{"id":1132,"date":"2017-08-21T11:32:11","date_gmt":"2017-08-21T18:32:11","guid":{"rendered":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/?page_id=1132"},"modified":"2017-12-14T17:10:13","modified_gmt":"2017-12-15T01:10:13","slug":"abrar-abidi","status":"publish","type":"page","link":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/life-as-a-scientist\/abrar-abidi\/","title":{"rendered":"Abrar Abidi, BS"},"content":{"rendered":"
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\"\"\u201cYou can go down many different roads before discovering what it is you actually want to do . . . it\u2019s often an unpredictable, winding path.\u201d<\/i><\/b><\/h6>\n

\u201cWhat is your current project and position here at ISB?\u201d<\/i><\/b><\/p>\n

\u201cI\u2019m an ISB fellow. I graduated from college a little over a year ago with a degree in physics, after which I wanted to transition into biology. I was given the fantastic opportunity to come here, essentially, to become a biologist. I am the inaugural ISB fellow, which has been an extraordinary thrill and privilege and honor.\u201d<\/p>\n

\u201cMy research focuses on Mycobacterium tuberculosis<\/i>, the bacterium responsible for tuberculosis, which is currently the deadliest infectious disease in the world. Typically MTB infects people by burrowing in their lungs in a deactivated, latent state, where the bacteria slow down their metabolism and can persist for years, undetected, before some ancillary illness distracts the immune system, allowing the bacteria to activate, wake up, and wreak havoc in the body. How it is that MTB enters and emerges from this latent state is a major question in infectious disease research. My project is to understand those transitions, to discover the genetic program\u2014the genes that get sequentially turned on and off\u2014through which MTB adapts to the host environment. The hope is that once we figure out the architecture and logic of these genetic circuits, we will be able to target combinations of genes that stall the latency program, which could lead to new drugs. I work on both the computational end, developing predictive quantitative models of MTB\u2019s gene regulatory network, as well as on the experimental end, designing and performing elaborate experiments that can validate whether those models represent the reality of MTB\u2019s biology. I do these experiments in a Biosafety Level 3 lab, dressed in something resembling a hazmat suit. There\u2019s often months of training you have to go through to get into one of these labs by yourself. Inside, you have to be extremely careful and vigilant\u2014the organisms you\u2019re working with are highly dangerous\u2014but the science that goes on in these labs is crucial, not just for our basic, curiosity-driven biological understanding of this organism, but in helping find cures for the almost two million people who suffer horribly and die from tuberculosis every year.\u201d<\/p>\n

\u201cHow have you found your unique physics background applicable to your study of tuberculosis?\u201d<\/i><\/b><\/p>\n

\u201cNot at all in an obvious way. In physics you are taught about fundamental laws that govern the behavior of matter and energy in the universe. From these laws you can construct mathematical models to understand all sorts of the things that happen in the world around us, but underlying that understanding are always those few, general, governing principles. Except for perhaps the theory of evolution by natural selection, there isn\u2019t much resembling law in biology. There are, however, a few ideas, a few basic models, that seem to govern life across all scales, from bacteria to human beings. The lac operon model, for example, helps us to understand how it is that genes are turned on and off in an organism. The MWC model for allostery, another example, gives us a picture of how proteins assume different conformations, essentially contorting themselves to bind other molecules and perform specific functions. While both of these ideas are descriptive and not exactly mathematical, as physical laws typically are, they certainly resemble<\/i> physical law in the extremely wide range of phenomena that they explain across the whole span of living organisms. In fact, the brilliant guy who helped discover both of those ideas\u2014to my mind, the smartest biologist since Darwin\u2014was a Frenchman named Jacques Monod, who used to say: \u201cWhat is true for E. coli<\/i> is true for the elephant.\u201d So if you find a genetics or cell biology textbook, you\u2019ll see hundreds, often well over a thousand, pages of detailed information about cellular processes. But my training in physics gave me an ability to hone in on the really fundamental ideas, which are often very simple and easy to state, but that in no small part undergird the reams of details that fill those textbooks. In light of these principles, the details become a lot less bewildering.\u201d<\/p>\n

\u201cI think this perspective has fed directly into my style of research. I\u2019m interested in the details of a problem insofar as they help lead me to construct a model whose components consist of much more fundamental notions. The power of these models, then, is that they are predictive. Not only do they describe what we already know, but they describe things that, until that point, we might have had no idea of. This is the kind of thinking that physicists are experts at. In my own research, I\u2019ve been constructing models that we believe underlie the phenomenon of latency in MTB. These models are in the form of genetic circuits that, if they behave the way we think they do, should not only explain what people have learned about the genetics of latency over the last few decades, but also should be able to predict exactly which genes to target in order to prevent the bacteria from being able to enter into latency in the first place. This is a prediction that we will have to go and test in the lab, and if it\u2019s right, it\u2019ll say something about not only the validity, but also the predictive power, of our model. This is an unusual form of biological research, certainly pretty remote from the way MTB has largely been studied in the past; but this is the kind of biology I\u2019m most interested in, and it is directly inspired by my training in physics.\u201d<\/p>\n

\u201cDo you have any type of graduate school plans?\u201d<\/i><\/b><\/p>\n

\u201cYeah, definitely! I didn\u2019t want to go straight to graduate school after college because, I don\u2019t know, I\u2019m a master procrastinator. I thought as an intermediate step I could get shoulder deep in research. I\u2019m not and never have been much of a classroom student, but I do love research. I like tussling with a really hard problem over the course of months and years. So I knew I wanted to go straight into research. Now as we\u2019ve made significant progress on this project, and we\u2019ve started to reach conclusions, we\u2019ve been brought closer and closer to the point of publication. After wrapping up this project my next destination will likely be a doctorate program. I\u2019m applying this fall for PhD programs in biology.\u201d<\/p>\n

\u201cDo you wish you had taken biology right at the start as an undergrad or do you like that you got your physics background?\u201d<\/i><\/b><\/p>\n

\u201cNo, I\u2019m really glad that I didn\u2019t take any biology at the start because I\u2019m just not good at memorizing lots of facts. That\u2019s not what biology is, but that\u2019s often how you\u2019re taught and evaluated in biology. You\u2019re tested by whether you have memorized all the different detailed points across some number of chapters in a monstrous textbook. That\u2019s just not how I learn, and I hated<\/i> biology in high school. Most of the biology I know now, I\u2019ve taught myself, often in an on-the-spot and haphazard way. Research works in a far less linear way than classes, and so my learning through self-study has been unsystematic, but often more thorough than if I\u2019d learned the same things in a classroom. I find that trying to do good research is a far, far greater incentive to learn with depth than trying to get a good grade on some tedious exam. I\u2019ve learned through an intense reading of review papers and monographs and a few really excellent textbooks (I find most textbooks to be unreadable and awfully written, but there are exceptions). Learning in this way has been, I\u2019m sure, far more fun and fulfilling than had I majored in biology in college and been bored to tears by lectures and Powerpoints and the inevitable cram for multiple choice exams. That might have killed any nascent interest I had in the subject.\u201d<\/p>\n

\u201cSo you talked about how you came to work at ISB. How do you think you balance your work and personal life? Is there a balance or?\u201d<\/i><\/b><\/p>\n

\u201c*laughs* Oh man, um\u2026 I\u2019m working on it. The truth is, science is just one among many of my interests. All of my other passions matter a great deal to me, but when I first got here I had to subdue them for a bit. Earlier on, I was spending a lot of nights in the lab. I was nervous and anxious and afraid: I had no background in this stuff, I had no idea what on earth I was doing. I\u2019d never been formally taught sterile technique, so I was contaminating my bacterial cultures for weeks, and there was nobody to tell me so. I was learning everything from scratch. So during that initial period I was very intimidated, and I spent all my time here thinking about the science, thinking about the problem I was trying to solve, even if I didn\u2019t yet know a whole lot of the biology and wasn\u2019t making much progress on my project.\u201d<\/p>\n

\u201cEventually, after lots of hard work and lots of thinking, I had a few lucky breaks, a few times where I discovered something conceptual or experimental that was really cool, and seemed to solve the complicated problem at hand. And that finally put me at ease. To take a very insignificant but recent example, there was this great moment, just two days ago. Did you see those Eppendorf guys? At those tables over there? They were showing off these fancy experimental platforms they were trying to sell, and after asking about them, I said, \u2018That\u2019s exactly what I\u2019ve been doing! What you have right there, is exactly what I\u2019ve been building for our experiment!\u2019 I didn\u2019t even know there was a commercial version of this thing that you could just go out and buy. We thought what we\u2019d made for our experiment was on its own really expensive; after all the troubleshooting, we\u2019d probably spent upwards of $6,000 on the equipment. And seeing these Eppendorf guys, I was wondering, Oh boy, how much money, how much time, would we have saved if we\u2019d used their platform? So I asked one of the representatives, \u2018How much does this cost?\u2019 He said, \u2018Well this one starts at $160,000.\u2019 At that moment I realized that all the flailing around that I\u2019d been doing for weeks and weeks, and those late nights that I\u2019d been spending in the lab\u2014all of it paid off.\u201d<\/p>\n

\u201cSo earlier on my time at ISB was a lot more intense. I remember once I went on a date with a girl, and in the middle of the date I needed to check the growth of my bacterial culture. So I brought her into ISB (I\u2019m not even sure if that\u2019s allowed) and said, \u2018Hey, I need to check the growth of my microbes for a second.\u2019 So\u2026 probably something like that wouldn\u2019t happen anymore.\u201d<\/p>\n

*laughing*<\/p>\n

\u201cThat\u2019s, uh, that\u2019s work-life balance, right? There wasn\u2019t so much balance then, unfortunately\u2026 *laughs* Now there\u2019s more. After making headway, you feel more secure about your position, and about what you can accomplish, and what\u2019s within your control and what\u2019s not. Then you start valuing your free time much more and making good use of it.\u201d<\/p>\n

\u201cWhen you got to ISB, did you learn anything about yourself? Besides thinking, \u2018Oh my gosh, I\u2019m so intimidated.\u201d<\/i><\/b><\/p>\n

\u201cI think there\u2019s a few traits which have brought me farther than I might have otherwise gotten. One of them is an ability to be beaten, defeated, floored, then to get back up on my feet, and to try again, over and over. That\u2019s because when you suddenly come here with no training, not only in the particular project you\u2019ve been assigned but in biology in general, and you\u2019re suddenly given all these responsibilities\u2014it\u2019s been such a privilege because they gave me the responsibilities of being able to go to the meetings and make decisions with the rest of the group, and right now, for example, I\u2019m helping to write a grant proposal for something like a one-and-a-half million dollar grant. They gave me a lot of responsibilities and assumed a lot of maturity, and, at the same time, I didn\u2019t know any biology! So sometimes I would say something in the middle of a meeting, and people would look askance at me and think, \u2018\u2026What?\u2019 At some point I developed an ability to recover from humiliation, to tell myself, \u2018Ok, next time I\u2019m going to do this better.\u2019 Now I feel utterly at ease with biologists, and I love talking with them, speaking in their language. At first I had such a difficult time reading papers. Someone would give me a paper and I would sort of pretend like I had read and understood it, when in truth I found it totally opaque. Now I can read them far more easily. So, just an ability to get my butt kicked, over and over again, and get bummed out, but nevertheless to stubbornly refuse to give up, and keep pushing myself until things change. And eventually, things get better, much better. You learn, you grow, you mature.\u201d<\/p>\n

\u201cWhen you were in undergrad, high school, did you find that trait in yourself? Or did you admit that you didn\u2019t understand?\u201d<\/i><\/b><\/p>\n

\u201cSo in undergrad if I didn\u2019t understand something I was probably much shyer about it. Because I felt like I was supposed to understand, you know? Everyone else was at the same level as me. So it was very different when I didn\u2019t understand there and I felt that my peers understood something; then I knew, \u2018Oh, I better figure this out quickly because I\u2019m behind.\u2019 Whereas here, everyone I work with is at least a decade older than me. I think, by way of this position, I\u2019m by far the youngest researcher at ISB, and so that helped me momentarily justify those earlier moments when I felt I was behind. It helped me forgive myself sometimes if I didn\u2019t understand something, because I knew my being here was an unusual thing. I knew I was kind of a guinea pig. My position here was an experiment just to see, is this possible? Where you could just take some kid who studied physics and thrust him into the deep end of a research question and see if he does something significant. The defeats were definitely more frequent early in my time here, but I\u2019m resilient. I recover from them, and I think that\u2019s a good thing. That\u2019s a trait I\u2019ve learned about myself.\u201d<\/p>\n

Katherine: \u201cThat\u2019s the important thing, right?\u201d<\/p>\n

\u201cYeah, just being able to look like a fool from time to time, and realizing that anyone who never makes a fool of themselves is probably an alien\u201d<\/p>\n

*laughing*<\/p>\n

\u201cDo you remember why you went into physics? Did you have a field in mind? Or like a job you thought you\u2019d go into?\u201d<\/i><\/b><\/p>\n

\u201cI knew I liked physics, I knew that I enjoyed it. During high school I had done a physics internship, I liked reading about the lives of physicists and solving problems, but when I went to college I really wanted to study English, actually. I spent much of my time taking classes on Shakespeare and poetry and things like that. So how did I get into physics? The truth is, there\u2019s a lot about physics that I love, and certain classes that were really exciting and have been important in my scientific development. Part of why maybe I was drawn to English initially was that I felt like it came more easily to me. Physics, on the other hand, often involved a lot of difficulty and struggle for me. So I guess I was drawn toward what, to me, felt like the greater challenge.\u201d<\/p>\n

\u201cHow much do you still struggle now working every day in the lab, still answering your question?\u201d<\/i><\/b><\/p>\n

\u201cAll the time! I mean, it\u2019s different: the struggles have to do with \u2014 it depends! Once you get into the field and you\u2019ve really immersed yourself in the literature and you understand many of the techniques, new things will come to you faster, much faster than they did initially. You\u2019re able to pick things up quicker, but sometimes when you\u2019re trying to talk to someone who\u2019s doing something quite outside of your area, then you\u2019ll suddenly feel a lot less knowledgeable. As a consequence, I try to read a lot from fields that are not my own specialty. Over time, you get less intimidated! There\u2019s this basic rule, which I think has entered my head, that anything is comprehensible. If there\u2019s a paper, humans wrote that paper, and because I\u2019m a human, I should be able to understand it… Right?\u201d<\/p>\n

Lauren: \u201cThat\u2019s a quote we should put on the website\u201d<\/p>\n

\u201c*laughing* I\u2019m telling you this is not going to be a normal interview! This is not going to be \u2014 you have to let me cut out all the weird parts!<\/p>\n

*laughing*\u201d<\/p>\n

\u201cWhat would be your advice to someone who is our age who is thinking about going into a field in science?\u201d<\/i><\/b><\/p>\n

\u201cSo, I read a lot about the history of science, and about the lives of biologists, biographies, autobiographies, to know what were these people \u2014 these people who discovered these incredible things \u2014 what were they going through? You come across stories which utterly destroy notions which have infected our minds before we first go into science. There\u2019s often the idea that you have to be that kid who is winning all the science fairs and competitions and whatnot. You know, who has the best grades in science, and who goes to college and knows exactly what they want to do, and graduates with flying colors. If you look at the people who\u2019ve really made the most spectacular discoveries in science, they\u2019re an extremely heterogeneous bunch, and often their lives often did not follow that trajectory at all. Strangely, many of the people in your own life who you think are prodigies and geniuses will just burn out. They won\u2019t end up doing very much at all. Growing up, I knew people who bragged about their high IQ scores and joined weird, self-congratulatory organizations like Mensa who, now, are total layabouts.\u201d<\/p>\n

\u201cTo give you a concrete example of the kind of scientist I\u2019m talking about, take Harold Varmus, the guy who basically discovered how mutated proto-oncogenes could lead to cancer. He\u2019s a very famous biologist now. He went to college, majored in English, had no interest in science whatsoever, nearly failed his organic chemistry class, and graduated with an English degree. He then went on to pursue a PhD in English Literature. Eventually, when he realized his med school friends were having a lot more fun than he was, he decided he wanted to go become a doctor. When he was in his late 20\u2019s, he got a trainee position at the NIH as a way of escaping the draft for the Vietnam war. You might have assumed by then he knew what he was doing with his life, that his course was set. But it was at this late stage that he first started learning about biology from other scientists, and finally himself got involved in basic research. He eventually figured out something that revolutionized our understanding of cancer genetics. He\u2019s a Nobel Prize winner. He was the director of the National Institutes of Health. And there are many other similarly improbable stories I can tell you about people who went on to discover extraordinary things in science.\u201d<\/p>\n

\u201cThe point is, people can come into science from so many different directions, from so many different backgrounds; they can find out early or late. I just think, you don\u2019t need to go into college with an absolute certainty about what you\u2019re doing. You can go down many different roads before discovering what it is you actually want to do. You\u2019ll meet many people who are really certain they want to do something, and then get deeply involved in it, only to find out somewhere down the line, \u2018You know what, this is not for me.\u2019 Then they find something else. This is a wonderful advantage of living in the United States; in other countries, where cultural pressures often predestine you for one career or another, or force you to choose very early on, you might not have that flexibility. Here, on the other hand, it\u2019s not necessarily that way, and circumstances may require that you take an unpredictable, winding path towards your ultimate destination. That\u2019s a privilege inherent in this society. We\u2019re the lucky ones. Don\u2019t be afraid of uncertainties. Take the plunge.\u201d<\/p>\n

 <\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"

\u201cYou can go down many different roads before discovering what it is you actually want to do . . . it\u2019s often an unpredictable, winding path.\u201d \u201cWhat is your current project and position here at ISB?\u201d \u201cI\u2019m an ISB fellow. I graduated from college a little over a year ago with a degree in physics, […]<\/p>\n","protected":false},"author":22,"featured_media":0,"parent":44,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"jetpack_post_was_ever_published":false,"footnotes":""},"class_list":["post-1132","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/P91cRS-ig","_links":{"self":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/pages\/1132","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/users\/22"}],"replies":[{"embeddable":true,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/comments?post=1132"}],"version-history":[{"count":39,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/pages\/1132\/revisions"}],"predecessor-version":[{"id":1960,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/pages\/1132\/revisions\/1960"}],"up":[{"embeddable":true,"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/pages\/44"}],"wp:attachment":[{"href":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2017\/wp-json\/wp\/v2\/media?parent=1132"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}