input so that they can focus on analyzing their results and other creative work.” 

In addition to the command-line interface geared toward more experienced theoretical chemists, AutoSolvate includes an intuitive graphical interface that is suitable for graduate students who are learning to run simulations. 

Labs can now efficiently generate many data points for solvated molecules and then use the dataset to build machine-learning models for chemical design and discovery. AutoSolvate also makes it easier to build and share datasets across different research groups. 

Setting the stage for machine learning 

“During the past 10 years, machine learning has become a popular tool for chemistry but the lack of computational datasets has been a bottleneck,” Liu says. “AutoSolvate will allow the research community to curate a huge number of datasets for molecular properties in the solution phase.” 

Determining the redox potential of a solvent molecule, or the likelihood for an oxidation to occur, is just one example of a key research area that AutoSolvate could help advance. Redox-active molecules hold potential for applications in the development of anticancer drugs and chemical batteries for renewable-energy storage. 

“Building up redox-potential datasets will then allow us to use machine learning to look at millions of different compounds to rapidly find the ones with redox potential within the desired range,” Liu says.

Instead of a black-box result, such analyses of large datasets can yield interpretable artificial intelligence, or basic rules for molecular models.  

“The ultimate goal is to identify rules that can then be applied to solve a broad range of fundamental science problems,” Liu says. 

The development of AutoSolvate was funded by Emory University with computational resources provided by the National Science Foundation.


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Wednesday, November 2, 2022

Ancient DNA analyses add new complexity to South America settlement

"As more genomes from South America are sequenced and published, they are likely to reveal more nuances about how South America was first settled," says Emory anthropologist John Lindo. His ancient DNA lab specializes in mapping little-explored lineages of the Americas.

By Carol Clark

Genomic analyses of ancient individuals from South America add surprising twists in the story of early human settlement of the continent. The Royal Society Proceedings B published the results, which show ancestral evidence in the Americas for extinct hominins known as Denisovans. 

The work, providing the most complete genetic evidence to date for ancient Central American and South American migration routes, was led by anthropologists at Emory University and archeologists at Florida Atlantic University. 

Identification of Denisovan DNA goes back only to 2010, after Russian scientists uncovered a finger bone dated 50,000 to 30,000 years ago in a cave in the Altai Mountains of Siberia. Additional specimens from the Siberian cave were subsequently tied genetically to Denisovans, an archaic hominin with an affinity to Neanderthals, along with a single specimen from a cave on the Tibetan Plateau in China. 

“It’s phenomenal that Denisovan ancestry made it all the way to South America,” says John Lindo, a co-corresponding author of the paper and an anthropologist at Emory who specializes in ancient DNA analysis. “The admixture must have occurred a long time before, perhaps 40,000 years ago.” 

The fact that the Denisovan lineage persisted and its genetic signal made it into an ancient individual from Uruguay that is only 1,500 years old suggests that it was a large admixture event between a population of humans and Denisovans, Lindo says. 

First author of the paper is Andrew Luiz Campelo dos Santos, an archeologist now at Florida Atlantic University who was formerly at the Federal University of Pernambuco in Recife, Brazil. Dos Santos uncovered the remains of two individuals from northeastern Brazil, who date back 2,000 years and are included in the analyses. 

Co-corresponding author is Michael DeGiorgio from Florida Atlantic University, a population geneticist specializing in human, evolutionary and computational genomics. 

The Americas were the last continents that humans populated. Evidence suggests that Paleolithic hunter-gatherers entered North America from a land bridge that formed between northeastern Siberia and western Alaska during a period of lower sea level around 26,000 to 19,000 years ago. 

The current analyzes compared two newly sequenced ancient whole genomes from northeastern Brazil with present-day genomes and other ancient whole genomes from South America and Panama. The results showed distinct relationships between Meso America, or parts of the modern-day countries of Mexico and Central America, and both present-day South Americans and ancient individuals from northeastern and southeastern Brazil, Uruguay and Panama. The analyses also detected a strong Australasian signal in the ancient genomes from near the Atlantic coast in Brazil. 

These ancestral connections provide new genetic evidence — in support of existing archeological evidence — for an ancient migration route through Panama and along the Atlantic coast of South America. 

Adding to the complexity is the detection of a stronger signal for Denisovan ancestry in the ancient Uruguay and Panama individuals than in those from ancient Brazil. That suggests multiple waves of ancestral migrations along the Atlantic coast, the researchers conclude. 

The Lindo ancient DNA lab specializes in mapping little-explored human lineages of the Americas. Previously, little focus has been put on sequencing ancient DNA from South America. One reason is that warmer, more humid climates throughout much of the continent have made it more challenging to collect usable ancient DNA specimens, although advances in sequencing technology are helping to remove some of these limitations. 

As of the publication date of this paper, Lindo notes, only 12 ancient whole genomes from South America have been sequenced and published, in contrast to hundreds from Europe. Other published ancient genomic sequences from the continent have been limited to mitochondrial DNA (which is typically transmitted exclusively by maternal inheritance) and targeted DNA sequencing (which captures less than one percent of the genome). 

“In this paper we’ve analyzed all of the ancient whole genomes available for South America and found some surprises,” Lindo says. “As more whole genomes from South America are sequenced and published, they are likely to reveal more nuances about how South America was first settled.” 


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