Share

The Graduates

KALX Radio

The Graduates is the talk show where we interview UC Berkeley graduates students about their work here on campus. Hosted by graduate students Ashley Smiley, Andrew Saintsing, and others, The Graduates airs every other Tu
Latest Episode3/10/2021

Kailey Ferger

Serrano: Hello, you've tuned in to 90.7 FM KALX Berkeley. I'm Karen Serrano and this is, The Graduates, an interview talk show where we speak to UC Berkeley graduate students about their work on campus and beyond. I'm joined by Kailey Ferger today from the Center of Computational Biology. Welcome to the show, Kailey!Ferger: Thanks. Thanks for having me.Serrano: Yeah, we are so happy to have you! So Kailey, tell us a little bit about the research you conduct on campus.Ferger: Yeah, so I'm a graduate student at the Center for Computational Biology, like Karen just said. So my work is entirely computational. I don't do any wet lab research. And so what that means for a PhD is essentially like designing pipelines or designing software or doing data analysis with various different programming languages. So at the end of my PhD, I hope to eventually either create some software or design a pipeline that other computational biologists can implement for their own data. And so I guess I'll tell you a little bit about what I specifically do. So I work with human genetics. I look at human genomes from populations across the world. Specifically, I am looking at two kind of different spheres of human populations, the first being modern-day Europeans and Asian populations and the second being South Asian populations and like Native American populations. So for the part where I'm analyzing like Eurasian populations like modern-day, I'm specifically investigating the effects of admixture in those populations. So what that means is essentially many many thousands of years ago humans lived on Earth with other ancient hominids, including neanderthals and denisovan hominids as well as potentially other hominids. Of course, they're extinct now, but there has been a lot of evidence in the past decade probably that humans actually kind of mixed with the Neanderthal population and I guess, like, had children with neanderthals and denisovan populations. And so even today there are still signatures in our own genomes of these archaic hominids, like their genomes in our own genomes. So a large portion of my project focuses on identifying these segments along all of the genomes and kind of characterizing how that like the archaic, you know, genome content that kind of remains in our own genomes has kind of affected the way we evolved and affected how we moved and affected the way that selection acts in our genomes. So I'm characterizing the distribution of archaic genomic segments in the genome and also looking at how natural selection has selected some of the variants that were kind of mixed into our own genomes. So I'm specifically developing a computational method right now that will let us do just that! So essentially, if we're able to identify where these archaic segments are in our genomes, hopefully, once we identify where they are we can also start to look at how natural selection is acting on these segments. So I hope to identify various like genes that are actually Neanderthal origin or denisovan origin and see kind of like when and how these genes have been selected throughout history and in what populations. So kind of what advantages they confer in the population and kind of just further characterizing archaic genomics.Serrano: Great. Wow, that's super cool and interesting and also something I know nothing about. I have a few questions. First of all, how.. how do you obtain this ancient DNA? Do you have samples that you maybe collect from museums or how?? Yeah, how do you basically get these genomes, right?Ferger: So it's cool because we're actually able to leverage modern human data. So basically we're just using.. so there's various models that exist today that are able to infer these tiny little bits of archaic segments in modern human genomes. So most Asian and European human populations still have kind of these signatures across their whole genome of these archaic genomes that at one time were highly prevalent at the time of the admixture event that occurred. So we can kind of leverage all of these different human genetic databases around the world, like for example the Thousand Genomes Project which aims to capture, I think, human genomes from Asia Europe, America, South Asia, and maybe Oceania and then I'm also using a really cool database that actually just came out so a bunch of new sequences from East Asia, North East Asia, Southeast Asia and in areas like that. And so that part I'm actually really excited about because many of these populations have not been studied extensively at all. Because I think sampling in these areas has been really scarce and like a lot of funding has been allocated towards kind of European and Asian populations and a lot of the major universities are located there and a lot of interest has been there especially in things like genomic medicine and things like that. So a lot of other populations like in South Asia, especially have not even been closely looked at so I'm looking at kind of populations from India populations in Southeast Asia and some like Oceanian populations too. So that's kind of going to be like the novel aspect of my analysis and those areas!Serrano: That's really cool. So I'm not a computational biologist. I don't know many things about you know, the programs that you're using. How do you recognize these stretches of ancient DNA in our genomes? Is it like, are you mapping it back to a known ancient DNA sequence or how does that work?Ferger: That's a really great question. So there are several ways to do this and one of them is doing just that! Where essentially you're taking a reference genome from one of the hominid species that we've been able to actually sequence to high coverage just because scientists have been working a really long time at it and have really been careful at preserving the remains that we found and so you could match the segments in a genome back to that reference. But I'm actually using a method that is reference-free and so it involves essentially using what's called a Hidden Markov Model, which is essentially just a kind of machine learning algorithm and it basically just uses, like, it leverages private variation that's found in the genome. So if you can imagine a human genome and an archaic hominid genome, it's going to have a lot more genetic differences across the whole genome compared to like a human population or human individual from a European population compared to like an American individual or something or like a Native American individual. You're just going to have a lot more fixed differences between an archaic genome. And so essentially that algorithm is leveraging a lot of those fixed differences in the population. What I mean by fixed differences, so we all have kind of like that four letter code that defines our whole genome and humans are actually extremely consistent. There really isn't as much variation among populations as you might think but compared to an archaic genome, there's a lot more differences. And so yeah this this algorithm essentially just leverages a lot of those differences and then it basically just uses the idea that if you input a human genome into the algorithm, it basically just scans along the genome and uses kind of a reference human population and then calculates the probability that a certain segment is human or archaic based on how different it is from like a human reference genome or another human individual or something.Serrano: I think I'm following. So basically this algorithm can compare how different two genomes are to each other and if it's more different than two human genomes are to each other, it will assume that it's actually hominid.Ferger: Yes, exactly!Serrano: Okay.Ferger: So yeah, the thing about that is it can't really identify what hominid it is. And that's kind of where my project comes in a little bit more but it can identify that it's probably not human given other genomes that you feed in and the reference genome and things like that.Serrano: So I might ask a silly question because I probably read too much sci-fi. But I've heard that like certain people with more neanderthal DNA have certain personality traits. Is there any like validity to that at all?Ferger:Yeah. I mean, I won't cast anything out of the realm of possibility just because we're discovering more and more about archaic genetics and the truth is that we don't really know. I would say it's probably unlikely. Just because there is only around 2 percent of our genome that is Neanderthal and of course two percent total of our genome is coding. And so the chance that a coding part of our genome will be Neanderthal or Denisovan or some other archaic type is very miniscule. But yeah, we're still doing research and a lot is still unknown. Like we have discovered various genes that are selected that are confirmed to be Neanderthal-derived or Denivosan and we're able to characterize, kind of, the selective event and why it was selected and what advantage it confers in the population and things like that. But yeah, I guess I guess that remains to be seen! Such a funny question.Serrano: Yeah. I don't know. I keep seeing articles, like, I don't know, if you have more Neanderthal DNA, you're like more aggressive or something. I'm sure they're false, but I didn't know if there's actual science behind that.Ferger: Yeah, I think another point to bring up to is that whatever amount of variation that people across the world have in terms of the amount of archaic ancestry is also very small. So it's within the range of a single percentage. So I'd say the populations with the most archaic DNA is like the Oceanian population. So like New Zealand Australia and the Pacific Islands and then across Europe Asia even America, we all have around two percent. Maybe, maybe a little over.Serrano: So we're all pretty similar, right?Ferger: Okay, we're pretty similar on that front. So there isn't going to be an individual you meet that has drastically more archaic DNA and maybe have noticeable effects.Serrano: What kind of genes, or I don't know if you've gotten to this part of the project, but what kind of genes have been conserved from ancient hominids?Ferger: Yeah. Yeah. So, um surprisingly, there's a lot of like immune system functions that have been selected.Serrano: Oh! That's interesting.Ferger: Yeah. Um, so that's, that's one category. Perhaps even more surprisingly, like fertility genes are not selected at all. And that's like actually a surprising result. So there's like a complete desert in the whole all of the sex chromosomes basically of archaic ancestry. And so I think that's kind of interesting. We don't really know what that means. Yeah, but definitely some immune functions have been selected. There's a really cool example actually in the Tibetan population. So there's individuals living on the Tibetan Plateau, which means they live at very high altitude. But genetically they're very similar to Chinese populations in the surrounding area, with one large exception, which is they actually have a gene that was conferred by Denisovans actually in their genomes and this gene allows them to be adapted to high altitudes. So if you ever, if you've ever been kind of at a really high altitude area for a long time, you probably know that you'll start to get altitude sickness or high altitude sickness. So I think your breathing shortens, like your blood doesn't flow as well. And it's just not good for you. You become very ill. But individuals who live in Tibet and at this very high altitude actually have an adaptation where they don't experience hypoxia, which is what you experience when you are really high up for a long time and they basically, luckily, have a mutation on this gene that was conferred from Denisovans where it modifies, I believe, some structure in their red blood cells. So they aren't susceptible to kind of hypoxic conditions. So I think that's a really cool example of a really unique signal that was conserved.Serrano: Yeah, and that was probably, I'm just kind of guessing here, that was probably so conserved in that population because it's so isolated from other populations, right? So they're living up in these mountains and that's kind of like separating them from other poptulations!Ferger: Yeah, yeah exactly. So they don't have a ton of admixture with other populations. And so we were able to characterize this signal really well and that's why it's so well conserved in this population.Serrano: Wow. That's pretty interesting.Ferger: Yeah.Serrano: So besides this project that you're working on, are there any like smaller projects that you're interested in as well?Ferger: Yeah. Yeah. So the main portion of the project I describe was essentially developing this method that scans the genome for selection on like these segments that were conferred to these individuals through gene flow. So once I develop that method and it is tested and works really well in the conditions of like archaic introgression, we're hoping to apply it to various different populations that are relatively understudied and so populations like Native American populations across North and South America as well as a lot of populations in South Asia. Like populations in India and Malaysia and kind of places like that. And so for a lot of these populations, kind of the reason they have been pretty understudied, other than the fact that there hasn't been a ton of kind of like funding for sampling in this area, is because they also are genetically really complicated. Because European and kind of a lot of Asians are relatively homogeneous from a genetic perspective meaning just that their genomes are all pretty similar in their kind of own groups. But in the cases of like South Asian populations and smaller populations, they have kind of signatures of recent like population mixture events. So when populations kind of come together and merge and start to like mix with each other and start to have children and create this admixed population, it makes your genome actually really difficult to study. This is because you basically have this, kind of, if you can imagine, this mosaic of different ancestry blocks across your whole genome and this is because every generation when you reproduce you kind of get this recombination event in your chromosomes. This is really getting in the weeds, but you kind of get these recombination events every generation in your chromosomes, which just kind of breaks up all of these ancestral blocks in your genome and so you end up with kind of this huge mosaic of ancestry. So kind of it models a lot of signals and it makes it really hard to study selection in these populations and to kind of delve in and analyze these populations to the same level as you can with a more homogeneous European population or something is difficult. So kind of the main goal of the method that I'm trying to develop is to try to overcome a lot of the challenges that come with populations being of smaller size or populations that have recently mixed with other populations and just kind of different populations that have more complicated genomes essentially to study. Basically, I don't have to get into the details. But that's the part of the project. I'm really excited about is the fact that once we kind of have this method that's really robust to a lot of these different conditions that make genomes really complicated. We can kind of apply this method across the world and discover some really cool things about populations that have really just never been studied before. This is really relevant to like genomic medicine or gene-association studies and things like that. So a lot of disease associations and medicine based on genomics are based on like European populations, some Asian, but mostly European populations. When you apply a lot of these methods and things that were designed for these populations, they're actually pretty in-applicable to other populations that aren't European and in some cases, they might even be dangerous to implement in populations of non-european origin. So the overarching hope of my project is to kind of open the door to an easier investigation of some of these other worldwide populations that typically haven't really been studied from like a medical perspective either.Serrano: Wow, that's really cool and something that I rarely think about. That's also like an area that isn't really often considered in these studies, the applicability of it across different populations, especially in medicine because I know that there's a lot of diseases that vary depending on your background. And so I think it's really important to have information about the genomes of different populations as well as Eurasian.Ferger: Yeah. Yeah. No, I totally agree. And I honestly think it's pretty surprising that we haven't gotten to that point yet. But you know, we've been doing precision medicine for a very long time and we've kind of been designing various treatments based off of genomic information for a very long time, but it's still you know, the vast majority is just using European-like variance and kind of genotyping data and things like that. But these can vary so widely like you said and so it's really important to kind of have accurate information about the kind of the individual you're treating especially their genetic background in their genetic history.Serrano: Yeah, so that's great. So what made you want to study this in the first place?Ferger: Yeah. So when I was an undergrad, I knew that I kind of fell into the field of computational biology. I kind of went to a seminar about the field and about the major that was offered at my undergrad, the computational biology major, and I kind of just like quickly realized that that was the path for me. It kind of had biology which I loved but it also had this aspect of like like problem solving on the scale of a few hours or days since that you can run an experiment computationally really quickly and kind of problem solve and come up with a new pipeline or solution and it's kind of very fast-paced like that. So I knew kind of that was the field I wanted to pursue and then I took a few courses. One was called Molecular Evolution and it kind of got me into the field of population genetics because it was essentially all of kind of like the underlying math for how we can infer different things about populations using their genomes. So kind of inferring different parameters about populations and kind of different statistics you can use to infer how populations have moved and you know what their size was and how similar two populations are to another one another and it kind of like really just captured my imagination how you can just use a couple of simple mathematical ideas and kind of infer all of these really cool things about populations just using you know information you can gather from a genome, or just from little base pairs or bases, I guess DNA bases. Um, but yeah so that kind of triggered my interest in population genetics. And then I took another course with the same professor about specifically human population genetics and about our history with archaic hominids. And so I kind of really just thought that was a super cool area of research. I didn't know a ton about archaic hominids and it just I think the idea of trying to paint our history back from you know, our our dawn of civilization and the kind of like where we came from and how we've moved throughout time and kind of being able to use genetics to paint this picture of who we are and where we came from and kind of why we are the way we are today. I was looking at various different grad programs and I found my advisor really early on even before I decided to move or even to apply to Berkeley because she specializes in kind of this idea of like human evolutionary genetics. And so I did yeah, I think I reached out to her and I applied to Berkeley and interviewed with her and I was kind of pretty immediately sold on working kind of on problems that she was doing with human evolution and kind of ancient human genetics.Serrano: Yeah, I was about to say it sounds like you had a really clear idea of what you wanted to study and you found someone who studied that exact thing. That's a really really lucky situation!Ferger: Yeah. Yeah. It was kind of.I came to grad school a little open to other avenues just in case that kind of research wasn't all it was cracked up to be. I hadn't really had experience in research doing that particular thing yet. So I shopped around but I ended up just picking that avenue because I really loved it once I tried it.Serrano: That's awesome.Ferger: Yeah.Serrano: Were you involved in any other kind of research as an undergraduate before Berkeley?Ferger: Yeah, it's funny. I actually I did three years of research on snails.Serrano: Oh that's so cute!Ferger: Yeah. Yeah so our lab was like a Marine Lab and we did snail genetics.Serrano: So wow, very different from humans.Ferger: But yeah, so I was the computational biologist of the lab. I was essentially the only one running like computational analyses, but I joined that lab for that very purpose because I wanted some experience doing computational stuff in a research setting and so I basically was running a lot of genetic analyses on the DNA of snails and specifically looking at gene expression during different stages of snail development and we don't have to get to into this.Serrano: No, but I'm kind of interested! What are the stages of snail development?Ferger: Yeah. There's.. I think I should know this better, but I think there's like five or six different distinct developmental stages of the snail. We were looking at really specific stages and so I was looking at kind of the patterns of gene expression throughout their development. So it's actually interesting because like mollusk organisms, like a lot of snail organisms and spiral organisms, have a really set and distinct pattern of how they develop with respect to what genes are expressed during that development. And so we were looking in our organism to kind of look to see how the expression patterns compared to like this very well-known kind of theory of development for others by spiralians and we found very contradictory evidence of kind of the expression patterns of our little snail. So that was kind of a cool project because I got to take the lead on some of the computational analyses and it was kind of cool because we found some contradictory evidence to a theory that we I guess other evolutionary biologist kind of thought was... what's the word for...Serrano: Standard?Ferger: Yeah, very standard scenarios.Serrano: Yeah. That's the thing I love about research. You can apply the same method to study like human populations or a very specific kind of snail.Ferger: Yeah. Yeah. It's pretty much just a genomic analysis so a lot of the tools work the same way. So yeah, it's definitely really cool.Serrano: What about your plans for the future? What do you want to do after you graduate?Ferger: Yeah. So our program, my program specifically, is actually pretty new. I think we only have... I think we have under 10 graduates so far and most of them have actually gone on into like Biotech Industry, which is I think where I also will end up. I've never really envisioned like leading a lab myself and I kind of really like the flexibility of an industry position and, kind of, in terms of geography and what I might be doing and kind of like as as well as like the stability that comes with just, you know, working at a company and getting paid the same amount instead of having to always apply for grants and kind of having that that uncertainty aspect where you would if you were a professor. But I haven't really narrowed it down as far as kind of what type of biotech. I think maybe I will end up doing some sort of like genetics-based biotech company. So think like 23andMe or Ancestry. Actually, several of the graduates of the program have gon onto both of those companies and they're working kind of in the R&D Realms of those companies. But I haven't given it a ton of thought other than I know I'm pretty industry oriented already.Serrano: Nice. Well, so you have a lot of time.Ferger: Yeah. I think, I think eventually I'll probably intern somewhere to kind of solidify what type of research I want to end up doing and then kind of decide from there, but it's pretty open-ended as far as kind of what I want right now.Serrano: Nice. I'm glad that you brought up those kind of companies like 23andMe because I had a question earlier that I forgot to ask. So whenever you sign up, you know to get your genome sequenced by those companies... could that information then be used with the project that you're developing?Ferger: Yeah. Yeah. I mean technically yes.Serrano: Um, I'm sure there's a bunch of privacy laws...Ferger: Yes. Yes, and also I believe that 23andMe and ancestry doesn't sequence the entire genome. They just genotype because sequencing is really expensive. And so I think they just narrowed down to kind of like gene-rich areas of the genome and just do like a genotyping array kind of thing. So, I mean a lot of the principles still apply where you can kind of compare genotype arrays between individuals and kind of compared to a reference which is essentially what they do. So they have you know, a standard they compare your genome to like all of the quote "European" genomes that they have in their database and like all of their other clients. So they're able to kind of infer all of these different things about like what your variants say about your ancestry in a certain area of your chromosome or whatever. So, I think yeah a lot of the a lot of the principles carryover, of course, there's a ton of privacy things going on with that but I think once you're in 23andMe, yeah, a lot of that stuff is definitely possible even with just you know, genotype arrays.Serrano: Yeah. This might bea little bit of a tangent but I know there's a new kind of sequencing company that can basically take your genome and then build a picture of what it predicts you to look like.Ferger: Oh, yeah. I think I actually have heard of that!Serrano: Yeah, they used it to identify the Golden State Killer! I guess one of his family members had submitted their DNA and like they were like able to compare it to old samples or something.Ferger: Yeah. Yeah. I don't know a ton about typically the cases where you can project kind of different phenotypes from genomes. I will say I think some of that is still like... I think accurate predictions for some physical attributes is still kind of a long ways away just because we're learning more and more about just how much your environment affects how you look and your different phenotypes and kind of your susceptibility to different diseases and all like a whole host of different phenotypic things. It could be possible. But I think right now maybe we're still a bit a bit a ways away from that.Serrano: Right, from getting like a perfect snapshot of what you look like!Serrano: Our time is actually coming to a close. Kailey, it has been so great to have you on here! Is there anything that you would like to leave the audience with?Ferger: I think I'll just say if you ever get the chance to, you know, do one of these private ancestry tests you should absolutely do it. I did one for myself and it's actually really interesting and you might find some things you didn't know about your own past. So I'd really, I'd really recommend it and it's kind of a really cool way to just learn about your heritage and kind of use the genetics that maybe someday I'll contribute to!Serrano: Yeah, I'll definitely have to try out one of those myself because I haven't done one yet! All right. Well, thanks so much Kailey!Ferger: Yeah. Thanks so much for having me!
3/10/2021

Kailey Ferger

Serrano: Hello, you've tuned in to 90.7 FM KALX Berkeley. I'm Karen Serrano and this is, The Graduates, an interview talk show where we speak to UC Berkeley graduate students about their work on campus and beyond. I'm joined by Kailey Ferger today from the Center of Computational Biology. Welcome to the show, Kailey!Ferger: Thanks. Thanks for having me.Serrano: Yeah, we are so happy to have you! So Kailey, tell us a little bit about the research you conduct on campus.Ferger: Yeah, so I'm a graduate student at the Center for Computational Biology, like Karen just said. So my work is entirely computational. I don't do any wet lab research. And so what that means for a PhD is essentially like designing pipelines or designing software or doing data analysis with various different programming languages. So at the end of my PhD, I hope to eventually either create some software or design a pipeline that other computational biologists can implement for their own data. And so I guess I'll tell you a little bit about what I specifically do. So I work with human genetics. I look at human genomes from populations across the world. Specifically, I am looking at two kind of different spheres of human populations, the first being modern-day Europeans and Asian populations and the second being South Asian populations and like Native American populations. So for the part where I'm analyzing like Eurasian populations like modern-day, I'm specifically investigating the effects of admixture in those populations. So what that means is essentially many many thousands of years ago humans lived on Earth with other ancient hominids, including neanderthals and denisovan hominids as well as potentially other hominids. Of course, they're extinct now, but there has been a lot of evidence in the past decade probably that humans actually kind of mixed with the Neanderthal population and I guess, like, had children with neanderthals and denisovan populations. And so even today there are still signatures in our own genomes of these archaic hominids, like their genomes in our own genomes. So a large portion of my project focuses on identifying these segments along all of the genomes and kind of characterizing how that like the archaic, you know, genome content that kind of remains in our own genomes has kind of affected the way we evolved and affected how we moved and affected the way that selection acts in our genomes. So I'm characterizing the distribution of archaic genomic segments in the genome and also looking at how natural selection has selected some of the variants that were kind of mixed into our own genomes. So I'm specifically developing a computational method right now that will let us do just that! So essentially, if we're able to identify where these archaic segments are in our genomes, hopefully, once we identify where they are we can also start to look at how natural selection is acting on these segments. So I hope to identify various like genes that are actually Neanderthal origin or denisovan origin and see kind of like when and how these genes have been selected throughout history and in what populations. So kind of what advantages they confer in the population and kind of just further characterizing archaic genomics.Serrano: Great. Wow, that's super cool and interesting and also something I know nothing about. I have a few questions. First of all, how.. how do you obtain this ancient DNA? Do you have samples that you maybe collect from museums or how?? Yeah, how do you basically get these genomes, right?Ferger: So it's cool because we're actually able to leverage modern human data. So basically we're just using.. so there's various models that exist today that are able to infer these tiny little bits of archaic segments in modern human genomes. So most Asian and European human populations still have kind of these signatures across their whole genome of these archaic genomes that at one time were highly prevalent at the time of the admixture event that occurred. So we can kind of leverage all of these different human genetic databases around the world, like for example the Thousand Genomes Project which aims to capture, I think, human genomes from Asia Europe, America, South Asia, and maybe Oceania and then I'm also using a really cool database that actually just came out so a bunch of new sequences from East Asia, North East Asia, Southeast Asia and in areas like that. And so that part I'm actually really excited about because many of these populations have not been studied extensively at all. Because I think sampling in these areas has been really scarce and like a lot of funding has been allocated towards kind of European and Asian populations and a lot of the major universities are located there and a lot of interest has been there especially in things like genomic medicine and things like that. So a lot of other populations like in South Asia, especially have not even been closely looked at so I'm looking at kind of populations from India populations in Southeast Asia and some like Oceanian populations too. So that's kind of going to be like the novel aspect of my analysis and those areas!Serrano: That's really cool. So I'm not a computational biologist. I don't know many things about you know, the programs that you're using. How do you recognize these stretches of ancient DNA in our genomes? Is it like, are you mapping it back to a known ancient DNA sequence or how does that work?Ferger: That's a really great question. So there are several ways to do this and one of them is doing just that! Where essentially you're taking a reference genome from one of the hominid species that we've been able to actually sequence to high coverage just because scientists have been working a really long time at it and have really been careful at preserving the remains that we found and so you could match the segments in a genome back to that reference. But I'm actually using a method that is reference-free and so it involves essentially using what's called a Hidden Markov Model, which is essentially just a kind of machine learning algorithm and it basically just uses, like, it leverages private variation that's found in the genome. So if you can imagine a human genome and an archaic hominid genome, it's going to have a lot more genetic differences across the whole genome compared to like a human population or human individual from a European population compared to like an American individual or something or like a Native American individual. You're just going to have a lot more fixed differences between an archaic genome. And so essentially that algorithm is leveraging a lot of those fixed differences in the population. What I mean by fixed differences, so we all have kind of like that four letter code that defines our whole genome and humans are actually extremely consistent. There really isn't as much variation among populations as you might think but compared to an archaic genome, there's a lot more differences. And so yeah this this algorithm essentially just leverages a lot of those differences and then it basically just uses the idea that if you input a human genome into the algorithm, it basically just scans along the genome and uses kind of a reference human population and then calculates the probability that a certain segment is human or archaic based on how different it is from like a human reference genome or another human individual or something.Serrano: I think I'm following. So basically this algorithm can compare how different two genomes are to each other and if it's more different than two human genomes are to each other, it will assume that it's actually hominid.Ferger: Yes, exactly!Serrano: Okay.Ferger: So yeah, the thing about that is it can't really identify what hominid it is. And that's kind of where my project comes in a little bit more but it can identify that it's probably not human given other genomes that you feed in and the reference genome and things like that.Serrano: So I might ask a silly question because I probably read too much sci-fi. But I've heard that like certain people with more neanderthal DNA have certain personality traits. Is there any like validity to that at all?Ferger:Yeah. I mean, I won't cast anything out of the realm of possibility just because we're discovering more and more about archaic genetics and the truth is that we don't really know. I would say it's probably unlikely. Just because there is only around 2 percent of our genome that is Neanderthal and of course two percent total of our genome is coding. And so the chance that a coding part of our genome will be Neanderthal or Denisovan or some other archaic type is very miniscule. But yeah, we're still doing research and a lot is still unknown. Like we have discovered various genes that are selected that are confirmed to be Neanderthal-derived or Denivosan and we're able to characterize, kind of, the selective event and why it was selected and what advantage it confers in the population and things like that. But yeah, I guess I guess that remains to be seen! Such a funny question.Serrano: Yeah. I don't know. I keep seeing articles, like, I don't know, if you have more Neanderthal DNA, you're like more aggressive or something. I'm sure they're false, but I didn't know if there's actual science behind that.Ferger: Yeah, I think another point to bring up to is that whatever amount of variation that people across the world have in terms of the amount of archaic ancestry is also very small. So it's within the range of a single percentage. So I'd say the populations with the most archaic DNA is like the Oceanian population. So like New Zealand Australia and the Pacific Islands and then across Europe Asia even America, we all have around two percent. Maybe, maybe a little over.Serrano: So we're all pretty similar, right?Ferger: Okay, we're pretty similar on that front. So there isn't going to be an individual you meet that has drastically more archaic DNA and maybe have noticeable effects.Serrano: What kind of genes, or I don't know if you've gotten to this part of the project, but what kind of genes have been conserved from ancient hominids?Ferger: Yeah. Yeah. So, um surprisingly, there's a lot of like immune system functions that have been selected.Serrano: Oh! That's interesting.Ferger: Yeah. Um, so that's, that's one category. Perhaps even more surprisingly, like fertility genes are not selected at all. And that's like actually a surprising result. So there's like a complete desert in the whole all of the sex chromosomes basically of archaic ancestry. And so I think that's kind of interesting. We don't really know what that means. Yeah, but definitely some immune functions have been selected. There's a really cool example actually in the Tibetan population. So there's individuals living on the Tibetan Plateau, which means they live at very high altitude. But genetically they're very similar to Chinese populations in the surrounding area, with one large exception, which is they actually have a gene that was conferred by Denisovans actually in their genomes and this gene allows them to be adapted to high altitudes. So if you ever, if you've ever been kind of at a really high altitude area for a long time, you probably know that you'll start to get altitude sickness or high altitude sickness. So I think your breathing shortens, like your blood doesn't flow as well. And it's just not good for you. You become very ill. But individuals who live in Tibet and at this very high altitude actually have an adaptation where they don't experience hypoxia, which is what you experience when you are really high up for a long time and they basically, luckily, have a mutation on this gene that was conferred from Denisovans where it modifies, I believe, some structure in their red blood cells. So they aren't susceptible to kind of hypoxic conditions. So I think that's a really cool example of a really unique signal that was conserved.Serrano: Yeah, and that was probably, I'm just kind of guessing here, that was probably so conserved in that population because it's so isolated from other populations, right? So they're living up in these mountains and that's kind of like separating them from other poptulations!Ferger: Yeah, yeah exactly. So they don't have a ton of admixture with other populations. And so we were able to characterize this signal really well and that's why it's so well conserved in this population.Serrano: Wow. That's pretty interesting.Ferger: Yeah.Serrano: So besides this project that you're working on, are there any like smaller projects that you're interested in as well?Ferger: Yeah. Yeah. So the main portion of the project I describe was essentially developing this method that scans the genome for selection on like these segments that were conferred to these individuals through gene flow. So once I develop that method and it is tested and works really well in the conditions of like archaic introgression, we're hoping to apply it to various different populations that are relatively understudied and so populations like Native American populations across North and South America as well as a lot of populations in South Asia. Like populations in India and Malaysia and kind of places like that. And so for a lot of these populations, kind of the reason they have been pretty understudied, other than the fact that there hasn't been a ton of kind of like funding for sampling in this area, is because they also are genetically really complicated. Because European and kind of a lot of Asians are relatively homogeneous from a genetic perspective meaning just that their genomes are all pretty similar in their kind of own groups. But in the cases of like South Asian populations and smaller populations, they have kind of signatures of recent like population mixture events. So when populations kind of come together and merge and start to like mix with each other and start to have children and create this admixed population, it makes your genome actually really difficult to study. This is because you basically have this, kind of, if you can imagine, this mosaic of different ancestry blocks across your whole genome and this is because every generation when you reproduce you kind of get this recombination event in your chromosomes. This is really getting in the weeds, but you kind of get these recombination events every generation in your chromosomes, which just kind of breaks up all of these ancestral blocks in your genome and so you end up with kind of this huge mosaic of ancestry. So kind of it models a lot of signals and it makes it really hard to study selection in these populations and to kind of delve in and analyze these populations to the same level as you can with a more homogeneous European population or something is difficult. So kind of the main goal of the method that I'm trying to develop is to try to overcome a lot of the challenges that come with populations being of smaller size or populations that have recently mixed with other populations and just kind of different populations that have more complicated genomes essentially to study. Basically, I don't have to get into the details. But that's the part of the project. I'm really excited about is the fact that once we kind of have this method that's really robust to a lot of these different conditions that make genomes really complicated. We can kind of apply this method across the world and discover some really cool things about populations that have really just never been studied before. This is really relevant to like genomic medicine or gene-association studies and things like that. So a lot of disease associations and medicine based on genomics are based on like European populations, some Asian, but mostly European populations. When you apply a lot of these methods and things that were designed for these populations, they're actually pretty in-applicable to other populations that aren't European and in some cases, they might even be dangerous to implement in populations of non-european origin. So the overarching hope of my project is to kind of open the door to an easier investigation of some of these other worldwide populations that typically haven't really been studied from like a medical perspective either.Serrano: Wow, that's really cool and something that I rarely think about. That's also like an area that isn't really often considered in these studies, the applicability of it across different populations, especially in medicine because I know that there's a lot of diseases that vary depending on your background. And so I think it's really important to have information about the genomes of different populations as well as Eurasian.Ferger: Yeah. Yeah. No, I totally agree. And I honestly think it's pretty surprising that we haven't gotten to that point yet. But you know, we've been doing precision medicine for a very long time and we've kind of been designing various treatments based off of genomic information for a very long time, but it's still you know, the vast majority is just using European-like variance and kind of genotyping data and things like that. But these can vary so widely like you said and so it's really important to kind of have accurate information about the kind of the individual you're treating especially their genetic background in their genetic history.Serrano: Yeah, so that's great. So what made you want to study this in the first place?Ferger: Yeah. So when I was an undergrad, I knew that I kind of fell into the field of computational biology. I kind of went to a seminar about the field and about the major that was offered at my undergrad, the computational biology major, and I kind of just like quickly realized that that was the path for me. It kind of had biology which I loved but it also had this aspect of like like problem solving on the scale of a few hours or days since that you can run an experiment computationally really quickly and kind of problem solve and come up with a new pipeline or solution and it's kind of very fast-paced like that. So I knew kind of that was the field I wanted to pursue and then I took a few courses. One was called Molecular Evolution and it kind of got me into the field of population genetics because it was essentially all of kind of like the underlying math for how we can infer different things about populations using their genomes. So kind of inferring different parameters about populations and kind of different statistics you can use to infer how populations have moved and you know what their size was and how similar two populations are to another one another and it kind of like really just captured my imagination how you can just use a couple of simple mathematical ideas and kind of infer all of these really cool things about populations just using you know information you can gather from a genome, or just from little base pairs or bases, I guess DNA bases. Um, but yeah so that kind of triggered my interest in population genetics. And then I took another course with the same professor about specifically human population genetics and about our history with archaic hominids. And so I kind of really just thought that was a super cool area of research. I didn't know a ton about archaic hominids and it just I think the idea of trying to paint our history back from you know, our our dawn of civilization and the kind of like where we came from and how we've moved throughout time and kind of being able to use genetics to paint this picture of who we are and where we came from and kind of why we are the way we are today. I was looking at various different grad programs and I found my advisor really early on even before I decided to move or even to apply to Berkeley because she specializes in kind of this idea of like human evolutionary genetics. And so I did yeah, I think I reached out to her and I applied to Berkeley and interviewed with her and I was kind of pretty immediately sold on working kind of on problems that she was doing with human evolution and kind of ancient human genetics.Serrano: Yeah, I was about to say it sounds like you had a really clear idea of what you wanted to study and you found someone who studied that exact thing. That's a really really lucky situation!Ferger: Yeah. Yeah. It was kind of.I came to grad school a little open to other avenues just in case that kind of research wasn't all it was cracked up to be. I hadn't really had experience in research doing that particular thing yet. So I shopped around but I ended up just picking that avenue because I really loved it once I tried it.Serrano: That's awesome.Ferger: Yeah.Serrano: Were you involved in any other kind of research as an undergraduate before Berkeley?Ferger: Yeah, it's funny. I actually I did three years of research on snails.Serrano: Oh that's so cute!Ferger: Yeah. Yeah so our lab was like a Marine Lab and we did snail genetics.Serrano: So wow, very different from humans.Ferger: But yeah, so I was the computational biologist of the lab. I was essentially the only one running like computational analyses, but I joined that lab for that very purpose because I wanted some experience doing computational stuff in a research setting and so I basically was running a lot of genetic analyses on the DNA of snails and specifically looking at gene expression during different stages of snail development and we don't have to get to into this.Serrano: No, but I'm kind of interested! What are the stages of snail development?Ferger: Yeah. There's.. I think I should know this better, but I think there's like five or six different distinct developmental stages of the snail. We were looking at really specific stages and so I was looking at kind of the patterns of gene expression throughout their development. So it's actually interesting because like mollusk organisms, like a lot of snail organisms and spiral organisms, have a really set and distinct pattern of how they develop with respect to what genes are expressed during that development. And so we were looking in our organism to kind of look to see how the expression patterns compared to like this very well-known kind of theory of development for others by spiralians and we found very contradictory evidence of kind of the expression patterns of our little snail. So that was kind of a cool project because I got to take the lead on some of the computational analyses and it was kind of cool because we found some contradictory evidence to a theory that we I guess other evolutionary biologist kind of thought was... what's the word for...Serrano: Standard?Ferger: Yeah, very standard scenarios.Serrano: Yeah. That's the thing I love about research. You can apply the same method to study like human populations or a very specific kind of snail.Ferger: Yeah. Yeah. It's pretty much just a genomic analysis so a lot of the tools work the same way. So yeah, it's definitely really cool.Serrano: What about your plans for the future? What do you want to do after you graduate?Ferger: Yeah. So our program, my program specifically, is actually pretty new. I think we only have... I think we have under 10 graduates so far and most of them have actually gone on into like Biotech Industry, which is I think where I also will end up. I've never really envisioned like leading a lab myself and I kind of really like the flexibility of an industry position and, kind of, in terms of geography and what I might be doing and kind of like as as well as like the stability that comes with just, you know, working at a company and getting paid the same amount instead of having to always apply for grants and kind of having that that uncertainty aspect where you would if you were a professor. But I haven't really narrowed it down as far as kind of what type of biotech. I think maybe I will end up doing some sort of like genetics-based biotech company. So think like 23andMe or Ancestry. Actually, several of the graduates of the program have gon onto both of those companies and they're working kind of in the R&D Realms of those companies. But I haven't given it a ton of thought other than I know I'm pretty industry oriented already.Serrano: Nice. Well, so you have a lot of time.Ferger: Yeah. I think, I think eventually I'll probably intern somewhere to kind of solidify what type of research I want to end up doing and then kind of decide from there, but it's pretty open-ended as far as kind of what I want right now.Serrano: Nice. I'm glad that you brought up those kind of companies like 23andMe because I had a question earlier that I forgot to ask. So whenever you sign up, you know to get your genome sequenced by those companies... could that information then be used with the project that you're developing?Ferger: Yeah. Yeah. I mean technically yes.Serrano: Um, I'm sure there's a bunch of privacy laws...Ferger: Yes. Yes, and also I believe that 23andMe and ancestry doesn't sequence the entire genome. They just genotype because sequencing is really expensive. And so I think they just narrowed down to kind of like gene-rich areas of the genome and just do like a genotyping array kind of thing. So, I mean a lot of the principles still apply where you can kind of compare genotype arrays between individuals and kind of compared to a reference which is essentially what they do. So they have you know, a standard they compare your genome to like all of the quote "European" genomes that they have in their database and like all of their other clients. So they're able to kind of infer all of these different things about like what your variants say about your ancestry in a certain area of your chromosome or whatever. So, I think yeah a lot of the a lot of the principles carryover, of course, there's a ton of privacy things going on with that but I think once you're in 23andMe, yeah, a lot of that stuff is definitely possible even with just you know, genotype arrays.Serrano: Yeah. This might bea little bit of a tangent but I know there's a new kind of sequencing company that can basically take your genome and then build a picture of what it predicts you to look like.Ferger: Oh, yeah. I think I actually have heard of that!Serrano: Yeah, they used it to identify the Golden State Killer! I guess one of his family members had submitted their DNA and like they were like able to compare it to old samples or something.Ferger: Yeah. Yeah. I don't know a ton about typically the cases where you can project kind of different phenotypes from genomes. I will say I think some of that is still like... I think accurate predictions for some physical attributes is still kind of a long ways away just because we're learning more and more about just how much your environment affects how you look and your different phenotypes and kind of your susceptibility to different diseases and all like a whole host of different phenotypic things. It could be possible. But I think right now maybe we're still a bit a bit a ways away from that.Serrano: Right, from getting like a perfect snapshot of what you look like!Serrano: Our time is actually coming to a close. Kailey, it has been so great to have you on here! Is there anything that you would like to leave the audience with?Ferger: I think I'll just say if you ever get the chance to, you know, do one of these private ancestry tests you should absolutely do it. I did one for myself and it's actually really interesting and you might find some things you didn't know about your own past. So I'd really, I'd really recommend it and it's kind of a really cool way to just learn about your heritage and kind of use the genetics that maybe someday I'll contribute to!Serrano: Yeah, I'll definitely have to try out one of those myself because I haven't done one yet! All right. Well, thanks so much Kailey!Ferger: Yeah. Thanks so much for having me!
2/16/2021

Jane Henderson

Andrew Saintsing: Hi, you're tuned into 90.7 FM KALX Berkeley. I'm Andrew Saintsing, and this is The Graduates, the interview talk show where we speak to UC Berkeley graduate students about their work here on campus and around the world. Today I'm joined by Jane Henderson from the Department of Geography. Welcome to the show, Jane.Jane Henderson: Him thanks for having me, Andrew.Saintsing: So great to have you here. I'm really excited to have you here because I've never had anybody from the Department of Geography, and I really want to know more about geography. Do you just like know all the state capitals and like you can put them all on a map?Henderson: It's… I think you could appreciate this as a graduate student that we often explain what we do as kind of completely different from what we actually do when people ask us. So, sometimes I will say like, “Yeah, I just studied capitals.” Kind of ironically, I would say many geographers don't actually have a good sense of what most people think of as geography, like capitals, where to place countries on a map, and things like that. Which is kind of the funny part of our discipline. But it is… that is part of it and part of how you would teach that to younger students (especially like the K through 12 level). But it's also a lot broader than being able to sort of memorize and or locate places and countries on a map.Saintsing: Right. That's kind of like the foundation, right? I guess like being able to localize things in space. It's kind of like you need to have that in order to get to actually what you're really interested in in research in terms of geography?Henderson: In geography, I would say a core tenant especially when we study it at the university level and the PhD level is to always question and pay attention to power and political relationships that create space. To not take space and spatial locations for granted. But actually, to question the power and the development of space over time or throughout time. So, geography is not just memorizing and taking a state capital as is.Saintsing: In general, you know, we use maps because they're helpful, right? And so, like a lot of us are just assuming we just look at a map, and we're like, “This is the way the world looks.” But you're kind of interested in how that map came to be our representation of the way the world works and potentially like what are the reasons it could be different or the problems with the way it is represented on the map?Henderson: Correct. That's I think a big piece of geography and a good entry point into questioning how space is developed. Because it's often developed unevenly which is another concept that we look a lot at in geography. Why is it that we have separations between urban space and rural space? And why is it that the economies of urban spaces are different than rural spaces? How did those things develop? And how did investment in one also lead to disinvestment in the other? And what is the relationship between that across space? So, to your point, like say you were to pull out your Google Maps app on your phone and ask for directions to a certain location. There are some locations that Google doesn't offer you directions to, for example, because those locations may be for one reason or another invisible (in the sense that either people in power have made it so you can't locate them as a site of resistance, or people who have less power, marginalized peoples whose geography knowledge is also often overlooked, may also be invisiblized by some of these things). But we tend to take Google Maps as fact or as like a hard truth that this is how a city or a landscape or the planet essentially is laid out. And in geography we're just always questioning that, questioning these things like land, like space, like cities even, that seem to just be as opposed to processes that are made or spaces that are made.Saintsing: Okay, so there are locations, right? Like absent of human ideas about these locations. They're just like physical… The world is physically there, but then you're saying humans situate themselves and say what each place is. And so, when you say you can't get to that place on Google Maps, you're saying that maybe Google Maps tells you a place in this location that doesn't match another person's understanding of that location?Henderson: Essentially, yeah. So, the second part that you're saying, yes. You're correct that like people, places are imbued with meaning that we provide. And meaning is contested. It is given. It's like giving value to something, and just like any social relation or social process, that meaning, and that value given to a place necessarily has all of the other things that come with social relation: like difference, power inequality. I'll end there for that section. I want to address the first part because that does get into some of like the deep like, “Is there space?” Like that it just is without people giving it meaning. That's some of the like philosophy of geography, and there are… I could give listeners a recommendation to check out Henri Lefebvre if they… That's spelled H-E-N-R-I L-E-F-E-B-V-R-E if folks are interested in that. Because there is lively debate in geography. Just as we might think about time in different ways (like you can think about it linearly, circularly, and in all sorts of different ways), you can also think about space differently. It's not, what we call it in geography, like an empty vessel or an empty container upon which things just happen. But the very process of time passing is that things happen to create space as well. So, there… But there's different camps. Like some people disagree about how that happens. Like if there's something like absolute space or not.Saintsing: So, which camp do you fall into, would you say?Henderson: Okay, so I tend to agree with Lefebvre, which is the person I just referenced. In this textwhich takes like somewhat of a… It questions this very idea that I've also been trying to explain so far which is that we take space for granted as sort of the container or the cup that everything else happens in. So, racism just happens in space, but space is neutral. Historical events happen through time, but the place where they're happening is just – it just is. It's just neutral. And what Lefebvre does is say, “No, no, no. We're taking this for granted. We're not actually looking at how space and time are connected and how they're made together. How space is actually produced.” Yeah, I tend to agree with that because it makes a lot of sense when we're thinking about other geographic or like geopolitical forms that we take for granted. Something like the US-Mexico border for example. We just take for granted and assume that there is this line drawn in the sand, basically, that will delineate where one country's power ends and where another one’s begins. Another one, another country's power begins. But when you really look at it, there's all sorts of contestations along borders. There's power that extends beyond a border line, for example. There are a lot of different life forms, for example, certain types of migratory birds or monarch butterflies, things like that that wouldn't… that don't understand space in the same way that we as humans would understand it. Such that a border like the US-Mexico border doesn't really mean a lot unless there's a giant fence that prevents them from flying over to migrate, for example. So, I had set up this to say that that was like an example of that: space isn't just neutral. It's also contested the same way that time is, the same way that things we may know about science is contested, the same way that other kinds of politics are constantly being debated and kind of battled out in a political arena. We just tend to assume that space is the arena that everything happens on, but we don't tend to ask questions like: Who built this arena? Why do we use an arena at all? Where did the materials come from to create the arena that we're now battling out our political ideas on? And so, in geography we ask questions about that.Saintsing: I guess in science, you know, like we're limited by our questions and our understanding. And I guess we're striving towards something, though, that is universal maybe, you know. At least we try to like move towards that truth that isn't necessarily hinging on what questions we're asking, but like the actual fundamental principles. Like in physics, we're trying to find like the laws that hold the universe together. And I guess in geography, are you… Yeah, I guess you're basically, though, studying how humans occupy space, which can never… which doesn't… wouldn't ever really get you to a fundamental place, right? Because like you're not ultimately just trying to get to like, “This is where a mountain range is.” Like that's… that would be something that you could… that everyone could say like, “Yes, this mountain range occurs here.” But like it's what that mountain range means to the people around it and that live in it and that travel through it.Henderson: Yeah, I think this can get us into like a distinction that we have in geography between physical geography and human geography which… There is a lot more overlap and our department at Berkeley has graduate students and faculty in both camps. (Not every geography program is like that.) But the easiest way to define that division is that physical geography is a physical science, hard science. And then human geography is a social science more akin to anthropology and/or some humanities even. So, the way that you described it is that people in physical geography may, yes, look at mountain ranges or river patterns, watershed flows from that mountain range, and tell us sort of data about perhaps the sediment in the water or how to use these different watersheds in order to fight wildfires or things like that. And also there's a lot of like climate change science that happens in geography. And then what I do is on the human geography side. So, it is more of a social science. Which is to ask about, yes, like not only our human relationship or like people's relationship to this mountain range and (like in your example), but also to think… to read against and with the very scientists who are coming up with universal truths about this mountain range. Because what I think is really important in our field is basically acknowledging that even the things that we find to be universal truths are still using a particular framework of viewing the world. One that's couched in like the scientific method, for example, as like a way of knowing. But there are many other ways of knowing, and knowledge isn't like a capital K knowledge, and there's only one. But there might be knowledges or things like that that would help us understand the world around us. What I think human geography and where the social science side of geography can offer is just the reminders that even in science we take a lot of things for granted as being quote unquote “natural.” Human geography is… destabilizes that a little bit or a lot a bit, I guess. So, yeah. But I'm definitely on the human geography side. So, I would say I'm more akin… my methods, my research is like… is couched mostly within African American studies or Black studies, history, anthropology. The methods I use aren't quantitative methods typically.Saintsing: This has been very interesting stuff.Henderson: Oh, great. Okay.Saintsing: All of like the philosophy of geography and all of that. But it would be… We are moving through the time we have for the interview, so it would be really cool to know a little bit more about like actually what you are studying, you know, using these research approaches that you've discussed. So, like what kind of is your… the area of your research for your dissertation?Henderson: Yeah, my research site is in Minnesota, in Minneapolis, which is where I grew up. And I've kind of taken a winding route to get back here. Mostly or sort of broadly, my research is on Black experiences in Minnesota. And that stems from my own experience as a Black Minnesotan and my family's experiences as Black Minnesotans. But also, the kind of surprise around Blackness in Minnesota, which is to say that people don't expect there to be Black people in Minnesota or in a place in the Midwest or so far north or things like that. Why is it that some places are more intimately tied with the Black experience than others? And so, that to me is a really geographic question because it's asking us about the process of how place gets made and how people come to understand that place. So, Minnesota is a state that is understood to be a white place and pretty much exclusively a white place. Blackness is often not only invisibilized, but as Black people we have to constantly mediate our knowledge of this place against the sort of common perceptions (or a word that we use is imaginary) of Minnesota as a kind of nice liberal white state. So, I would say that's the basis of my work. And then, in order to get at some of these questions, I'm trying to put forth an intervention, which is in the field of Black geographies, which is where I'm kind of situated. My work is to think about geographies, Black geographies beyond the plantation. And what other geographic locations and sites, but also like words like other than the plantation we can use to understand Black experience of space. So, for me in Minnesota, this looks like: if I were to bring up to just general Minnesotans that there is racism in Minnesota, they might answer me by saying, “No, there isn't. Minnesota was one of the first states to give Black people – Black men the right to vote prior to any amendments in the federal constitution. And we didn't have slavery because we didn't have plantations in the North. So, therefore we don't have racism in Minnesota.” It's kind of like how the saying goes. And so, the plantation itself as like a place, like a geography just does not fit anywhere in Minnesotan's minds. It's like, “That is an elsewhere. That happens in the South. That doesn't happen here.” And it makes it really hard then to have a discussion about like anti-Black racism and or racism in general in Minnesota because the core geography, like the core site that we often use to explain racism, is the plantation. But what does that… what does that do if you don't… if people have no reference point to the plantation at all? There has to be other ways to explain the experience of Black people in a place. What my research does is try to think about other geographic forms. So, my research looks at the frontier because that does have a lot of purchase here in Minnesota as like how… like how to play… how do Black people understand themselves as like frontiers people? As opposed to like people tied to the plantation. And I'm hoping (because I'm not that far in my research yet) will be another way of just getting to this kind of Black way of knowing place and knowing our environment. Which is… tends to be different than sort of geographic knowledge that is taken as natural.Saintsing: So, you brought up like talking about the Black experience in relation to a plantation. Are you using it kind of like as a historical basis of rooting the black experience? Like where the Black experience originates? Is that kind of the idea with using that term?Henderson: The plantation?Saintsing: Yeah, yeah. The term the plantation. Specifically in the context of your… of like what you were discussing with your research.Henderson: The plantation is both like a historical site. Like you could go on a plantation tour in parts of the US South or things like that. But it's also a description of like a geography, meaning a place that can travel. And it travels because the way it organizes space might be similar. The kinds of logics that are developed or the kind of knowledge that's developed may be similar. And that's how it would travel.Saintsing; So, it's this kind of way in which people are interacting with each other. And like that's kind of like what's traveling. But then, that's interesting that… when you were talking about how white Minnesotans can say like, “Oh, there aren't plantations here.” So, I guess, yeah. Like the idea in geography that you can… that spaces replicate and like that something that occurs physically in one space can then like metastasize and like affect people in other places is a good… it's like a good way to describe something. But then, on the other side people who are looking to avoid grappling with this complex and harsh reality can then turn that around and say, “Okay, you're talking about this space, but it's somewhere else. And so, I can like physically locate this issue that I don't want to deal with in a completely other place. And then, I can say it doesn't happen. I don't have any part in it because I don't belong to that space.” So, that's very interesting.Henderson: And that is another key key site that geographers look at. Are the connections and the flow of resources (money, actual materials) through these spaces that people don't think of as being connected at all. And this happens every day. Like all the time we think about that something that is happening to us, a way that we are experiencing space in a city like in Berkeley has nothing to do with what people in Oklahoma City or in rural Oklahoma are experiencing. That there is no connection. But what we often times can uncover is that there are real connections between these places that don't only have to do with people moving from one place to another necessarily but all sorts of other ties and kinds of interconnectedness between spaces. So, you're right in seeing this as kind of a… it's both a helpful way of thinking about the Black experience as like plantation travels, but then it also… there's this kind of catch-22, which is people can skirt responsibility because that geography doesn't resonate with their lived experience or even their history. Like not even their lived experience but the history of the place that they live in. The kind of important thing for me to do is to try to understand what geographies do resonate with people here, and like how Black people both in history and in the present navigate that understanding of space. We have a lot of research on how Black people have resisted the plantation, how Black people have resisted and lived through the violence of the historical plantation and also the ways that the plantation has traveled. We don't have as much research on other geographies and how black people live through, in, and through those places as well. So, that's really what my work is trying to do.Saintsing: So, you're trying to root the Black experience in Minnesota without using this terminology of the plantation. You talked about frontier. You're trying to say like how we can root our understanding of the Black experience in Minnesota in this idea of frontier? And with the ultimate goal to then like have this framework that people can, I guess… Is the idea to better communicate to the Black experience outside of the Black community to the wider community? Or to kind of have a framework to talk within the Black community? Or both?Henderson: Yeah, I would say, perhaps prematurely, the hope would be for both. But another key part of my research that I have not yet talked to you about is that the main point of my intervention is to try and think about Black and Indigenous geographies together. And oftentimes discussions of the plantation and slavery alongside things like Indigenous genocide and dispossession of land, they don't always come together neatly in terms of a conversation both in academia and in sort of activist spaces. But what I have noticed so far in Minneapolis is that there is a lot of attention on Indigenous dispossession, Indigenous geographies, and Indigenous knowledge here that I have not always experienced in other places that, I mean, that I've lived and that I've researched. And so, my hope is that with thinking about other places that Black people live that might not have the plantation kind of hanging over us that we might come to better understandings and relationships with Indigenous peoples, as Black people with Indigenous peoples. So, in Minnesota that would be like the Dakota, Ojibwe peoples. And that just gives us a totally new way of understanding space. A new way of understanding geography and a new set of values around who matters in these places that I think, if we can get outside of some of the plantation and the really terrible violence of the plantation, we can think about how to be together differently. So, it is both for like white Minnesotans to be able to like understand their… like how they're implicated in racism. Because I'm not using the plantation. I'm using something that has… that resonates to white Minnesotans. But it's also more than that. It's more than like humanizing Black people for white people. My project is also trying to think more broadly about Black claims to land, how we interact with land, and how we do that with respect to the original inhabitants of this land. Indigenous Dakota people.Saintsing: This has been really interesting, but we're running out of time on the interview. Usually at the end of the interview we give our guests a chance to address the audience on any matter that they'd like to bring up or re-emphasize. Is there anything you'd like to leave us with before we go?Henderson: Yes. Hello, audience, all the listeners. It's been really great to talk with you, Andrew, about my work, and I would definitely encourage any listeners who are interested in geography to not only check out our department website at UC Berkeley, but also to think about your own neighborhoods, the places that you tend to go to. And even now during COVID to take a really close look at the spaces that you're in and try and think about like how they came to be that way. And look at those things with a critical eye. Like, “Why does the street that you lived on have this certain name? Or why is the school, the elementary school down the block, named after a certain person?” And I'd also encourage everybody to look up the (whichever place you might be), to look up whose Indigenous homelands you're on and how you might be able to ensure that Indigenous sovereignty is an active practice in your own work. And when you talk about like where you're from, there's a lot of resources on that. So, you could also email me for those if you have trouble.Saintsing: Thanks so much, Jane. Yeah, so if you're interested in getting in touch with Jane… And remember: we're speaking to Jane Henderson from the Department of Geography, and you can find her email on that website. Again, thank you so much for being on the show.Henderson: Yeah, thanks for having me. This was awesome.Saintsing: Tune in in two weeks for the next episode of The Graduates.
2/2/2021

Mohamad Jarada

Andrew Saintsing: You're tuned into 90.7 FM KALX Berkeley. I'm Andrew Saintsing, and this is The Graduates, the interview talk show where we speak to UC Berkeley graduate students about their work here on campus and around the world. Today I'm joined by Mohamad Jarada from the Department of Anthropology. Welcome to the show, Mohamad.Mohamad Jarada: Hey, hey. How are you? How's it going? Thanks for having me.Saintsing: It's great. I'm so glad you're here. How are you doing?Jarada: I'm doing well. Beautiful day in Berkeley today.Saintsing: Yeah, weirdly unseasonably warm when we're interviewing this in January – doing this interview in January.Jarada: Yeah.Saintsing: So, I'm so glad to have you on here. I don't think I've had anyone from the Department of Anthropology, yet. And so, I'm really interested to hear more about your research. I'm also really interested to hear about your research because I saw that you do a lot of it in North Carolina, which is where I'm from. Could you just kind of introduce us a little bit to what you're doing? What your research is?Jarada: Yeah, sure. So, my research essentially takes civil rights as its focal point, but it does so by expanding our understanding historically and in the contemporary about how civil rights is practiced within local communities and how civil rights gets shaped within legal, political, and social discourses throughout post-Reconstruction United States of America. So, what I try to do in my research is look at certain communities certain, racialized communities, in particular communities who are criminalized, to see how they have used and construed the concept of civil rights and how that has been developed historically since again the late 19th century up until the present. And I do this in particular by trying to look at certain security documents because what I'm trying to do with the civil rights focal point is expand our understanding of civil rights beyond questions of voting political participation, etc., etc. And to think about how communities could protect themselves and defend themselves against things like hate violence and austere surveillance from the government or something of that sort.Saintsing: Wow, so your research is very relevant right now, right? It's… you're getting a lot of news stories that could probably be something you could look at for your research?Jarada: Absolutely, yeah. I mean right now civil rights is certainly a hot topic to discuss. I think it's sometimes, it's over-determined and misplaced about where it could be talked about or addressed publicly.Saintsing: What do you mean by over-determined?Jarada: I think that sometimes when we talk about racial struggles in the United States or communities who are criminalized by law enforcement agencies, oftentimes civil rights gets tokenized as the only resource or only form of recourse that these communities can seek. I think that it's important for me in my dissertation and in my research is to kind of delimit that space of what civil rights can do for these communities and the limits of what it can do for these communities as well.Saintsing: Sorry, but can you just say what you mean specifically by civil rights then?Jarada: Yeah, so the way I understand civil rights and the way I construe it as a, both as a historical concept and as a legal concept in my dissertation is something that is particularly referring to certain legal entitlements that are, that is offered by the state or by the federal government or by, depending on the time or era you're speaking about, by state government. And so, when I say civil rights I say the particular legal entitlement that a citizen, or a non-citizen for that matter, is given by the state generally and historically speaking. And this is where it gets kind of confusing or complex. It's differentiated especially by the Supreme Court by two different kinds of rights. So, there’s civil, there’s social, and there's political rights. And so, often times the Supreme Court, at least in the post-Reconstruction era, they differentiated these three different kinds of rights in order to address how they should matriculate formerly enslaved people into the national citizenry. So, the goal of civil rights is to ensure those legal entities and legal entitlements that are essential to being a citizen or living in the United States.Saintsing: Okay, and so you're saying that maybe the other rights that you talked about are not as emphasized and could be more important to the discussions that we're having in racial justice and social justice issues?Jarada: Precisely. So I mean these are discussions that are happening within political activists, social activist communities, where civil rights is often not really a significant part. Or it is a significant part, but the problem with civil rights is the legal regiment in order to get some kind of redress or get some kind of cure for a political, social, or legal injury. So, for example, if a civil rights of mine is transgressed, in order for me to get that remedied I would have to go through a large and extensive legal process that is a headache. And so, there are these other kinds of rights, particularly social, political. There are things like economic rights, too, that people are considering on the local level as well, to think about different ways or different forms of recourse that these communities could find in times of need or in times of vulnerability.Saintsing: Okay, and so civil rights we're saying we have to go through legal channels to address injustices or to make sure that people have these civil rights. But these other rights, political, economic, social rights, these are things that are addressed outside of court systems?Jarada: Well, no, they're… So, they are outside of court systems in the sense that they could be used or addressed or spoken about outside of legal processes and court systems, precisely. But they're highly defined by and created and constructed out of the Supreme Court essentially because… or legal debates that were happening, or presidential debates. So, part of my research is looking at this really funny early debate between this guy named Stephen Douglas and Abraham Lincoln. So, before Abraham Lincoln was the President of the United States, he was running for the Senator in Illinois. And he ran up against this kind of robust racist Stephen Douglas who truly believed in the institution of slavery. And so, it's in these debates (these are really famous debates) where the idea of social, political equality and rights somehow gets differentiated from legal, civil equality, rights, and entitlements. And it's so… they're constructed within these legal these legal arguments, these political debates, the court system. But they are… they have a more expansive capacity, or they're more expansive in the sense that communities can use them or address them or speak about them in a way that isn't limited by the courts per se. Okay, it is confusing. It definitely is. But it's both confusing, ambivalent, and unstable, and for all those reasons it makes political and social rights all the more contested and gives them potential to be used for these social justice or political justice initiatives.Saintsing: Okay, so you research specific case studies around this. So, could you kind of walk us through like a specific example that could help illustrate you know the intersections of these rights and how communities use different rights to address different issues/Jarada: Sure, so the community that I work in particularly is in North Carolina, and I've done research across the South. I've tried to do stuff in Virginia and Tennessee, but I chose North Carolina just because it was a pragmatic decision that I made. And it's kind of high… it's been highlighted within public channels especially within the communities I work with (which are particularly Muslim communities) because there was a kind of a brutal murder of these three Muslims in Chapel Hill, North Carolina by this guy named Craig Hicks. And so, after this kind of tragic situation where these three Muslims, you know, Yusor, Deah, and Razan (that's what their names were) were murdered, the question about how to protect the community and what resources to use in this community to protect them was, you know, kind of got, kind of exploded. It's like, “how can these Muslim Americans protect themselves both from the fact that they're being surveilled by the government and at the same time being, you know, hurt, murdered, assaulted, vandalism on their on their religious basis, etc. And so, what I do with this community, or what I examine in particular this community is the kind of language they use, and the kind of resources they use. And essentially to get to the nitty-gritty and to reduce it to one element it goes back all the way to the question about civil rights and how they're differentiated from things like political and social rights. And so, for example, this community wants to protect themselves from, let's say, the possibility of their space being vandalized. So, what do they do? Some communities find recourse in law enforcement. So, some communities, say in Raleigh, North Carolina, are engaging with federal and state law enforcement, particularly the FBI and local police departments in order to protect themselves. And the language that they're using is civil rights, but on the side of things they're talking about how they could actually protect themselves socially and politically (precisely because the state or the federal government hasn't done their job) in order to protect themselves. Or those civil entitlements that they're given isn't sufficient to take care of themselves. So, how do they wield this concept of political, social rights is what I try to look at and what my conclusion essentially (or one of my conclusions is) that political and social rights get used to secure these communities. And it gives them impetus or motivation to take seriously their security. Like quite literally. So, they buy CCTV cameras. They go through the process of getting a license, a permit to carry a handgun. They are highly aware of their spatial awareness, and they take part in social initiatives to mend relationships between themselves and other communities. Or they take on political initiatives to make sure that people are voting for whoever they desire to vote for. In a place like North Carolina, which is a is a heavy purple state you know. North Carolina, when Trump won for the first time, he won by 0.5 percent. And so, it's these initiatives that they're focusing on. These social initiatives and these political initiatives that focus on their security, right? The focus on the security, not only of the physical livelihood, but the security of the religious practice that is outside of this boundary or this limited space of what we know as civil rights.Saintsing: Okay, right. So, you're going through the materials that these groups, like Muslim American groups in North Carolina are putting out, both in like legal documents and just in materials that (maybe like pamphlets they're handing out or like materials they're using to communicate with other groups or within their own group) and you're just kind of seeing the language they use and seeing the strategies they use?Jarada: Precisely, yeah. I mean, you're a great listener. I mean that is exactly what they're doing there. That's exactly what I'm doing as a researcher to kind of hone in on those like little sensibilities, those strategies, those relationships that they create that can't be reduced to simple civil rights or civic participation. There's something far deeper, and there's a deeper motivation, and there's a bigger stake at hand when we think about political and social justice in the United States for racialized and criminalized communities like Muslim Americans. The majority of Muslim Americans I worked with were either brown or are Black Muslims. And so, this was a heavy topic at hand that constantly got discussed in a lot of the meetings and interviews I had with my interlocutors.Saintsing: So, I saw also that you kind of look at things from a historical perspective. So, what were… was there like a big change (you mentioned the specific event in Chapel Hill) was there like actually really a big change in the way the Muslim community in North Carolina started interacting with other groups and started looking at themselves? Like what were, what were kind of… how did they view themselves before the incident? And what were really the changes we saw afterwards?Jarada: Great question. So, I mean… should… can I address the historical part?Saintsing: Yeah, definitely.Jarada: So, historically… I try to historically (again I said I look at Supreme Court cases and see how civil rights gets construed, but) I'm also attentive to the fact that, you know, North Carolina is a Southern state. And so, as a Southern state, we know that racism and racialization functions in pervasively… it's a huge part of a state like North Carolina. The first thing I remember when I got to North Carolina, and I first went when I was in… 2017. In the summer of 2017, I went to Durham. I got to Durham. I went on the bus, and the first thing I noticed was that everyone on the bus was a Black person and everyone near the bus station, which is near downtown Durham right next to Duke was white. And so, from the outset you could tell that there's these… there are these forms of racism or racialization or segregation that was just inherent to this part of the country. And so, the historical part both looks at, you know, Supreme Court cases (reading those cases trying to figure out how civil rights and social rights and political rights were construed). But the other part is being attentive to these kinds of ghostly specters that still reside and still have vestiges in a place like the American South. And so, I try to attend to that part as well in my research. But in terms of what had happened after the community had dealt with this big blow, this tragedy of these Muslims being murdered, there was a drastic change. I mean that event was a national event, not only for the Muslims in North Carolina. At that time, I was in Boston. I was doing my master’s degree at Boston in Harvard. And students across the campus were worried. They were scared. They felt a sense of anxiety about whether or not they were being protected. And this is in Boston. And so, in North Carolina, where this had happened, (and all of my interlocutors the majority of which always point to this event as a threshold) security became the essential issue in this community about how to protect themselves. And the way they did it was they created relationships with law enforcement, and they try to amend relationships with their particularly Christian neighbors and Jewish neighbors as well. And so, you see like a wave a wave of like civic, political, and social activism that's happening from the generation that grew up after 2015 when this event happened. And so, there were a lot of drastic changes after that event.Saintsing: And this was nationally. Like Muslim Americans in general. This is a huge event, and it's shaped across the country not just North Carolina.Jarada: Absolutely, and I can only speak about the effects that have happened in places that I've lived (so North Carolina, Boston, and California now) where I've seen communities take this question about security far more seriously than ever before. And that event was only one of a series of events that happened, like the Dylan Roof shootings in South Carolina at a Methodist church also was impetus. The Christchurch shootings in Australia were also an event that happened. And so, that event in particular focusing on Muslims in the United States pretty much changed a lot of the things in a lot of the ways that Muslims and mosques and the wider community thought about themselves and how they arranged their communal makeup and their spatial makeup. Yeah.Saintsing: Right, yeah, you brought up a bunch of different attacks on different denominations, different faiths and then there was also the Tree of Life massacre. Yeah. Is this, you know, thinking historically, is this an exceptional moment that all of these attacks are happening in these places of worship or on people specifically for their faith?Jarada: Yeah, I mean it's really hard to tell just because I mean historically, you know, speaking of Black churches, Black churches have been arsoned or been used as a as a tool by the KKK in particular or other white supremacy and hate groups to be to be arsoned or vandalized to foster fear and anxiety within Black communities for a very long time. Albeit these things aren't reported or documented because when you burn something it's, you know, it just disappears, or we don't have those or at least I don't have the resources to know historically about how these things have happened within the United States. But I can say that in the past two decades… I could say this. I could say that the events that have occurred within religious spaces like murders, stabbings, shootings have had a kind of singular response that has been significant. It's a significant change in religious communities in the United States, I think, where these communities are now fully taking security into their own hands. They're soliciting not only the help of law enforcement, but (I mean we could call them mercenaries) like private security firms who take care of religious communities. There are now, I know of two security firms that are particularly focused on religious communities. And they have a kind of like Christian Biblical motivation, you know. And so, I know that in the past two decades those events related to religious spaces have taken on this question of security far more seriously. So, it's interesting, you know, as a Muslim myself, when I'm in a mosque and you see a man with a handgun, that's something new. That isn't something that I was always privy to or aware of or I had to care for growing up as a young Muslim in California. So, yeah.Saintsing: It's so interesting to think about. You know, obviously this danger in public spaces in general is problematic and scary. But I guess in particular thinking about religious sites, you know churches, mosques, synagogues, temples… the fact that people have to worry about this and have to think about security when these spaces are supposed to be these welcoming spaces in general, you know. This is like a place where theoretically everyone could just come in and you know be welcome to worship. So, do you have any… has your research shown you anything about the way that, you know, these new security… thoughts about security and movement towards increasingly secure spaces has altered that aspect of places of worship?Jarada: Wonderful question. I mean you're asking a really great question, Andrew. I really appreciate this. Yeah, so this is an essential question that I'm trying to ask in my research about how is it possible that these traditions, right? These are religious traditions, like Islam, Christianity, Judaism, that's really kind of honing in on the question of neighborliness or being a neighbor with someone or helping someone out or being hospitable to people and attending to the poor, you know. And creating these virtues within a community, right? Things like charity, things like service. How do they do that given this fact that now mosques are (they quite literally… this one mosque in particular the Islamic Association of Raleigh has built a, you know… fortified their entire space with a wall, with a gate). And so, it's interesting to ask you know how the hell is someone going to know whether or not to come into space or feel welcomed into space if there's a wall blocking them from this and if they're not already part of the community. And so, the conclusion I've come to or from the interviews I've had and the people I've spoken to, it's really interesting. They believe that (and I would agree with them that) the construction of these walls, which creates a space or creates a division between oneself and one’s community and another community outside, is actually the condition for hospitality. It's the condition for a healthy relationship to one’s social world outside of themselves or welcoming someone inside the mosque, right? So, when you build a wall, one interlocutor would tell me, you're doing something to invite people in to ask questions and to be provoked in a particular way such that they ask “why is this Muslim community building a wall? And for what reason?” Or in the scenario where there was, there was cases where people would come outside the mosque wearing things like a pig, a hat with bacon and saying kryptonite for muslims or stuff like that, where they would stand outside of these mosques, and imams would come and invite them in. And so it's in this like really interesting scenario where you would think that building a wall and you would think that carrying guns and you would think that all these protective strategies that these communities are building and implementing are ways of pushing people away. But for them it's actually an invitation to both ask questions and to be welcomed inside the mosque. So long as they're safe, right? So, long they're also prepared in the situation in which someone wants to do something out of the ordinary. And I think that is where we get to the question of political and social justice or political and social rights. Where these communities take it seriously that the state or the federal and state government won't protect them. In these everyday situations, you won't have… 911 won't come immediately. And so, building these walls and holding guns, etc., etc. are both strategies to invite people in – strategies for hospitality – and strategies to protect themselves and their religious tradition. And so that they can have some kind of psychic relief when they're praying.Saintsing: Okay, yeah. So I'm really interested… I think your research is super interesting, and like the content of your research is really interesting, but I'd love to know more about like what it actually looks like when you go out and do research as an anthropologist. So, are you… so, you talk a lot about interviews? So, you're going actually into communities and interviewing people. But then you're also like looking at documents. Like how do you choose what to look at? How do you identify people for interviews? Just tell us a little bit about that process.Jarada: Yeah, I should say first and foremost, you know, I got really lucky. I mean the community I worked with in North Carolina were probably the most lovely people I've met in my life. I mean these people are caring, loving, welcoming, concerning, you know. Highly political and socially aware people that really care about both the community that are, that they live in (the non-Muslim community) and the communities they're a part of. And so, for me, I was, my job was really easy. I mean I woke up in the morning excited to do the research that I was doing. As an anthropologist, the first step for me is to gain some kind of trust between myself and this community, right? And that was kind of… I have to admit it was easy just because my name is Mohamad. I'm Muslim myself. I speak Arabic. And you know I pray. And so, I was first intending to kind of put myself within this community as a Muslim, right? And as a researcher. They knew from the outset that I was a researcher. I first… what I first did was just attend a bunch of meetings. I mean I would attend things from like random-ass dinners to you know events about civil rights to concerts to gatherings, social gatherings. I mean fires, what are they, bonfires. I mean I went to everything for like the first four months. I mean I was exhausted. But it was a lot of fun. And then people got to know me, and I got to know them. And so, as I started going to the more important events, events surrounding questions about political rights or social rights or activism or people running, Muslims running for mayor or Muslims running for political office. When I went to these events, that's when the question started happening. And because they knew me as a familiar face, and they were so kind, they were so open to giving me, giving me interviews. And so when I would do these interviews, they were just… they were just a lot of fun, man. You know you get excited about these things and these people are as excited as you, and the people I would talk to range from people who worked in tech to people who devoted their entire life to the religious communities like imams and other religious leaders. Or people who own subways. Or people who were financial advisors or people who wanted to be lawyers, et cetera, et cetera. And so, you get a diverse group of people all who are concentrated on this one task: security. And when you ask them and you provoke them, boy are they willing to talk. The job of an anthropologist is, or the job that I took as an anthropologist for the way I see, is to kind of get to know these little social minutia that surround these really important issues, right? Like you hear about these things on the news every day. You hear about these things on your podcast. You hear about these things everywhere, but nobody really knows what goes into those little interactions or those little happenings in the everyday in order to protect a community. In order to garner your social, political, and civil rights. And that was my goal, and I enjoyed it very much.Saintsing: Well, unfortunately, it looks like we're running out of time. It's been so great talking to you, Mohamad. Just a reminder: today I've been speaking with Mohamad Jarada from the Department of Anthropology about civil rights and other form of rights among different groups in America with a focus on Muslim Americans in the American South. Thank you so much for being on the show, Mohamad.Jarada: Andrew, it's been honestly my pleasure. And I really thank you for giving me the time and space to speak about my research. And truly your questions were really great. And I appreciate that.Saintsing: Thanks for saying that. Tune in in two weeks for the next episode of The Graduates.
1/19/2021

Giovana Figueroa

Andrew Saintsing: You're tuned into 90.7 FM KALX Berkeley. I'm Andrew Saintsing, and this is The Graduates, the interview talk show where we speak to UC Berkeley graduate students about their work here on campus and around the world. Today I'm joined by Giovanna Figueroa from the Department of Integrative Biology. Welcome to the show, Giovanna.Giovanna Figueroa: Hey there.Saintsing: How's it going?Figueroa: It's going. I'm happy to be here.Saintsing: We're happy to have you. We're really interested in hearing about your research. So, you do field work in the Amazon rainforest, right?Figueroa: Yeah, that's true. I do field work in Peru, and my home base when I'm there is Iquitos.Saintsing: That's really cool. What do you? What are you looking at?Figueroa: So, I'm focusing my research on a genus of palm trees Oenocarpus, and specifically I'm focusing on Oenocarpus bataua, which is a really abundant palm tree in the Amazon. So, it's the seventh most abundant tree in the Amazon basin, and it spans like northern South America. So, I'm really interested in I guess like kind of people-plant interactions and also tropical ecology in general. So, I want to understand floristic abundance and diversity patterns and also how humans might have influenced these patterns. So, something interesting about this palm tree is that its fruit is really nutritious, and it's used to make like this beverage. It's called chapo de Ungurahui, and it's just like macerated pulp with some water. And sometimes folks will add some sugar also.Saintsing: Cool, okay. So, you're studying this palm tree that grows throughout the Amazon rainforest, and you're mostly focused on how people interact with it?Figueroa: That's like… that's a component of it. So, I want to look at the like finer scale, like variation of this palm tree. So, when I do my field work, I'm collecting a lot of fruit specimens and leaf specimens to do some molecular work to understand like the population-level structuring.Saintsing: And what do you mean by population-level structuring?Figueroa: Oh, so I want to see if there's any… like how much, I guess, structuring… like genetic structuring there is between populations. So, I visit different communities along different river, rivers in the Amazon, and I'm just, I want to like compare the genetic structuring to see if there's like any sort of like distinct genetic differences between these different populations along different rivers. But I'm also recording morphological variation in the fruits, so this… it can be related to like the size, the weight, but specifically the pulp color, So, I found fruits that are like a really deep purple. Some that are white, and then some that are like some like intermediate pinkish version of that. And then, there are some where the pulp looks like it's like essentially rotted, but when I talk to people, they're like, “this is the best one for oil content.” So, you wouldn't expect that because it looks really dry, but apparently, it's really rich in oil content. So, that's a lot of variation I'm looking at.Saintsing: Okay, cool. Okay, so this is one species of palm tree, but you're looking to see if there just happens to be differences genetically and morphologically across this range. I guess it's kind of like how a lot of agricultural plants, like you see big differences in the way their fruits and different parts of their vegetative structures look. Like that's kind of like what you're looking at in this palm tree?Figueroa: Yeah, I'd say that's correct. And I'm also looking across the genus also. Just so I have like a baseline to do evolutionary like comparisons I suppose. So, I'm not just looking at this one specific species. I'm looking at other related species which also produce fruit that's like similar in nutritional content some are also used to make beverages similar to the chapo de Ungurahui, but they're not as popular. And so, I'm like curious to see if there's like significant differences in the nutrition of these like lesser used foods. Or if maybe they're just not as popular because they're not as abundant.Saintsing: So, you you're saying that people just don't see them as much, so they don't go to them basically.Figueroa: Yeah, essentially. I don't know if that's why they're not as used because they're not as encountered or if they're actually just not as great of a food source. And I'm curious to like kind of explore that realm of my research, to like kind of also understand if people have influenced the geographic distribution of Oenocarpus bataua, this really, really abundant tree. Whether it's being used as much because it's been so abundant, it's so abundant, or if somehow through migration and past human management, this species has benefited from that and become more abundant.Saintsing: Right. Okay, so that's interesting. So, I guess when you first started talking about it, it kind of seemed like this was, we were talking about just kind of a wild plant, but is it kind of undergoing cultivation? Like people are…Figueroa: There's no, there's no evidence of like it being actively domesticated. Some folks consider it like incipient domestication, where it's just kind of like a byproduct of human presence. So, what I've noticed is that when people go collect, harvest this fruit, they just go into the surrounding forest to harvest it. But they don't actively plant it. However, like you know as you're walking through the forest and eating the fruits you can drop the seeds, and it will grow, and then when I see folks who are working their chacras, their plots of lands where they have their own like crop rotations for food, if there is one of these palm trees growing on that plot of land, they won't chop it down. They'll just like let it be because it takes a while for these to start producing fruits. So, it's more beneficial to just like leave it there but it's actually pretty difficult for, it's difficult for them to just start growing in like full sun areas. And so, a lot of these like agricultural plots are not shaded. They're full sun.Saintsing: So, these plants kind of have to be growing before people have moved in to like actually farm is what you're saying? I see. That's interesting. Yeah, in the Amazon is farming generally how we think of it in the US, or you know like people go in and clear a forest and then plant crops? Or do people kind of try to integrate into the existing ecosystem to grow? Because I assume a lot of the useful crops that would come out of the Amazon kind of work well in the natural ecosystem.Figueroa: Yeah, I think there's like a big spectrum of agricultural systems in the Amazon. And so, where like the places I visit specifically, what I notice is that folks have like an area of land that they just cut, they work. And that's their area of land. And they will just rotate through crops seasonally, but it's not like a huge chunk of land. And it's not monoculture like what we see here. So, it's kind of like mixed in. A few different crops. There might be some yucca, or like there will be plantains or something. And it's just kind of like all integrated. And then when that plot of land has kind of become like nutrient-deficient, they'll just like burn it. Let it rest for a bit, and it'll like regenerate into a second forest over time, and they'll move to like a second plot. But then they can go like switch off between these like new and like the secondary growth so that they're letting regeneration happen.Saintsing: Okay, so how much of your research would you say is actually interacting with local people in the Amazon, who are farmers or who just happen to live there and can guide you around and things like that?Figueroa: Quite a bit I'd say. So, I go to a lot of different communities, and every time I go I have to like present my like research ideas to either like the community members or the whole community. Each place has like their own protocols of like what is standard, and so I always have to like make sure that I have the permission from locals to actually carry on my work. And I always hire like a local guy to take me to the palm trees or like areas where they know that these palm trees grow. I learn a lot just like in my interactions. Like for example when I was telling you about the Oenocarpus variety, the one that looks like it's like rotted but is actually really high in oil content. Like I wouldn't have known that otherwise. And folks are just like, “oh, yeah this is good for this.” You know? So, just like in my like conversations I learned a lot.Saintsing: Yeah, definitely. Is that, is that trick (this kind of rotted-looking fruit) something that was specific to a like local area? Or was that kind of like commonly known throughout the places you're looking?Figueroa: I think it's… I think a few folks like when I like start talking to more people like here and there in different communities, they're like, “oh, yeah, those.” I think it is kind of known, but it… this variety isn't like really good for making like beverages the chapo de Ungurahui. So, people usually just let this one like stay on the tree. Or, they know this tree does not give good fruit, so like we're not going to collect them. So, like some people are just like, “Yeah, that's not good for like what we're looking for.” The beverage is like one of the main uses of these fruits. The oil is like secondary. But in some places I'm guessing like the oil is really popular. But once I start talking to other people, they're like, “yeah, yeah, those are really like fatty and oily. Not great for beverage, but good for like oil.”Saintsing: Okay, so what is this beverage exactly? Like what are people drinking it for? Or is it just kind of like a good drink?Figueroa: It's just a good drink. Yeah, but it's, I find it kind of rich. And a lot of people like don't drink… like they'll drink a lot of it, but they're like cautious to not drink too much of it like too close to like bedtime because it's like heavy. So, it's just like this fruit. You let the fruits soak in warm water to kind of soften them up a bit, and then you macerate everything, and you have this like mixture of pulp and seeds. And so, what folks do is they'll like remove the seeds and then pass this pulp with some water through like a sieve. And then, you have this like really like thick mixture of like water and pulp, and you can thin it out by adding more water. You can add some sugar to it to make it a little sweet, but on its own, it's pretty, it's like creamy. And I'd say it's like nutty tasting. And it's really good. It's just, like I say, it's heavy because it's really like fatty and protein rich. So, it's like a really great source of nutrition. It's actually a complete protein. It's like, it's important for the local, like just like subsistence level economy. But what's being seen now is that it's, we're starting to see these fruits like move out of the local communities into cities. And folks are like making ice creams or just like other yummy beverages or candies out of these fruits.Saintsing: So, it's being kind of commercialized you would say?Figueroa: Yeah, yeah. I think it's like being integrated into like a larger economy. So, that's something else that's kind of interesting. Because there's like a higher demand for the fruits now, a lot of folks have turned to like felling trees to collect fruits instead of climbing palm trees which is like the traditional and like I guess more sustainable, less destructive way of harvesting. I don't really know what the implications of that are. That's something that I want to explore. But I think that's going to come later in my research. Just kind of understanding like what exactly is over harvesting of a dominant tree… like what is the role of a dominant tree in the Amazon? Does something else take over? Like fill in its place? Or is this actually not that destructive? (Which I don't believe is the answer, but I'm not sure right now.) When I do my research, I partnered with this local fruit pulp company, processing company, and it's based in Iquitos. And they've developed this specialized climbing system. It's like a harness with two loops. And two loops for your feet. And it allows you to essentially just like walk up the palm trunk. And you can, it's really easy, and it's safe, and you can just like get up to the trunk in (if you're really good) like five minutes. It takes me a little longer. And then you just cut a mature raceme of fruits instead of having to like cut the whole tree down. And you lose a lot of potential with future fruits, you know,Saintsing: Because the tree is going to put out the fruit like every year?Figueroa: It's kind of continuously putting out fruit, and there's not like a real understood pattern of like when it's like fruiting period is. And there's a lot of like variation between populations also. Like every place I have visited, except for one community, I have always found ripe fruits. And I visited at like different times of the year because that's just how I can visit. So, yeah, they're kind of continuously producing fruits. And like most individuals, it's like there will be like one raceme with really ripe fruits, there will be a green raceme that will probably be ready like next year, and then there's like a little bud that will be a raceme in a year also or something like that. It's like an abundant source of really nutritious food. It's always producing.Saintsing: Yeah. So, okay. So, you go into, you fly into Peru, right? And then you have to just get yourself around to different communities that are kind of in remote areas in the rainforest? How? What is that like?Figueroa: Yeah, that's tough. So, I'm really lucky that my advisor Paul Fine, he has been working in Iquitos for like over 20 years. So, he has a really great network of collaborators and folks that he's, yeah, just worked with over the years. So, I'm able to meet with those people when I get to Iquitos. And they kind of help me out. So, like I will like… before I start my river travel, I like sit down and like ask for their advice on like where they recommend would be a good place to go. Like just telling them like, “this is what I'm looking for. I'm looking for a place that has Oenocarpus bataua. I'm also looking for a place that has Oenocarpus bacara. Like, where are some areas where you have seen this? And like what are some like good base communities that you think I can like go to and find folks to help take me to these places?” So, yeah, that's like my first step when I arrive to Peru. And then once that is done, oftentimes I'll try to establish contact before I go to these communities. But sometimes that's really difficult because, like some places, there's like one cell phone for the whole community. And like there might not be great cell phone reception, or like whoever has a hold of the cell phone, like maybe he's on a fishing trip and can't answer. So, sometimes it's difficult. So, I'll either keep trying to contact folks, or like send word of mouth through the rivers. Just be like, “oh, yeah.” Like, I'll meet someone like at one place, and then I'll like find out that this person is going to keep traveling, and I'll be like, “oh, if you stop in this community, will you just like kind of give folks a heads up that I am interested in working and will like probably be showing up in a week.”Saintsing: That's really interesting. When you say “river travel,” you mean you're on a boat?Figueroa: Yeah, let's see. What I usually do is, when I leave Iquitos, I will either have like, try to coordinate with someone from the fruit pulp company to take me to like a large, larger like central community in the river. And then from there I'll organize, like I'll like hire someone with a smaller boat to start taking me further out. Or sometimes I'll take like a public transportation or like a public boat. There are like so many different varieties. Like I can take a fast one. It'll get me there like relatively faster. I can take a slow one if I like feel like I have time, and it's like an overnight river trip. And I just hang a hammock and can like sleep. And it's more comfortable because we're not like crammed together. And then I just show up somewhere and like ask around and find someone who can/is willing to take me to my next site.Saintsing: And people are pretty friendly about it? They're… you don't really… you kind of always have somebody that'll help you when you get to these places?Figueroa: Yeah, I usually do. So, at least for like my… like wherever that first place is, I know, I like… I go with like a name or like someone in mind that I'm looking for specifically, or like people from Razac already know folks there. And they'll go with me and like will like ask. And if that person can't, they'll be like, “oh, but like you know my neighbor probably can.” So, then we'll go ask the neighbor, and as long as like I’m paying for the gas and like also like paying for the services, like people are happy to help me get to my places.Saintsing: So, you have to I guess tell people a plan, right? Before you start these trips. But how often would you say that plan is actually what happens on the ground?Figueroa: Yeah, I'd say like, maybe like 80 percent of the time that's what happens. Sometimes I have to switch the community site or like whatever. Like I thought there was going to be trees like immediately outside this forest. And like no. We have to actually go like 30 minutes up the river or something. So… But I mean it's not like a huge change in plans. Well, except for this past year.Saintsing: Right, yeah, that's what I was going to say.Figueroa: It's like probably like most unexpected of my trips.Saintsing: Yeah, so obviously this past year the issue was COVID-19. So, like what happened while you were on location? What was going on?Figueroa: I had planned for a two-week trip down the Nanay River, which is pretty like easy. I've traveled on the Nanay many times. So, I didn't think it was going to be a huge deal. But I was going further than I ever had. So, I made it about like (it was a 16-hour boat ride to this community called Tucaurco), and I was able to get all my collections done and everything. And then just by chance one night someone had turned on their TV and heard that there is like a lockdown in place for COVID-19. So, all like travel, like ground and fluvial (like river) travel was like suspended. And they told me that, and I was like, “oh, interesting. Okay.” And like in my head, I was just like, “I don't know how you like shut down river travel. Like that doesn't make sense.” Especially, a lot of folks like fish on the rivers. Like that… like this is how people get their food. Like I don't know how like you stop this. But luckily I had this GPS that the Field Safety Office let me borrow. And I was able to contact Paul, my advisor. And I just sent him a message. And I was like, “hey, I am hearing this stuff. I don't know what this means. Can you like do some research and let me know?” Because I couldn't get a hold of Julie, who's this other grad student from Princeton that I usually do a lot of, we try to coordinate our field work to overlap. Everything was just like still like really uncertain. So, I was like, “okay. I think maybe I should like make my way back to Iquitos.” And I got really lucky, and I found a team of medical workers that was in… they were doing malaria tests, and they were going to head back down the river towards Iquitos. And so I asked them if it would be possible for myself and Chapi, my field assistant, to like get a ride with them. And they were like, “yeah, of course.” So, they like took us pretty far down the river. Up to like right before the first, where the first river checkpoint would be. So, my plan was the following day was to like go to the river checkpoint and like talk to the national police who were there and just kind of like explain my situation and try to see if like I could get back to Iquitos. But before I could do that the national police showed up to this town Yamanote, where I was, and were like (and just kind of like went door to door) and just said, “this community is on a full lockdown. You can't leave.” I was there for almost two or like to the end of the lockdown because it was only supposed to be until the end of the month or something. But while this was all happening, I was like finally able to contact Julie, and she was like, “the US is like trying to like plan a like repatriation flight. You have to get to Iquitos.” And I was just like, “I don't know how I'm going to get to Iquitos. I have to pass two checkpoints. Like the military police showed up at the door and said I can't leave. Like, yeah, we’d get arrested.”Saintsing: What happened?Figueroa: I like went to the first checkpoint. They weren't going to let me go unless I had like proof that my name was like on a roster or like, yeah, a manifest sheet. A flight manifest. And I was like trying to like get in contact, like send WhatsApp messages to the embassy, so they can send me a PDF. But like it just wasn't working out. And then Chapi was able to talk to the police officer. And then I'm not sure what happened, but they let me go. So, we made it through like the first checkpoint to a little town that was like maybe two hours from that checkpoint. And from there Chapi had been able to contact someone that he had worked with before who he knew had a boat and would be willing to take us to Iquitos. And this man was like, “yeah, yeah. I'll take y'all to Iquitos, but I'm not going to be able to take you until tomorrow.” And I thought that was fine. But then I got a call from Julie saying like, “the flight's leaving tomorrow at 10 AM. You have to be here.” And I was like, “okay. I don't know if that's going to happen.” So, like I talked to the boat driver, and I was like asking him if it would be possible to leave like immediately. And he's like, “no, we can't because of the curfew and the checkpoint. Like, we have to leave tomorrow, or we have to leave at night.” And there is a curfew that started at I think at 8. And it was like from eight to like five in the morning. And so, like at seven, the man comes up to my like (our like little campsite), and he was like, “we should just leave now.” And I was like… I was really scared because I was like, “well, the curfew's about to start, and I am not Peruvian. And if I like… I don't want any of us to get caught. But like I… like from what I’ve heard from my friends in Iquitos is that like the consequences for being like breaking this curfew (especially if you're not a citizen) are like much more severe. But I, at the same time, I was like, “this is my one chance to like catch this flight. I don't know when there's going to be another repatriation flight straight out of Iquitos that's like a direct flight.” And so, we just went, and I don't know like how… like I'm not sure what happened. I fell asleep, and then like at six, five thirty, six in the morning, we’re in Iquitos. I was like, “okay?” And then it was just like a rush to get to my… the place I had been staying (a little like office apartment place), shower, and just pack up my essentials and get to the airport. And it was just… yeah, I was running on a lot of adrenaline and didn't really process how bizarre just like the whole journey back had been.Saintsing: Down the road, not on this particular project, but you are excited to be able to do more work like you have, you had done more freely before COVID in the future?Figueroa: Definitely, I really like field work. I think I like the fact that it keeps me on my feet a lot. I don't know. I don't… I don't think I do very well with like a lot of strict structures. So, like because things come up while I'm in the field, and I have to kind of like adapt, I like that. And I like being outside, too. I find it really rewarding just like interacting with plants and people and like just being immersed in it.Saintsing: Before you started your dissertation (actually going out and doing the field work) were you kind of more on the side that you were going to do like the evolutionary relationship, the genetic, you know, makeup of these communities of plants and the morphology and all of that? And then like communicating with the people kind of drew you also to the plant-human interactions? Or was that always like part of it all together before you started?Figueroa: That was always part of it. I've always been really drawn to like people-plant interactions. And just kind of looking at like, explicitly looking at like human and human participation in our environment as an ecological force. I think, up until recently, oftentimes the academic literature, just the way we like perceive ourselves has been really kind of to remove humans from the environment. So, I was really like, “I really wanted to explore these interactions in a non-domesticated species” for that reason. Because I think like domestication is like one extreme of a spectrum. And then we have like wild plants. But like what is this like in between space? And like how have humans been a part of this you know like spectrum? I suppose. So, that's always been one of my interests, and it was just trying to find a manageable species that like I felt like comfortable like studying during my PhD that fit those criteria that I was looking for.Saintsing: Right, yeah. And like how accurate is it to say anything is really wild, right? Like absent of human interaction.Figueroa: Yeah, I think there's like this like false notion of the Amazon and like a lot of forest as being pristine when like that's not really true. It's like humans have been here for a really long time and have been interacting with these forests.Saintsing: Yeah, it's like in California, you know, with fire management. We're figuring out how important it was to have people…Figueroa: …actively managing the forests.Saintsing: Yeah, exactly. Well, unfortunately it looks like we're running out of time on the interview. Is there anything you'd like to leave us with before we go?Figueroa: I think the aspect of my research that I like find most rewarding and that like I'd like to stress is just like how much there is to learn from like non-traditional, like non-academic settings. Like I learned so much just like on the like on the ground in the field just through my like interactions. And a lot of that has like really like helped how I like, how I shape my research. So, you know I think there's like knowledge to be learned like everywhere. And not just in textbooks, so yeah.Saintsing: Definitely. Thanks so much for that. Today, I've been speaking with Giovanna Figueroa from the Department of Integrative Biology, and we've learned a lot about her really cool work in the field in the Amazon rainforest in Peru. It's been so much fun talking to you, Giovanna.Figueroa: It’s been great talking to you, too.Saintsing: Tune in in two weeks for the next episode of The Graduates.
1/5/2021

Joshua Benjamins

Andrew Saintsing: Hi, you're tuned into 90.7 FM KALX Berkeley. I'm Andrew Saintsing, and this is The Graduates, the interview talk show where we speak to UC Berkeley graduate students about their work here on campus and around the world. Today I'm joined by Joshua Benjamins from the Department of Classics. Welcome to the show, Joshua.Joshua Benjamins: Thanks so much, Andrew, for having me on. It's good to be with you.Saintsing: Yeah, it's great to have you here. Really interested to hear more about what you study. So, you are in the Department of Classics. So, what are the classics?Benjamins: Right, that's a good question. I get asked that a lot because Classics is a term that doesn't really have the same currency it used to. But in this context Classics really means having to do with the classical civilizations, which means Greece and Rome. So, essentially, I'm in the discipline that studies Ancient Greece and Ancient Roman civilization, culture, literature, all the things that are involved with the ancient world in that part of the Mediterranean. So, it's a bit of a heterogeneous discipline in that it's not defined necessarily by a set of guiding questions or particular methodology the way that a lot of other disciplines are, but it's really defined more by some loose chronological and geographical boundaries. And, within that, anything that falls within the purview of Greek and Roman culture could be a part of Classics. So, it could be anthropology, could be linguistics, could be history, could be religion. All of that falls into the discipline of Classics. So, it's a bit of a heterogeneous and even an interdisciplinary field to be in. And that's one thing I really like about Classics.Saintsing: And so, you can study anything that uses… basically it has to be rooted in the Greek or Latin language essentially?Benjamins: It’s not even necessarily the languages. The languages are kind of the foundation for doing everything else because, if you really want to get into the culture, you really have to know the languages. But you can address any kind of question that touches on Greek and Roman culture that may not involve language directly. So, you might be interested in the development of astronomy in the Roman world, for example. Or the transition of astronomical knowledge from Persia to Rome or Greece. Or you might be interested in purely political questions. What kind of state was the Roman state? How did it operate? How did it come to be? How is power managed? How was the grain supply managed? Or all kinds of different sorts of questions you might be interested in that have to do with the ancient world. And so, the languages are a useful and even in most cases a necessary step towards formulating answers to those questions, but you might be pretty unconcerned with the languages themselves as anything more than a tool. Then there is another part of the discipline that would be very concerned with the language itself. Maybe if you're a philologist and you really want to know how the Latin language came to be and how it evolved from Indo-European and how word formations came to be the way that they are. All that could be part of Classics. But sort of a different sector, as it were, of the field. And literature of course is a big part of Classics. But you don't need to work on literature to be in Classics. It's just one way that you can go. One direction you can take. Greek and Roman language and culture broadly defined.Saintsing: I got you. So, essentially you can study whatever you want just as long as it's based in Roman culture or Greek culture.Benjamins: Yeah, and often the sorts of questions that you might ask would require you to bring in a couple of different lenses or a couple different kinds of knowledge. Maybe if you're interested in religion, you also have to look at literature on the one hand. But also, let's say cults. And maybe even archaeology. The archaeology of temples. The evidence that we have for certain rites and their development. And so, often there's a sort of interdisciplinarity that comes along with answering questions about the Classical world. And that's something that I really enjoy about the discipline. Because I've always been a lover of interdisciplinarity and multi-disciplinarity, and this is one way to avoid being really tied down to a very tightly confined space and be able to roam freely as it were, at least within the boundaries of space and time that are set by the discipline.Saintsing: Are you more Roman or Greek? Do you at least have that defined?Benjamins: Yes, I'm more on the Roman side, and I'm also more on the late side. As I said, there's a chronological range, and the end point of that range is not clearly defined. But I work on the later end, so let's say 300 to 600 AD. So, chronologically later than most people. And I also work primarily on Roman authors and Roman texts, and my research focuses on Italy and the city of Rome especially. But the thing about Classics, especially for those of us who are Latinists (are interested in Roman culture), is that Roman culture and Roman literature are both so heavily dependent on Greek culture and Greek literature that if you want to be a Roman historian, it's an absolute prerequisite to be really familiar with Greek culture and Greek literature. Because all the authors that you're studying were intimately familiar with and constantly shaped by and constantly interacting with their Greek predecessors. And to understand them at all you have to know that world that was also their world. And so Latin and Greek always really do go together. But I'm on more on the roman side.Saintsing: So, you read Latin?Benjamins: Yes.Saintsing: And, do you read Greek as well?Benjamins: I do read Greek as well. Also, a little bit of Syriac, which is another ancient language not quite as often studied. And then of course the modern languages are really important just for the sake of scholarship. So mostly German, French, Italian, a bit of Spanish.Saintsing: Oh, wow, so you can read all of these language as well?Benjamins: Yes, not with equal fluency, but yes. It’s a very language-heavy course of study to involve oneself in, and it's a little bit frustrating early on because so much of your time kind of has to be devoted to cultivating the languages because that's as it were the passageway into all the other things that you want to do. So, languages are definitely a big part of the discipline, but once you've mastered the languages you can really branch out into lots of other things.Saintsing: Right, yeah that sounds… how long would you say it took you to get to a place where you felt comfortable saying you just were fluent reading all these languages?Benjamins: Yeah, it varies by the language I think, and it also depends on what you mean by fluency. I think to really get to the place where you understand the language inside and out and, as it were, think in terms of the language takes longer than it does to get to a point where you can decipher the words on the page. So, I think Latin and Greek would be the languages I feel that I have the most intimacy with. And that probably takes about – it might vary by the person, but – six or seven years or so to really feel like you know it inside and out.Saintsing: Right, yeah. That's interesting. I guess I think of, you know, Classical studies. Like people are, you know, looking back at things, at records and trying to bring them into modern languages, right? Like, you know, thinking about people translating Egyptian hieroglyphs or translating, you know, runes or something. But I guess with you, you don't really… I mean you want to be able to translate obviously, but like you want to also be able to be fluent in Latin. And be able to like think in Latin. Is that accurate?Benjamins: Yeah, that's a great point. And there are, I think, two things to say there. One is that the way that we tend to teach Classical languages is very translation-based. So, the way you learn Latin is by constantly translating Latin into English, and that's the established pedagogical method that we've had for Latin and Greek for the longest time. And it's still persistent, and it's not necessarily the method that you'll see used in teaching modern German or modern French or modern Spanish. But it's been very persistent in the Classical languages specifically. And so students, when they're at that level of language learning, are always being prompted to translate into English. But really as you go farther along in the field you want to and should move away from that and get to the point where you can work with a lot of facility with the languages without having to or even tending to then convert it back into your own language. So, that's one thing I would say. And then the other thing is that translation itself is a really important work, and it's not necessarily part of Classics, but there are people in Classics who do a lot of translation work. And, I've done quite a bit of translation work myself. And I find it a very challenging and rewarding enterprise to figure out how to convey something best in English that was written in a remote context both in time and space.Saintsing: Right, yeah, that would be so challenging. Yeah, I think about… I took some Latin in high school, and it's always… it was kind of funny seeing things pop up. Like at one point, I was reading I think the Aeneid or something, and it was like, they talked about an ear of corn. And I was like, I don't think they would have had corn. But yeah, I mean obviously there's obviously much more… there are like examples of technologies, right, that people wouldn't have had. But then also just like the connotations that like you know you would completely miss, right?Benjamins: Exactly. And often it's the less obvious things that are the biggest obstacles or challenges that you maybe don't even see. Like the whole conceptual world of Rome is different than that of ours. And simple ideas like space and time for example don't translate easily from one culture to another because they're inhabiting different idioms of thought and of language.Saintsing: Right, yeah. And that kind of brings us to your research, right? You actually are studying the concept of time in Roman culture, right?Benjamins: Right, yeah, I'm interested in both ways that romans thought about time and ways that they divided and marked time. That's kind of on the granular uh easily approachable level, but then also kind of broader questions about how Romans thought about history and the relationship of past, present, and future. And how they saw their place within that broader movement, if there was a movement from past to present to future. So, that brings in questions about what is history and what is progress. And I'm interested in how Romans thought about those sorts of questions as i say especially in this period called Late Antiquity, so between roughly 300 to 600 AD.Saintsing: Is there an idea of progress in Rome like we have the idea of progress now? Like has that already started to develop? That we're like kind of in a linear history?Benjamins: I think in some ways we can see some of the genesis of the idea of progress in my period. But certainly, the ancient world doesn't have an established notion of the necessary betterment and progression of things over time in the way that moderns are very attached to. That idea is a very modern supposition. And it's actually one that's especially dangerous for historians. I'm mostly an ancient historian. And as an historian it's very easy to tell the story of the past in terms of this necessary guaranteed progression of things from a less civilized or more barbarous or less enlightened age to more enlightenment, more progress, revolution, improvement, betterment. That's the way we tend to think about how history goes in the modern age. But that's a very modern notion, and it's not one that was endemic to ancient culture necessarily at all. As you say, the difference… one way to think about that would be the difference between kind of cyclical time and linear time. That once you have a strong notion of beginning and end and the idea of history as a kind of timeline moving from some origin to some destination, then the idea of progress becomes very natural. But ancients didn't have that assumption of the linearity of time in the way that we do, in the way that we naturally conceive of time with a timeline, as it were.Saintsing: So, ancients. You are referring to your time period with the word ancients?Benjamins: YeahSaintsing: So, you're… you said the progress idea or linearity kind of had started to appear, but wasn't really cementing in your time period, right?Benjamins: Right, so one of the most famous markers of linearity is this division of history into BC and AD, for example. And that's a sort of unifying and homogenizing way of plotting time because everything has a place on the number line. And that division in terms of BC and AD didn't even come into existence until the first half of the sixth century. It was this Scythian monk named Dionysus Exiguous who came up with this pattern of AD and BC, before Christ and after Christ, anno Domani. And he didn't even come up with that with the intent of providing a convenient dating era. He actually came up with it because there are a lot of disputes over how to calculate Easter, and this was one way of answering those disputes. So, that whole notion didn't even come into existence until the sixth century, and it didn't take root until much, much later. It really wasn't until the 18th century actually that it became really conventional to use BC and AD. So, that's just one example of a very abstract dating scheme that we all take for granted because we all are used to calculating dates this way. But it was not endemic to the ancient world at all. Another example would be centuries and decades, you know. We easily think about the past in terms of centuries, the 18th century, the 16th century, the 14th century. And then decades as ways of plotting and subdividing the contents of a century. But those also are very recent notions. In fact, the idea of a century has only been around for about three and a half centuries. There's a famous poem which says the 19th century the 20th century, there never were any others because we didn't invent the idea of the century until that recently. And the notion of decades is even more recent. It's only been seven decades that we've thought about the past in terms of decades. And these sort of homogenizing schemes for time are very new, and it takes a little bit of work to put ourselves outside of those time schemes. That's really what we have to do if you want to understand how the ancients thought about and placed themselves in time. They didn't have these all-encompassing, homogenizing schemes in the way that we do. And they didn't think about the past in terms of dates. They thought about the past in terms of events instead of numbers, which is a very different way of conceptualizing the past and situating yourself in in the past or in the present.Saintsing: So, I guess like what intervals were present in the Roman concept of time?Benjamins: Right, so Roman conceptions of time really come out of Greek conceptions of time. And the way that Greeks situated themselves in time was really with the use of events. And actually a date really is an event if you think about it. That fact is concealed by the homogenizing force of the BC/AD or BCE/CE framework. But even that framework is kind of event laden because there's some event that's taken to be the dividing point between BC and AD. And so, event dates really are events whether we notice that or not. We're always plotting a date with reference to some event, and you can see that because once you move away from events you find it really hard to have a date number make sense to you. It's easy to say 1960 and come up with some correlates for that date because we have events we can link with that decade: Lyndon Johnson, the Vietnam War, any number of the, you know, various kinds of Cultural Revolution. And it's those events that help us quickly place ourselves in 1960, for example. Similarly, with 1940 you can think of the World War. And the farther back you go in time the less you have the benefit of those events to latch onto like hooks to place yourself. So, you know, if you're reading about the history of China a very, very long time ago a date like 2200 BC or 3000 BC really doesn't mean anything to you because you don't have events to link it with. And so, I would say a date really always is an event, but we've lost that recognition. And, in the ancient world, if you don't have the timeline, you don't have an all-encompassing numerical scheme, all you have are the events. And that's kind of neat because that kind of shows the conceptual work that always goes into placing yourself in time. You always use an event. So, for an ancient historian they might use the Trojan War, a really big important event. Or the death of Alexander, something that got recognized pretty soon after as a really epochal event. And then, you can date yourself by measuring the interval of distance either before or after. So, five years before the Trojan War. Ten years after the death of Alexander. 20 years before the founding of Rome. The date of the founding of Rome becomes a really foundational date in Roman culture for how you situate yourself in the past. 200 years after the foundation of Rome. So, how you might use an event to set you up yourself in time if you're in ancient Rome or in ancient Greece.Saintsing: All right, so you talked about BC/AD is like this cut off that like we use in modern times. Or I guess people try to make it like BCE and CE. But I guess with that, you know, when people first implemented it, right, there was this idea of like, “this was like this really important date.” But now I guess we've kind of moved to this idea that like, “okay, we're all using this date as like a standard cut off so that we can all situate ourselves like universally.” But essentially I guess you're talking about in Rome they just… or in this time period every culture would have its own signifying dates. And like people wouldn't really, you know, be able to communicate about large time scales with each other because they would have… they would be all like, “I don't know what event that is,” if you went to another culture.Benjamins: Yep, exactly right. Every culture has its own. And not even necessarily every culture, but every city might have its own calendar and its own rulership. And it might count its years by the reign of a certain ruler, but if you don't live in that region in that polis and that city, that ruler’s dates of reign don't mean anything to you. And so, it's really a world of local time. And that's something that's so foreign to us because in the modern world we've adopted universal time. This is a world that doesn't have universal time. Each city, each local area has its own time. So, there's no such thing as Greek time for instance. You might have Athenian time and Sicilian time and Spartan time and Argive time. And those are all different. They all have their own calendar. They all have their own rulerships. And there's a complex and difficult process of adjustment if you want to place an event in one region in terms of the calendar and civic regime of another region. And one of the interesting things about that is that of course this world doesn't have the pressures of mass media and mass communication and mass transportation which really were the driving forces behind the synchronisms that we've developed in the modern world. It's especially the industrial revolution that presses us to have these kind of synchronizing time scales. So, in some ways interestingly that the conquest of space necessitates then the conquest of time. If you're moving around really quickly from place to place, it becomes necessary to have these homogenizing schemes. But if life is lived on a smaller scale, it's not as important to be able to frame events in one place in terms of events in another place. I think it's the problem of synchronizing railway timetables for instance that drives the creation of time zones. This is the world that doesn't need that because it doesn't have that kind of conquest of space.Saintsing: Right, yeah, I see that, in terms of like high-speed transportation and things like that, the Romans obviously wouldn't have had access to that yet. But I guess the difference in my mind between Rome and Greece, right? Greece is, at least like in my… you know, pre-Alexander, maybe, it's a bunch of city-states. So, the idea of local time really makes a lot of sense because it's just people like living locally. But then Rome came in and created an empire, right? So, they had to coordinate across a vast amount of space. I guess they wouldn't have had to move quickly between those places necessarily, but I mean there, there is an idea of like conquesting space there.Benjamins: Right. Yep, exactly right. And that's why the conquest of space drives the conquest of time. Once you have a world empire the pressures upon you to synchronize all of these areas become really strong. And that starts already with Alexander because Alexander unifies the Greek world in a way that hasn't been done before. And that's why the third century BC is when we start to see universal histories, histories that aspire to cover the vast span either of space or of time. You know, if you think about it, a universal history can be universal in space, covering all places, or universal in time, aspiring to cover all times, or both. But both of those impulses become strong in the age of Alexander when the Greek world is unified as never before. And then they grow stronger when Rome becomes a world empire and the history of this one city eventually becomes the history of the world. So, by Late Antiquity, the period that I'm looking at, to write the history of Rome and to think about the future of Rome and to situate Roman time is really to write the history of the world and the future of the world and to situate the world in time. Because the city and the world had become, to some degree, one in the same. And so, a date like the beginning of the city of Rome can be a universalizing axis or coordinate on which to map the history of all places in all times.Saintsing: And so, people are at this point trying to, you're saying, like tell the story of humanity essentially by writing these histories?Benjamins: Yeah, exactly. And one of the new currents that you see in my time period is Christianity. And people often point to Christianity as the source of a new conception of time: linear time, where you have a clear idea of an origin, which is the creation of the world, this hard and fast beginning point instead of sort of the hazy mists of mythical time. You have creation, and then you have the end of the world or judgment of some kind that's a clear end point. And so, one of the interesting features of my period is to look at what happens when Christianity comes on the scene and how do Christian authors map their, what you might call, their sacred history, all these events of the Bible, and both the Old Testament events that come in biblical literature, and then more recent events with Jesus and his coming. And so, on all of these events that are seen to have a religious or sacral import how they take those events and then map them on to existing dates from what you might call secular or mundane history. And so, for example we get this Christian bishop called Eusebius who around the year 300, he creates this work called the Chronicon, or the chronicle. And what he does in this chronicle, it's one of the important steppingstones in the development of this universal history genre, is that he has a bunch of columns. And each column represents the key dates for an empire. So, you'll have the Persian empire, you have the Macedonian empire, you have the Athenian empire. You also have the Hebrew people and the Persians and the Asian peoples. And he'll list the regnal years for each king within the column. And then, on the left-hand side you'll have the Olympiads (the Olympics occur every four years so that's one of these universalizing measuring sticks you can apply), so you have the Olympiads in one column, then you have each empire, and then that goes on page after page after page. You have all these columns, and as the pages go on, you see columns appear and columns disappear. So, for a while you have all these Asian peoples that eventually go, Greek antiquity, but as you go on through time more and more empires disappear. The Persian empire disappears. The Babylonian disappears. The Macedonian disappears. Eventually, you only have the Romans and the Jews, and then the Jews disappear from his column after AD 70, when the temple is destroyed. And then you only have Rome. And so, that's a really interesting development. It's a kind of pictorial representation of the supremacy of Rome on the axis of time. For a long time, there's this miscellany, but by the last page, the only column left is Rome. Rome has triumphed in this representation of time. And he also melds biblical events with Roman events. So, it's a Christian Rome, so Christianity and Rome kind of share the supremacy or hegemony of time. So, that's one way of mapping Christianity on to Roman time and also showing the supremacy of Roman time as it were over all the times and places of these other empires that have now succumbed eventually to Rome.Saintsing: Right. I guess, so you said like the linearity that, you know, modern people kind of ascribed to history hadn't really appeared then, but I feel like that kind of suggests like, you know, this guy is like saying everything was moving towards having Rome. And then I assume in his mind probably that Rome would just be what was going for the rest of time, right?Benjamins: Yeah, that's kind of the assumption that Rome keeps on going. And that's not a new idea. The idea of Rome, that Rome will go on forever is a very old idea. Virgil, you see it in Virgil, where Jupiter prophesies that this empire will have no boundaries of either space or time. It will be an empire without end. And that's a shared notion in the Roman world. That Rome is destined to endure on and on and on. And one interesting place that we see that idea is in this ancient habit of thinking about the history of Rome (and hence, by this time, the history of the world because those two are very closely connected) in terms of the ages of a human life. So, there's this interesting idea that a human life has these different periods, your ages. You have infancy, you have boyhood, you have young manhood, you have adulthood, you have old age. And the world goes through these ages similarly. And that's an oldie in Greek culture and then Roman culture, that there's this homology between the ages of a human life and the ages of the world. And you can apply that then to the history of Rome. And we know that Seneca did this. And the historian Florus did this. He told the story of Rome in terms of these ages of infancy, boyhood, manhood, and so on. And that scheme implies that you're going to get to the end because a human lifespan has an end. We can see that at least in the classical Roman world, there's a resistance to the idea of saying that Rome will have an end. So, you know Cicero for example in his On the Republic uses this simile and talks about Rome in its boyhood, and then eventually verging on manhood, and now it's in its prime. and so on. But then, he also wants to say that it's not going to die. He says there is no death of the state. The state should be so constituted as to be eternal and for the state to die would be like the cosmos collapsing.Saintsing: Well, unfortunately it looks like we're running out of time. So is there anything you'd like to leave us with before we go?Benjamins: Sure, I'll say first: Latin and Greek are wonderful languages, and the literatures are marvelously complex and variegated. And so, for those of you who have the chance to learn Latin or Greek and enter into this wonderful space, I highly recommend it. But I know many of us don't have the time or leisure to do that. But I would maybe just put in a little word for the value of history. Not necessarily ancient history, but maybe ancient history especially. There's a lot a lot of benefit to be gained from going through the challenge of thinking through a culture in a world and an idiom that's different from our own. And it's both challenging and very rewarding, and it frees us from a lot of the assumptions and prejudices that we share with our culture and even with our language that we have often without thinking about it just because of the way that our language and our culture tends to divide up the world. And so, it's very rewarding in a lot of ways to take advantage of these opportunities to enter a different time space in whatever way that might be. In the original language or in translation. And have some of our ideas challenged and just exposed to very different ways of thinking about such basic ideas as space or time or anything else.Saintsing: Thanks so much. Today I've been speaking with Joshua Benjamins from the Department of Classics. Thanks so much for being on the show, Joshua.Benjamins: My pleasure, Andrew. Thank you so much for having me.Saintsing: Great. Tune in two weeks for the next episode of The Graduates.
12/10/2020

Nina Maryn

Serrano: Hello, you've tuned in to 90.7 FM KALX Berkeley. I'm Karen Serrano and this is The Graduates, an interview talk show where we speak to UC Berkeley graduate students about their work on campus and around the world today. I'm joined by Nina Marin from the Department of Plant and Microbial biology. Welcome to the show, Nina!Maryn: Hey, thanks for having me.Serrano: It's great to have you here. How’ve you been doing?Maryn: Oh, you know, just apocalypse adjusted. I think things are going pretty well.Serrano: Nice. Yeah, I think we're all feeling the same way. Could you tell us a little bit about what you do on campus?Maryn: Yeah, so I am a relatively new PhD student in the Krishna Niyogi lab in the Plant and Microbiology department and I study photoprotection in plants, which is how plants respond to stress from high light. When there's too much light in the environment and they can't use it all to perform photosynthesis, they want to avoid the generation of reactive oxygen species, which are basically molecules that are created from radicalized oxygen which is kind of a byproduct of photosynthesis in plants that are unable to have mechanisms to protect themselves.Serrano: That sounds super interesting! For people who aren't plant people like us... I thought light was required for photosynthesis. Why is too much light bad for plants?Maryn: Right, so light is required for photosynthesis, but plants can only cope with so much. So there are only so many photosystems which are the molecular protein complexes that process photons of light. There are only so many in a leaf for example, and they can only perform it a certain density and at a certain rate. So, in kind of the middle of the day at High Noon, there’s almost twice as much light as the plants can process. And what happens to the light when they're absorbed by a leaf is that they get absorbed by these chlorophyll molecules, which people should generally be familiar with chlorophyll, it’s a pretty famous pigment molecule, and when the light is absorbed their electrons get excited and if there's no photosystems available to process that light, which is what happens in middle of the day when there's too much light around, is that energy from that will end up going to molecular oxygen which is present because the byproduct of photosynthesis and as a result that can start shredding apart the proteins in the chloroplast and in the leaf itself, and so in order to prevent that from happening they have to have another way to redirect all that extra energy.Serrano: So it sounds like the leaves just get really overwhelmed with all the energy they're taking in and they have to kind of shuttle it to other places so that it doesn’t settle into those bad oxygen species. That's pretty cool. How are you studying that?Maryn: So I actually study the natural variation of this process. So what I've looked at are a bunch of wild species at the University of California Botanical Gardens, and I'm looking for plants that are abnormally good at doing this and better at doing it than the crop species that we grow for food are so that we can kind of understand how those mechanisms work in the wild, especially in plants that are adapted to environments with really high sunlight. So where there’s lots of shade, but also a lot of kind of excessive sunlight as well, like, in dense forest canopies and Rocky deserts, I study the natural variation of these photoprotective mechanisms in wild species.Serrano: So how can you tell which plants are good at this and which plants aren't good at it?Maryn: Through this really fancy measurement system called a “fluorometer”. So what happens after that chlorophyll pigment absorbs a photon of light and its electrons get excited, there are a few different places it can go. So it can either go to perform photosynthesis, which is what it normally does when there's not too much excess light. Or it can go to and be released back into the environment as light again, and that's fluorescence. So all pigment molecules pretty much fluoresce. So, chlorophyll is a fluorescent molecule. So when it absorbs that photon of light it can either use it for photochemistry, which is what we call photosynthesis, or it can be released back into the environment as light again, and that's what we would call fluorescence. Like, fireflies also have molecules that fluoresce. Yes, and you can measure how much fluorescence there is. Fluorescence is correlated to how much photochemistry is happening. And so when fluorescence goes down, this is actually a sign that the plant is beginning to perform photo protection instead of photosynthesis and we can measure that by using a fluorometer.Serrano: Oh, I see, so the higher fluorescence measures the worse the photochemistry then?Maryn: No, it's the opposite. So yeah, fluorescence is correlated with photochemistry. So the more fluorescence there is the more likely the rest of the energy is being used for photosynthesis. But when the fluorescence goes down that means the plant is performing photo protection and it's very very efficiently funneling that light to other funneling that light energy to the other molecules.Serrano: I see, so do you like just go to the Botanical Gardens and measure the plants fluorescence? Is that how you take your data?Maryn: So that's one way of doing it, but I wanted to measure almost a hundred plants in the first data collection that I did.Serrano: Oh wow!Maryn: Yeah, so I did a survey of 100 species and what I did was I took a bunch of their leaves which I got special permission from the garden to do, and I brought them back to the lab. Made the measurements there.Serrano: Oh, I see. It must be nice going to Botanical Gardens!Maryn: Very, very lovely. I mean, I feel like I'm good friends with the curators there now. It’s so fun.Serrano: So what is your hope for your research outcomes? So do you think that you'll be able to find or use this natural variation to maybe engineer plants with better photosynthesis?Maryn: Yeah, so in my first screen I actually found a really interesting group of plants that are all fern species and most of which are xerophytic. So they're adapted to live in the Rocky desert and the southwestern United States and these were incredibly efficient at turning on and off photo protection. So when there's too much highlight, they immediately perform enormous amounts of photoprotection, way higher than both of the model organisms, Nicotiana tabacum which is a tobacco species and Arabidopsis, which is kind of this model weed. Well, they perform way better photochemistry or photo protection then those species and they're able to turn it off much more quickly when the light goes back down to a low level where they can start performing photochemistry again, and so we suspect that they're able to kind of optimize their photosynthesis and photoprotection for whatever the light regime is and we are hoping to be able to kind of understand what that mechanism is and then put it into crops to improve biomass .Serrano: That’s super cool. Do you have any hypotheses to why these ferns might be better at that?Maryn: Yeah, so ferns are a really interesting group of plants.They diverged very early in the land plant lineage. So they're very far removed evolutionarily from angiosperms, which are most of what we eat. Those are the flowering plants and you know angiosperms really didn't evolve to optimize photo protection because their biomass field is not directly correlated to how good they are at reproducing because they produce fruit and flowers. But ferns actually reproduce by forming spores on the backs of their leaves and so their leaves are their reproductive organs and so being able to optimize this photoprotection/photochemistry mechanism might be more useful for ferns because optimizing their biomass and growing bigger and better leaves actually increases their chance of fecundity or their reproductive success. That’s my pet hypothesis for why they might be better at it.Serrano: Yeah. I was kind of thinking since ferns evolved earlier than yeah gymnosperms and angiosperms that they maybe have had to deal with harsher environmental conditions than those and so they would have different mechanisms to adapt to those conditions prior to the rest of the land plants.Maryn: Yeah, I mean that's definitely one reason. So a lot of ferns grow in forest understories and the ones that I've been looking at primarily actually have adapted away from growing in forests and into the Rocky desert and so my hypothesis is that they first adapted to optimizing photosynthesis in low light and then moved to being able to do high-capacity photoprotection and high light. One of the other fun things about these species is that they perform phototropism. So in high light, when they're not being clamped to a fancy lab machine like a fluorometer, they curl their leaves and so they kind of do this self-shading and I think that that's one of the other reasons why the rate of transitioning from photosynthesis to photo protection and back is really high because as soon as there's too much light, the photosystems shade and they perform self-shading so they can still absorb a lot of light from the environment but it's not an excess wow optimize that transitionSerrano: So what would it entail for you to kind of steal these photosynthesis mechanisms from ferns and place them into crop plants?Maryn: So the project that I'm planning for my dissertation is to look at their light-harvesting complexes. So this is the part of the photosystem that holds a lot of the chlorophyll that captures light from the environment and directs it to the photosynthesis reaction center. And this is the site of that photoprotective mechanism because you have to stop the excess energy from getting into the reaction center where the molecular oxygen is. And so my project is to look at the genes in the light harvesting complexes in these plants and see how they may be structurally different to be able to redirect that energy to other molecules that bind to these light-harvesting complexes.Serrano: I see. So you're focusing on like one really specific part of the chain, basically?Maryn: Well, I'm focusing on the site of photo protection in the photosystem.Serrano: I see. Hi, just a reminder that you're tuned in to 90.7 FM KALX Berkeley. I'm Karen Serrano and I've been speaking to Nina Maryn from the Department of Plant and Microbial Biology and she's been talking about her work in photosynthesis. So Nina, have you always been interested in plant molecular biology or what did you do before your time at Berkeley?Maryn: No, I was not a plant biologist before I started my PhD. In undergrad, I worked in very basic genetics and molecular biology. So I studied sex determination in C. elegans, which is a model worm. It's super common for studying how genes are regulated and how genomes function because they have very small, well-characterized genomes. And then when I graduated, I worked for two years as a microbiologist in a lab at New York University and I studied kind of biophysics and also the formation of spores in some bacterial subspecies and then I decided that I wanted to work on something that had possible implications for climate science. I thought that, you know, doing a PhD is a really big commitment and it's a very long time and there's not necessarily the biggest payoff at the end in terms of money or fame. So I wanted to work on something that I felt had a moral resonance and I think that working on a project where I get to do basic biology and learn a lot about some of the molecular mechanisms of a really interesting system, but meanwhile hopefully down the line that will help to actually make people's lives better and help improve crop yield in places where climate change will be likereally affecting how much food people can produce for their communities down the line.Serrano: Right. Yeah, I think definitely now more than ever climate change has been on our minds. It seems like you just wanted to go into maybe like a more applied field of study.Maryn: Yeah, I think specifically I yeah, I was interested in something that would have kind of an environmental.Serrano: What made you want to study photosynthesis in particular?Maryn: I didn't plan to be a photosynthesis researcher, but I was interested in the lab when I was doing rotations in my first year because a lot of the people in the lab seemed really happy and it seemed you know, professional and well-funded and when I got in I got this like really big kind of fishing expedition of a project to do this survey the botanical garden and I ended up finding something really interesting and I felt very dedicated to solving the problem that I discovered.Serrano: I see. So it wasn't it wasn't planned at all? It was just..Maryn: Nope.Serrano: It was just something you found really interesting when you encountered and then fell into it. Were you always interested in science or were you ever interested in anything besides science?Maryn: Ever since high school. I was definitely interested in science. I always felt that at least in my science classes, I had enough questions where we reached the end of our knowledge that we could get from the textbook and I think I always had a very research-oriented personality, but it was not the only thing I ever wanted to do. I've always really enjoyed writing and performing and I seriously considered a career in stand-up comedy which I'm deeply glad I did not pursue during this time! But yeah, I've definitely considered other things besides science.Serrano: So you said you considered a career in stand-up comedy. Do you ever do that in your free time?Maryn: Not anymore, but I did during the “before time”.Serrano: I guess now you can't really! Maybe there's like a zoom comedy show, but definitely less funny that way.Maryn:Yeah.Serrano: But you also mentioned, or, you mentioned writing! How do you kind of incorporate writing into your life now?Maryn: So I do write fiction in my spare time. I like to write snow funny short stories, but science itself has a lot of writing involved. I'm writing my thesis proposal right now and it’s a lot of work and that's kind of one of the things that I love about science is that it's so interdisciplinary and on a given day, there are so many different things you could be doing. You can be planning an experiment or doing lab work, writing, presenting work, and it kind of has it all.Serrano: Yeah, I would definitely say as a fellow PhD student, there's definitely more writing than you ever expect there to be in stem fields. And so you’ve also mentioned that you were really research-oriented. Did you have undergrad experience in research or what kind of opportunities that you have there?Maryn: Yeah, so the work I did in C elegans. I did for my sophomore year through my senior year in undergrad at New York University. And then yeah, and then I worked as a laboratory technician for two years before I came to grad school.Serrano: So you got to get a feel for what research is like before you considered grad school. And then you said you worked for two years after your undergrad, right?Maryn: Yeah.Serrano: Did you ever consider going straight from undergrad to your PhD or did you want that kind of buffering time.Maryn: I did consider it but I think that the concern that I had was that I felt that I didn't have the confidence to break out of my comfort zone in undergrad and I think that I would have ended up applying to something that was very similar to what I had already been doing because it was what I felt confident in it was what I felt comfortable with and I knew that if I was going to spend five to seven years working on something I wanted it to be more thought out than just what I felt comfortable with. So taking two years to go into a different field and start over.. and start over with a little bit more experience. I think, it prepared me better and gave me more time to go to talks and go to seminars and do more reading and figure out what kind of project I really wanted to do for my PhD.Serrano: Nice. Yeah, so you mentioned that you're writing your thesis dissertation right now or your thesis project? How is that going?Maryn: I think it's going well. I guess we'll find out I guess if I become a PhD candidate in two and a half weeks!Serrano: Yeah. Wow!Maryn: I think I think it's going well. I've gotten some good feedback from my postdoc and some professors that I've been working with.Serrano:Nice! What do you think you’d like to do after you graduate?Maryn: The world scariest question, Karen!Serrano: You don’t have to have a real answer. I don’t even have a real answer to this question.Maryn: I mean, I think the honest answer is that I'm trying not to make too many decisions for my future me. A year ago. I would not have predicted anything about my life as it currently is, but I think that I don't have any answers.Serrano: All right. So I mean usually grad students are usually stuck between staying in Academia and then moving into the private research sector. Do you have any kind of preferences at the moment?Maryn: I really don't because I think that, I mean, my understanding of Academia and my experience with it is that it can be really wonderful and fulfilling but there are not very many spots for professorshipat the highest level and it it takes a lot of luck to get there and I think that if I get that luck and I get postdocs and opportunities that I'm excited about I would absolutely pursue that, but barring that I think that I would probably have it, into a career that is more writing and communication oriented rather than just doing bench work at an industry level.Serrano: Yes. You're a little interested in more science communication right now.Maryn: Yeah.Serrano: Cool. Have you had a chance to try out teaching yet?Maryn: Not yet. Not yet. I'm planning to teach next year.Serrano: Oh cool. Do you know what you'll be teaching?Maryn: No, the next academic year, so I’m not sure what’s on the …Serrano: Oh right, okay! What do you do on campus besides research right now?Maryn: I've been working on campus in the graduate student union. I'm a steward for our department in the graduate student union. And so I act as a representative of my fellow graduate students in how we collectively bargain with the university to make sure we are paid enough to live and we have rights..Serrano: That's definitely important and thank you for your work in that! Are there any other clubs or organizations that you’re also part of or is the union work your main sort of focus right now?Maryn: The union is my main focus. In my spare time, I used to also do swing dancing occasionally on campus. There is a Lindy Hop on Saturdays, which was so much fun.Serrano: Oh that’s so fun!Maryn: But alas so many of my hobbies were social so they've been rendered illegal.Serrano: Are you still in Berkeley this semester or have you decided to go home?Maryn: I am still in Berkeley. I currently live in Oakland.Serrano: I wonder if.. I wonder if they'll approve any sort of outdoor activities soon such as swing dancing because I feel like that could be done outdoors. And I think I have in fact seen people do it like in the main little square like next to Sather Gate.Maryn: Yeah, but it does require touching strangers… Which I don't know about.Serrano: Oh wow! Yeah, you need a partner to dance, don't you? Yeah, I guess you could do like the Middle School.. like six feet apart.Maryn: I think yeah six feet apart is farther than middle school dancing!Serrano: But yeah, I think we all struggle with lost hobbies now. Since you’re studying plants, what’s your favorite plant?Maryn: Ooh, that's a good question. So I'm going to say that it's one of the ferns that I study. One of the plants that I study is a maidenhair fern called Adiantum raddianum and you can buy it as a houseplant and they are absolutely beautiful. They have very like tiny and delicate leaves that are just like a very Vivid bright shade of light green and I highly recommend it as a lovely addition to your home.Serrano: Do you have one in your house?Maryn: I do not have one in my house. But I am going to probably grow them in the greenhouse soon at school and steal some home for free.Serrano: I imagine ferns are a little bit hard to take care of because they require a lot of water, right?Maryn: It depends on the species. But yeah, this is probably so far is quite a bit of water.Serrano: I'm glad you had a real answer to that because every time someone asks me, and for the audience, I also am a plant biologist. So people often ask me what my favorite plant is and I always blank on every single plant I know when I hear that question! So it’s nice that you had one.Serrano: You know, we end the show with usually asking our interviewees what they like to leave the audience with. Do you have anything you'd like to leave the audience with?Maryn: Yes, so I like to listen to podcasts when I'm working in the lab on something that’s tedious and my number one recommendation for podcast listening for the scientifically minded is the podcast 0% scared and it’s a podcast where a viral biologist and a person who believes in the Paranormal argue about paranormal topics.So the scientist likes to break down why the logic of the paranormal thing makes no sense! But occasionally she says “this is plausible” and it’s real fun. It's a real fun time.Serrano: I actually have to start listening to that. I love it. I listen to a lot of crime podcasts when I work, but I recently started listening to one called “Two Girls One Ghost”. I don’t know if you’ve ever heard of that one but it’s just to best friends and they talk about paranormal experiences, but I’d love to hear a scientific debate between a believer and a scientist.Maryn: It's fun, I think because she's genuinely aggressive about it. Like she's like “No! This doesn't make any sense astrology isn't real.” So sorry to the astrology believers out there in the audience, but it's great. It's really fun.Serrano: Sorry, I'm really interested haha! Is this, are they like reviewing cases that have happened to other people or is it like their own experiences?Maryn: It's like topic by topic. So there's one episode about mermaids and the paranormal believer co-host…Serrano: Oh so it’s not like “this is a ghost story, do you think this is real?”Maryn: It’s like “Are mermaids real?” So it’s the funniest! Okay so this is a great episode because the Paranormal believer is like “I've seen a mermaid” and she was like, “you definitely did not see a mermaid, you saw something else” and then she goes through like the history of like mermaid debunkings and she brings in like scientific papers and she's like here's why mermaids can't exist because of evolution and it's great.Serrano: I love that. That's a great recommendation! All right, we're coming to the end of our time here. So thank you so much again, Nina and great to have you on here and tune in next week for the next episode of The Graduates.Maryn: Thanks so much!
11/24/2020

Karen Serrano

Andrew Saintsing: You're tuned into 90.7 FM KALX Berkeley. I'm Andrew Saintsing, and this is The Graduates, the interview talk show where we speak to UC Berkeley graduate students about their work here on campus and around the world. Today, I'm joined by Karen Serrano from the Department of Plant and Microbial Biology. Welcome to the show, Karen.Karen Serrano: Thanks, thanks for having me.Saintsing: Karen is actually about to be our newest host of The Graduates, so you can look forward to new interviews hosted by Karen. Are you excited to be hosting The Graduates, Karen?Serrano: Yeah, I'm super excited. It'll be nice to be on the other side of this soon.Saintsing: Have you ever done anything like interviewing before? What made you get interested in The Graduates?Serrano: I've been interviewed for a show like this, but I haven't been the interviewer, so I thought it would just be kind of interesting to be on the other side and then get to hear about all the cool research that's going on that I never really get to hear about, so yeah, that's kind of what made me decide.Saintsing: Nice. Oh, you have been interviewed before? When were you interviewed?Serrano: As an undergrad we had like a similar program at the University of Arizona, and it was called Thesis Thursday with the local radio show, so I was interviewed a couple of times about my research on that. It was pretty cool.Saintsing: So, you've been doing research, you were doing research all throughout undergrad to have enough to get a couple interviews?Serrano: I did have like basically the same interview. One year I was part of this research program called the Undergraduate Biology Research Program, and one of the requirements was to do a radio interview each summer. And so yeah, every summer I would get interviewed. I only did research for two years, but I got to be interviewed twice, so that was fun.Saintsing: Oh, that's cool. They had a requirement that you had to be interviewed?Serrano: They had to do a radio interview, yeah, and they also had a requirement that you had to write like a small like press release about your research, so that was also fun. Yeah, just like some activities to get you into communication.Saintsing: Oh, cool, so you're like well-versed in science communication now. Sounds like this...Serrano: I'm a beginner.Saintsing: But, well, you know, you have a good starting point relative to some other people. This is just like a thing at the University of Arizona where you went to undergrad?Serrano: It was kind of like a summer program that you had to apply for, but yeah, it was fun. I was happy to be a part of it.Saintsing: Well, let's put those science communication skills to the test. So, you are in the Department of Plant and Microbial Biology. So, you are studying, I guess, some kind of interaction between plants and microbes or something along those lines?Serrano: Yeah, so I'm a plant biology PhD student, but I do study an interaction between plant and microbes. I study the interaction between plants and a fungus called arbuscular mycorrhizal fungi.Saintsing: Can you repeat that one more time?Serrano: Yeah, it's a mouthful. It's called arbuscular mycorrhizal fungi.Saintsing: Okay, and what are those?Serrano: Yeah, so to kind of break down the name: mycorrhizae. They're called ‘fungus root’ because they're fungi that live in plant roots. And then, they're also called arbuscular because they form these little structures called arbuscules when they get into the plant root.Saintsing: What is an arbuscule?Serrano: It's kind of just like a little fungal structure that serves as kind of a hub for metabolite exchange. So, the fungi will like crawl into the plant root, and when they get there the plant will like entirely rearrange its whole cell to let the fungi grow this arbuscule.Saintsing: What do you mean by crawl?Serrano: They actually like seep into the plant cell walls.Saintsing: Okay, so the fungus, they're moving like an animal? Like they are controlling their movements? Or, I guess I'm wondering: is it kind of like how plants roots grow through the soil? Is that kind of how the fungi are moving?Serrano: Yeah, it's exactly like that. They just grow longer and longer in a certain direction.Saintsing: Okay, cool. Sorry, I interrupted, though. And you got to tell us more about how the plant rearranges itself to accommodate the fungus.Serrano: Yeah, so the fungus actually provides a lot of nutrients and water for the plant, and so the plant actually accommodates them like by rearranging its entire cell wall to let them fit in there. So, it's like a symbiotic relationship the plant gets more nutrients and water out of the soil because of the fungi, and the fungi gets a house and carbon from the plant.Saintsing: So, what kind of nutrients are the plants getting out of the relationship?Serrano: So, they've been shown to provide like, I don't know, so many nutrients. The main ones are phosphorous and some like small micronutrients that the plant usually has to scavenge for. Yeah, these fungi are really, really, really good at taking up phosphorus. Usually because phosphorus is present in like a non-available form in the soil that plants have to like work really hard to convert to an available form that they can use. And these fungi do it really easily, and so that's kind of a mechanism that yeah allows them to get more nutrients from these fungi.Saintsing: Do you know more about the like why is it unavailable to the plants or like what what's going on with the phosphorus? What, it's like energetically costly to convert it?Serrano: Yes and no, but the kind of hard part about phosphorus is that there's a lot of phosphorus in soil, but it gets tied up with metals just because it likes to interact with them more. So, it's not existing in like a free form that plants can just like suck up when they suck up water. It's tied up with other things, and so the work is trying to get it to untie from those other things.Saintsing: And the fungus just has like good metabolic pathways or something that let it break those interactions down?Serrano: Yeah, exactly. I don't study the fungus specifically, so I don't know more about it, but I’m assuming, yeah, they do. Plants also release like little, small like metabolites that convert the phosphorous, but it takes a lot more for them to do that than for the bacteria and fungi to do that.Saintsing: I see, so you don't study the fungus. You study the plant, I guess. Like the how the plant does this interaction.Serrano: Yeah, um so this fungus is actually like the worst behaved lab specimen ever. It's really hard to study the fungus specifically because it's multikaryotic. So, what that means is that each of the cells can have like hundreds of nuclei.Saintsing: Wait, so like the cell are like fusing together you mean? Or like what what's going on there?Serrano: So, the fungus is like eukaryotic. There are multiple cells that make up the organism. Those cells instead of just having one nucleus, it has like hundreds of them.Saintsing: So, it just like has a bunch of DNA that it can make its proteins with.Serrano: Exactly. So, it's really hard to actually genetically study them, and then there's like recent research has shown that like those nuclei will just like divide and multiply kind of at will. So, that makes it increasingly hard.Saintsing: Interesting, so wait, but I mean that seems like you have a bunch of DNA to study, right?Serrano: It’s hard to tell exactly like what DNA comes from what cells, which is pretty important.Saintsing: I see. Yeah, so like a cell could have slight deviations in DNA within the cell.Serrano: Exactly, yeah so just as like we have millions of cells but some of our cells are like eye cells and some of our cells are only expressing you know finger things (I don't know much about humans) but the fungi also like kind of separate these functions, and so, if we want to study them, we just get like hundreds of DNA we don't know actually where they're coming from.Saintsing: So, the fungus is poorly behaved. It's not something that's easy to study.Serrano: Right and they will die outside of the plant host, like they have to be studied within the plant, and so, it's really hard to separate like to get really clean fungal tissue first also. So, anyway they're just really hard to study, and so, we kind of have to get creative, and so, my research is trying to apply a transcriptomics technique that was developed for human biology and trying to use this technique and apply it to the symbiotic system.Saintsing: What is transcriptomicsSerrano: Transcriptomics… you've probably heard of genomics (the study of all the DNA within an organism). Transcriptomics takes a step further and only studies the genes that are actually being expressed.Saintsing: So, it's a transcript because it's like been transcribed.Serrano: Yeah, exactly right,Saintsing: Because you're not worried about genes or you're not worried about all the DNA that like doesn't get transcribed is basically the idea behind this, right?Serrano: Exactly, if you want to know like, for example, I only want to know about the genes that are related to the symbiosis, so I don't really care about everything else or the DNA that's not being transcribed at the moment. And it's kind of a new field, but it's developing really rapidly, and now we've gotten to the point where we can tell exactly what genes are being expressed and exactly what cells so it's pretty crazy.Saintsing: Oh, cool, so that's why the fungus is useless. Kind of like: what are you doing with that because you can't differentiate cells, so it doesn't really help you, right?Serrano: Exactly, and this company 10x Genomics has taken it a step further, so now they created this slide, which is what I'm going to be using, and it basically… like you can take a little slice of tissue and then like paste it on the slide that has DNA markers on it which will capture the DNA that's released, and so, you can take the plant tissue that's been infected with this fungus and then you stick it on the slide and you apply some chemicals that will let you see what like cells there are and what structures within the cells and if the structure is fungal or plant and then you release the DNA onto the slide and then you get information from a computer which I don't know actually much more about, but it will tell you exactly what DNA is coming from exactly what part on the slide. And so, you basically get like a picture and then all the DNA information next to it.Saintsing: Wait, wow, so you're saying that like essentially all you – I mean I'm not saying it's not work, but like all you have to do is take a slice of the plant, the root that you're looking at and just put it on slide and then you're just going to get all of this data about DNA?Serrano: Basically.Saintsing: Wow, yeah, that's really cool. Is this really new, the technology?Serrano: Yeah, it's really new. So, it was developed actually for like human cell biology, so like histologists that would take like – I don’t know, whatever histologists do. And they take like human tissue, and they try to study like what genes are being turned on which cells like for cancer or something. So, it was developed for that, and then a couple of scientists I think in 2016 applied it first to plant tissue, and they got some really good results. So, this will be the first time that's applied to both plant and fungal tissueSaintsing: Wow, yeah and the… So, it recognizes DNA. So, does that mean it, you have to program it in whatever way you program it? With the knowledge of the genes that you’re like… You already know what genes you're looking for essentially? So, you're trying to say like when are genes that you're interested in are activated? Or, are you actually going to find genes from this?Serrano: Yeah, so it'll actually just capture like everything that it's expressed. So, you don't need any prior knowledge about the genes and then from the data that'll give you that's when you kind of look at okay which genes were the most expressed in which areas and it'll give you kind of like a list of candidates that you can now go through each gene one by one and see okay does this gene actually do something.Saintsing: So you're going to maybe find a bunch of genes that people haven't ever seen before or like is this pretty well studied, and so, you'll find things that people have been talking about for a while now?Serrano: Hopefully a bit of both. So, there have been transcriptomic studies done on the system before, but it hasn't been… so, this kind of technique that I described to you, it's called “spatially resolved.” So, other techniques, they'll have single cell data, but they won't know exactly where the data came from, like which cells it came from because they have to pool them all together. So, this will be the first time that we get like both all the data and then where exactly it came from in the tissue. It can be used to validate other people's work, but we're hoping to actually find some new genes as well. It sounds very easy, but it'll take years. The slicesSaintsing: Yeah, have you started already?Serrano: Yeah, so COVID kind of threw a wrench in things, but this summer we mainly focused on getting the staining techniques down. So, there's a couple of different staining techniques that will allow us to see like exactly where the fungus is in the root tissue which is what we'll have to do for the slide to be visualized correctly. So, that's kind of what I've been focusing on, and then COVID also kind of delayed my training on the device that lets you actually slice the tissue so thinly. So, I hope to be doing that next week.Saintsing: Oh, cool. Nice. Are you looking at a particular plant?Serrano: Yeah, so I work with Medicago sativa, which is more commonly known as alfalfa.Saintsing: Is there a reason why?Serrano: It's kind of the model plant that's been used for this just because it's a legume and legumes tend to form these relationships more than other plants.Saintsing: Do you know why that is?Serrano: I think they were the – I don't know why exactly, but if I can remember I think it's because they were the first ones to evolve this interaction. This actually is the oldest like symbiotic interaction between plants and microbes.Saintsing: So, this interaction between this fungus and legumes is the oldest interaction because they were the first one to develop it?Serrano: I don't know about legumes specifically. This fungus and plants is the oldest known like interaction. Arbuscular mycorrhizal fungi are actually living fossils because identically similar fungi were found to be like associated with the oldest plant fossils we have. So there's a lot of research that basically points towards these fungi being the things that actually allowed plants to colonize land.Saintsing: How widespread is this? Is it like all plants are doing this?Serrano: It's about 80% of land plants, so it's pretty common.Saintsing: And what's up with the other 20?Serrano: Yeah, I don't know. That's probably something I should know, but they just have their own thing.Saintsing: Okay, so that's… so you're working towards like really getting into data collection at this point, and so you'll be hopefully like actually getting data maybe next semester even.Serrano: Yeah, hopefully.Saintsing: That's cool. So, you're in your second year. What brought you to Berkeley? How did you end up deciding Berkeley was the school for you, and this program, the Plant Microbial Biology program was the program for you?Serrano: Yeah, so in undergrad I did a lot of research in mining reclamation, so helping mines re-vegetate their land. Through that I got to kind of not only do like plant-related research but also like interact with like the mining companies themselves. And like getting to know like what the actual industry side of things was like, that's kind of what attracted me to Berkeley because we have so many partnerships with industry here, and that's what led me to my lab specifically. I work with Henrik Scheller at the Joint Bioenergy Institute, and so, it's like just a really collaborative environment, and that's exactly what I wanted. I wanted to be like working side by side with like industry scientists.Saintsing: And now, I guess the industry scientists that you're working with would be more like agricultural sciences or people that are involved in agriculture, right?Serrano: Yeah, and a lot of like bioenergy scientists.Saintsing: Oh, right. You said bioenergy. So, you're trying to help people improve like corn ethanol, things like that. Like the production of that.Serrano: Yeah, exactly. We have like another project that I work on which is studying the same interaction but in sorghum, which is a really important biofuel crop. So, hopefully the research I do with Medicago, like the model plant, will be translatable into sorghum also, so we can start trying to use this fungus to help us grow biofuel crops.Saintsing: So, you said like 80% of plants have these interactions, and sorghum is one of these plants, so what are you trying to improve? The interaction between the fungus and the plant? What is the ultimate goal there that could actually be an improvement on the industry?Serrano: Yeah, so as I mentioned before, there's so many benefits that these fungi bring to plants. They're improving their nutrient status; they help them survive better in drought… And so, we're hoping that we could like strengthen the interaction between these plants, between like these important crop plants and the fungi so that in field conditions you know, as climate change happens and we get worse soil and hotter and hotter weather, the fungus will better help the plant to survive in those conditions. And we'll have to put less input into the system.Saintsing: Okay, and by input you mean like fertilizer?Serrano: Yeah, fertilizer, water.Saintsing: So, ideally the ultimate goal of this would be to have improvements that you could genetically engineer into the fungus, or into the plant, or both?Serrano: Yeah, probably easier to do the plant.Saintsing: And these would just help it be a better host or something for the fungi, or help it to get the most it can out of the fungus?Serrano: Yeah, one of the things that we're looking at is the first interaction between the fungus and the plant. So, when it you know first kind of crawls into the cell wall, there's a lot of cell wall engineering that we could do to help the fungus kind of penetrate that wall. So, that's an example of something that we could engineer.Saintsing: I see, and if the… well, I guess I'm just wondering… because the fungus does ultimately penetrate that wall, that cell wall, right? Like, these interactions are occurring, so having that improvement would maybe make that interaction happen faster and speed up the plant growth. Is that the idea?Serrano: I don't know if speed is a factor but definitely the extent of colonization.Saintsing: I got you. Like maybe some plants that aren't growing as well or don't look as healthy don't have as much colonization in their roots of these symbiote relationships?Serrano: Right, exactly, yeah, the extent of colonization differs a lot across even just like different varieties of sorghum. And so, if we could make that more consistent, or if we could find a way to make it… if we could find a way to increase that colonization, it would really help the plant.Saintsing: I got you. So, you're improving yield, and then you'll have more source for fuel.Serrano: Exactly. With less input, which is important.Saintsing: Right, yeah. Well, that sounds really interesting. I'm also really interested in the mining reclamation. So, what, kind of briefly, were you doing there?Serrano: Yeah, so I worked with, it's called the Center for Environmentally Sustainable Mining, which is also a mouthful. And I worked with three southern Arizona copper mines, and two of them were legacy sites. So, those are mining sites that have kind of been abandoned and need to be revegetated. And then, one was an active site, and I worked more closely with the active site. And they basically had these gigantic mountains of just waste soil/rock. More rock than soil. And it was on national forest land actually, and so, they had this really tight deadline to get that stuff revegetated. But, as I said earlier, it's like mostly rock, so it's really hard to revegetate that stuff, and so what our lab did was we basically did a lot of soil sampling, vegetation sampling. And we wandered patterns across the mountains and tried to come up with ways that they could like cost effectively revegetate that area.Saintsing: And were you doing similar things? Like thinking about the genetics of the plants you were interested in and ways you could improve how, you know, well they grew in different situations?Serrano: I was actually looking at phosphorus really specifically. Which is kind of why I started getting into arbuscular mycorrhizal fungi because they're so good at scavenging phosphorus. But we were really focused on kind of just sampling everything we could just to get a better sense of: okay what are these slopes made out of? Because this is just like material that the mine dumps there from all of their other activities. And so, we would just sample and then try to analyze trends. So, over years, like, is the pH going down? How is the phosphorus different? Is carbon different? What plants are associated with different carbon? Different phosphorus? Different soil nutrients? Stuff like that. And then we would try to piece together what was actually happening.Saintsing: And I guess the interest there is like figuring out what the best way to colonize this area with plants was? Like maybe you would figure out which plants to introduce first or something like that?Serrano: Exactly. For example, we had we had two different slopes that we looked at. One, they had previously tried to seed, so there was like a few plants that they planted themselves. And then one they left alone. And the pH on the slope that they seeded was a lot lower and a lot more optimal for plant growth than the other slope that they had left alone. And so, one of the questions we were asking was: was the pH of that slope brought down by the plants, or did that pH just happen to be lower to begin with? And so, those were the kind of questions that we asked there. Because if it had just been lower to begin with, they would just have to wait a few years for the other slope to go down before planting.Saintsing: That sounds super interesting. So, when you got to undergrad, did you start like doing research as an undergrad like right when you got to undergrad?Serrano: Oh, no. Definitely not. I was a very lost freshman. I mean I've always known that I was interested in science, and I really liked genetics. But I started out with like human stuff and quickly realized I didn't like human stuff. It wasn't until I kind of randomly volunteered to be like a mountain guide with really no experience (I'm from the suburbs of Dallas). So, I don't know. They kind of just accepted me. They paired me up with a graduate student who happened to be a graduate student studying plant biology, and he was just like absolutely infectious with like his love of plants. And I just really got into plants after that. And especially because in Tucson there are so many weird desert plants that it's kind of like impossible to miss them. And so, yeah that was that was kind of the story of how i got into plants. And I just started reaching out randomly to professors, and like: do you work on plants? Can I work with you?Saintsing: Wow, yeah that's really cool. So, this grad student was really like when you figured out what… or talking to him was really when you figured out you like really were interested in plants?Serrano: Yeah, exactly. He had this ability to just like look at a field and be like: this is that plant. That's that plant. This is how they interact. This is why they're cool. And I was like: yeah, I totally see that now.Saintsing: Are you at that level now?Serrano: You know my friends always try to get me to identify plants, and I'm like, that's not really what plant biologists do. I work with one plant, who I forget the common name of.Saintsing: So, you're going to be… you're always on trips with your friends, and then that one time, you're going to be like: that is alfalfa.Serrano: Yes, exactly. That's Arabidopsis.Saintsing: So, what turned you off of working with people? Were you going to be a doctor?Serrano: That was my initial thought. Or like a genetic counselor. I was also thinking about doing that. And then I was trying to be proactive, and so, I signed up for this health skills clinic that the university was offering, and you could do like a suture lab, and they had like this fake human tissue that you could practice like sewing on. And I just got like, just so very creeped out by that. And I remember I was like walking home from the place, and I called my mom, and I was like: yeah, I don't know about this. I got that creeped out by like fake tissue. I don't think I could handle it if it was actually bleeding.Saintsing: Yeah, that makes sense.Serrano: Yeah, and plants don't bleed, so you can't really – I mean, you can hurt plants, but they won't sue you.Saintsing: Yeah, that's true. So, okay you figured out you wanted to do plant biology, and then you went to your undergrad research experience, and you found these cool opportunities where you could work with industry partners, and you had all these collaborations. So, do you think after graduate school that you're kind of interested in more like the industrial side, actually working at these companies and doing the reclamation project yourself? Or do you want to pursue academic research, do you think? Or maybe something else entirely?Serrano: Yeah, I'm more leaning on the industry side just because I've always kind of just thrived in that environment. But I am interested in teaching, so I'm kind of torn right now because I love both.Saintsing: Why do you think you thrive in the industrial side of things?Serrano: I kind of like application-based problems. There's like an immediate kind of solution to a problem right in front of you, which is a little different than like doing science for science’s sake.Saintsing: So, you really enjoy teaching. What are you teaching?Serrano: I'm teaching intro bio right now. Bio1B.Saintsing: Is this the first time you've taught?Serrano: Yes.Saintsing: Did you know beforehand that you would be interested in teaching? Or you just found out you like teaching now, this semester?Serrano: I was interested in teaching prior to this, but I didn't expect liking it so much. So, as an undergrad, I served as like an undergraduate TA. It's kind of like the TA's helper. And I always found that really fun and like a good way to practice like learning concepts on my own. Like keeping refreshed with the material. I guess I had really been missing that personal component of things, like interacting with the students every day and like learning more about their lives. Because as an undergraduate you kind of just like go over concepts and like hold reviews and stuff. You don't really get to like make those connections. So, I've really enjoyed that and like learning about what makes them excited and like telling them probably way too much about my research. So, yeah, I think that's kind of why I like it.Saintsing: All right, well it looks like we're actually running out of time now. Usually at the end of the interview we have a moment where guests can take an opportunity to directly address the audience. Is there anything you'd like to leave us with?Serrano: I’d just like to say if you are interested in these fungi, you can actually buy these products yourself now. There's a lot of companies that sell like little inoculants for your own garden that you can try out and see if they help your own vegetables or anything like that. So, if you're interested just Google them: arbuscular mycorrhizal fungi. And you can buy them for yourself and try them out.Saintsing: Oh, cool. A way to minimize the amount of fertilizer you have to use in your own gardening.Serrano: Exactly.Saintsing: Today's guest was Karen Serrano, and she will also soon be a host. Thank you, again, Karen.Serrano: Thanks for having me. I'm so excited.Saintsing: Tune in in two weeks for the next episode of The Graduates.