Season 2 |
Episode 4: From Childhood Curiosity to Bioinformatics Breakthroughs with Dr. Mary Jo Ondrechen
[00:00:00] RORI: Welcome to ScienceWise, a podcast where we learn from stories from experienced badasses in science to figure out how we're going to navigate today.
[00:00:09] EMILIA: So that when you have a question about what to do under a specific situation, you can get some guidance.
[00:00:15] RORI: I'm Rory. I'm the hildegard Lamfrom
Associate Professor in Data Science at the University of Oregon.
[00:00:20] EMILIA: And I'm Emilia, an Associate Professor in the Department of Ecology, Evolution, and Organismal Biology at Brown University.
[00:00:29] RORI: Today, we are thrilled to interview Mary Jo Ondrechen. Dr. Mary Jo Ondrechen is an incredibly productive computational chemist and has truly made science a more robust space that can support Indigenous scientists.
For years, Dr. Ondrechen has been developing models to predict protein function on a granular level. And she's gone further to develop protein design principles to create useful proteins, for example, to break down harmful chemical byproducts. She's made loads of software to predict protein functions, like Salsa Pool and thematics. And she's been using machine learning for these projects before it became popular to apply in biology. She continues to run a full and vibrant lab today. Her creative research is why she was awarded a Fulbright Faculty Research Fellowship and the 2024 Technical Excellence Award from ACES.
The American Indian Science and Engineering Society. Along with her science, Dr. Andrakin has been improving science culture for folks who came after her. For years, she has contributed to fellowship programs through ACES and has helped create Lighting the Pathway, a program to support Indigenous scientists as they become faculty.
Dr. Andrakin has been in the leadership of ACES and contributed to SACNAS for years and was appropriately awarded the 2018 SACNAS Outstanding Mentor Award. We are thrilled to talk with Dr. Mary Jo Andrakin today.
Well, we are very happy to interview you today. So honored to have a conversation with you. When you were growing up, you were really fascinated with the natural world and you dreamt of being a scientist and a professor, but you didn't know anybody who did those things. How did you learn that this profession existed?
[00:02:08] MARYJO: My mom would take us. On the weekends to the Natural History Museum, and every time we would learn something different back then, there was a lot of emphasis on science that you don't see in this country today.
[00:02:23] RORI: Oh, interesting.
[00:02:24] MARYJO: Now, in the, in the 1950s, when Russia launched the Sputnik. The oh it was oh my god, we're behind the Russians.
What are we gonna do?
[00:02:34] RORI: So it's kind of this like kind of competitive Cold War emphasis on
[00:02:38] MARYJO: absolutely. Yes And and there were all kinds of things to get kids interested in science There were these little 45 rpm vinyl records with songs of science
[00:02:49] RORI: and it sounds like your mom your mom really supported you in that.
She was like, yeah, let's go to the museum. Let's learn about snakes. Let me get you some records.
[00:02:56] MARYJO: My dad too. My dad was very interested in astronomy. And so we go out in the night and, and, uh, he'd tell me all about the stars and the constellations of the galaxies and everything. So
[00:03:08] RORI: You had pretty strong support from your parents to explore some of these, explore the natural world in different ways.
[00:03:14] MARYJO: Yes. Yes.
[00:03:15] EMILIA: Were you interested in biology then? Because that was maybe the closest to the natural world.
[00:03:19] MARYJO: Well, I was, I was interested in all kinds of things, you know, astronomy and plants and animals. Um, but then in high school, I had a very good chemistry teacher. You know, I went to the kind of high school where you don't learn much.
And, uh, a lot of the teachers had low expectations of us, but the chemistry teacher taught an honest to God college prep, you know, chemistry course. Her name was Mrs. Prime. Mrs. Prime was. Barely five feet tall. I can still picture her. She wore a red lab coat.
[00:03:53] RORI: Oh, stylish.
[00:03:54] MARYJO: Yeah. Before she was a teacher, she worked in industry.
And, you know, in most cases, probably the only woman and, uh, she really made chemistry fun and she taught a rigorous course, but she made it fun. She got a big kick out of life. She got a big kick out of chemistry.
[00:04:13] EMILIA: What was fun about it? Was it the experiments or was it the, because chemistry can be really technical.
[00:04:19] MARYJO: Yes, we did lots of experiments. He did lots of labs and so he had this sort of fun war going on with one of the biology teachers. We would send stink bombs to his class and things like that.
[00:04:33] RORI: Wow, serious pranking. What did they do to you?
[00:04:37] MARYJO: He would, well, they would fight biologically. So they would send this jar with the sheep's eye in it and things like that. It was all in fun.
[00:04:47] RORI: But you learned about the chemistry of making a stink bomb.
[00:04:50] MARYJO: Oh yeah.
[00:04:52] RORI: That's special. It's also special that this, this teacher was an industry and then went. To be a high school teacher. That's an unusual trajectory. So she was like a practicing chemist who then was like, no, I will actually want to, I want to share this with high school students.
[00:05:07] MARYJO: Mrs. Prime lived well into her nineties and through the magic of the internet. I was able to find her. So when she was about 90 years old, I went to visit her. We went out to lunch. Uh, she said, the restaurant's about a mile away. Is that all right walking? I said, sure. And I was able to thank her for introducing me to chemistry and giving me my career.
[00:05:33] RORI: So after you took her class, did you, did you think to yourself, this is it? I'm going to go into chemistry. Was it really clear to you right then?
[00:05:40] MARYJO: Yeah, because that fall as a senior, I applied to colleges and I wrote that I wanted to major in chemistry. I did not know anything about college applications or how to write them.
[00:05:51] RORI: So you didn't know how to do a college application. Can you tell us a little bit about your family? Like, had anyone in your family written a college application? Like, was this a totally new idea?
[00:06:01] MARYJO: My dad, he was in the Navy, and when he got out of the Navy, he took courses part time on the GI Bill. It was around, around between my junior and senior year when dad finally got his bachelor's degree.
But he didn't go, you know, through the college process by the typical path. Mom had no money for college, but during the Second World War, the government needed nurses, so they offered qualified young women, you know, a free ride through nursing school. They didn't call it a bachelor's RN back then, but it was the same thing as a modern-day bachelor's RN.
You take academic courses at the university and clinical and the nursing school. She didn't get into college by the path that most of us do now, where you write applications and everything. So, so it was a whole different story.
[00:06:53] EMILIA: Did you have siblings?
[00:06:55] MARYJO: We were five children and I was the oldest and one of my jobs, one of my many jobs growing up was reading to the younger children.
So they love Dr. Seuss. So to this day I have Dr. Seuss memorized. Oh, we, we did bad things too. We made gunpowder.
[00:07:15] RORI: Oh, wow.
[00:07:16] MARYJO: We, we got, we got chemicals and mixed them and made gunpowder.
[00:07:20] RORI: Whoa, was that before you were in, was that before Mrs. Pryne's class?
[00:07:24] MARYJO: Yeah, that was actually before Mrs. Pryne.
[00:07:26] RORI: Okay, okay, so you were already doing chemistry, naughty chemistry.
[00:07:30] MARYJO: Yes.
[00:07:32] EMILIA: You mentioned that you, you wanted to do chemistry. So that was your major.
[00:07:35] MARYJO: Yeah.
[00:07:36] EMILIA: Did you always wanted to do a PhD
[00:07:38] MARYJO: or? Sometime during undergrad, I guess. Yeah, I decided I wanted to be a professor. So I knew I had to get a PhD.
[00:07:43] RORI: So you were excited about the research. There are some questions you wanted to ask.
And I mean, of course, being a professor is a great way to be able to ask. your own questions, like the questions of your design, like what were you excited to explore?
[00:07:55] MARYJO: Well, in my senior year of college, I took a course in group theory. I was really impressed with how much you could say about molecules using this mathematical theory.
So that, that's kind of the direction I went, uh, in grad school, uh, doing theory and, and computation theory. Mostly theory.
[00:08:17] EMILIA: So when did you become interested in biology?
[00:08:20] MARYJO: Really the late 90s, as the human genome was being sequenced, I decided that there's got to be things that, uh, there's got to be ideas, progress that a theoretical chemist can contribute to.
[00:08:35] EMILIA: Were you waiting for that genome to be sequenced or, uh, did you start collaborations with people who were doing some sequencing, even though it wasn't, it was probably not. the human genome? Or were you just thinking theoretically, if we had this data, what could we do? Um, what, how could we contribute as theoretical chemists?
[00:08:54] MARYJO: Well, the genomes were being sequenced and a lot of those genes code for proteins. And a lot of those proteins are of unknown function. And so I took a sabbatical in 2000, 2001 to learn biochemistry because the biochemistry I learned as an undergrad was, was not good anymore. No, when I was an undergrad, you couldn't sequence nucleic acids.
Now you can, uh, everything, everything's changed. So I took a sabbatical and.
[00:09:26] EMILIA: Where did you go?
[00:09:27] MARYJO: I went to Brandeis University.
[00:09:29] RORI: That's cool. That's cool. To be like, oh, I'm gonna change, I'm gonna learn something new. Like, you had been a professor for, what, 15 years or something? By then, you're like, no, I'm gonna
[00:09:38] MARYJO: Yeah.For 20 years. Yeah,
[00:09:38] RORI: for 20 years by then. Okay.
[00:09:40] MARYJO: Mm-hmm . And, yeah, I joined the faculty in 1980. Yeah. And, uh, so, uh, I, I, uh, worked with Jag Maringa at Brandeis, and we, well, I, I said I, if you gimme the structure of any protein, I'll tell you which amino acids. are important for the function.
[00:09:57] RORI: Oh, that's a nice offer.
[00:09:59] MARYJO: And, uh, so she gave me some examples of proteins that she'd work with and saw that I was predicting the active amino acids. And so she knew there was something to it because here was this person who didn't know any biochemistry who knew exactly where the active residues were. So she knew there was something, something to it.
So, and so, uh, that we we've. Carried those ideas, my group and I have carried those ideas on to other things, uh, but, uh,
[00:10:28] EMILIA: I'm curious, how do you know what is active from the structure of the protein?
[00:10:32] MARYJO: We calculate them from the three-dimensional structure.
[00:10:35] RORI: So you go from the sequence to predict the three-dimensional structure.
And my biochemistry is pretty rusty, but you can predict like these alpha helixes and beta sheets. And things.
[00:10:47] MARYJO: Yeah. Yeah. You can build structures by homology to known structures. And nowadays, the alpha fold programs are very good at omniscio predictions.
[00:10:58] RORI: So you've been doing this kind of work, this protein function prediction, for quite a while and you've published some pretty key software in the field.
[00:11:06] MARYJO: Yeah.
[00:11:06] RORI: You were applying, you know, machine learning to these problems kind of before it became in vogue to apply machine learning to biological questions. I mean, I guess it sounds like Your collaborator at Brandeis was like, well, Dr. Rakin is predicting things correctly, so she must be doing something right here.
[00:11:25] MARYJO: I published my first machine learning paper applied to Biomolecules in 2008. That was kind of before the, the big wave of interest in, in machine learning ai,
[00:11:36] RORI: like by quite a lot. By like a decade. Yeah.
[00:11:39] EMILIA: Um, I'm still stuck in this other question about the protein structure and how you find out what's by, uh, active.
So, how would you test that your prediction
was correct?
[00:11:48] MARYJO: Yeah, we, we've done a collaboration. We've done, I collaborate with Penny Boyning here at Northeastern. Uh, you, you mutate out the amino acid. That's, that you say is important and see if you lose activity.
[00:12:01] EMILIA: And lose activity means like the protein doesn't fold or?
[00:12:06] MARYJO: No, no, the proteins usually fold, but they, you, you know, enzymes catalyze reactions. So to measure whether it's, you see, you test how fast. It can generate product.
[00:12:20] EMILIA: Okay, so using kinetic experiments.
[00:12:22] MARYJO: Or binding experiments, yeah.
[00:12:24] EMILIA: Okay, um, if you had to describe right now what you study and how you describe whatever you do, how would you, I guess, how would you describe that?
Like, would you say you're just a theoretical chemist or you've done, you're more than that obviously, but how would you describe it?
[00:12:40] MARYJO: It's a combination of theoretical chemistry and computational biology and bioinformatics.
[00:12:45] EMILIA: Okay, so very interdisciplinary.
[00:12:47] RORI: Where did you go to PhD school?
[00:12:49] MARYJO: Northwestern.
[00:12:50] RORI: And over in Evanston, you're doing computational chemistry.
And from there, you decided you wanted to do a postdoc. You were like, yes, I want to be a faculty member.
[00:12:59] MARYJO: Yeah, yeah. You know, computers couldn't do a lot back then. And so we did a lot of. Sort of deriving equations kind of theory, you know, um.
[00:13:08] EMILIA: Did you do
any programming when you were at school?
[00:13:10] MARYJO: Yeah, I
did, I did. I had programs that they were on punch cards.
[00:13:15] RORI: Yeah.
[00:13:16] MARYJO: So I had this big box and I'd carry it on my shoulder to the computer center.
[00:13:21] RORI: Like some people carry a boom box, you're carrying your punch cards.
[00:13:28] EMILIA: And graduate school, did you feel like, did you feel like you belong there? What was the environment like back then?
[00:13:34] MARYJO: Yeah, I thought graduate school was easy compared to undergrad.
[00:13:37] EMILIA: Really?
[00:13:39] MARYJO: You know, except in chemistry, I was not real well prepared for undergrad school. And it was, it was a bit of a struggle to catch up with everybody else. Yeah, so I, yeah, I tell, I tell kids, I say, you know, I got a bachelor's degree and a doctorate.
I'm proud of both degrees, and I worked hard for both degrees. But it was the bachelor's degree that was harder.
[00:14:00] RORI: Like what did your struggle in undergrad look like?
[00:14:03] MARYJO: Well, everybody else was ahead of me.
[00:14:07] EMILIA: But not in chemistry, you were, you were okay in chemistry.
[00:14:10] MARYJO: I was okay in chemistry.
[00:14:11] EMILIA: Why do you think that is?
Was it just because that was what sparked your interest or?
[00:14:16] MARYJO: No, it's because of Mrs. Brine who taught a real class.
[00:14:19] EMILIA: I see.
[00:14:21] MARYJO: I mean, this was a high school, no AP, no calculus. No, you know, no advanced courses. I mean, my senior year, I only went to school half a day. The school was underfunded and we had double sessions.
So, so yeah, I only went to school for half a day.
[00:14:38] EMILIA: How do you approach this with students when they, they feel like some things were not covered in class or that they don't know how to do this or that?
[00:14:47] MARYJO: I think when you come, from an underserved community, you tend to study in high school on your own, you tend to learn on your own, and in college and in grad school, you could do better.
If you connect with other people and learn from them, like they might know something that you don't know, or they may know workarounds or a good source on the subject, or you know, how to succeed in professor so and so's class. And Just working, you know, just, just being involved with other students can be a big help and, and sometimes it's hard to break out of that mold of, okay, I'm on my own. I've got to learn all this stuff by myself.
[00:15:34] EMILIA: Yeah. I think, uh, learning from others and also teaching others what you know that they don't know is it's a good strategy. What about the tenure process? Did you, did you just fly through that? You said undergrad was hard. Grad school was. easier. What about faculty life? Or did you do a postdoc?
[00:15:52] MARYJO: I did. I did. I postdoc at the University of Chicago. And then I was, I was a NATO fellow at Tel Aviv University in Israel.
[00:16:00] EMILIA: Have you been outside of the country before that?
[00:16:02] MARYJO: Yes. As a member of a Navy family, I had done kindergarten and first grade in Japan.
[00:16:09] EMILIA: Oh.
[00:16:10] MARYJO: My younger sister was born in Japan.
[00:16:13] EMILIA: How do you think all those places shaped your view of the world? Or how did you approach the world based on those experiences?
[00:16:21] MARYJO: Um, it, it makes it hard personally because you make a friend and then you have to move away.
[00:16:29] RORI: And you started your faculty job in 1980 at Northeastern, and you've been there ever since.
[00:16:36] MARYJO: Well, Boston is a wonderful city. It's got a very good cultural life. It's easy to get around the city, but yeah, I like it here. I like it here.
[00:16:47] EMILIA: So you, you said you took your faculty, did you say you started your faculty position in, in the 80s?
[00:16:53] MARYJO: 1980, yeah.
[00:16:55] EMILIA: Okay, so you've seen, I mean, Boston has probably evolved a lot.
[00:16:59] MARYJO: And Northeastern has evolved. It's hard to get in now. It's very hard to get into Northeastern. And, uh, you know, we're, we're now in an R1, highly research-intensive university.
[00:17:10] EMILIA: But you've always gone on sabbatical. So it's not that you've been there since then. You've, you've
[00:17:15] MARYJO: Well, once every seven years, I go on sabbatical.
[00:17:18] RORI: As often as they come up.
[00:17:20] EMILIA: How do you choose where to go on sabbatical?
[00:17:22] MARYJO: Well, you want to go someplace where you can do something new, learn something new. And you want to go someplace that's a good place to be, you know. So, and, and, uh, personal considerations, like when my parents were elderly, and I, I would take my sabbatical in Southern California.
[00:17:40] EMILIA: And did you encounter any challenges as, as faculty? Or has it been an okay experience? At Northeastern. And maybe that's why you've been there for so long.
[00:17:50] MARYJO: Yeah. Well, there've been challenges. You know, we, we have right now we have, I have an excellent department chair, an excellent Dean. When you have good leadership, things go, go well.
[00:18:00] RORI: Totally.
[00:18:01] MARYJO: And there were, there were times in the distant past when we did not have good leadership.
[00:18:05] RORI: That's so hard.
[00:18:06] MARYJO: And that hurts morale. It hurts progress. Um, But, uh, for the quite a long time now, we've had, we've been in very good shape, very good leadership. We're doing very well.
[00:18:15] RORI: That's good. When you had weaker leadership, how did you cope?
[00:18:20] MARYJO: Well, you know, that that person is not going to stay there forever. You know, we, we tell each other, we're going to outlast this guy. Yeah. I mean, weak leaders are bad because they don't push the unit forward, but jerks are even worse because they hurt morale. And they set the tone and, you know, for some time now we've had a tone of collegiality, respect, people like each other, have fun together and do a lot of good things.
And, and that, that's what happens when you have, you know, good leadership.
[00:18:54] RORI: But you've done a lot in kind of like non-university leadership.
[00:18:58] MARYJO: Oh, y Like, like chairing the board at ACEs.
[00:19:01] RORI: Yeah. Like ACEs, like the American Chemical Society. I see that you ran for the Health Board of Hopkinton, which I don't even know how to pronounce.
[00:19:09] MARYJO: I am, I am. You're on the board of Health of Hopkins. Mm-hmm.
[00:19:12] RORI: You take a lot of leadership roles in these kind of like society, uh, frameworks, either like academic society or, you know, kind of like social. Health board of a, of a town.
[00:19:25] MARYJO: Well, uh, you know, sometimes people ask you to step up and when people who you respect say you're needed, would you please step up?
You do it.
[00:19:33] EMILIA: You're still mentoring students and, and, uh, maybe postdocs or undergrads?
[00:19:38] MARYJO: I'm still working right now I got, I got seven PhD students, four master's students.
[00:19:45] RORI: That's big.
[00:19:46] MARYJO: And a couple undergrads, a visiting scholar on sabbatical.
[00:19:50] RORI: Wow. That's a popping lab.
[00:19:52] EMILIA: I know. How do you manage such a big lab?
[00:19:55] MARYJO: The more experienced people I count on to help the newer people. Because I can't, I can't help everybody directly myself.
[00:20:01] RORI: No, that's
so many people, like even just meeting with everybody for an hour a week, that's like half your week.
[00:20:06] MARYJO: Can't do that, yeah.
[00:20:08] RORI: Okay, so you kind of have like structures.
[00:20:10] MARYJO: Yeah. Groups and subgroups, yeah.
[00:20:13] RORI: What motivated you? Why do you have a big lab now?
[00:20:15] MARYJO: Well, I, I, more people wanted to work with me when I started doing bioproblems.
[00:20:19] RORI: Oh, there you go. Yeah, there's a lot of biologists, there's a lot of NIH funding.
[00:20:25] MARYJO: Well, the hardcore, you know, hardcore physical chemistry, non-linear optical properties, you know, not, not many students want to do stuff like that.
[00:20:35] EMILIA: You received a letter about whether or not you were suitable for biology.
[00:20:39] MARYJO: I took a biology class my freshman year. And I got a letter from the chair of biology saying that it was the policy of their department to inform all the students who took, I forget what they call biology 101, first year biology, to inform all the students about your prospects to be a biology major.
And I had never asked to be a biology major, I was a chemistry major. Uh, but the letter said that they did not think I, would make a very good biology major. So I tore up the letter into a million pieces and threw it away, but I wish I had kept it because I would frame it. Because I think by any fair analysis, I've done far more to contribute to biological knowledge than the dude that wrote that letter.
[00:21:25] RORI: I'm sure. Also, what a weird policy. We're going to send unsolicited letters to everyone telling them to or not to. Like, who would think that's a good idea? Yeah,
[00:21:35] MARYJO: I mean, yeah.
[00:21:36] RORI: And, and clearly you're right. You've contributed so much more.
[00:21:39] MARYJO: Yeah, but it hurt. At the time it, it hurt. And, um, I don't know, maybe it subconsciously discouraged me from going that way and going more in the direction of the mathematics and theory, you know, physical theory stuff. Yeah.
[00:21:52] RORI: You know, undergrad was difficult. You were doing a lot of catching up. You were working very hard. And then to get this unsolicited letter saying that you shouldn't be in biology. Yikes.
[00:22:02] EMILIA: So how did you shake those feelings away?
[00:22:04] MARYJO: I don't know what I did, uh, other than to tear the letter up.
[00:22:08] RORI: But that's something.
[00:22:09] MARYJO: I think that fundamentally I did believe in myself because my mom, my mom told me over and over again You can do anything you want if you try, you can do anything you want if you work, you can do anything. So, so, and, and from the time I was little, like probably too young to fully understand, she kept telling me over and over and over again.
So I, I, by the time I was in college, I believed it. So even though it was hard. I still believed I could do it. And you know, and I, I was very naive. I was very naive. Like, I probably didn't understand just how in over my head I was, but I pushed through and I, and I, I was making very good grades by the time I got to my junior senior year.
[00:22:55] RORI: And then you did make these major contributions to biology. And you were doing some work recently that I just wonder what it was even like in 2020, you started doing work to try to understand the function of SARS CoV 2 proteins, no?
[00:23:12] MARYJO: Uh huh, uh huh.
[00:23:12] RORI: Like, what was it like to be doing that research at that time?
Like, We were all having our own early pandemic experience and the mm-hmm . You were characterizing protein function of this virus? Like what was it like?
[00:23:25] MARYJO: Well, I mean, the function of the proteins was, was, was pretty much known because other coronaviruses had been studied, but I remember it was February of 2020.
We were still all coming in in person and I said to, in our group meeting, I said, there's. There's an epidemic coming. I had no idea it was going to be as bad as it was, but I said, there's an epidemic coming. We should help. Who wants to help? And two grad students and one undergrad raised their hands. So then came the lockdown, but we were working on COVID 19.
The people who, those of us in the group who were working on COVID 19 had permission to come in. Well, we were able to do most of our work offsite, but I would come in one day a week. Um, I drive in even though I normally take the train. Because I didn't want to ride the train, and we worked on it. Uh, the functions of the proteins were known.
But what we were looking for was possible sites to target for drugs and, you know, that are there other sites besides the obvious ones that could be targeted? And we wrote a paper about it.
[00:24:28] RORI: And so you were there, you were some of the few people on campus. And it's kind of incredible that you, uh, you know, you kind of forecast that this is going to be an epidemic like in, in February.
You were already like, this is really clear and let's get started on it.
[00:24:42] MARYJO: Yeah. And the, the sequences of the viral proteins were known and, and the structures of the viral proteins were just starting to appear. And so then we were able to work on those structures.
[00:24:56] RORI: And then what about your findings? Did you find any drug targets that? We're actioned upon.
[00:25:03] MARYJO: Yeah, we, we, we found some possibilities and we wrote about it.
[00:25:07] RORI: So I, I guess I imagine it must have felt good to do something that is actively contributing to useful knowledge in that time when so many of us were, uh, you know, viscerally feeling the limits of our control over our.
[00:25:21] MARYJO: And in the summer, then some undergrads joined remotely and helped.
Yeah. So we had a bunch of undergrads helping. It did help to say, okay, well, you know, we're, we're studying the virus. We're, we're doing something where, you know, we're not just victims of this, this pandemic, you know, but it was, it was hard on the students. No, because I think it was probably harder for the younger people as they're, they're just programmed to be social and to connect with people.
And I think it was, it was hard on them to be isolated.
[00:25:52] RORI: Yeah, I think the people who were particularly like in high school at that time, it's really tough time to have to separate from your peers.
[00:26:02] EMILIA: I think COVID changed everybody's concept of like work time. And you know, now people want to be more flexible, have people into people in your lab.
Do they still come in person or are they remote more now?
[00:26:16] MARYJO: Yeah, we do both. I come in about four days a week. I work from home maybe one day a week. And my students, they come in for meetings. Some of them come in to work. Some of them work at least part of the time at home.
[00:26:28] RORI: Dr. Ondrechen, I would love to talk to you a little bit about gender and sexuality.
[00:26:34] MARYJO: Sure.
[00:26:34] RORI: Because, for me, this is, uh, you know, I'm a femme dyke, and it's a very important identity for me. And when, I feel like we don't talk too much about gender and sexuality in science, uh, but I know that you're a two spirit. I actually don't know how you identify your sexuality.
[00:26:52] MARYJO: I'm gay.
[00:26:53] RORI: Gay? Okay. So, I'm curious, did you have a coming out moment or have you like always been out as gay and two spirit?
[00:27:01] MARYJO: No, I, I didn't talk about my private life early on in my career.
[00:27:07] RORI: At what point did you, did it feel like the right thing to be able to come out in your professional life?
[00:27:13] MARYJO: Um, there was no real coming out moment. I think I think I assume people knew.
Um, then I guess it was maybe it was 2004. I could legally marry in Massachusetts.
[00:27:28] RORI: Massachusetts was one of the first.
[00:27:29] MARYJO: Massachusetts was the first.
[00:27:31] RORI: Was the first. Okay.
[00:27:31] MARYJO: Was the first. And, uh, and then, of course, um, on the public record as married to a woman. So, uh, we went to town hall on the first day that it was legal.
[00:27:44] RORI: Oh, wow.
[00:27:45] MARYJO: And got a marriage license.
[00:27:48] RORI: You and like many other people, right?
[00:27:50] MARYJO: Well, in, in our little town, there was no line.
[00:27:53] RORI: Okay.
[00:27:55] MARYJO: And then, and then that afternoon I came to work and I was in a suit and tie. And, and so my students were, were teasing me. You had business in town hall. I heard there was a long line.
I said, well, in Boston and Cambridge, yes, but not in our little town.
[00:28:10] RORI: That's sweet. Yeah.
[00:28:11] MARYJO: And the, the town clerk had a sign up that said fishing, marriage, and dog licenses. So, so I asked the town clerk, is that in order of importance?
[00:28:22] RORI: Yeah. Yeah.
[00:28:23] MARYJO: I said, well, there actually, there was a young couple that came in and the young man asked if he could get his fishing license first.
[00:28:30] RORI: I was going to say, you could get a little two for one there, you know, you're like, Oh, so long as I'm here, did I get a fishing license? Earlier, when you weren't talking about your personal life and who you were dating at work, like, were you actively worried about it or did you fear that something wouldn't go well if you did?
[00:28:49] MARYJO: I guess I was, I was probably an assistant professor when Northeastern Uh, passed the, the policy that we did not discriminate on the beck basis of sexual orientation. Um, I was, I was an assistant professor. Our vice provost for faculty affairs was a lesbian, so I, I kind of, I, I wasn't too worried.
[00:29:10] RORI: No, you didn't feel uncomfortable.
[00:29:11] MARYJO: Not in Massachusetts. No,
[00:29:13] RORI: not in Massachusetts. And before then in Illinois, and
[00:29:16] MARYJO: Yeah, I did. I didn't talk about it in grad school.
[00:29:18] RORI: Yeah, that's, I mean, in so many cases, that's a very practical, self preserving and, um, giving us access to the things that we need approach.
[00:29:28] EMILIA: When did you meet your partner and where?
[00:29:30] MARYJO: Uh, we met on a blind date 25 years ago. We had actually had talked on the phone first and had a very nice conversation. We said, let's meet and we met on a date and we hit it off. We just clicked.
[00:29:46] EMILIA: Is your partner a scientist or?
[00:29:48] MARYJO: She's an engineer.
[00:29:49] RORI: Okay. So it's all STEM all the time in your household.
[00:29:53] MARYJO: Yeah, I guess so.
But you know, I tell students, I say, you know, the most important decision you make in life is who you marry and the second most important decision is who's your PhD advisor. But you know, you've found the right person to marry. If that person makes every aspect of your life better. If it makes you a better scientist, if it makes, you know, maybe it made me a better scientist, better professor, better person.
A better everything, and if everything in your life is better with that person, then you know you've found the right person. I found it, I hope you do too. That's what I tell my students.
[00:30:27] RORI: That's beautiful.
[00:30:29] EMILIA: Choosing a PhD advisor has to be, is important. Could you expand on that?
[00:30:34] MARYJO: Well, it's just like, you know, if you, if you marry the right person, uh, you know, you can be happy.
If you marry the wrong person, you can be unhappy. And it's the same kind of thing. You know, is that person going, your PhD advisor, is that person going to support you? Is that person going to help you move on when you finish? Is the person going to help you succeed? Will you be part of the group? Will you, will you flourish and thrive in that group?
[00:31:01] RORI: Yeah, shorter relationship than a marriage, but at a pivotal moment,
[00:31:05] MARYJO: it's pretty much a lifelong relationship.
[00:31:07] RORI: You met your wife on a blind date and you talked on the phone first. I'm curious, how did you find other gay community?
[00:31:15] MARYJO: Well, you know, many years ago, it was a lot more, I don't know, underground. If you thought somebody was probably gay, you couldn't just ask them.
[00:31:25] RORI: Yeah, so what kind of signals did you use?
[00:31:27] MARYJO: Things that you'd ask, like, do you ride the bus? You know, I ride the bus. Do you ride the bus?
[00:31:33] RORI: Oh yeah.
[00:31:34] MARYJO: Are you family? I get asked, are you family?
[00:31:36] RORI: We're like hanky codes or those pins. What did people have? Like Lambda pins that they would wear, like, like a frat, but not a frat.
[00:31:44] MARYJO: Was that a thing that would, a lot, a lot of meeting took place in bars, which is not necessarily a good thing.
[00:31:50] RORI: Totally. This is a challenge about queer culture.
[00:31:54] EMILIA: What about your family? Was your family okay, uh, with you being gay?
[00:31:58] MARYJO: Yeah.
[00:31:59] RORI: That's, that's very rad.
[00:32:00] MARYJO: You know, Native people never had a problem, gays or genderqueer people.
I mean, the missionaries came and messed everything up, but traditionally our people never cared. The local Indian center had a federal grant to serve women who were affected by domestic violence. That's And the federal program officer said to our executive director, you know, we would like for you to serve transgender women also. And our executive director said, our people never had a problem with that.
[00:32:35] RORI: Like, it's already done.
[00:32:37] EMILIA: So we have a segment called Revise and Resubmit.
[00:32:42] MARYJO: Okay.
[00:32:42] EMILIA: And so here we talk about your own career journey that you'd like to change or revise. What would you like to revise and resubmit?
[00:32:52] MARYJO: Okay. Yeah. It went, I was a student, uh, uh, an undergrad.
I kind of was, was worked pretty much on my own. I was pretty isolated. And, you know, it would have been good to ask other students, what are professor so and so's tests like? What, you know, is there a good source on this subject? You know, it, it, uh, I wish that I had connected with people more. I wish that I had sought mentors more.
[00:33:18] RORI: Like in your undergrad, like early on.
[00:33:20] MARYJO: Yeah. And, and, and later. Well, I wish I had sought mentors more, uh, later in my career, yeah.
[00:33:26] RORI: Totally. Like you were saying earlier, our, our peers who can help guide us and our mentors who can help guide us are so invaluable. And so getting more earlier, make a difference.
[00:33:38] EMILIA: Yeah. And I think it's also hard for a single person to know everything. And so you have to ask around and find information that way. Thank you so much for, for coming and sitting down with us and, uh, you know, telling us your story. I really, um, enjoy hearing about it and I am definitely taking some lessons from it.
[00:34:01] MARYJO: Pleasure to talk with you.
[00:34:04] EMILIA: Thank you for listening. The hosts of ScienceWise are Rory Rolfes and me, Emilia Huerta Sanchez.
[00:34:10] RORI: This episode was produced and edited by Maribel Quesada Smith, with sound engineering by Keegan Stromberg. Special thanks to Dr. Mary Jo Ondrechen.
.
[00:00:09] EMILIA: So that when you have a question about what to do under a specific situation, you can get some guidance.
[00:00:15] RORI: I'm Rory. I'm the hildegard Lamfrom
Associate Professor in Data Science at the University of Oregon.
[00:00:20] EMILIA: And I'm Emilia, an Associate Professor in the Department of Ecology, Evolution, and Organismal Biology at Brown University.
[00:00:29] RORI: Today, we are thrilled to interview Mary Jo Ondrechen. Dr. Mary Jo Ondrechen is an incredibly productive computational chemist and has truly made science a more robust space that can support Indigenous scientists.
For years, Dr. Ondrechen has been developing models to predict protein function on a granular level. And she's gone further to develop protein design principles to create useful proteins, for example, to break down harmful chemical byproducts. She's made loads of software to predict protein functions, like Salsa Pool and thematics. And she's been using machine learning for these projects before it became popular to apply in biology. She continues to run a full and vibrant lab today. Her creative research is why she was awarded a Fulbright Faculty Research Fellowship and the 2024 Technical Excellence Award from ACES.
The American Indian Science and Engineering Society. Along with her science, Dr. Andrakin has been improving science culture for folks who came after her. For years, she has contributed to fellowship programs through ACES and has helped create Lighting the Pathway, a program to support Indigenous scientists as they become faculty.
Dr. Andrakin has been in the leadership of ACES and contributed to SACNAS for years and was appropriately awarded the 2018 SACNAS Outstanding Mentor Award. We are thrilled to talk with Dr. Mary Jo Andrakin today.
Well, we are very happy to interview you today. So honored to have a conversation with you. When you were growing up, you were really fascinated with the natural world and you dreamt of being a scientist and a professor, but you didn't know anybody who did those things. How did you learn that this profession existed?
[00:02:08] MARYJO: My mom would take us. On the weekends to the Natural History Museum, and every time we would learn something different back then, there was a lot of emphasis on science that you don't see in this country today.
[00:02:23] RORI: Oh, interesting.
[00:02:24] MARYJO: Now, in the, in the 1950s, when Russia launched the Sputnik. The oh it was oh my god, we're behind the Russians.
What are we gonna do?
[00:02:34] RORI: So it's kind of this like kind of competitive Cold War emphasis on
[00:02:38] MARYJO: absolutely. Yes And and there were all kinds of things to get kids interested in science There were these little 45 rpm vinyl records with songs of science
[00:02:49] RORI: and it sounds like your mom your mom really supported you in that.
She was like, yeah, let's go to the museum. Let's learn about snakes. Let me get you some records.
[00:02:56] MARYJO: My dad too. My dad was very interested in astronomy. And so we go out in the night and, and, uh, he'd tell me all about the stars and the constellations of the galaxies and everything. So
[00:03:08] RORI: You had pretty strong support from your parents to explore some of these, explore the natural world in different ways.
[00:03:14] MARYJO: Yes. Yes.
[00:03:15] EMILIA: Were you interested in biology then? Because that was maybe the closest to the natural world.
[00:03:19] MARYJO: Well, I was, I was interested in all kinds of things, you know, astronomy and plants and animals. Um, but then in high school, I had a very good chemistry teacher. You know, I went to the kind of high school where you don't learn much.
And, uh, a lot of the teachers had low expectations of us, but the chemistry teacher taught an honest to God college prep, you know, chemistry course. Her name was Mrs. Prime. Mrs. Prime was. Barely five feet tall. I can still picture her. She wore a red lab coat.
[00:03:53] RORI: Oh, stylish.
[00:03:54] MARYJO: Yeah. Before she was a teacher, she worked in industry.
And, you know, in most cases, probably the only woman and, uh, she really made chemistry fun and she taught a rigorous course, but she made it fun. She got a big kick out of life. She got a big kick out of chemistry.
[00:04:13] EMILIA: What was fun about it? Was it the experiments or was it the, because chemistry can be really technical.
[00:04:19] MARYJO: Yes, we did lots of experiments. He did lots of labs and so he had this sort of fun war going on with one of the biology teachers. We would send stink bombs to his class and things like that.
[00:04:33] RORI: Wow, serious pranking. What did they do to you?
[00:04:37] MARYJO: He would, well, they would fight biologically. So they would send this jar with the sheep's eye in it and things like that. It was all in fun.
[00:04:47] RORI: But you learned about the chemistry of making a stink bomb.
[00:04:50] MARYJO: Oh yeah.
[00:04:52] RORI: That's special. It's also special that this, this teacher was an industry and then went. To be a high school teacher. That's an unusual trajectory. So she was like a practicing chemist who then was like, no, I will actually want to, I want to share this with high school students.
[00:05:07] MARYJO: Mrs. Prime lived well into her nineties and through the magic of the internet. I was able to find her. So when she was about 90 years old, I went to visit her. We went out to lunch. Uh, she said, the restaurant's about a mile away. Is that all right walking? I said, sure. And I was able to thank her for introducing me to chemistry and giving me my career.
[00:05:33] RORI: So after you took her class, did you, did you think to yourself, this is it? I'm going to go into chemistry. Was it really clear to you right then?
[00:05:40] MARYJO: Yeah, because that fall as a senior, I applied to colleges and I wrote that I wanted to major in chemistry. I did not know anything about college applications or how to write them.
[00:05:51] RORI: So you didn't know how to do a college application. Can you tell us a little bit about your family? Like, had anyone in your family written a college application? Like, was this a totally new idea?
[00:06:01] MARYJO: My dad, he was in the Navy, and when he got out of the Navy, he took courses part time on the GI Bill. It was around, around between my junior and senior year when dad finally got his bachelor's degree.
But he didn't go, you know, through the college process by the typical path. Mom had no money for college, but during the Second World War, the government needed nurses, so they offered qualified young women, you know, a free ride through nursing school. They didn't call it a bachelor's RN back then, but it was the same thing as a modern-day bachelor's RN.
You take academic courses at the university and clinical and the nursing school. She didn't get into college by the path that most of us do now, where you write applications and everything. So, so it was a whole different story.
[00:06:53] EMILIA: Did you have siblings?
[00:06:55] MARYJO: We were five children and I was the oldest and one of my jobs, one of my many jobs growing up was reading to the younger children.
So they love Dr. Seuss. So to this day I have Dr. Seuss memorized. Oh, we, we did bad things too. We made gunpowder.
[00:07:15] RORI: Oh, wow.
[00:07:16] MARYJO: We, we got, we got chemicals and mixed them and made gunpowder.
[00:07:20] RORI: Whoa, was that before you were in, was that before Mrs. Pryne's class?
[00:07:24] MARYJO: Yeah, that was actually before Mrs. Pryne.
[00:07:26] RORI: Okay, okay, so you were already doing chemistry, naughty chemistry.
[00:07:30] MARYJO: Yes.
[00:07:32] EMILIA: You mentioned that you, you wanted to do chemistry. So that was your major.
[00:07:35] MARYJO: Yeah.
[00:07:36] EMILIA: Did you always wanted to do a PhD
[00:07:38] MARYJO: or? Sometime during undergrad, I guess. Yeah, I decided I wanted to be a professor. So I knew I had to get a PhD.
[00:07:43] RORI: So you were excited about the research. There are some questions you wanted to ask.
And I mean, of course, being a professor is a great way to be able to ask. your own questions, like the questions of your design, like what were you excited to explore?
[00:07:55] MARYJO: Well, in my senior year of college, I took a course in group theory. I was really impressed with how much you could say about molecules using this mathematical theory.
So that, that's kind of the direction I went, uh, in grad school, uh, doing theory and, and computation theory. Mostly theory.
[00:08:17] EMILIA: So when did you become interested in biology?
[00:08:20] MARYJO: Really the late 90s, as the human genome was being sequenced, I decided that there's got to be things that, uh, there's got to be ideas, progress that a theoretical chemist can contribute to.
[00:08:35] EMILIA: Were you waiting for that genome to be sequenced or, uh, did you start collaborations with people who were doing some sequencing, even though it wasn't, it was probably not. the human genome? Or were you just thinking theoretically, if we had this data, what could we do? Um, what, how could we contribute as theoretical chemists?
[00:08:54] MARYJO: Well, the genomes were being sequenced and a lot of those genes code for proteins. And a lot of those proteins are of unknown function. And so I took a sabbatical in 2000, 2001 to learn biochemistry because the biochemistry I learned as an undergrad was, was not good anymore. No, when I was an undergrad, you couldn't sequence nucleic acids.
Now you can, uh, everything, everything's changed. So I took a sabbatical and.
[00:09:26] EMILIA: Where did you go?
[00:09:27] MARYJO: I went to Brandeis University.
[00:09:29] RORI: That's cool. That's cool. To be like, oh, I'm gonna change, I'm gonna learn something new. Like, you had been a professor for, what, 15 years or something? By then, you're like, no, I'm gonna
[00:09:38] MARYJO: Yeah.For 20 years. Yeah,
[00:09:38] RORI: for 20 years by then. Okay.
[00:09:40] MARYJO: Mm-hmm . And, yeah, I joined the faculty in 1980. Yeah. And, uh, so, uh, I, I, uh, worked with Jag Maringa at Brandeis, and we, well, I, I said I, if you gimme the structure of any protein, I'll tell you which amino acids. are important for the function.
[00:09:57] RORI: Oh, that's a nice offer.
[00:09:59] MARYJO: And, uh, so she gave me some examples of proteins that she'd work with and saw that I was predicting the active amino acids. And so she knew there was something to it because here was this person who didn't know any biochemistry who knew exactly where the active residues were. So she knew there was something, something to it.
So, and so, uh, that we we've. Carried those ideas, my group and I have carried those ideas on to other things, uh, but, uh,
[00:10:28] EMILIA: I'm curious, how do you know what is active from the structure of the protein?
[00:10:32] MARYJO: We calculate them from the three-dimensional structure.
[00:10:35] RORI: So you go from the sequence to predict the three-dimensional structure.
And my biochemistry is pretty rusty, but you can predict like these alpha helixes and beta sheets. And things.
[00:10:47] MARYJO: Yeah. Yeah. You can build structures by homology to known structures. And nowadays, the alpha fold programs are very good at omniscio predictions.
[00:10:58] RORI: So you've been doing this kind of work, this protein function prediction, for quite a while and you've published some pretty key software in the field.
[00:11:06] MARYJO: Yeah.
[00:11:06] RORI: You were applying, you know, machine learning to these problems kind of before it became in vogue to apply machine learning to biological questions. I mean, I guess it sounds like Your collaborator at Brandeis was like, well, Dr. Rakin is predicting things correctly, so she must be doing something right here.
[00:11:25] MARYJO: I published my first machine learning paper applied to Biomolecules in 2008. That was kind of before the, the big wave of interest in, in machine learning ai,
[00:11:36] RORI: like by quite a lot. By like a decade. Yeah.
[00:11:39] EMILIA: Um, I'm still stuck in this other question about the protein structure and how you find out what's by, uh, active.
So, how would you test that your prediction
was correct?
[00:11:48] MARYJO: Yeah, we, we've done a collaboration. We've done, I collaborate with Penny Boyning here at Northeastern. Uh, you, you mutate out the amino acid. That's, that you say is important and see if you lose activity.
[00:12:01] EMILIA: And lose activity means like the protein doesn't fold or?
[00:12:06] MARYJO: No, no, the proteins usually fold, but they, you, you know, enzymes catalyze reactions. So to measure whether it's, you see, you test how fast. It can generate product.
[00:12:20] EMILIA: Okay, so using kinetic experiments.
[00:12:22] MARYJO: Or binding experiments, yeah.
[00:12:24] EMILIA: Okay, um, if you had to describe right now what you study and how you describe whatever you do, how would you, I guess, how would you describe that?
Like, would you say you're just a theoretical chemist or you've done, you're more than that obviously, but how would you describe it?
[00:12:40] MARYJO: It's a combination of theoretical chemistry and computational biology and bioinformatics.
[00:12:45] EMILIA: Okay, so very interdisciplinary.
[00:12:47] RORI: Where did you go to PhD school?
[00:12:49] MARYJO: Northwestern.
[00:12:50] RORI: And over in Evanston, you're doing computational chemistry.
And from there, you decided you wanted to do a postdoc. You were like, yes, I want to be a faculty member.
[00:12:59] MARYJO: Yeah, yeah. You know, computers couldn't do a lot back then. And so we did a lot of. Sort of deriving equations kind of theory, you know, um.
[00:13:08] EMILIA: Did you do
any programming when you were at school?
[00:13:10] MARYJO: Yeah, I
did, I did. I had programs that they were on punch cards.
[00:13:15] RORI: Yeah.
[00:13:16] MARYJO: So I had this big box and I'd carry it on my shoulder to the computer center.
[00:13:21] RORI: Like some people carry a boom box, you're carrying your punch cards.
[00:13:28] EMILIA: And graduate school, did you feel like, did you feel like you belong there? What was the environment like back then?
[00:13:34] MARYJO: Yeah, I thought graduate school was easy compared to undergrad.
[00:13:37] EMILIA: Really?
[00:13:39] MARYJO: You know, except in chemistry, I was not real well prepared for undergrad school. And it was, it was a bit of a struggle to catch up with everybody else. Yeah, so I, yeah, I tell, I tell kids, I say, you know, I got a bachelor's degree and a doctorate.
I'm proud of both degrees, and I worked hard for both degrees. But it was the bachelor's degree that was harder.
[00:14:00] RORI: Like what did your struggle in undergrad look like?
[00:14:03] MARYJO: Well, everybody else was ahead of me.
[00:14:07] EMILIA: But not in chemistry, you were, you were okay in chemistry.
[00:14:10] MARYJO: I was okay in chemistry.
[00:14:11] EMILIA: Why do you think that is?
Was it just because that was what sparked your interest or?
[00:14:16] MARYJO: No, it's because of Mrs. Brine who taught a real class.
[00:14:19] EMILIA: I see.
[00:14:21] MARYJO: I mean, this was a high school, no AP, no calculus. No, you know, no advanced courses. I mean, my senior year, I only went to school half a day. The school was underfunded and we had double sessions.
So, so yeah, I only went to school for half a day.
[00:14:38] EMILIA: How do you approach this with students when they, they feel like some things were not covered in class or that they don't know how to do this or that?
[00:14:47] MARYJO: I think when you come, from an underserved community, you tend to study in high school on your own, you tend to learn on your own, and in college and in grad school, you could do better.
If you connect with other people and learn from them, like they might know something that you don't know, or they may know workarounds or a good source on the subject, or you know, how to succeed in professor so and so's class. And Just working, you know, just, just being involved with other students can be a big help and, and sometimes it's hard to break out of that mold of, okay, I'm on my own. I've got to learn all this stuff by myself.
[00:15:34] EMILIA: Yeah. I think, uh, learning from others and also teaching others what you know that they don't know is it's a good strategy. What about the tenure process? Did you, did you just fly through that? You said undergrad was hard. Grad school was. easier. What about faculty life? Or did you do a postdoc?
[00:15:52] MARYJO: I did. I did. I postdoc at the University of Chicago. And then I was, I was a NATO fellow at Tel Aviv University in Israel.
[00:16:00] EMILIA: Have you been outside of the country before that?
[00:16:02] MARYJO: Yes. As a member of a Navy family, I had done kindergarten and first grade in Japan.
[00:16:09] EMILIA: Oh.
[00:16:10] MARYJO: My younger sister was born in Japan.
[00:16:13] EMILIA: How do you think all those places shaped your view of the world? Or how did you approach the world based on those experiences?
[00:16:21] MARYJO: Um, it, it makes it hard personally because you make a friend and then you have to move away.
[00:16:29] RORI: And you started your faculty job in 1980 at Northeastern, and you've been there ever since.
[00:16:36] MARYJO: Well, Boston is a wonderful city. It's got a very good cultural life. It's easy to get around the city, but yeah, I like it here. I like it here.
[00:16:47] EMILIA: So you, you said you took your faculty, did you say you started your faculty position in, in the 80s?
[00:16:53] MARYJO: 1980, yeah.
[00:16:55] EMILIA: Okay, so you've seen, I mean, Boston has probably evolved a lot.
[00:16:59] MARYJO: And Northeastern has evolved. It's hard to get in now. It's very hard to get into Northeastern. And, uh, you know, we're, we're now in an R1, highly research-intensive university.
[00:17:10] EMILIA: But you've always gone on sabbatical. So it's not that you've been there since then. You've, you've
[00:17:15] MARYJO: Well, once every seven years, I go on sabbatical.
[00:17:18] RORI: As often as they come up.
[00:17:20] EMILIA: How do you choose where to go on sabbatical?
[00:17:22] MARYJO: Well, you want to go someplace where you can do something new, learn something new. And you want to go someplace that's a good place to be, you know. So, and, and, uh, personal considerations, like when my parents were elderly, and I, I would take my sabbatical in Southern California.
[00:17:40] EMILIA: And did you encounter any challenges as, as faculty? Or has it been an okay experience? At Northeastern. And maybe that's why you've been there for so long.
[00:17:50] MARYJO: Yeah. Well, there've been challenges. You know, we, we have right now we have, I have an excellent department chair, an excellent Dean. When you have good leadership, things go, go well.
[00:18:00] RORI: Totally.
[00:18:01] MARYJO: And there were, there were times in the distant past when we did not have good leadership.
[00:18:05] RORI: That's so hard.
[00:18:06] MARYJO: And that hurts morale. It hurts progress. Um, But, uh, for the quite a long time now, we've had, we've been in very good shape, very good leadership. We're doing very well.
[00:18:15] RORI: That's good. When you had weaker leadership, how did you cope?
[00:18:20] MARYJO: Well, you know, that that person is not going to stay there forever. You know, we, we tell each other, we're going to outlast this guy. Yeah. I mean, weak leaders are bad because they don't push the unit forward, but jerks are even worse because they hurt morale. And they set the tone and, you know, for some time now we've had a tone of collegiality, respect, people like each other, have fun together and do a lot of good things.
And, and that, that's what happens when you have, you know, good leadership.
[00:18:54] RORI: But you've done a lot in kind of like non-university leadership.
[00:18:58] MARYJO: Oh, y Like, like chairing the board at ACEs.
[00:19:01] RORI: Yeah. Like ACEs, like the American Chemical Society. I see that you ran for the Health Board of Hopkinton, which I don't even know how to pronounce.
[00:19:09] MARYJO: I am, I am. You're on the board of Health of Hopkins. Mm-hmm.
[00:19:12] RORI: You take a lot of leadership roles in these kind of like society, uh, frameworks, either like academic society or, you know, kind of like social. Health board of a, of a town.
[00:19:25] MARYJO: Well, uh, you know, sometimes people ask you to step up and when people who you respect say you're needed, would you please step up?
You do it.
[00:19:33] EMILIA: You're still mentoring students and, and, uh, maybe postdocs or undergrads?
[00:19:38] MARYJO: I'm still working right now I got, I got seven PhD students, four master's students.
[00:19:45] RORI: That's big.
[00:19:46] MARYJO: And a couple undergrads, a visiting scholar on sabbatical.
[00:19:50] RORI: Wow. That's a popping lab.
[00:19:52] EMILIA: I know. How do you manage such a big lab?
[00:19:55] MARYJO: The more experienced people I count on to help the newer people. Because I can't, I can't help everybody directly myself.
[00:20:01] RORI: No, that's
so many people, like even just meeting with everybody for an hour a week, that's like half your week.
[00:20:06] MARYJO: Can't do that, yeah.
[00:20:08] RORI: Okay, so you kind of have like structures.
[00:20:10] MARYJO: Yeah. Groups and subgroups, yeah.
[00:20:13] RORI: What motivated you? Why do you have a big lab now?
[00:20:15] MARYJO: Well, I, I, more people wanted to work with me when I started doing bioproblems.
[00:20:19] RORI: Oh, there you go. Yeah, there's a lot of biologists, there's a lot of NIH funding.
[00:20:25] MARYJO: Well, the hardcore, you know, hardcore physical chemistry, non-linear optical properties, you know, not, not many students want to do stuff like that.
[00:20:35] EMILIA: You received a letter about whether or not you were suitable for biology.
[00:20:39] MARYJO: I took a biology class my freshman year. And I got a letter from the chair of biology saying that it was the policy of their department to inform all the students who took, I forget what they call biology 101, first year biology, to inform all the students about your prospects to be a biology major.
And I had never asked to be a biology major, I was a chemistry major. Uh, but the letter said that they did not think I, would make a very good biology major. So I tore up the letter into a million pieces and threw it away, but I wish I had kept it because I would frame it. Because I think by any fair analysis, I've done far more to contribute to biological knowledge than the dude that wrote that letter.
[00:21:25] RORI: I'm sure. Also, what a weird policy. We're going to send unsolicited letters to everyone telling them to or not to. Like, who would think that's a good idea? Yeah,
[00:21:35] MARYJO: I mean, yeah.
[00:21:36] RORI: And, and clearly you're right. You've contributed so much more.
[00:21:39] MARYJO: Yeah, but it hurt. At the time it, it hurt. And, um, I don't know, maybe it subconsciously discouraged me from going that way and going more in the direction of the mathematics and theory, you know, physical theory stuff. Yeah.
[00:21:52] RORI: You know, undergrad was difficult. You were doing a lot of catching up. You were working very hard. And then to get this unsolicited letter saying that you shouldn't be in biology. Yikes.
[00:22:02] EMILIA: So how did you shake those feelings away?
[00:22:04] MARYJO: I don't know what I did, uh, other than to tear the letter up.
[00:22:08] RORI: But that's something.
[00:22:09] MARYJO: I think that fundamentally I did believe in myself because my mom, my mom told me over and over again You can do anything you want if you try, you can do anything you want if you work, you can do anything. So, so, and, and from the time I was little, like probably too young to fully understand, she kept telling me over and over and over again.
So I, I, by the time I was in college, I believed it. So even though it was hard. I still believed I could do it. And you know, and I, I was very naive. I was very naive. Like, I probably didn't understand just how in over my head I was, but I pushed through and I, and I, I was making very good grades by the time I got to my junior senior year.
[00:22:55] RORI: And then you did make these major contributions to biology. And you were doing some work recently that I just wonder what it was even like in 2020, you started doing work to try to understand the function of SARS CoV 2 proteins, no?
[00:23:12] MARYJO: Uh huh, uh huh.
[00:23:12] RORI: Like, what was it like to be doing that research at that time?
Like, We were all having our own early pandemic experience and the mm-hmm . You were characterizing protein function of this virus? Like what was it like?
[00:23:25] MARYJO: Well, I mean, the function of the proteins was, was, was pretty much known because other coronaviruses had been studied, but I remember it was February of 2020.
We were still all coming in in person and I said to, in our group meeting, I said, there's. There's an epidemic coming. I had no idea it was going to be as bad as it was, but I said, there's an epidemic coming. We should help. Who wants to help? And two grad students and one undergrad raised their hands. So then came the lockdown, but we were working on COVID 19.
The people who, those of us in the group who were working on COVID 19 had permission to come in. Well, we were able to do most of our work offsite, but I would come in one day a week. Um, I drive in even though I normally take the train. Because I didn't want to ride the train, and we worked on it. Uh, the functions of the proteins were known.
But what we were looking for was possible sites to target for drugs and, you know, that are there other sites besides the obvious ones that could be targeted? And we wrote a paper about it.
[00:24:28] RORI: And so you were there, you were some of the few people on campus. And it's kind of incredible that you, uh, you know, you kind of forecast that this is going to be an epidemic like in, in February.
You were already like, this is really clear and let's get started on it.
[00:24:42] MARYJO: Yeah. And the, the sequences of the viral proteins were known and, and the structures of the viral proteins were just starting to appear. And so then we were able to work on those structures.
[00:24:56] RORI: And then what about your findings? Did you find any drug targets that? We're actioned upon.
[00:25:03] MARYJO: Yeah, we, we, we found some possibilities and we wrote about it.
[00:25:07] RORI: So I, I guess I imagine it must have felt good to do something that is actively contributing to useful knowledge in that time when so many of us were, uh, you know, viscerally feeling the limits of our control over our.
[00:25:21] MARYJO: And in the summer, then some undergrads joined remotely and helped.
Yeah. So we had a bunch of undergrads helping. It did help to say, okay, well, you know, we're, we're studying the virus. We're, we're doing something where, you know, we're not just victims of this, this pandemic, you know, but it was, it was hard on the students. No, because I think it was probably harder for the younger people as they're, they're just programmed to be social and to connect with people.
And I think it was, it was hard on them to be isolated.
[00:25:52] RORI: Yeah, I think the people who were particularly like in high school at that time, it's really tough time to have to separate from your peers.
[00:26:02] EMILIA: I think COVID changed everybody's concept of like work time. And you know, now people want to be more flexible, have people into people in your lab.
Do they still come in person or are they remote more now?
[00:26:16] MARYJO: Yeah, we do both. I come in about four days a week. I work from home maybe one day a week. And my students, they come in for meetings. Some of them come in to work. Some of them work at least part of the time at home.
[00:26:28] RORI: Dr. Ondrechen, I would love to talk to you a little bit about gender and sexuality.
[00:26:34] MARYJO: Sure.
[00:26:34] RORI: Because, for me, this is, uh, you know, I'm a femme dyke, and it's a very important identity for me. And when, I feel like we don't talk too much about gender and sexuality in science, uh, but I know that you're a two spirit. I actually don't know how you identify your sexuality.
[00:26:52] MARYJO: I'm gay.
[00:26:53] RORI: Gay? Okay. So, I'm curious, did you have a coming out moment or have you like always been out as gay and two spirit?
[00:27:01] MARYJO: No, I, I didn't talk about my private life early on in my career.
[00:27:07] RORI: At what point did you, did it feel like the right thing to be able to come out in your professional life?
[00:27:13] MARYJO: Um, there was no real coming out moment. I think I think I assume people knew.
Um, then I guess it was maybe it was 2004. I could legally marry in Massachusetts.
[00:27:28] RORI: Massachusetts was one of the first.
[00:27:29] MARYJO: Massachusetts was the first.
[00:27:31] RORI: Was the first. Okay.
[00:27:31] MARYJO: Was the first. And, uh, and then, of course, um, on the public record as married to a woman. So, uh, we went to town hall on the first day that it was legal.
[00:27:44] RORI: Oh, wow.
[00:27:45] MARYJO: And got a marriage license.
[00:27:48] RORI: You and like many other people, right?
[00:27:50] MARYJO: Well, in, in our little town, there was no line.
[00:27:53] RORI: Okay.
[00:27:55] MARYJO: And then, and then that afternoon I came to work and I was in a suit and tie. And, and so my students were, were teasing me. You had business in town hall. I heard there was a long line.
I said, well, in Boston and Cambridge, yes, but not in our little town.
[00:28:10] RORI: That's sweet. Yeah.
[00:28:11] MARYJO: And the, the town clerk had a sign up that said fishing, marriage, and dog licenses. So, so I asked the town clerk, is that in order of importance?
[00:28:22] RORI: Yeah. Yeah.
[00:28:23] MARYJO: I said, well, there actually, there was a young couple that came in and the young man asked if he could get his fishing license first.
[00:28:30] RORI: I was going to say, you could get a little two for one there, you know, you're like, Oh, so long as I'm here, did I get a fishing license? Earlier, when you weren't talking about your personal life and who you were dating at work, like, were you actively worried about it or did you fear that something wouldn't go well if you did?
[00:28:49] MARYJO: I guess I was, I was probably an assistant professor when Northeastern Uh, passed the, the policy that we did not discriminate on the beck basis of sexual orientation. Um, I was, I was an assistant professor. Our vice provost for faculty affairs was a lesbian, so I, I kind of, I, I wasn't too worried.
[00:29:10] RORI: No, you didn't feel uncomfortable.
[00:29:11] MARYJO: Not in Massachusetts. No,
[00:29:13] RORI: not in Massachusetts. And before then in Illinois, and
[00:29:16] MARYJO: Yeah, I did. I didn't talk about it in grad school.
[00:29:18] RORI: Yeah, that's, I mean, in so many cases, that's a very practical, self preserving and, um, giving us access to the things that we need approach.
[00:29:28] EMILIA: When did you meet your partner and where?
[00:29:30] MARYJO: Uh, we met on a blind date 25 years ago. We had actually had talked on the phone first and had a very nice conversation. We said, let's meet and we met on a date and we hit it off. We just clicked.
[00:29:46] EMILIA: Is your partner a scientist or?
[00:29:48] MARYJO: She's an engineer.
[00:29:49] RORI: Okay. So it's all STEM all the time in your household.
[00:29:53] MARYJO: Yeah, I guess so.
But you know, I tell students, I say, you know, the most important decision you make in life is who you marry and the second most important decision is who's your PhD advisor. But you know, you've found the right person to marry. If that person makes every aspect of your life better. If it makes you a better scientist, if it makes, you know, maybe it made me a better scientist, better professor, better person.
A better everything, and if everything in your life is better with that person, then you know you've found the right person. I found it, I hope you do too. That's what I tell my students.
[00:30:27] RORI: That's beautiful.
[00:30:29] EMILIA: Choosing a PhD advisor has to be, is important. Could you expand on that?
[00:30:34] MARYJO: Well, it's just like, you know, if you, if you marry the right person, uh, you know, you can be happy.
If you marry the wrong person, you can be unhappy. And it's the same kind of thing. You know, is that person going, your PhD advisor, is that person going to support you? Is that person going to help you move on when you finish? Is the person going to help you succeed? Will you be part of the group? Will you, will you flourish and thrive in that group?
[00:31:01] RORI: Yeah, shorter relationship than a marriage, but at a pivotal moment,
[00:31:05] MARYJO: it's pretty much a lifelong relationship.
[00:31:07] RORI: You met your wife on a blind date and you talked on the phone first. I'm curious, how did you find other gay community?
[00:31:15] MARYJO: Well, you know, many years ago, it was a lot more, I don't know, underground. If you thought somebody was probably gay, you couldn't just ask them.
[00:31:25] RORI: Yeah, so what kind of signals did you use?
[00:31:27] MARYJO: Things that you'd ask, like, do you ride the bus? You know, I ride the bus. Do you ride the bus?
[00:31:33] RORI: Oh yeah.
[00:31:34] MARYJO: Are you family? I get asked, are you family?
[00:31:36] RORI: We're like hanky codes or those pins. What did people have? Like Lambda pins that they would wear, like, like a frat, but not a frat.
[00:31:44] MARYJO: Was that a thing that would, a lot, a lot of meeting took place in bars, which is not necessarily a good thing.
[00:31:50] RORI: Totally. This is a challenge about queer culture.
[00:31:54] EMILIA: What about your family? Was your family okay, uh, with you being gay?
[00:31:58] MARYJO: Yeah.
[00:31:59] RORI: That's, that's very rad.
[00:32:00] MARYJO: You know, Native people never had a problem, gays or genderqueer people.
I mean, the missionaries came and messed everything up, but traditionally our people never cared. The local Indian center had a federal grant to serve women who were affected by domestic violence. That's And the federal program officer said to our executive director, you know, we would like for you to serve transgender women also. And our executive director said, our people never had a problem with that.
[00:32:35] RORI: Like, it's already done.
[00:32:37] EMILIA: So we have a segment called Revise and Resubmit.
[00:32:42] MARYJO: Okay.
[00:32:42] EMILIA: And so here we talk about your own career journey that you'd like to change or revise. What would you like to revise and resubmit?
[00:32:52] MARYJO: Okay. Yeah. It went, I was a student, uh, uh, an undergrad.
I kind of was, was worked pretty much on my own. I was pretty isolated. And, you know, it would have been good to ask other students, what are professor so and so's tests like? What, you know, is there a good source on this subject? You know, it, it, uh, I wish that I had connected with people more. I wish that I had sought mentors more.
[00:33:18] RORI: Like in your undergrad, like early on.
[00:33:20] MARYJO: Yeah. And, and, and later. Well, I wish I had sought mentors more, uh, later in my career, yeah.
[00:33:26] RORI: Totally. Like you were saying earlier, our, our peers who can help guide us and our mentors who can help guide us are so invaluable. And so getting more earlier, make a difference.
[00:33:38] EMILIA: Yeah. And I think it's also hard for a single person to know everything. And so you have to ask around and find information that way. Thank you so much for, for coming and sitting down with us and, uh, you know, telling us your story. I really, um, enjoy hearing about it and I am definitely taking some lessons from it.
[00:34:01] MARYJO: Pleasure to talk with you.
[00:34:04] EMILIA: Thank you for listening. The hosts of ScienceWise are Rory Rolfes and me, Emilia Huerta Sanchez.
[00:34:10] RORI: This episode was produced and edited by Maribel Quesada Smith, with sound engineering by Keegan Stromberg. Special thanks to Dr. Mary Jo Ondrechen.
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