{"id":113,"date":"2021-07-22T00:11:32","date_gmt":"2021-07-22T00:11:32","guid":{"rendered":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2021\/?page_id=113"},"modified":"2021-08-21T08:29:04","modified_gmt":"2021-08-21T08:29:04","slug":"andrew-baumgartner-phd","status":"publish","type":"page","link":"https:\/\/baliga.systemsbiology.net\/see-interns\/hs2021\/minds-of-isb\/andrew-baumgartner-phd\/","title":{"rendered":"Andrew Baumgartner, PhD"},"content":{"rendered":"\n
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In this down to earth interview, intern partners, Kalea and Yannell, got to talk with Dr. Baumgartner, a theoretical physicist in the Hadlock Lab at ISB. He discusses various aspects of his job, his hopes for the future, and provides relatable advice for anyone in or aspiring to be in STEM or medicine:\u00a0<\/p>\n<\/div><\/div>\n\n\n\n

Can you talk a little bit about what a theoretical physicist does. What was your journey to becoming a theoretical physicist and what inspired you to pursue this as a career? <\/strong><\/p>\n\n\n\n

It was probably around high school, junior or senior year, when I was really kind of thinking of what to major in in college and what kind of career to go through. I\u2019ve always really loved the stars, looking up at space, and all the constellations. My mom is a science teacher, so growing up she would always kind of hammer that stuff home for me. She really wanted to be an astronomer, so that kind of sparked my interest in science. I started taking more math classes, AP Calculus, AP Physics, and I was really enjoying them. Then I went to undergrad and started studying physics full time. It went well, I luckily had a really supportive and small department at my undergrad, so it really fostered a lot of personal interest in various fields of physics. It all started liking space stuff and then I kept thinking deeper and deeper about astronomy and it all came back to Physics! Then the more I learned about quantum mechanics and string theory I was like \u201coh this stuff is so cool!\u201d<\/p>\n\n\n\n

What a theoretical physicist does in a physics context is use whatever mathematics is at your disposal to understand the mechanics of the universe at a fundamental level. Really, what that means is studying matter and energy in various forms. Those are the two main drivers, everything kind of boils down to that. There\u2019s a number of different types of theoretical physicists too. There\u2019s people who would build mathematical models to describe phenomena that people would observe in a lab (which is more similar to what I\u2019m doing now). In comparison, what I studied in grad school was more abstract physics. It was more using math and manipulation, of not only using calculus and differential equations, but a lot of higher pure mathematics such as differential geometry, topology, and group theory to really gain new insights into the physical world through the mathematics alone rather than using math to explain something that came up in an experiment. There\u2019s kind of a flip side there. <\/p>\n\n\n\n

How do you apply your theoretical physicist background in physical and mathematical principles into your current work with biology and medicine?<\/strong><\/p>\n\n\n\n

Obviously, being good at math is a strong advantage to that. Now I do a lot of statistics and machine learning which is different math than what I was doing before, but it all comes from the same place. Definitely having a strong mathematics education helped me land this job for sure! As far as philosophy for approach to problems, it\u2019s much different than bio. Most biologists and people in medicine study the interacting parts of the body such as how Rna gets translated into protein, what different genes do and how that might affect pathology of certain diseases, but there\u2019s a whole lot going on. Biology and medicine is very very complex and complicated. Physics on the other hand, especially the physics I was doing, while it may sound very hard and complex, the ideas are actually extremely simple. That\u2019s kind of why you can do theoretical physics, because you have a strong set of really simple kinds of baselines to go off of. Then as you go up in length scales, let’s say, going from nuclei and atoms to molecules to biomolecules to DNA, it just gets so so so complicated so fast that those core principles that allow you to do theoretical physics kind of don’t really help you as much anymore. Thus, what I really try to do is bring it back to that. I try to approach problems by looking at the simplest baseline. What are the simplest variables and assumptions that I need to kind of explain what is going on in this problem.  That is really where my physics education kind of seeps into what I\u2019m doing now. I have a number of friends who also study biophysics that I met in grad school, and one of them put it really kind of perfectly in that <\/p>\n\n\n\n

As a physicist with a physics training going into biophysics you kind of learn to filter out all the noise and whatever you don\u2019t necessarily need to solve the problem at hand.<\/span><\/strong><\/p><\/blockquote>\n\n\n\n

I think that is an invaluable lesson that I learned in my education. <\/p>\n\n\n\n

Can you describe your current research projects in the Hadlock Lab and how they contribute to what is being developed such as new technologies, cutting edge research, etc.?<\/strong><\/p>\n\n\n\n

This is also kind of motivated by my physics background because obviously in physics things move through time. We\u2019re all moving through time. Most of the things you do in physics is time dependent. Through physics, you learn how to study the evolution of systems through time. Really, energy when it boils down to it is fundamental to how we move through time. So where I was coming from, time played an incredibly important role in everything I was doing, but coming to once again biology and specifically the medicine we do here is the time factor. Things are already so complex when you\u2019re dealing with static data and so kind of bringing in time, how systems will evolve over time, how cells will differentiate, how different diseases take hold in your body, the temporal aspect is incredibly difficult to deal with. I\u2019m hoping and kind of what I really want to do, is kind of focus on these temporal aspects and how do you put into context certain longitudinal data and extract time dependence from it. <\/p>\n\n\n\n

Currently, I\u2019m working on a project with Jenn that is doing exactly that. I\u2019m looking at the Electronic Health Records and what I\u2019m trying to do is infer trajectories of vital signs or lab results, so you that you can really see that if you\u2019re hypothetically sick, how your blood pressure changes over time or how your pulse changes over time, and is it different for different diseases, etc. Dealing with the EHR in particular is incredibly difficult because it\u2019s not an easy data set to work with because there\u2019s a lot of missing values due to it\u2019s sporadic nature. In EHR there\u2019s a lot of irregularity in how the temporal aspects of the data is collected which makes it hard to do analysis on. <\/p>\n\n\n\n

One of my projects is attempting to kind of untangle that and give everybody in your data set (all your patients) kind of a similar temporal profile so it\u2019s easier to compare things across the board. I\u2019m also working on another one that deals with Alzehimers disease, which is actually worked with people in the Hood-Price Lab, but I\u2019m also trying to use not so much the same ideas, but the tantamount concept of velocity. There\u2019s a lot of work that\u2019s been done in recent years to kind of bring these ideas of velocity into the biological domain so you can kind of see and visualize how your cells can change and stuff like that. We\u2019re still kind of exploring things and I\u2019m still kind of running some data, but we\u2019re trying to use these ideas of Rna velocity to understand how different cell types are implicated in Alzehimers disease. Those are kind of the two main projects and I\u2019ve also got things in the wings that are kind of half baked ideas that are in various stages of becoming projects for real.<\/p>\n\n\n\n

What research do you hope to continue or start in the future of your career?<\/strong><\/p>\n\n\n\n

There\u2019s a ton of different tools, mathematical frameworks, and ways to analyze data that I just want to apply to some sets and see what happens! You know a lot of it boils down to this time dependent concept still. It gets a little more tricky when you\u2019re dealing with populations of people for individual counts of Rna because there is so much fluctuations and variance in your data. It\u2019s so noisy that it\u2019s kind of hard to look at an individual’s profile and really get a sense of a deterministic trajectory. For example, I do something over here and there\u2019s a predefined way of telling what it\u2019s going to do over here in a year or something. That\u2019s really hard because these are such noisy systems. <\/p>\n\n\n\n

Luckily, there are certain frameworks that allow you to instead of studying an individual’s profile, you can study probabilities. You can build models that determine what\u2019s the probability that I\u2019ll be sick, what\u2019s the probability that I\u2019m going to get better, and things like that. From these, you can shift from saying \u201cOkay if I give you this medicine you\u2019re definitely going to get better\u201d to \u201cIf I give you medicine, there\u2019s a probability that you\u2019ll get better in two days, the probability increases in four days, and it decreases in eight days\u201d or something like that. It\u2019s actually a pretty big shift from understanding and analyzing systems in the first way versus the second way. So, the projects I want to get going on are kind of more towards that second way and really kind of looking at these probabilities and the ensembles of the patients as a whole to not tell you exactly what\u2019s going to happen, but give you a list of likely outcomes. <\/p>\n\n\n\n

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Interns Yannell (upper left hand corner) and Kalea (bottom middle) with Dr. Baumgartner (upper right hand corner).<\/span><\/figcaption><\/figure><\/div>\n\n\n\n

What is an ugly truth of your research\/job and what are some ways that you\u2019ve found help you navigate through that? <\/strong><\/p>\n\n\n\n

Oh, I can break that down into a couple of different things. There\u2019s ugly truths about data and that is usually, especially EHR, things are not really recorded uniformly, they\u2019re not inputted uniformly, it\u2019s very noisy like I said, there\u2019s a lot of missing data, etc. It is really kind of hard to deal with that stuff. People in the lab and elsewhere have come up with great ways to do that, but once again it kind of makes it difficult for this kind of personalized trajectory approach to deal with. There\u2019s also a lot more software debugging and just general computer nuisances that I didn\u2019t really have to deal with in my former life because I wasn\u2019t doing so much computer work, but that definitely is a learning curve to get used to. For example, how to troubleshoot and debug code and install packages and stuff like that. It can really be a pain in the butt. Part of living in the 21st century that\u2019s nice is that there\u2019s so many options for things, like you have many different kind of platforms that you can run your code on, but what is unfortunate about capitalism is that they\u2019re all competitors, so a lot of there platforms are very different. If you want to use them, you kind of have to relearn all the different features for one platform.<\/p>\n\n\n\n

Those are kind of typical nuisances, typical hurdles, and there are of course the environmental hurdles. Everyone at ISB is really great, but part of the ugly truth about being a scientist, especially one of the young scientist in the field, is dealing with imposter syndrome, constantly kind of dealing with the competitiveness of the field, feeling like you\u2019re not good enough, trying to keep up, etc. Those definitely take a toll on your mental health and learning how to compartmentalize those aspects of the job and deal with them in a healthy way is difficult. It\u2019s something that a lot of people have to learn. Luckily, we have a really great group and Jenn is an understanding boss, so there\u2019s not so much external pressure where it\u2019s kind of really crushing down on your mental health, but it\u2019s more like you know \u201cpublish or perish\u201d type of deal. That\u2019s kind of always living over your head. If you want a career in this stuff, you\u2019ve got to be grinding, but you know “do you have to be grinding?\u201d I don\u2019t know, maybe you just got to be really efficient and good at your work. It\u2019s definitely hard to strike that balance and it\u2019s something if you\u2019re going into STEM or medicine you\u2019ll have to tackle with down the line. But, I wouldn\u2019t worry about it too much until you have to. Meanwhile just have fun because that\u2019s what life is all about. <\/p>\n\n\n\n

Where do you hope to see your field go in the future\/what do you hope to see change over time?<\/strong><\/p>\n\n\n\n

I think the biggest thing I want to see change is definitely more diversity and inclusion in the fields. Historically, access to higher education has been reserved for few privileged individuals and people who generally look like me. That\u2019s not how you foster a good kind of scientific environment. The ideal goal would be to have equal access for everyone and everyone to have a chance to succeed in the fields they want to succeed in while not being hindered by jerks at the top. Aside from that, which is obviously super important, is having a variety of different viewpoints from a variety of different people from different backgrounds. This will help inform important research questions that help solve problems or answer questions that will help different communities that people like me might not necessarily know because we\u2019re not existing within them.<\/p>\n\n\n\n

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I think it\u2019s definitely for the benefit of humanity as a whole and science as a whole to have as heterogeneous of a scientific population as possible, so that we can just kind of tackle all the important questions from everywhere around the world and provide equal access to everyone.<\/span><\/strong><\/p>Andrew Baumgartner, PhD<\/span><\/cite><\/blockquote>\n\n\n\n

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I think it was a lot worse in physics than it is in bio from my experience in terms of diversity, but I really hope going forward that a lot more energy and resources will be allocated to increase that diversity at the top.That\u2019s kind of the main thing. As far as scientific questions, where the scientific questions are leading, you know, I just hope that important questions are being answered. I don\u2019t really know\/think I have enough knowledge at this point to know what those questions are, but yeah. <\/p>\n\n\n\n

How has COVID-19 hampered or enhanced your research\/job? <\/strong><\/p>\n\n\n\n

I actually got this job during COVID-19. I got hired back in November, so you know it was kind of weird being hired to a new job and not having to go onsite somewhere and talk to people in person. It was kind of isolating at first, but at the same time, because of the nature of my work in grad school I was kind of used to it. I came from a small research group and I was my advisor’s only student. It was in a small group and there was some collaboration, but a lot of it involved reading, doing math, writing a little computer code here and there and that was kind of isolating in and of itself. I was kind of used to working alone and working in isolation, so in that regard COVID didn\u2019t really change that much, especially as a theorist or now someone who writes more computer code. I don\u2019t really need to go into the lab to do it, I can just do it on my laptop from anywhere. I guess one thing I really miss is that I used to go to a lot of coffee shops and work. Obviously I haven\u2019t done that in COVID, so that would be a nice thing to do when 4 oclock rolls around in the afternoon and I\u2019m kind of sick sitting at my desk in the office. Having a change of scenery and being surrounded by other people just living their lives is kind of refreshing and it gives me a little more energy and helps me focus. I guess now that places are opening up again I could do that, but you know I\u2019m still kind of iffy. <\/p>\n\n\n\n

What advice would you give to high schoolers or anyone else who may be hoping to pursue a career in healthcare or the STEM field?<\/strong><\/p>\n\n\n\n

I would say, first and foremost, time management is a huge one. This kind of goes back to what I was saying about the fields being very competitive in the first place. As long as you manage your time well during the day and in college, getting all your work done and studying hard and all that stuff, you will be able to have a good balance between your work and life. This is super important because having a life is fun, but it also informs the type of work you do and the questions you answer. If you go out and interact with people, you kind of know what people who aren\u2019t scientists and specialists care about. This is important especially in being able to communicate scientific ideas and stuff to other people!<\/p>\n\n\n\n

I would say managing your time well and being able to do both good and hard work and still have a life and have fun is some of the best advice I could give.<\/span><\/strong><\/p>Andew Baumgartner, PhD<\/span><\/cite><\/blockquote>\n\n\n\n

Sometimes you can\u2019t always do that because you\u2019re under pressure or whatever, but trying as hard as you can is also good. Another one would be don\u2019t compromise who you are for the sake of a career. I think that is important for any career. It\u2019s important to kind of not change who you are and how you operate as a person just so that you can get a job or appease your boss or something and that\u2019s true across the board with any job. People like us, we don\u2019t really consider a research institution to be part of the capitalistic machine but it is in some sense. There is some external spending to benefit corporations, and it\u2019s not worth giving your life away to be a cog in that machine, even if it seems to be more important because it\u2019s medicine or science. I still think having a life is the best thing you can do. Don\u2019t compromise who you are and don\u2019t compromise all your time and within those kinds of restraints just do the best work you can and work as hard as you can.I think you\u2019ll find the more you have a normal life and hangout with friends and family and stuff like that, the harder you will work during the day. Part of it being because you know you compartmentalize that time to be like these 8, 9, ten hours, whatever I\u2019m working today, I\u2019m getting it done. Then I\u2019m going to go home and have fun. I think that\u2019s very important for individual mental health and the work you do as a scientist.<\/p>\n\n\n\n

Link to ISB Profile:<\/strong> Andrew Baumgartner, PhD | The Hadlock Lab (isbscience.org)<\/span><\/a><\/p>\n\n\n\n

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

In this down to earth interview, intern partners, Kalea and Yannell, got to talk with Dr. Baumgartner, a theoretical physicist in the Hadlock Lab at ISB. He discusses various aspects of his job, his hopes for the future, and provides relatable advice for anyone in or aspiring to be in STEM or medicine:\u00a0 Can you talk a little bit about what a theoretical physicist does. What was your journey to becoming a theoretical physicist and what inspired you to pursue this as a career?  It was probably around high school, junior or senior year, when I was really kind of thinking of what to major in in college and what kind of career to go through. I\u2019ve always really loved the stars, looking up at space, and all the constellations. My mom is a science teacher, so growing up she would always kind of hammer that stuff home for me.…<\/p>\n

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