Chris Sasaki

A team of researchers has developed a new approach to analyzing DNA evidence in sexual assault cases – one that could reduce lengthy delays in the processing of evidence.

While there are almost half a million sexual assaults in Canada every year, many more go unreported because victims are reluctant to come forward.

One of the reasons cited by victims is that analysis of forensic evidence is too slow.

Mohamed Elsayed (supplied image)

“For this research, we read reports and surveys that asked victims why they weren’t reporting assaults,” says the study’s lead author Mohamed Elsayed, who worked on the project as part of his PhD in biomedical engineering at the University of Toronto. “And the most common answer was that they didn't have confidence in the justice system – and that lack of confidence was partly because of how long the process takes.”

Elsayed, now a post-doctoral researcher in the department of chemistry in the Faculty of Arts & Science, co-authored the study with, among others, Leticia Bodo, a master’s student in the department of chemistry, and Aaron Wheeler, a professor in the department of chemistry, the Institute of Biomedical Engineering and the Centre for Research and Applications in Fluidic Technologies, a �鶹��Ƶ institutional strategic initiative.

All three researchers are also affiliated with the Donnelly Centre for Cellular and Biomolecular Research.

Processing forensic evidence in sexual assault cases is a technical, multi-step process that involves collecting DNA evidence and sending it to a well-equipped forensic laboratory for analysis by a skilled technician. Once there, the sample is first processed to isolate the assailant’s DNA from the victim’s so the assailant’s DNA can then be analyzed and used to identify a suspect.

The entire process can take days, weeks or longer. Most of that time is taken up with transporting the evidence to the lab, where its analysis can be further delayed depending on how many other cases are being investigated.

To speed things up, researchers focused on the first step: separating two individuals’ DNA from a single sample. At present, this is usually done manually by trained and experienced experts.

Elsayed and his collaborators, by contrast, developed a process called ’differential digestion” using digital microfluidics that helped simplify the overall process and reduce the number of manual steps needed to isolate the assailant’s DNA from 13 to five. “Also, because micro-fluidic processes tend to be faster, we expect that one of the eventual benefits will be shortening the overall time needed,” says Elsayed.

What’s more, the new approach could lead to a mobile solution that no longer requires a lab. For example, testing could be done at a hospital, circumventing the lab’s queue.

The new technique, described in a paper published in the journal Advanced Science, is compatible with the technology known as Rapid DNA analysis that is already in use for the second step of identifying an individual from their DNA. The study’s authors, which included researchers from �鶹��Ƶ Mississauga’s forensic science program, say the long-term goal is to integrate the two technologies to make the process even more streamlined.

While there remain several challenges to deploying the new technique, Elsayed says he is confident they can be overcome and has turned his efforts toward making it widely accessible and commercially viable.

“Our plan is to develop an instrument that will do in five minutes what currently takes 45,” says Elsayed. “And to run many more samples than previously. Once we do that, the next step would be to introduce the technology to forensic labs and hospitals.

“It will take years, but the potential is very exciting.”

The research was supported by the ANDE Corporation and NSERC Alliance Society.

"I’m grateful to NSERC for having the foresight to establish the ‘Alliance Society’ program which has a mission to ‘address a societal challenge that will result in new natural sciences and engineering knowledge and societal impact,” Wheeler says.

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Forensic Science

Supermassive black hole mergers could be explained by dark matter: Study

Christopher.Sorensen — Tue, 06 Aug 2024 15:35:00 +0000

Supermassive black hole mergers could be explained by dark matter: Study

Christopher.Sorensen Tue, 08/06/2024 - 11:35

Cutline

A visualization of two supermassive black holes in orbit around each other (image by NASA's Goddard Space Flight Center/Scott Noble; simulation data, d'Ascoli et al. 2018)

Chris Sasaki

Topic

Breaking Research

Department of Physics

Faculty of Arts & Science

Research and Innovation

Space

Subheadline

A team of researchers that includes a �鶹��Ƶ postdoc may have solved the "final parsec problem" of astrophysics

A team of astrophysicists that includes the University of Toronto’s Gonzalo Alonso-Álvarez has shown that pairs of supermassive black holes can merge together into a single, larger black hole – a major breakthrough in addressing what is known as the "final parsec problem."

Gonzalo Alonso-Álvarez (supplied image)

The longstanding astrophysics problem refers to a discrepancy between the detection of gravitational signals permeating the universe – which astrophysicists previously hypothesized had emanated from millions of merging pairs of supermassive black holes (SMBHs) – and theoretical simulations which showed that the approach of SMBHs stalls when they’re roughly one parsec (about three light years) apart.

Not only did the final parsec problem conflict with the theory that merging SMBHs were the source of the gravitational wave background, it was also at odds with the theory that SMBHs – each billions of times more massive than our Sun – grow from the merger of less massive black holes.

The new research, published in Physical Review Letters, has shown that pairs of SMBHs can indeed break through the one-parsec barrier and merge into a single black hole. This is demonstrated by calculations showing that SMBHs continue to draw closer because of previously overlooked interactions with particles within the vast cloud of dark matter surrounding them.

“We show that including the previously overlooked effect of dark matter can help supermassive black holes overcome this final parsec of separation and coalesce,” says Alonso-Álvarez, a post-doctoral fellow in the department of physics at �鶹��Ƶ’s Faculty of Arts & Science and the department of physics and Trottier Space Institute at McGill University, who is first author on the paper. “Our calculations explain how that can occur, in contrast to what was previously thought.”

SMBHs are thought to lie in the centres of most galaxies. When two galaxies collide, the SMBHs fall into orbit around each other; as they revolve around each other, the gravitational pull of nearby stars tugs at them and slows them down, causing them to spiral inward toward a merger.

Previous merger models showed that when the SMBHs approached to within roughly a parsec, they begin to interact with the dark matter cloud or halo in which they are embedded. These models indicated that the gravity of spiraling SMBHs throws dark matter particles clear of the system.

The new model introduced by Alonso-Álvarez and co-authors James Cline, a professor at McGill University and the European Organization for Nuclear Research (CERN) in Switzerland, and Caitlyn Dewar, a graduate student at McGill, reveals that dark matter particles interact with each other in such a way that they are not dispersed. The density of the dark matter halo remains high enough that interactions between the particles and the SMBHs continue to degrade the SMBH’s orbits – clearing a path to a merger.

“The possibility that dark matter particles interact with each other is an assumption that we made, an extra ingredient that not all dark matter models contain,” says Alonso-Álvarez. “Our argument is that only models with that ingredient can solve the final parsec problem.”

The background hum generated by these colossal cosmic collisions is made up of gravitational waves of much longer wavelength than those first detected in 2015 by astrophysicists operating the Laser Interferometer Gravitational-Wave Observatory (LIGO). Those gravitational waves were generated by the merger of two black holes, both some 30 times the mass of the Sun.

The background hum has been detected in recent years by scientists operating the Pulsar Timing Array. The array reveals gravitational waves by measuring minute variations in signals from pulsars, rapidly rotating neutron stars that emit strong radio pulses.

In addition to providing insight into SBMH mergers and the gravitational wave background signal, the new result also provides a window into the nature of dark matter. “Our work is a new way to help us understand the particle nature of dark matter,” says Alonso-Álvarez. “We found that the evolution of black hole orbits is very sensitive to the microphysics of dark matter and that means we can use observations of supermassive black hole mergers to better understand these particles.”

For example, the researchers found that the interactions between dark matter particles they modeled also explains the shapes of galactic dark matter halos.

“We found that the final parsec problem can only be solved if dark matter particles interact at a rate that can alter the distribution of dark matter on galactic scales,” says Alonso-Álvarez.

“This was unexpected since the physical scales at which the processes occur are three or more orders of magnitude apart. That’s exciting.”

16-year-old physics grad completes ‘incredible journey’ at �鶹��Ƶ

Christopher.Sorensen — Mon, 03 Jun 2024 15:33:09 +0000

16-year-old physics grad completes ‘incredible journey’ at �鶹��Ƶ

Christopher.Sorensen Mon, 06/03/2024 - 11:33

Cutline

Daniel Honciuc Menendez, 16, is the youngest to graduate from the Faculty of Arts & Science, �鶹��Ƶ Scarborough or U of Mississauga since at least 1979 (photo by Diana Tyszko)

Chris Sasaki

Topic

Our Community

Convocation 2024

Faculty of Arts & Science

International Students

Physics

University College

Subheadline

Daniel Honciuc Menendez carried out research on dark matter detection and theoretical quantum optics

Daniel Honciuc Menendez was 11 years old when he took part in a summer program in theoretical physics at the Perimeter Institute in Waterloo, Ont., in 2019.

“I’d known for a long time that I wanted a career in physics. But it was in this program that I learned for sure that this was what I wanted to do with my life,” says Honciuc Menendez, who is Ecuadorean and was living in the country's capital Quito at the time.

The trip was his first visit to Canada – and made a big impression. “I liked the openness of the people and the diversity. So I decided that when I applied to universities, I would make sure to apply to universities in Canada.”

After completing high school at age 12, Honciuc Menendez received offers of admission from 12 post-secondary institutions in Canada, the U.S. and Ecuador. He chose the University of Toronto, where he received an International Scholars Award, and began his undergraduate studies as a member of University College.

Honciuc Menendez at 11 years old at the launch of one of his experiments on a rocket with the NASA Cubes in Space program at the Wallops Flight Facility (photo courtesy Daniel Honciuc Menendez)

Now 16 years old, Honciuc Menendez is graduating with a specialist in physics and a major in mathematics with high distinction. He’s the youngest to graduate from the Faculty of Arts & Science, �鶹��Ƶ Scarborough or �鶹��Ƶ Mississauga since at least 1979, the year the university began tracking such data.

“I’m proud and excited to be graduating,” he says. “It’s the culmination of four years of hard work, research and volunteer experiences. I’m really looking forward to convocation.”

Faculty of Arts & Science writer Chris Sasaki spoke to Honciuc Menendez before his convocation.

When did your interest in science begin?

I started reading at an early age. When I was very young, my mother and I moved often to different countries because of her career. During this time, I was surrounded by a variety of books, including math books, puzzle books, encyclopedias and atlases. They became my early companions and mentors. Also, even before starting school, I was captivated by educational videos, websites and apps about math, physics, chemistry and other subjects. Then, at 4 years old, while living in the U.K., I gained early entrance into grade school and became interested in programming and robotics. I attended every science festival I could. It became clear to me that I wanted to pursue a life in the sciences.

What was your early education like?

Early entrance into grade school in the U.K. was my first ‘grade-skip.’ When I was six years old, we moved back to Ecuador and I wanted to learn more challenging material during my classes. After meetings with my new school, I was encouraged to apply to the Johns Hopkins University (JHU) Centre for Talented Youth. Upon passing the entrance tests, I was admitted into the program, which allowed me to take advanced courses.

At nine years old, I skipped another grade and started auditing International Baccalaureate (IB) diploma classes in physics and music. Then, when I was 10 years old, I also took the SAT and with its results, I was allowed to skip four more grades to 11th grade and was also able to join other programs like JHU’s Study of Exceptional Talent. From there, I took a full IB diploma program and graduated from high school at 12 years old.

What research projects were you able to take part in at �鶹��Ƶ?

The first was with Professor Miriam Diamond in dark matter detection with the Super Cryogenic Dark Matter Search experiment at SNOLAB, an underground research facility near Sudbury for neutrino and dark matter studies. I developed and tested dark matter detector simulations and conducted data analysis on remote servers.

The second was in theoretical quantum optics with Professor John Sipe at the Centre for Quantum Information & Quantum Control, in which I investigated the theoretical optical response for waveguide-quantum dot systems that could be used as the basis for optical quantum computers.

Throughout both experiences, the collaborative and inclusive spirit of the physics community really inspired me. The professors and researchers provided invaluable mentorship to me and have significantly shaped my decision to pursue a physics research career involving high-energy physics and quantum information.

Honciuc Menendez pursued his interest in music with the Hart House Chamber Strings ensemble (photo courtesy Daniel Honciuc Menendez)

What field are you most interested in now?

I’m interested in quantum information and high-energy physics. Quantum information is a unique field that has applications to various disciplines, since quantum computers can solve various problems that classical computers cannot. I want to specialize in quantum algorithms since they’re essential to realizing the potential of quantum information in its applications, including in my other field of interest, high-energy physics. The more I learn about quantum information's capabilities and its synergy with high-energy physics, the more I realize the significant impact these technologies could have on our understanding of the universe and on advancing computational sciences.

What are your plans after graduation?

I was honored to receive a full scholarship from the European Union to pursue a master's of science in physics with a concentration in quantum science and technology. The program will take place over two years at the Sapienza University of Rome in Italy, then at Université Paris-Saclay in France, and lastly at �鶹��Ƶ. I’ll be taking courses and developing my career in quantum technology in academia and industry, and exploring the interdisciplinary possibilities of the quantum science landscape, including in high-energy physics, medicine, cybersecurity and finance. Later, I want to pursue a PhD in physics where I can go deeper into the intersection between quantum information and high-energy physics.

What are your thoughts as you look back at the past four years?

Throughout these years, the support from my friends, professors and mentors at �鶹��Ƶ, and the resources provided by University College and �鶹��Ƶ’s Accessibility Services have been invaluable and have helped me navigate the complexities of academic life and the personal challenges of being a young student. Plus, all of this would not have been possible without the unconditional support from my mother, a single mom who has been my constant source of strength and inspiration, and who accompanied me as I pursued my studies in Canada.

These past four years have been transformative for me — not just academically but also personally — and were filled with challenges, achievements and growth. It’s been an incredible journey, and I step forward with a heart full of gratitude for the �鶹��Ƶ community, ready for the next chapter of my life.

�鶹��Ƶ researchers identify 'degrees of Kevin Bacon' gene in fruit flies

rahul.kalvapalle — Fri, 24 May 2024 20:22:51 +0000

�鶹��Ƶ researchers identify 'degrees of Kevin Bacon' gene in fruit flies

rahul.kalvapalle Fri, 05/24/2024 - 16:22

Cutline

(photo by janeff/iStock)

Chris Sasaki

Topic

Breaking Research

Ecology & Evolutionary Biology

Faculty of Arts & Science

Genes

Genetics

Research & Innovation

�鶹��Ƶ Mississauga

Subheadline

Researchers studied two distinct strains of fruit flies and found that one group showed different patterns of connections within their networks

A team of researchers from the University of Toronto has identified a gene in fruit flies that regulates the types of connections between flies within their “social network.”

The researchers studied groups of two distinct strains of Drosophila melanogaster fruit flies and found that one strain showed different types or patterns of connections within their networks than the other strain.

The connectivity-associated gene in the first strain was then isolated. When it was swapped with the other strain, the flies exhibited the connectivity of the first strain.

Researchers named the gene after Hollywood star Kevin Bacon (photo by Theo Wargo/Getty Images)

The researchers named the gene “degrees of Kevin Bacon” (dokb), for the prolific Hollywood star of such films as Footloose and Apollo 13. Bacon’s wide-ranging connections to other actors is the subject of the parlour game called “The Six Degrees of Kevin Bacon,” which plays on the popular idea that any two people on Earth can be linked through six or fewer mutual acquaintances.

“There's been a lot of research around whether social network structure is inherited, but that question has been poorly understood,” says Rebecca Rooke, a post-doctoral fellow in the department of ecology and evolutionary biology in the Faculty of Arts & Science and lead author of the paper, published in Nature Communications. “But what we’ve now done is find the gene and proven there is a genetic component.”

The work was carried out as part of Rooke’s PhD thesis in Professor Joel Levine’s laboratory at �鶹��Ƶ Mississauga before he moved to the department of ecology and evolutionary biology, where he is currently chair.

“This gives us a genetic perspective on the structure of a social group,” says Levine. “This is amazing because it says something important about the structure of social interactions in general and about the species-specific structure of social networks.

Post-doctoral researcher Rebecca Rooke (supplied image)

“It's exciting to be thinking about the relationship between genetics and the group in this way. It may be the first time we’ve been able to do this.”

The researchers measured the type of connection by observing and recording on video groups of a dozen male flies placed in a container. Using software previously developed by Levine and post-doctoral researcher Jon Schneider, the team tracked the distance between flies, their relative orientation and the time they spent in close proximity. Using these criteria as measures of interaction, the researchers calculated the type of connection or “betweenness centrality” of each group.

Rooke, Levine and their colleagues point out that individual organisms with high betweenness centrality within a social network can act as “gatekeepers” who play an important role in facilitating interactions within their group.

Gatekeepers can influence factors like the distribution of food or the spread of disease. They also play a role in maintaining cohesion, enhancing communication and ensuring better overall health of their group.

In humans, betweenness centrality can even affect the spread of behaviours such as smoking, drug use and divorce.

Professor Joel Levine (supplied image)

At the same time, the researchers point out that social networks are unbiased and favour neither “good” nor “bad” outcomes. For example, high betweenness centrality in a network of scientists can increase potential collaborators; on the other hand, high betweenness centrality in another group can lead to the spread of a disease like COVID-19.

“You don't get a good or a bad outcome from the structure of a network,” explains Levine. “The structure of a network could carry happiness or a disease.”

Rooke says an important next step will be to identify the overall molecular pathway that the gene and its protein are involved in “to try to understand what the protein is doing and what pathways it’s involved in – the answers to those questions will really give us a lot of insight into how these networks work.”

And while the dokb gene has only been found in flies so far, Rooke, Levine and their colleagues anticipate that similar molecular pathways between genes and social networks will be found in other species.

“For example, there's a subset of cells in the human brain whose function relates to social experience – what in the popular press might be called the ‘social brain,’” says Levine.

“Getting from the fly to the human brain – that's another line of research. But it almost has to be true that the things that we're observing in insects will be found in a more nuanced, more dispersed way in the mammalian brain.”

Students tackle impact of climate change at �鶹��Ƶ Climate Impacts Hackathon

Christopher.Sorensen — Mon, 06 May 2024 16:44:57 +0000

Students tackle impact of climate change at �鶹��Ƶ Climate Impacts Hackathon

Christopher.Sorensen Mon, 05/06/2024 - 12:44

Cutline

Students, instructors and organizers participate in the inaugural Climate Impacts Hackathon (photo by Milan Ilnyckyj, CC BY-NC-SA 2.0 DEED)

Chris Sasaki

Topic

Our Community

Climate Positive Energy

Data Sciences Institute

Institutional Strategic Initiative

Climate Change

Faculty of Applied Science & Engineering

Faculty of Arts & Science

Undergraduate Students

Subheadline

Teams of undergraduate and graduate students grappled with problems that ranged from altering irrigation practices in Sudan to adapting snow-clearing plans in Ottawa

In the wake of Toronto’s warmest winter on record, students at the University of Toronto recently gathered for the inaugural �鶹��Ƶ Climate Impacts Hackathon.

The event asked students to tackle several challenges brought by a warming planet: How should the City of Ottawa adapt its snow clearing plan in response to increased precipitation caused by our warming atmosphere? How should irrigation practices in Sudan change in response to higher temperatures and reduced rainfall? And where should new cooling stations – swimming pools, libraries, community centres, shopping malls – be located in an increasingly sweltering City of Toronto?

Participants included undergraduate and graduate students from a range of natural science and engineering disciplines, as well as from the humanities and social sciences. They were divided into teams and competed for prizes.

The hackathon was led by Paul Kushner, a professor of Earth, atmospheric and planetary physics in the department of physics in the Faculty of Arts & Science; and Karen Smith, an associate professor, teaching stream, in the department of physical and environmental sciences (DPES) at �鶹��Ƶ Scarborough. Co-organizers included Michael Morris, a PhD candidate in the department of physics, and Francisco Camacho, a masters of environmental science student at DPES.

The event was hosted by the department of physics and the DPES; sponsors included Climate Positive Energy (CPE) – a �鶹��Ƶ institutional strategic initiative – the Centre for Climate Science and Engineering (CSE) and the Cosmic Future Initiative.

The event kicked off with a wide-ranging discussion from a panel of climate experts with diverse perspectives.

Steve Easterbrook, director of the School of the Environment in the Faculty of Arts & Science, spoke about how climate models work and why we can trust them. Lisa MacTavish, project lead in resilience, climate resilience policy and research for the City of Toronto, shared how the city uses climate projections to manage infrastructure and crisis planning. And Daniel Posen, an associate professor in the department of civil and mineral engineering in the Faculty of Applied Science & Engineering, talked about his expertise at the intersection of climate change and engineering.

To develop their solutions, students used the University of Toronto Climate Downscaling Workflow (UTCDW) which includes the UTCDW Guidebook developed by Morris, Smith and Kushner, and the UTCDW Survey, a project design tool. The UTCDW was developed with the support of the CSE, CPE and the Data Sciences Institute, another �鶹��Ƶ institutional strategic initiative.

Climate models or simulations typically work on a global scale; the UTCDW is designed to help researchers “downscale” what the models do in order to understand how smaller regions and even individual cities are being affected by climate change. The resulting projections can then inform decisions on a local level.

“In our proposal for support to develop these tools, we committed to holding this hackathon to roll them out,” says Kushner. “The intent is to encourage a better understanding of climate change impacts on different domains of application in an atmosphere of fun engagement and community cohort building.”

First prize was awarded to a team that tackled the cooling centre challenge. Using the downscaling tool, the team made detailed projections using temperature and humidity data. They considered vulnerable groups including children, the elderly, refugees and the underhoused; and they factored in education and income levels.

After surveying the current locations of the city’s cooling centres, the team came up with recommendations for six new centres located in areas that are currently underserved.

“We were very pleased and impressed at how far the student participants got in their analysis – how they creatively overcame technical and conceptual obstacles, and how they maintained a constructive and positive attitude as they grappled with the serious issues of climate change,” Kushner says.

�鶹��Ƶ researcher seeks out new insights on the universe's oldest galaxies

Christopher.Sorensen — Thu, 08 Feb 2024 19:27:46 +0000

�鶹��Ƶ researcher seeks out new insights on the universe's oldest galaxies

Christopher.Sorensen Thu, 02/08/2024 - 14:27

Cutline

Jacqueline Antwi-Danso, a postdoctoral researcher with the David A. Dunlap department of astronomy and astrophysics, is studying massive galaxies that formed “when the universe was still just a baby” (supplied image)

Chris Sasaki

Topic

Our Community

Astronomy & Astrophysics

Black

Dunlap Institute for Astronomy & Astrophysics

Faculty of Arts & Science

Indigenous

Space

Statistical Sciences

Subheadline

"We're trying to understand why these galaxies formed the way they did and how they became so big so quickly"

Jacqueline Antwi-Danso remembers a book from her junior high school library describing how stars are born and how the most massive stars die in gigantic explosions called supernovae.

“The book explained that there were objects out in space that gave off so much energy we could see and study them and make precise observations of their physical properties,” says Antwi-Danso, who credits her parents for nurturing her interest in education and reading while growing up in Ghana. “That just blew my mind.”

Today, Antwi-Danso is an NSERC Banting postdoctoral fellow at the University of Toronto’s David A. Dunlap department of astronomy and astrophysics in the Faculty of Arts & Science. Her work focuses on studying massive galaxies that formed “when the universe was still just a baby.”

She is also active in supporting Black, Latinx and Indigenous women who are interested in a career in science.

She recently spoke to �鶹��Ƶ’s Chris Sasaki about her career, research and goals.

Was there an important milestone in your journey to becoming an astronomer?

After high school, my plan was to take a gap year to figure out if I wanted to stay in Ghana and do something in the sciences at the university level or go elsewhere.

That’s when an opportunity came my way. There was a program run by the American Embassy in Accra for Ghanaian high school students interested in studying in the U.S. It provided mentorship for things like how to apply to schools in the U.S., how to write a good college application and how to select courses. They also helped you think about what you wanted to do in your career.

It was a big turning point in my life when I was selected to join the program. That’s how I learned about opportunities outside of Ghana and realized that if I was going to study astronomy, I would have to leave because we don't have astronomy at the collegiate level. And so, I made my decision to study astronomy at Texas Christian University.

Large, relatively nearby galaxies like this one took billions of years to form. Antwi-Danso is trying to determine how large galaxies in the very distant universe formed in a small fraction of that time (photo by ESA/Hubble & NASA, D. Jones Acknowledgement: G. Anand, L. Shatz.)

As an astronomer, what questions are you trying to answer?

I study massive galaxies in the very distant universe – some of the very first structures that formed after the Big Bang nearly 14 billion years ago. We're trying to understand why these galaxies formed the way they did and how they became so big so quickly. We’re finding them at increasingly earlier times, as far back as when the universe was just four per cent of its current age.

This goes against our understanding of the hierarchical formation of large structures – where massive galaxies like our Milky Way galaxy were formed from the merger of galaxies that were formed from stars, which, in turn, formed from clouds of gas and dust.

For our galaxy, it took billions of years to attain its current stellar mass. These distant, massive galaxies had only a fraction of the time to go through this process, so we have no idea how they formed so quickly. So, one of two things is happening: either there's something wrong with our observations or we need to revise our current models. That's the big problem I'm working on and I’m actually looking for a summer undergraduate student to work on this project.

Jacqueline Antwi-Danso speaks to students at a meeting of the American Astronomical Society (supplied image)

You’re working to support Black, Indigenous and Latinx women in science. Can you tell me more about that?

The League of Underrepresented Minoritized Astronomers (LUMA) is a peer mentoring organization for women in astronomy, physics and the planetary sciences that was formed in 2015 by Catherine Espaillat, who is the director of the Institute for Astrophysical Sciences at Boston University. She started LUMA because, as a Dominican American grad student, she felt isolated.

There weren’t many people in her field who looked like her, with whom she shared backgrounds. So, she created LUMA to be a community of people with similar experiences who could provide each other with support. I joined because I also realized there weren't many people in my field who looked like me. There were even fewer African astronomers. And, like Catherine, I wanted a place where we could come together as a community and support each other.

Do have you have plans to do the same type of work here in Canada?

I would like to continue this work, so I've been learning about and trying to understand what the Canadian science landscape looks like. I think the challenge in Canada is similar to the challenge that LUMA faces in the U.S. – there are very few Black, Indigenous or Latinx women in science in either country. So, yes, I would like to do similar work here. I just don't know what that looks like yet.

What about in Ghana?

One thing that I had in mind was trying to create some sort of pipeline for students in Ghana who might be interested in astronomy and might want to study in the U.S. or Canada. There are challenges, of course, but I’m talking to people who have been involved in similar projects and have found solutions to these challenges. For example, it might mean helping by providing mentorship to students who are already interested in physics and to students who are a little further along in their studies. I'm hopeful there are a number of ways to make this work.

How do you feel about receiving the NSERC Banting fellowship?

I’m very grateful and humbled to receive it. For me, it represents an exciting opportunity to work independently on my research, especially at �鶹��Ƶ with all the people in the Dunlap Institute (for Astronomy & Astrophysics), the department of astronomy and astrophysics, CITA (Canadian Institute for Theoretical Astrophysics) and the department of statistical sciences. I feel like �鶹��Ƶ is the perfect place for me because I’m combining astronomy with statistics and cosmological simulations to understand these really massive, distant galaxies. I’m having the time of my life, and I’m looking forward to seeing what the next few months will bring.

�鶹��Ƶ geoscientists shed new light on plate tectonics

Christopher.Sorensen — Tue, 06 Feb 2024 17:08:10 +0000

�鶹��Ƶ geoscientists shed new light on plate tectonics

Christopher.Sorensen Tue, 02/06/2024 - 12:08

Cutline

Researchers have discovered undersea faults on the Pacific plate, some of which are hundreds of kilometres long (image by NOAA/NASA GOES Project)

Chris Sasaki

Topic

Breaking Research

Earth Sciences

Faculty of Arts & Science

Research & Innovation

�鶹��Ƶ Scarborough

Subheadline

The researchers found that the Pacific plate is scored by large undersea faults that are pulling it apart

A team of geoscientists from the University of Toronto is shedding new light on the century-old model of plate tectonics, which suggests the plates covering the ocean floors are rigid as they move across the Earth’s mantle.

The researchers found that the Pacific plate is scored by large undersea faults that are pulling it apart. The newly discovered faults, described in a paper published in the journal Geophysical Research Letters, are the result of enormous forces within the plate tugging it westward.

Some of the faults are thousands of metres deep and hundreds of kilometres long.

Erkan Gün (photo by Don Campbell)

“We knew that geological deformations like faults happen on the continental plate interiors far from plate boundaries,” says Erkan Gün, a post-doctoral researcher in the department of physical and environmental sciences at �鶹��Ƶ Scarborough. “But we didn't know the same thing was happening to ocean plates.”

Russell Pysklywec, a professor in the department of Earth Sciences in the Faculty of Arts & Sciences, adds that the research contributes to a fuller understanding of the field.

“What we're doing is refining plate tectonics – the theory that describes how our planet works – and showing those plates really aren't as pristine as we previously thought.”

Other researchers involved in the study include Phil Heron, an assistant professor in the department of physical and environmental sciences at �鶹��Ƶ Scarborough, as well as researchers from the Eurasia Institute of Earth Sciences at Istanbul Technical University.

For millions of years, the Pacific plate – which constitutes most of the Pacific Ocean floor – has drifted westward to plunge down into the Earth’s mantle along undersea trenches or subduction zones that run from Japan to New Zealand and Australia. As the western edge of the plate is pulled down into the mantle, it drags the rest of the plate with it like a tablecloth being pulled from a table.

The newly discovered plate damage at the faults occurs within extensive, sub-oceanic plateaus formed millions of years ago when molten rock from the Earth’s mantle extruded onto the ocean floor; the faults tend to run parallel to the closest trench.

“It was thought that because the sub-oceanic plateaus are thicker, they should be stronger,” says Gün. “But our models and seismic data show it’s actually the opposite: the plateaus are weaker.”

In other words, if the Pacific plate is like a tablecloth being pulled across a tabletop, the plateaus are patches of weaker cloth that are more prone to tearing.

Russell Pysklywec on the south slope of Mount Tongariro in New Zealand (supplied image)

The researchers studied four plateaus in the western Pacific Ocean – the Ontong Java, Shatsky, Hess and Manihiki – in a vast area roughly bounded by Hawaii, Japan, New Zealand and Australia. They made their discovery using supercomputer models and existing data – some collected in studies done in the 1970s and ‘80s.

“There is evidence that volcanism occurred at these sites in the past as a result of this type of plate damage – perhaps episodically or continuously – but it isn’t clear if that’s happening now,” says Gün. “Still, we can’t be certain because the plateaus are thousands of metres below the ocean surface and sending research vessels to collect data is a major effort. So, in fact, we’re hopeful our paper brings some attention to the plateaus and more data will be collected.”

The theory of plate tectonics has been refined over many decades by numerous Earth scientists, including �鶹��Ƶ’s John Tuzo Wilson, who made significant contributions to it during his career.

“But the theory’s not carved in stone and we’re still finding new things,” says Pysklywec. “Now we know this fault damage is tearing apart the centre of an ocean plate – and this could be linked to seismic activity and volcanism.

“A new finding like this overturns what we’ve understood and taught about the active Earth,” he says. “And it shows that there are still radical mysteries about even the grand operation of our evolving planet.”

In his latest book, �鶹��Ƶ prof tells the story of the human mind

Christopher.Sorensen — Wed, 22 Nov 2023 19:10:20 +0000

In his latest book, �鶹��Ƶ prof tells the story of the human mind

Christopher.Sorensen Wed, 11/22/2023 - 14:10

Cutline

Paul Bloom, a professor of psychology, provides an overview of major aspects of psychology in his seventh book: Psych: The Story of the Human Mind (photo by Greg Martin)

Chris Sasaki

Topic

Our Community

Faculty of Arts & Science

Psychology

Subheadline

Paul Bloom says psychology is "about the most interesting topic there is – us"

Paul Bloom’s latest book kicks off by recounting a daydream in which he quits his job as a psychology professor to venture into the world of cosmology.

But his fantasy of studying the vast reaches of the universe was brief because, he writes, “...all of psychology gives me this buzz. It’s about the most interesting topic there is – us. It’s about our feelings, experiences, plans, goals, fantasies, the most intimate aspects of our being.”

A professor in the University of Toronto’s department of psychology in the Faculty of Arts & Science, Bloom’s research focuses on developmental psychology, personality and how we make sense of the world – with a particular interest in pleasure, morality, religion, fiction and art.

His seventh book, Psych: The Story of the Human Mind, had its origins in the introductory psychology course Bloom taught at Yale University and, as such, provides an excellent overview of major aspects of psychology.

In its pages, he attempts to “put forth the best answers we have” to the fundamental questions most have pondered: How does the brain give rise to intelligence and conscious experience? Where does knowledge come from? How and why do we differ in personality, intelligence and other traits? How does the mind of a child differ from that of an adult? What makes people happy?

He also provides an overview of the different schools of psychological thought that offered their own best answers to the queries.

He describes the mechanistic or materialist point of view that our thoughts and emotions are the output of a vast assembly of nerve cells and the result of interactions between various molecules – or as Nobel Prize-winner and co-discoverer of the helical structure of DNA Francis Crick wrote: “Brain makes thought.”

He also describes “Cartesian dualism,” named for French philosopher and scientist René Descartes – the idea that our minds and our physical selves are distinct entities. In other words, we are bodies and souls. We feel certain, Bloom writes, “we are not our bodies; we inhabit these bodies. We are Ghosts in the Shell.”

Psych is filled with anecdotes and intriguing facts that help explain psychological principles and bring them to life – insights that would’ve sparked curiosity and interest among the students who either enrolled in the Yale course or took the online version of it that Bloom later developed.

He tells the story of Phineas Gage, who in 1848, while working on the construction of a railway, had a metal rod blasted through his brain. Gage survived and retained the ability to speak and understand language, as well as other intellectual capacities. However, Gage eventually suffered severe changes to his personality and emotional states, began having seizures and died – a clear demonstration of how physical damage to the brain affects who we are.

Bloom wrote the book during COVID-19, and he uses the pandemic to discuss the question: “If we’re so smart, why do we often seem so dumb?” Why is Holocaust denial still rampant, why do some believe 9/11 was an “inside job,” why are there so many followers of QAnon who believe, among other absurdities, that the actor Tom Hanks is a Satanist?

And why has COVID-19 become so politicized with so little regard to science? In writing about conspiracy theories like these, Bloom describes how beliefs about the disease contrast starkly between Democrats and Republicans (with neither side having a monopoly on accuracy). He cites a study showing that subjects supported a hypothetical government program, not on its merits, but on whether they were told it was a Democratic or Republican initiative.

Nonetheless, Bloom is optimistic and writes that, despite our irrationality, “... we are also the animal that is capable of acting intelligently for the long-term good...and tries to see things as they really are.”

The questions of consciousness and mind that Bloom raises in his book point to just how vast the story of the human mind is – despite its miniscule size compared to, say, a galaxy.

“The more you look at the mind and how it works from a serious scientific point of view, the more you appreciate its complexity, its uniqueness, and its beauty.”

Researchers use powerful AI tool to gain new insights into protein structures

Christopher.Sorensen — Fri, 03 Nov 2023 16:35:45 +0000

Researchers use powerful AI tool to gain new insights into protein structures

Christopher.Sorensen Fri, 11/03/2023 - 12:35

Cutline

A protein containing amino acids with fixed spiral and ribbon structures, in blue and light blue, as well as thread-like disordered regions in orange (photo by AlphaFold Protein Structure Database (CC BY 4.0).

Chris Sasaki

Topic

Breaking Research

Temerty Faculty of Medicine

Cell and Systems Biology

Faculty of Arts & Science

Global

Hospital for Sick Children

Research & Innovation

Subheadline

The findings could lead to a better understanding of the role played by proteins in disease and the development of new treatments

An international team of researchers has revealed new insights about the three-dimensional structure of certain types of proteins by using the powerful artificial intelligence tool AlphaFold2.

Long molecules comprising strings of amino acids, proteins are folded into three-dimensional structures according to a strict set of rules. The myriad of different structures enable proteins to perform their functions. Within organisms, from bacteria to humans, they transport molecules, act as catalysts for chemical processes, operate as valves and pumps – and much more.

While AlphaFold2 has predicted the three-dimensional structure of some 200 million proteins, it has until now been unable to determine whether sections within certain proteins, known as intrinsically disordered regions (IDRs), have any structure at all – much less predict the shape of that structure.

Alan Moses (supplied image)

“This has been a long-standing debate amongst biochemists and molecular biologists – whether IDRs have fixed structure or whether they’re just ‘floppy’ parts of proteins,” says Alan Moses, a computational biologist and professor in the department of cell and systems biology in the University of Toronto’s Faculty of Arts & Science.

“We confirmed that, [while] AlphaFold2 still can't predict the structure of IDRs very well ... what it can do is tell us which IDRs are likely to have some structure – something that was previously impossible.”

Moses is a co-author of a new paper, published in the journal Proceedings of the National Academy of Sciences, that details the research team’s findings and could lead to a better understanding of the role played by these proteins in disease and to the development of new drug treatments.

His co-authors include Reid Alderson, a post-doctoral researcher with the Medizinische Universität Graz (MUG) who formerly did post-doctoral work at �鶹��Ƶ; Julie Forman-Kay, a senior scientist and program head of molecular medicine at the Hospital for Sick Children and a professor of biochemistry in �鶹��Ƶ’s Temerty Faculty of Medicine; Desika Kolaric, a research assistant at MUG; and Iva Pritišanac, an assistant professor at MUG and former post-doctoral researcher in Moses’s lab.

The team’s findings are significant because AlphaFold2 wasn't trained to predict structures in IDRs and IDRs were not included in its training data. “It's like AI being trained to drive a car, and then trying to see if it can also drive a bus,” says Moses. “It can't drive the bus all that well, but it can recognize that someone should be driving.”

The team is also the first to do it systematically for all the proteins in humans and other organisms. “So, for the first time we believe we know how often it is happening,” says Moses. “This is important because biology is full of exceptions. We need to know what’s common and what’s exceptional.”

The development of this powerful and unexpected application of AlphaFold2 demonstrates the power of using AI to solve the protein folding problem and will improve researchers’ understanding of IDRs and their role in disease.

“In the IDRs that AlphaFold2 predicts to have some structure, we’ve shown that mutations are far more likely to cause disease than mutations in other structureless IDRs,” says Moses. “This is an important advance in understanding how mutations in IDRs can cause disease, which is generally not well understood. We now believe that many of the mutations are disrupting the structure somehow.

“What’s more, because AlphaFold2 predictions are already available for all proteins, now we can say for the first time how many IDRs across the tree of life have structure. Our paper shows that bacterial IDRs are much more likely to have structure than human and animal IDRs. As far as we know, this is the first time this has been noticed and it may settle the ongoing debate about whether most IDRs have structures or not.”

We should believe what climate models are telling us: �鶹��Ƶ computer scientist

Christopher.Sorensen — Fri, 20 Oct 2023 17:55:44 +0000

We should believe what climate models are telling us: �鶹��Ƶ computer scientist

Christopher.Sorensen Fri, 10/20/2023 - 13:55

Cutline

In his new book, Computing the Climate, �鶹��Ƶ’s Steve Easterbrook explains why we can trust computer models when they say we’re in a climate crisis (supplied images)

Topic

Faculty of Arts & Science

School of the Environment

Sustainability

Subheadline

In his new book, Steve Easterbrook says climate models undergo a quality control process "that I believe is unique in the world of computational modeling"

Steve Easterbrook began thinking about his how his research might impact future generations shortly after he arrived at the University of Toronto.

“I came to �鶹��Ƶ in 1999,” says Easterbrook, now director of �鶹��Ƶ’s School of the Environment and a professor in the department of computer science in the Faculty of Arts & Science. “My partner and I had just started a family; we became very busy with young kids.”

Having previously worked as lead scientist at NASA’s software verification research lab, where he and his team studied flight software for the Space Shuttle and International Space Station, Easterbrook took a particular interest in the role computer science and software engineering play in understanding and combatting global climate change. He decided to investigate how climate models describe our warming atmosphere – and how well they work.

In his new book, Computing the Climate, Easterbrook explains what climate models are and why we can trust them.

Put simply, climate models are computer programs that simulate the Earth’s atmosphere. Typically, they divide the atmosphere and oceans into three-dimensional blocks – some as small as 30 by 30 kilometres. Mathematical equations simulate the flow of energy, air, moisture through the atmosphere, as well as how the atmosphere interacts with the oceans and land.

To conduct his research, Easterbrook visited climate change labs around the world, including the Meteorological Office in the U.K., the Max Planck Institute for Meteorology in Hamburg, Germany, the National Center for Atmospheric Research (NCAR) in Boulder, Colo., and the Institut Pierre-Simon Laplace (IPSL) in Paris, France.

Easterbrook says he saw first-hand how climate models show with remarkable accuracy how the atmosphere works over long periods. They have provided accurate predictions of the dire consequences of pumping carbon dioxide into the atmosphere for more than a century. He says even models that predated the modern computer, like that of 19th century Swedish chemist Svante Arrhenius, were accurate.

How is it that they’re so trustworthy? According to Easterbrook’s research, it’s because they involve a rigorous global collaborative effort on the part of hundreds of scientists across many disciplines. He says that makes climate models more reliable than most software, which is typically the product of a single, relatively small team’s efforts. While commercial software is tested, it does not undergo the same thorough and rigorous review as climate models.

We should believe these models, he writes in the book, because “climate modelers have built a remarkable set of design and testing practices that look quite unlike anything I've observed in commercial software companies. If you have a large enough community of experts who run the models over and over again, treating each run as though it were a scientific experiment, treating every quirk of the model with the utmost suspicion, it's possible to produce remarkably high-quality software. The result is a quality control process that I believe is unique in the world of computational modeling.”

A high-definition animation of global air circulation by Community Climate System Model (CCSM) and NCAR.

To demonstrate how well climate models work, Easterbrook uses an impressive model developed by NCAR as an example. The model’s output appears as a moving “map” of the world, showing land masses, oceans, clouds, air circulation and precipitation – and looks very similar to animated satellite images. The model correctly simulates details like the daily pulse of rainfall in the Amazon basin and in sub-Saharan Africa, as well as typhoons forming in the western Pacific Ocean that crash into Japan and China.

“None of the patterns you see in this model are directly programmed into it, none are written in the code,” Easterbrook says. “It shows that if you get the physics right, the rotation of the planet, the heating from the sun and cooling off at night, and you run that simulation – these patterns emerge. And they match the planet’s real patterns. That blows my mind.”