Audio-story: Opening doors in science

The doors to science are harder for people to open who are currently under-represented in science. Some labs have set out to change that.
Audio-story: Opening doors in science

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For the column Lab & Life in Nature Methods, I recently did a story called When labs welcome under-represented groups  Here is a bit more about the people in that story with a combination of text and audio. 

Science is about discovery and often also about self-discovery. Dr. Pavan Ramdya is a neuroscientist and bioengineer at EPFL in Lausanne Switzerland . 

"As neuroscientists we can be quite different from other scientists because we are trying to investigate ourselves. As much as I study a fly, it’s because I really truly believe there is something in the essence of the fly that will scale up to human behavior. "

Science, as is true in many areas of society, has issues. Among them is the fact that it has been hard for women, people of color, people who have been marginalized in society for any number of reasons, to enter science, work in science or become scientists. It’s also true that many researchers are aware of this and want it to change. Often, this desire stems from their own experience.  Things happen that are stigmatizing, that set one apart.

"Actually Vivien, I would say, people are stigmatized but I think there is something larger and much more subtle that has always been happening. Which I experienced and didn’t realize I experienced until recently.  Which is just the feeling that you don’t belong.

It’s not stigmatization exactly. There’s something about seeing somebody who looks like you doing what you want to be doing. That I now start to appreciate much more. Especially talking to my wife who is also a professor and realizing that I am one of the few brown folks that passed through the labs that I’ve been in in my career. It’s something I starting to be more aware of."

As he embarks on this process as he runs his lab and mentors others with this awareness of those under-represented in science, Ramdya knows that his role in the mentoring process is taking place only in one phase of that person's life. It's a bit later than when first experiences begin to shape someone and deter from paths they might otherwise take. 

"The biggest tragedy in my opinion, it’s a trajectory that starts early. If you look at a child on the playground, who is 3,4 years old, who is not-white. And I don’t mean to demonize people but it’s just the majority of a particular population, I already can anticipate that they’re unlikely to come to my lab. Or they’re unlikely to make it through the educational system feeling confident enough to come to my lab."

Making someone feel like they do not belong happens early. And there are ways to try and convert that feeling of not belonging. A number of labs have started summer programs to try and address some of the issues they see around them. 

At the University of California Irvine in the Department of Biomedical Engineering researcher Dr. Michelle Digman, who is Latina, develops imaging techniques and co-directs the Laboratory for Fluorescence Dynamics and directs the W.M. Keck Nanoimaging Laboratory. She shapes her department’s policies on equity matters and does outreach programs for local community college and high school students from minorities under-represented in science. She runs a summer program called Undergraduate Student Initiative for Biomedical Research.

It involves her lab group and some colleagues at University of California Irvine and participants. She wants to open the doors to to their lab and to science more generally to groups currently under-represented in science.

 One participant in this program is Angelica Rippee who describes herself like this before she applied.

"I was a very confused undergraduate student. I was at a local community college, I had moved to Florida to start my four years of school and I did not like it. I said I need to go back home and figure out what I want to do next. I knew I wanted to still study marine biology, but I didn’t know where. I go back home, I start going to my local community college. And that’s basically where I was in my life point just confused trying to figure out what my next big step was."

Being confused is not an untypical feeling for many people setting out to figure what they are interested in as a career. For women, people of color and minorities in general --Angelica Rippee is Latina, the hurdles are high. The UC Irvine program that Michelle Digman offered felt like a good idea .

"I’m Hispanic, my mom is from Columbia, I am Hispanic. She drew in from community colleges  and the STEM program I was in was for students who were diverse and from backgrounds where parents didn’t go to school. The people who applied with me were in the STEM club with me and kind of from the same boat."

In the program, Michelle Digman and her team let the participants choose from a variety of their projects.


"It was their projects. They welcomed us in for that week to help out and learn about them. Out of the list, you got to choose, and when it was my turn I chose to do orbital tracking on lysosomes around the cell.

We would track it around the cell with this very fancy optical imaging technology. It was really interesting. I have never seen anything like that before." 

"Learning about it from the biology side was amazing. I understand what a lysosome but I don’t understand how to track it or why it is we’re tracking it. Someone who is studying physics was in the department with us, our mentor, and he was telling us all about the physics. And then there was another woman who was all about the biology. So it was good to see two different collaborators on the project form two different backgrounds.

We weren’t required to know coding, even to analyze it you had to be able to code. But that wasn’t a problem, they told us though we could try it, and they set us up with little coding programs to use. They also showed us how to do it by hand on Excel. So I did try to learn how to do that. That was interesting. Then our mentors sat down with us helped us for maybe three hours one day so we could code it and present it the next day. "

The week was intense but intense a good way.

"Because without having the pressure of a grade  or 'I have to go home and study this.' You are put in a real-world situation. You get to pretend to be a researcher for a week. I would go to work everyday and research and help on this project. So it was very different from anything I had done before. It was the first time I was ever in a lab doing research. It' kind of kickstarted all my future researchI have ever done, too. 

Overall, she and others in her group were surprised about the experience. 

"I think a lot of other people felt that way as well. My family never went to higher education. My mother never went to college, my father dropped out of college. I was the first person to go to higher education in my family. So I didn't know about higher education. So when I met my mentors who were grad students, I was like

"whoa that is something you can do, you can continue after you get your degree?"

They showed us a whole bunch of options, basically. "

Another participant is Sabreen Alam, who is South Asian. She applied to the Undergraduate Student Initiative for Biomedical Research in the summer after 8th grade, participated in consequent USIBR programs and interned at Dr. Digman's lab ever since, she says. “Spending my summer in USIBR was the perfect way to begin my science research journey.”

She is now an incoming freshman at Princeton University who plans to major in chemical and biological engineering and will pursue minors in computer science, math and finance.

In the program Alam especially liked the hands-on experiences. And she liked the introduction to advanced principles of fluorescence microscopy and how they can be applied to imaging techniques in the lab. The projects she worked on in Dr. Digman's lab included analyzing the effects of mechanical loading on collagen fiber orientation and fibroblast proliferation, investigating mitochondrial movement in breast cancer cell lines, building an at-home gel electrophoresis system and exploring new kinds of imaging techniques.

“I enjoyed learning how to culture cells, prepare cell treatments, and analyze microscope images with various software applications. I also learned about the work being done by postdocs and other members of the lab, which enhanced my understanding of the many subfields and questions to investigate in biomedical engineering. This experience helped me adopt the creative and analytic mindset of a researcher, and prepared me for finding a potential career or research interest in this field.”

The work in the Digman lab helped her, she says, develop perseverance and critical communication skills.

“I learned the importance of meticulous planning before experimentation, and the dedication required to work on the cells’ schedule and not my own.”

Dr. Digman's support was crucial to her as this helped her discover her own passion for science research and identify what she wanted to study in college. “I sincerely recommend this experience to anyone with a desire to explore the field of biomedical engineering and participate in significant hands-on lab work.”

A short stay in a lab in which one receives guidance and hands on experience can make a difference. Michelle Digman explains a bit more about the program.

"So the official summer program is one week and it's an intense week, I started this for community college students, but many high school high school students added on. So I put the outreach program as community college, undergrads and exceptional high school students if they want to join. And so what we do is we have a formal process where they have to submit an application just to give you an idea. Before the pandemic, we had about 70 applicants, both high school and undergrad students from community colleges surrounding our area that applied for a program."

"But we could only take about twenty, twenty-five of them, max, because that's a lot of students for group. But I would also like to add that my lab is part of a resource here on campus, it’s called the P41 center, the Laboratory for Fluorescence Dynamics and the PI of the Resource Center is Professor Enrico Gratton who was also my postdoc mentor. H e's the director and I'm the co-director of the center. And we have 17 different types of imaging systems in the center."

 "The whole purpose of the outreach is to show students, undergrad students who are in our local community because we kind of, we live in Orange County, which has its own kind of little bubble. And outside of this bubble, there are communities that have high populations of under-represented minorities that live in these areas. And many of them go to community colleges. And even though they live maybe ten minutes away from us, they don't actually really know what UCI does."

 "And it's not just that they don't have access to these imaging systems or training that you would be exposed to when you go to a four-year institution. So I thought, why not try to engage these students, have them come over to our lab? And we started with a community college called Rio Hondo, which is actually about thirty five miles away from us. It's kind of far, but at the same time it's still drivable. And we had the first cohort were a group of twelve students and we would go over there and do the lectures and then they would come over and do the actual training."

"We changed that since then. That was the very first time we did it. And it was one whole week where we really immerse the students in the techniques that we offer in my lab and at the center. And some people come up to me and they said, but how on earth can they learn that in a week? And it's just amazing how much these students can do in a week. We really integrate what they're doing with our own research projects."

"And I tell my students, if there's something that you want to test that you haven't had the time to do, let's work on getting a one week, let's say, session with the students that you are able to test this out and that relates to their own research. So sometimes it's one of those things where I wish I had the time to test that. And then they just are doing so many other things they never get to it."

"Is the one week where they actually have that ability to test it. Sometimes it works out that way. Other things are like, ‘oh, we want to show students how a system is built, how does this operate? So how is this engineered?’"

"So we'll take it apart and then they'll have to piece it together. But while they're building it back, they learned what the components are for. What is the fundamental understanding of this piece of equipment that makes us able to see small structures using light imaging. "

One week indeed is not a lot of time but it can give students plenty in the experience. Michelle Digman has had a lot of students pass through this program.

"I think they are really transformed. They have to at the end of the week, on Friday, in the afternoon, they have to present their findings to each other. So they have to get up in front of the audience and discuss what they did. And they were amazing.

Those students really learn so much when they talked about the technology and they describe how something worked, whether it was fluorescence lifetime imaging or whether it was how our TIRF system works. They really understood it. I could tell based on their presentation that they understood it. And you could see the smile in their faces, you could see how happy they were, they accomplished something and they contributed to science. I think for me that's what keeps me motivated and continuing these kinds of projects."

I spoke to another researcher who offers a summer program of this kind. Dr. Mackenzie Weygandt Mathis, a researcher at EPFL Geneva. 

"I was actually born and raised in California, in Central Valley, A lot of nice cows, orange trees, peach orchards in the backyard, so very much a country upbringing. I grew up showing horses competitively.  Always had a lot of dogs around, almost a different life than a modern academic my parents are not in academia."

Mackenzie Weygandt Mathis decided at one point to not show horses competitively. 

After college I was going to go to medical school. I wanted to be a physician.I had never met a scientist. This just wasn’t a career. I saw Bill Nye, I just wasn’t so exposed to that."

She now runs an integrative neuroscience lab at EPFL’s Geneva campus, Campus Biotech. She and her colleagues, including her husband Alexander Mathis also an EPFL scientist have developed DeepLabCut and multi-animal DeepLabCut, which is open source software they and other scientists can use to track how animals move. It’s helpful when identifying multiple animals in a scene for example: who is doing what where.

To draw conclusions about the animals’ behavior, you need to be able to tell them apart, which the software can do. It’s been downloaded over 375,000 times and used by researchers studying many types of animals and how they move. She is committed to the culture of open-source software and she wants to democratize AI and make computer science more inclusive, more open to minorities currently under represented in computer science.

"Just to really home in on my commitment to democratizing AI culture and making it more diverse: the country girl from California can become an open-source developer. We‘re running a new DLC AI residency program. It’s only for underrepresented minorities in computer science. They’re going to come spend summers with us. Have all the resources, it’s sponsored by Nvidia and Chan Zuckerberg and Center for Intelligent Systems at EPFL. It’s an immersive  hand-on residency. We are launching it this summer, it’s a way to build people into the community.

"We want to teach you, and empower you, help you write better code, do better research but also bring people into the open-source ecosystem. Even if they don’t want to contribute to Deep Lab Cut for the rest of their lives. But if they feel comfortable contributing to Python, or sci kit learn, or other packages, I would be so elated, that for me is the biggest reward to enable others to do these types of endeavors."

"We’re absolutely for sure running it in future years. Obviously, it would be amazing, we’ve had so many incredible applicants. They had to do two-minute videos for applications. The people are amazing. The future is bright, the future is diverse, the future is empowered, I am super-excited."

Vic Shao-Chih Chiang 蔣紹志 at EPFL Geneva's Campus Biotech. He is one of this year's

DLC AI residency program fellows. (Stephen Renjie Hu )

Vic Shao-Chih Chiang 蔣紹志 is a gay cisgender male born in Taiwan who moved to New Zealand at age seven when his parents, and he, emigrated. “Being a newcomer that could not speak any English in a then-80% white country and effeminate, I faced racism and homophobia from a young age.”

He came to London UK as a student in 2015 and there, he says he was exposed to many influences. In this different environment where he attended a diverse range of events “I become more woke,” he says.

 He began hosting Open Mind debates and as part of that he began reading widely, also far beyond his discipline of study: neuroscience.

These experiences gave him a deeper cultural awareness, which partly shaped his motivation to empower marginalized minorities. “I find this social purpose soothing in my longstanding existential crisis similar to that described by Nietzsche’s “God is Dead.” It’s a desire for transcendence, he says “that I find unfulfilled in Western science.” He grew up under his grandmother’s influence, who held Buddhist-related beliefs; “ I also find this echoes her teachings on Dharma: the materialistic happiness and spiritual emancipation of all sentient beings.”

His objective to cultivate epistemological diversity, specifically through the lens of marginalized communities brought him to the US and to be a PhD student in the lab of Jin Ho Park where he studies the neuroscience of sexual diversity at University of Massachusetts, Boston, a minority-serving institution. Park, he says, helped him apply for the DeepLabCut AI Residency.   

Studies have emerged on same-sex sexual behavior, transgenderism, and heterospecific sexual behavior, but research on sexual diversity is still largely neglected in neuroscience, which is dominated by patriarchal, heteronormative, and cisnormative views, he says. This is further complicated by the politicization of the field, which experiences a tug-of-war between academic freedom, social values, such as gender equality, and inductive risks, due to the uncertainty and complexity of research findings, he says.

 His current projects look at sexual diversity from a multi-faceted perspective including how sexual behavior can be independent of sex steroid hormones, brain-skin interactions relevant to sexual behavior, sexual behavior in a collective behavior context and the evolutionary drives of mating systems.

“Understanding sexual diversity accurately is necessary to overcome the systemic and institutionalized barriers that contribute to the well-recognized underrepresentation of sexual minorities in STEM. This can be improved, for instance, by being aware of the sexual diversity within and across species, recognizing the social and historical context of research findings and using inclusive and precise language during discussions that don’t assume cultural norms.”

Diversifying STEM also means embracing perspectives beyond Western science, for example, by incorporating Indigenous communities and Arabic philosophies in science, he says. 

“When studying sexual behavior in animals, I came across several challenges,” he says. He found selection bias of only a few behavior parameters, he experienced how laborious manual annotation of behavior is and the fact that there are ‘inter-rater’ variations. 

Add to this, he says “our sensory detection limits and the limits of human language to comprehensively describe behavior.”  These factors further obstruct the accurate understanding of the neuroscience of behavior.

As he sought possible solutions, he came across different machine-learning-based high-throughput behaviomic approaches including DeepLabCut, which address the limitations of manual methods.

 “I don’t have any formal training in computer science, but I studied for a certificate in bioinformatics.” With this coding experience, he first explored DeepLabCut. The task he set out to achieve was one he did with his husband to label videos of a friend’s corgi. As Chiang explains “we found programming skills weren’t necessary to navigate the basics of DeepLabCut.” He add that his husband, too, helped him with his application for this residency.

 Among the positives he sees in DeepLabCut is that for example there is an animal ethics aspect “because we can obtain more data from a smaller number of animals.” The high throughput behavioral data this method obtains enables in silico and robotic models that can entirely replace animals in experiments. He also believes that DeepLabCut promotes biodiversity because videos need not only be from labs “so we are not limited to ‘labesticated’ model species” but can apply the tool to situations with wildlife. “Captivity is also not necessary since any type of camera can be used including footage from drones and satellites,” he says.

Manifold factors motivate him to participate in this DeepLabCut AI Residency .

“First, I want to support the residency’s cause to diversify AI. This field excludes marginalized minorities from its creations which led to race and gender misidentification problems, resulting in the ‘weapons of math destruction,’” he says.

The fact that DeepLabCut is open-source code makes it easier to democratize because it is  economically accessible to everyone, unlike software that must be bought and licensed. “To my knowledge, no one at my university has experience with behaviomics, so I am establishing DeepLabCut in my department, and from there, I want to extend it to the rest of the university..” he says.

In the fall of 2022, he be teaching a research methods class. “I will make DeepLabCut an integral part of the course,” he says. By taking part in this residency, he will get the technical support to become a DeepLabCut code contributor. “I want to shape DeepLabCut in a way that makes it even easier for marginalized minorities, a prevalent population in my university, to use and thereby, be more comfortable working with AI.”

 The residency, he says, also gives him community and credential support from prominent people in the behaviomics field, which also helps in a society like ours that “operates on a principle of affiliation and networks.” The residency, he says, will bring him closer to his “longer-term objectives to diversify AI beyond the university through citizen science approaches, “such as by building on DeepLabCut  in a way that focuses on marginalized minorities such as transgender, gender-queer and nonbinary youths.

Nirel Kadzo is also a fellow in the first residency. She is nearing the end of her undergraduate studies. She is to her knowledge the only undergrad student in the program, which “can be intimidating but I am more excited about the possibilities of how much I can gain from a minimal background."

I am here to explore and hoping to find my place and voice in science.”

She comes to the fellowship with knowledge of the basics and fundamentals in Java, C++ and self- taught Python. She also knows web development, HTML5, CSS and PHP. “I also realize that the knowledge I got of programming from a business school in Kenya is rather different from here- a science institution,” she says.

Over the course of her education, she has developed enterprise management systems for her university, as well as a clinic to optimize delivery of services. “Recently, I worked on a sentiment analysis model to better understand the views of Kenyan youth about the economy and identify where the biggest challenges are and with the upcoming elections whether a change will be seen in the leadership and economy.”

Apart from that, she says, she has been heavily involved in community development, especially with  education in digital skills for marginalized communities around Kenya. She has liked “interacting with different communities, most importantly empowering women, like me, who have been held down by community practices with skills to start their own venture- and also coming back months later to see the life they’ve created. And I have been doing this for 3 years now.”

It’s her first encounter with neuroscience , which  was a subject she had only read about. Now that she sees the many projects happening in Campus Biotech, “it’s just awesome!” she says. “I’ve just been to two labs and the joy is sparked. Looking forward to getting hands on this summer.”

A number of factors motivated her to apply for the residency: “my background, career and community,” she says but the core motivation is the offering itself: its resources also in terms of professors and facilities and the opportunity to be a fellow, he says.

“Where I come from, it’s hard to get into science and few people have the chance to do so, even less likely to contribute to open source.” She is also “keen on making science accessible for all.”

It helps that Geneva is a beautiful city, she says.  The stay offers the possibility of learning French as well. Geneva has mountains and lakes, “so this summer, I’m definitely getting the best of both worlds.”

“I’ve always been exceptionally curious,” she says. That’s one of the reasons she felt drawn to this program. She always wonders ‘how does this work?’ ‘What makes this move?’ This curiosity is what she sees as having propelled her through much of her life.

“I see AI as being at the heart of the future – not just flying cars, robots, and space exploration but also solutions to the common challenges we face,” she says. Those include climate change, biodiversity loss, also medicine as a way to better understand how bodies work, how the brain works, how we can improve the human experience. Especially in Africa, she says, AI can provide a lot of opportunity.

“Like in many poor countries, there aren’t many opportunities to engage these technologies in Kenya, where I’m from. So I see this program as a golden opportunity to be at the very epicenter of these advancements and the conversations which spur them.”

"I have great ideas that with AI-based behavioral analysis, it can create impact to the community, however, I have not known how to implement them and by the end of this program, I will be well-equipped to pursue something back home."

She has found both the campus and the people in the lab "super cool!,” she says.

“Looking forward to who Nirel will become after the two months

and possibly more :).”

 (olaser, Getty Images








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