Ologies with Alie Ward - Systems Biology (MEDICAL MATHEMATICS) with Emily E. Ackerman

Episode Date: August 4, 2021

Biological mysteries solved with numbers! Graphs! Patterns! Data points! Systems biology! You never knew it existed, yet it’s keeping us alive. Systems Biologist Dr. Emily E. Ackerman join to chat about why the field appealed to her, how her work shifted during the pandemic, why she wants to scream at Excel sometimes, how computing might replace specific types of animal testing, accessibility in STEM, the immune system, why she loves being a disabled scientist and advocate, the ethics of CRISPR, and some really nice guy named Doug. Dr. Emily E. Ackerman’s website emilyeackerman.com Follow her at Twitter.com/EmilyEAckerman More links at www.alieward.com/ologies/systemsbiology A donation was made to HEARD: https://behearddc.org/ Sponsors of Ologies: alieward.com/ologies-sponsors Transcripts & bleeped episodes at: alieward.com/ologies-extras Become a patron of Ologies for as little as a buck a month: www.Patreon.com/ologies OlogiesMerch.com has hats, shirts, pins, totes and now… MASKS. Hi. Yes. Follow twitter.com/ologies or instagram.com/ologies Follow twitter.com/AlieWard or instagram.com/AlieWard Sound editing by Jarrett Sleeper of MindJam Media & Steven Ray Morris Transcripts by Emily White of www.thewordary.com/Support the show: http://Patreon.com/ologies

Oh, hey, it's your co-worker that you had a dream about, who you will never tell what the dream was about. Allie Ward, backologies. This is an ology you've likely never even heard of. It was invented just around the turn of the century when Y2K fears were big, eyebrows were thin, systems biology, it's only been around about 20 years in name, and the National Institutes of Health says that different labs define it differently, but at its core. You ready for this?

Here it is. This is an approach in biomedical research to understanding the larger picture, be it at the level of an organism tissue or cell by putting its pieces together. It's like detective work, but with math and computers and graphs and stuff. I'd put money on at least one of you who have never heard of it before, falling in love with it and becoming this type of ologist in the future. But before that gamble, let's thank everyone at Patreon.com slash ologies for supporting the show.

It costs one cool American dollar a month to join, and you can submit questions. Also thanks Spotify for having us as your number one science podcast on there. Hot dang. Whoever thought, not me. We stay up in the charts thanks to every kind soul who leaves us ratings and reviews, like this one from Will Gollahue on Apple Podcasts who wrote, this show's like a red carpet premiere with scientists instead of celebrities, and I just can't get enough. I'm glad you can't because we have more for you in this episode, Will Gollahue.

Okay, so this ologist and I, we met via Twitter. Last year she wrote some really thought-provoking articles on the robotic scene in Pittsburgh and how errant delivery rovers cause a lot of problems for wheelchair users like herself, and she has written extensively about accessibility and STEM. She has a PhD in chemical engineering where she used data and math and modeling to figure out what the fuck happens in the body when we're infected with a virus like the flu and what drugs might work best for whom. We recorded this while she was still in the throes of finishing her dissertation, but

now this doc is off to Cambridge to start post-doc work at a little place called Harvard Medical School and it's the systems biology department there. She is smart, kind, funny, brilliant, and not at all a slacker, more on that later. So count your lucky stars. We're about to learn about mathematics, computational science, excel curses, career pivots, accessibility, identity, genomics, crisper, soapboxes, science, and more with advocate, scholar, and systems biologist Dr. Emily Ackerman. Her pronouns, she, her, cool.

And now you are a systems biologist, correct? I am. I mean, by my own definition, I'm a chemical engineer by training, but most chemical engineers don't want to do chemical engineering. So we do other stuff and my other stuff of choice is biology. When you say chemical engineering, what exactly does that encompass? Chemical engineering is very broad. We always think of it as the movement of heat, mass, and energy.

It's been around forever and it hasn't changed in forever. So like the core curriculum that you learn is like transport and thermodynamics and that hasn't changed in like 100 years. So I'm in a more biological area. There's also the energy area where people do alternatives, kind of energies and fuels, batteries, and then they also do things like solar or biofuels and things. So her chemical engineering department focused on petroleum and fuels, but she didn't work with petroleum.

Our work involved more living things. But you've always loved biology too? Yeah. Yeah? Yeah. I love, it's so cool, it's such a mystifying place, at least to me. Where did that start? Was it bird watching or was it documentaries about bugs or where did you start, did you

have a microscope growing up? Where did you start to get really interested in the natural world? So being disabled and having like medical conditions, I've always found the body very interesting and kind of understanding the ways that mine is different has led me to kind of explore a lot of biology from like a younger age, I think. Once I got to kind of high school when you really start learning and deciding what you want to do, I guess we forced 16-year-olds to decide to do it their lives. It was like a very interesting thing to me, but the definitions of types of engineering

were like a real mystery to me and I think for most people. So I chose chemical based on the fact that I liked chemistry, but I didn't want to do like lab science, so I thought, okay, I'll do more math. She says at 16 she thought, hey, math sounds like a good thing to commit to, math will always be there for you and math is in everything, it's all around us, like ghosts who make sense and have her back. So I went into chemical engineering and then slowly migrated more toward biology when I realized it was way more interesting.

And you, in order to be a biologist in the biological sciences, there's a ton of patterns and math and chemistry that needs understanding, right? For sure. I mean, my type of biology is like, I sat on a bench and I drew a picture of a mushroom because I'm not very gifted in the other way, but there need to be people like you who also can do applied topology and a lot of words I don't understand, which I understand on your CV and I don't even know what topology is. So how does math and systems and patterns, how do you get to apply that to the natural

world? Yeah, it's really, I think a lot about, I mean, the body specifically, the human body and I specifically work with the immune system, something that, like the rest of your body is in a very kind of precarious balance at all times. And the only time you really notice it is when it's out of whack. Your sick and your body is trying to compensate, so it starts giving you a fever and you start trying to cough and do all kinds of things to get rid of it. That's really the definitive example for me of kind of how much we rely on math to exist,

but we don't think about it. So what's happening is that really your body is the math is a spew, like things are out of balance, there's too much of something or too little of something, or even it showed up six hours too late, whether it's your T cells or something that you need to fight an infection, or even that a gene doesn't get turned on. It's really an interesting kind of view of math and we can use math to describe all of the relationships within ourselves and all of the interactions happening that kind of keep us alive, which is really, really cool.

I heartily agree on that staying alive is on my coolest. And if someone isn't sure what systems biology is and you have to describe it to them, how do you put such a big thing in such a small nutshell? Yeah, systems biology is, I like to think of systems biology as the Frankenstein of biology. It's very young, most definitions you would probably see like popping up 20, 30 years ago. It's really the result of having huge amounts of data and needing to process it and trying to do it in a way that you get a better system view.

So for example, you can invent algorithms to understand it, you can make models of it, and the goal is that you get kind of this picture that you wouldn't get from just doing an experiment. So if I want to understand the immune response, which is what I do, I take data from real mice and I try to represent it with maths or to work backwards if I don't understand really what's biologically happening. Maybe I can find some math that fits it and I'd say, oh, well then this must be what's happening.

It must be these two things interacting, causing maths. And one of the great things about what we do is that there's so much data out just in the world that if you have questions, you can sometimes just find data to help you answer them. And that's kind of what you see happening with COVID. There's this real huge emphasis on making data publicly available and easy to use, which is a great effect on the kind of scientific endeavor that I love. So Dr. Ackerman had analyzed infectious disease and influenza strains, but while getting her

PhD at the University of Pittsburgh, she did a little pivot to a different virus you probably have not heard a lot about. It's called SARS-CoV-2, just an intro to it, JK. I was eating fistfuls of sourdough all through 2020 and watching people make out on Outlander, but she was spending the pandemic trying to help us understand the pandemic while getting a PhD. I used to work only with the flu. Now I work with COVID-19.

Heard of it? Heard of it? Making headlines? Yeah. I have seen that. And so basically, my group deals with viral respiratory infection for the most part. I have kind of two major kind of projects. The first is trying to identify important proteins that we could use as drug targets.

And to do that, I use network topology and analysis, which is a very large-scale zoomed out view of a cell. And then my other project is a very specific zoomed in view where I write kind of mathematical equations to try to understand the dynamics of the immune response. So the timing and the kind of magnitude of response and how that differs between, say, strains of the flu or between males and females or any kind of relationship in hopes of better treatment strategies, better understanding of diseases of the flu, because frankly, we don't have a great idea of what's going on. And just kind of better understanding so that we can better address viral infection.

How was that pivot? How much of you had to pivot your research to COVID? Yeah. Which, by the way, that's amazing that you're working on it. Thank you. Yeah. Thank you for doing that on behalf of me and literally the world. What was that pivot like for you?

Was it exciting? Was it daunting? Was it really different from the flu? It was a lot at once. When it hit, I realized that I could very easily apply the network study methods to SARS-CoV-2. I did it, and it was just this giant whirlwind of trying to get things out. No, it was very stressful to be working under that kind of time-restring, kind of the magnitude of this problem.

It's kind of overwhelming. I know it. But it's really exciting at the same time to be able to help and contribute in the best way I know how. It's been a really interesting make women's out of women aid opportunity. That's not even the first. What is it? Make women out of women.

I was given women's. Tomato tomato. When life throws tomatoes at you, make salsa. Science is just all about confronting setbacks, head on, piecing things together with the info we do have and adapting to new circumstances. That's why it's high drama behind the scenes, and we love it. The problem with such a novel virus emerges is that we don't even know what it looks like.

It's different for every virus. They all have kind of different evasion mechanisms or ways that they try to hide themselves. What does your work look like? If you were to say, take your oligies host to work day, what is it? Is it like, I picture? Okay. Tell me if I'm wrong. I love it.

I picture that you have like six computer monitors and it's like when you walk into like the control room at NASA, and it's all spreadsheets and like minority report like, and you have maybe several different input devices like mouses or keyboards or lasers, and it's just numbers flying by. If I were there, I would just be trembling in a corner being like, how do you keep track of all the numbers? Is that correct? Do the same next time.

I've got two monitors, very high open moral, two monitors, five cups of coffee, and two keyboards because I spilled a full cup of coffee on my laptop last year. So that's not great, but yeah, I get told a lot that it looks very scary because I have learned to code from like, an old man who's been coding since coding existed, and so I code like in the terminal and like the worst visual way and it looks very scary and people tell me all the time that it looks horrifying, but yeah, it's, you're not too far off, except it's less, less fun than you would think. Okay.

Just telling us back like $100,000. Okay, so you're taking some funding away. Who was the old man that taught you to code? I picture like an old sailor in a park with an ancient laptop. I didn't internship with a pharmacy with a couple, and he's very much like the dad is dad, like every dad. He's just, he's just Doug, you know, kind of Doug. If anyone out there knows a very paternal guy named Doug who has taught people to code,

tell him I love him. Am I exaggerating? No. I love him. Yeah. I miss him. Do you dream in code at all? No, but I have dreamed about COVID and I've dreamed about like just school things in general.

It's a terrible experience. Oh no. Let's move on from nightmares to flimflam systems biology style. I guess like that we spend all of our time like actively coding is like the biggest thing. I spend most of my time either waiting for the code to run, like days, or googling the same error code in different ways, or downloading Excel files of data and then searching for the one gene that is the same as a date. So Excel like converts it to a date and then you end up with like errors in your, in your

code because, yeah, except for is my mortal enemy. Of course I had to look this up, but sep4 means septin4 and it's a protein that in humans is encoded by the sep4 gene, which also reminded me of the meme, which is a Venn diagram of Excel and incels both incorrectly assuming everything is a date. It hurts. So good. The amount of time I spend actually writing code is very, very small. Are there moments where you run data or run an algorithm or applied something computational

to see if it fits with data and it works? Like does your screen light up like in gold glitter? Like what happens when that works? I stop crying. Yeah, I mean, there's a problem in systems, biology and more computational fields where you don't always have validation for your answer. Maybe you need more data to prove that it's correct or you have to very carefully design training sets and things to prove that you have actually done something so it can feel

a little unrewarding, but sometimes it's the other way around and you're fitting to data that already exists or you have a way to validate it. So sometimes it just points you down the path, but you're not quite to the destination yet, but at least you know that your work isn't a mess. Are you a person that is super organized and analytical in the rest of your life? Are you like a person like friends go to with computational questions? Or are you like, I save that for work and I let the rest of my life be loosey-goosey? I'm a little bit of an unorganized person.

I'm a very stuck food person. I love having a schedule. I love having rules to follow. I'm that kind of person. At least rules have benefited me, but I'm also known as like, not in a serious way, but like the one who does math for a living but isn't very good at it. Wait, what? But I'm always doubting my ability to do math.

Do people ever tell you to stop doubting your ability to do math because you're probably so much better at it than other people? Yes. I need good constant reminders like, where am I? How I got this far? You mentioned something too about disability in STEM. And I'm wondering, is there anything that you wish you knew kind of coming up to do?

Do you wish other people in STEM with maybe any kind of disabilities knew? Yeah, so many things. I think... What do I want them to know? Sorry, that's a big question. No, I mean, this is what I really am so proud to know about. When I was... When I went to college, I was very unsure, like most, I think, college students are.

What they want to do or what they care about. I think one thing that is STEM particular is the fear that you... That STEM isn't made for you in a very physical way, but also in a... There's this emphasis on working long hours, on kind of devoting yourself and therefore your body to the cause, the STEM cause you've chosen. And I guess what I would tell people is that that's unhealthy and false. There's so much of a push to be a scientist or engineer and to devote your whole self and it should be first.

And I think what we know in the disability community is that our bodies and our minds have to come first and you can't do the science if your body's not there, right? So, and if you really want to be there, there has to be a way. So if you need to change your schedule, if you need to ask for accommodations and things because you want to be there, that's... You are so in the right to do that and there's always a way that you can get to it. When I... The reason I do computational work is that I am very weak.

I'm very small. I weigh like 50 pounds. I can lift like half a pound to a pound on a good day. And a lab is just not made for me. And in any way, it just will never work. And I knew that and it's part of why I chose engineering. And when I got to college, I was just by chance kind of complaining to a professor about how I was a little bit upset that I felt that there was no opportunities for me to do research

because it felt like my peers were doing research that was going to get them a grad school or a job and that I wasn't able to do it. And he was like, well, don't you know anything about computational work? And I was like, nope. Nobody told me about that. And he was like, oh, you got to meet this guy. And so I met my undergrad advisor, Dr. Kurt Brennan, who does computational chemistry. And it was nothing like anything I'd ever learned, but I could do it anywhere, anytime of day.

You didn't involve lifting anything except my computer. And it was such an opportunity that I didn't know existed. And so I didn't know anyone else that was disabled, students or faculty. And so I really just had no idea that there's this whole world out there when I consider way more accessible science. And so one tip I would definitely say is to explore computational science, et cetera, cool area. And it's so much more accessible with the timing and the physical demands of it. And it's super cool, and I want everyone to do it.

That's so wonderful that just someone suggesting something like that can, you know, it's so funny that those moments in our lives are like, wait, I could do that. Yeah, and if I knew someone who was disabled, it probably would have been way more clear to me. Well, at least I would have had some kind of hope that I could do it in the same way that my peers were just going up and asking for lab positions. I am really passionate about not only like getting more people into STEM, but making it a place they can stay. And foster the next generation of kids like I was who had no idea what the future could even look like, I guess. Yeah, it's so important that we make it equitable, because right now it's definitely not. Yeah, anything that would make it more equitable, any kind of moves that others could make or that you would love to see made?

Yeah, one big thing is just generally thinking about your lab space or your lab policies, or your classroom policies can be designed in a way that make it easier for disabled students and researchers to exist in your space. So for example, if you're teaching class and your policy in this strange pandemic time is that you have to always have your video on and you have to show up to every Zoom or you drop a letter grade, right? It's really difficult for a lot of us to attend a grade lecture on time when there's no difference between watching a recording of it and attending in real time. Or if your lab space, most lab spaces are disgustingly accessible. But what can you do? You can not load all of your pipette boxes and glove boxes and everything right inside the door so that I can't even enter a lab. And just a quick side note on identity and disability.

So Dr. Ackerman says she prefers identity first language, i.e. she is a disabled person rather than saying a person with a disability. And this discussion comes up in the disability community a lot. Many autistic folks prefer identity first, autistic person rather than person with autism. So deaf person, blind person are also common choices. And Dr. Ackerman pointed me to a really great article written by Molly Callahan for Northwestern University, which explains, quote, for people who prefer person first language, the choice recognizes that a human is first and foremost a person. They have a disorder, but that disorder doesn't define them. And for people who prefer identity first language, the choice is about empowerment.

It says that autism or a disability isn't something to be ashamed of. So now you know what person first versus identity first means. And when in doubt, just ask someone if they have a preference. Point being, disabled is not a bad word. It's especially great to know this on the heels of July's Disability Pride Month, which celebrated the ADA or Americans with Disabilities Act, which is an example of person first language on that one. But major point being disabled is nothing to ever feel ashamed of.

As my good friend TV writer, David Radcliffe says, quote, disability will be a part of everyone's life, whether through age, illness, or accident. So we are either disabled or we are temporarily non-disabled. And I love that sentiment. It's really true for everyone. And also David Radcliffe is David Radcliffe on Twitter, by the way. I'll link his Twitter on my website. It's great.

And it's also always wonderful to read articles by or follow folks on social media who are passionate about communicating these issues. Honestly, the best prevention for accidentally saying ignorant shit is just to learn and listen more in the first place. Boom. There are ways that you can minimize the kind of effect that you have on your surroundings. Because I think what people assume is that when they see someone who is disabled, they say, oh, they're disabled. But the truth is, you can't always see it. In fact, it's a lot of the time it's very difficult to see when people need you to change the way that you kind of operate.

And so instead of waiting for someone to ask for accommodation, just providing it is the best way to ensure that that person gets what they need without putting the onus on them to ask for. You could change the way that you operate from your kind of position of power. That makes so much sense and thinking about it ahead of time instead of waiting until you've put someone into crisis. Right. Sort of. And relying on that person to be able to convey to you that they need you to change is an even bigger barrier. A few, like, Twitter is popping up recently of kind of community building for specifically disabled and STEM folks.

And they're great. I love interacting with other people. Listeners, patrons have questions for you. Can I lob some at you? Ooh, yeah. Okay. Side note, those Twitter hashtags are disabled and STEM. That is a great one.

And you can follow disabled STEM, that account to listen to that community and to get more resources and speaking of resources. Before we lob questions, let's toss some money at a cause of theologist choosing. And Dr. Emily E. Ackerman asked that it go to herd, which she told me via email is an abolitionist disability org that does a lot of work around the incarceration of deaf and disabled people. She says, our current carceral system is built from and runs on ableism and disproportionately affects the lives of BIPOC disabled people. And herd does an incredible job of centering disability justice with abolitionist thinking. And they have trainings called the revolution must be accessible that I would urge people to take a look at. She says, especially those organizing in their own circles. So that donation went to beherdc.org.

That is linked in the show notes. And that donation from oligies in Emily's name was made possible by patrons of the show and sponsors who you may hear about now. Okay. Your systemic biological questions. Let's start basic. Dina wants to know, do you see chaos in the mathematical models that you work with? And if so, when? Yeah.

We see a lot of noise in the models because everyone is different. So for example, I use data from like triplicate mice experiments. Okay. Side note, I looked up triplicate mice and it's not a type of mouse. I found out, but rather experiments run in triplicate using mice. So more runs of the experiment means more data points. And then thanks to this episode, I now picture data points like coins or mushrooms in a video game. Just like ping, ping, ping, ping, ping, like get that data.

Just shove it in your pockets. Also, if you're still staring off thinking about the mousies, we address perspectives on animal testing and its future later in the episode. Anyway. And even within those three mice, there is so much variation and it causes a lot of mathematical issues. A lot of unstable systems. The nature of biological systems is feedback. Everything is a feedback system. And so when you make very small changes to components of that system, you can get some really out of proportion results.

And so yeah, we see a lot of problems with the noise and things like that. That chaos and noise are sort of correlated. Yeah. I don't know exactly the mathematical definition of chaos at the top of my head, but I'm willing to back that. But we see it. Chaos. Noun. Behavior so unpredictable as to appear random, owing to great sensitivity to small changes in conditions.

So little stuff makes things go sideways. The shorthand is the butterfly effect. Honestly, chaos is in everything, especially our bodies. Right. And Caitlin Allen, first time question asker, wants to know, and this is specific, but if you have a favorite mechanism in organic chemistry. Oh, I don't. Because I'm very fast on organic chemistry. It's funny.

There's this kind of like assumption that if you're a chemical engineer, you must be very good at like advanced chemistry. I haven't thought about chemistry in years, except for when I think about like protein binding, but what's a very specific kind of chemistry. If you're like, I need a whole episode about molecular proteins and also being a queen of psychom. See the molecular biology episode with Dr. Raven, the science Maven Baxter. Okay, onward. I thought Joe Porvito has a great question in it was second by Will Pliwa, Erica Perriandri, and Onyx Casale. Wanted to know if we could use viruses to cure a disease rather than cause one. Yeah, there's some really cool work that goes on with this.

I think it's called Uncle Virology or something. I made that word up, but it's probably close. It's the idea that you can treat tumors with modified viruses. So what happens when you get a virus enters yourself is that it triggers this kind of series of events where your body says, Oh, I need to start fighting. You know, I gotta do something. Are we in danger of a hull breach? So it alerts all the surrounding cells with these small molecules called interferon. And they trigger all of these events that start bringing in immune cells and giving immune processes to fight the virus.

And the idea is that let's say we could take all the scary stuff out of viruses and just leave the stuff that our cells recognize and then put them in the other tumor. And our cells would say, Oh, there's something bad like we have to fight it. It would start that interferon response. But instead of fighting a virus because it's harmless, it would fight the tumor. I don't do anything like that, but I have read about it and I think it is super cool. There's lots of things you can do as far as messing with the genomics of viruses and kind of knocking out the harmful stuff and using them to deliver parts of genes or just kind of cause controlled havoc. I think it looks promising and really cool. Oncovirology or tumor virology, it is, it's a thing.

So if anyone knows of a good oncovirologist, please holler at me at your dad war. I'm all ears. Zoltan Sazi says this is very interesting and an important scientific area. And question, is it possible to estimate with epidemiologic models? I don't know why I can't say that. How likely it is for animal influenza strains like pigs and birds to cross the species barrier into humans? And if that happens, is it possible to guess how well humanity will do if another big flu pandemic breaks out? Like, is it, is that a number crunching kind of a question?

To my knowledge, no one is crunching that number, et cetera, random event. Cause it really just takes one, one event of, of mutation and then jump from the animal to a human. I'm sure statistically you could figure out some kind of estimate. This is one of those family problems where you do exactly the envelope calculations. It's like, what will be the next pandemic? You could definitely try doing that. I've never thought about it. Ah, thinking about the next pandemic.

Well, maybe let's get through this one first. I don't know. I hope everyone's out there getting vaccinated if they can, because your health is worth it. And so are others health. It's been interesting as someone who, if I got COVID, I would be in very bad shape, just given the nature of my health. It's, it's been interesting to see the way that people kind of, I guess, write off other people in their, in their estimation of danger. So they're thinking about, oh, I'll be fine. I'm, I don't get very safe usually or whatever.

But they're not giving a lot of thought to people like me who can't leave their house at all. And when they do, I'm at a super high risk and what steps they could be taking towards helping people like me or their grandparents or their mom who just had surgery or whatever. This was actually recorded before the vaccines were widely available, when the best we could do was distance and mask up and wash our groceries. And as the Delta variant picks up right now and the masks go back on, just do what you can out there to protect each other. Some of the people you're protecting are the very people working on the science to get us through this, like Emily. Just to be like, do you realize what she's doing? I'm trying my hobbies. You're like the one that's next thing at, oh, there, oh, Michael McLeod has a question, first time question asker.

What are some advancements being made now using systems biology and synthetic biology approach that may not have even been possible 10 or 15 years ago? Well, we're always kind of coming up with new kind of experimental methods that give us better data, which is a big barrier to addressing these kinds of problems. Emily says that better imaging helps system biologists have a more accurate grasp of pathologies, which is helpful for number crunching and analysis. So what does this mean for you and your hot bod? Similarly, like putting humanized versions of cells into mice or rabbits and things so that we can get a closer idea of what the human response would be in a rabbit where we can test it. Well, that's a fairly new concept that's really kind of advancing our understanding of specifically human response. And then on the computational side, the more data we have, the more advanced algorithms we can develop and the models that we build are more kind of biologically accurate, more encompassing at least. And my goal kind of in everything I do is better personalization of treatment.

So how can we better understand late stage infection behavior based on early signs or early dynamics of immune cells and cytokines and things. And in the various coronasodes we've done over the last like year and a half, which seems longer. But we've mentioned that cytokines are the small proteins that allow your cells to communicate messages to each other, essentially. And a cytokine storm is like your immune system's phone just blowing up, just going on overdrive and having system wide inflammation that occurs. And it can be pretty dangerous, especially for COVID patients, sometimes leads to organ failure. And systems biologists help figure things out like, okay, based on a patient's day two COVID data, who's going to be in the ICU on day 10 and what medications are more likely to work on a system-wide inflammatory response. So she's working on that. So people who think that math is maybe not their thing or systems biology is not their thing, it's really like essentially a crystal ball.

You're essentially like a wizard. If you can predict the future, like what's cooler than that? That's the goal. Right? It's like the magic eight ball of, but based completely on math and accurately. And it's kind of almost like waving your hands and like clearing a weird farm. And you're like, what are these two proteins doing? And then I like wave my hands and they're finding that disability. That's so cool.

Speaking of looking into the future. Oh, and I have one more question and it deals a little bit with what you were just talking about with animal models too. Two different patrons, Ruby Ostrich and Erica Perry-Andre, both asked if you see us in the future moving away from animal models by using like bioengineered human models or just by using math. And Ruby says I really struggle with science and animal cruelty. And Erica says as a vegan and a scientist using animal models kind of hurts my heart. But maybe bioengineering or systems biology might be able to kind of get around that. Will quantum computing help us solve that? Where is it going?

Do you think? We're definitely headed in the right direction, I think, as far as we're always going to need data. Well, so it depends on your kind of application. I could see some of them going much closer to no animal models. I'm thinking like if you work with a very specific tissue type and you only look at that, you could be probably much closer to going animal free. Well, it's a much harder question, but I do completely agree. And to some extent, it's difficult to put out of my head the animals that we have to use. As computational researchers, I don't have to do it myself, which I'm thankful for.

I think I'd be a big chicken. Yeah. I think I'd be a big chicken too. Yeah. And I have friends who do it. I'm like, I don't know how you do it. We really do everything with the least amount of data that we can possibly scrape by with 90% of the time because it's so hard to get data. And so we really do try to minimize the amount of data that we use for that, among my new reasons.

And I mean, as long as I've taken us on a detour to Bummer Town, what is the thing that is the most upsetting thing about what you do or something unexpected that you just hate about systems biology? Any bones to pick or any grievances to air? Feel free to have a soapbox. You know, I do have a large soapbox. So this is something that I try to be vocal about whenever I can. The pervasiveness of eugenics in disease research can be very tough to be a disabled researcher and human and be exposed to. This is a systems biology specific problem.

There's a lot of assumptions that go into biological work as far as that people with diseases would not like to be the way that they are or that there's some kind of inherent goodness in insulting people in any ways based on genetics or some inherent truth, I should say. And so it's tough to watch people who do disease research and have probably not much exposure to those people who are affected. And from an activism standpoint, it's really scary to watch a lot of movement in that direction as a positive change. For example, like last year, I think when the genetically modified children were exposed in China, I don't know if you remember when that was like a thing. But for background, they basically had genetically modified the embryos so that the children didn't have whatever genetic disorder the parents had. I mean, in the science community, that was like enough of a red alarm for people to be like, no. On the whole, in kind of the world, it got a lot of traction as like, is this the future? Are we going to eradicate disease? And it's just such a harmful mentality to think that people would be better off without their genetic disorders.

And obviously, there are things about it that are valid to think about like life-setting illnesses and things like that. That's a conversation that should be had by the people with those disorders. The harmful nature of those conversations happens when it's just the people in power doing the science or funding the science or spreading the science who really don't consult with the people that are on the other end. And when you talk to the disability community, there's this huge push for the advocacy to call out these kind of eugenics for what they are because they're so accepted by the public as something that's good because it's eradicating something that's implicitly bad to them. That we don't get hurt when we say, I don't want to be different. I don't want to be genetically modified and I wouldn't want my children to be genetically modified and things. So I do wish that people would be much more cognizant of the ableism and the eugenics that are so deeply ingrained into science. And listening for people calling them out and people like me and there's a lot of us who are actively out there yelling about it. But yeah, it's been really interesting to see the way that non-disabled people have framed the conversation about disability and genetics in a scientific way. Where can people listen to your voices and get a more balanced picture of that?

Yeah, the great thing about the disability community is that we are all super online because of the nature of our lives. We organize virtually. So Twitter is a great place. I would recommend any written piece that is written specifically by a disabled person. Yeah, and I think just being cognizant that the opinions that really matter on this debate, which should not be a debate for most people, only for us who are affected. We are the ones who matter in kind of having our voices heard. There's a lot of articles written by people who have no connection beyond understanding CRISPR and it's very disappointing to see that platform be given to them when they don't frankly know what they're talking about. This is of course a really important topic and this conversation with Dr. Ackerman really opened up my own eyes to the issue and she sent me an email after we recorded because she just wanted to expand on it and get her thoughts down. And she wrote, quote, CRISPR and gene editing are absolutely incredible scientific technologies that have revolutionized the way we're able to address biological problems. She says, I know that as a scientist there are a million ways to use it for good. However, in combination with the ableism ingrained in our societal teachings, blatant or unrecognized, it stands as a not so farfetched weapon against the identities in the lives of the disabled. The failure of the scientific community to widely condemn the detrimental idea of editing our very disabled existence and the suggestion that it represents an optimal future to do so. Combined with the very extensive history of eugenics leads me to actively fear my colleagues potential role in the downfall of the community I love so much under the misguided, ableist idea that all those with disabilities would be better off without them, she says.

The day the Nobel Prize was announced for genetic scissors, a tool for rewriting the code of life, Dr. Ackerman continues, my Twitter feed was 50% scientists who were elated and 50% disabled people who were saddened, angry and scared. The science community needs to bridge this divide and seek out voices of disabled individuals themselves, not their families, who are proclaiming their joy and renouncing the idea that there's something wrong to be fixed. If we don't have this very personal conversation now, she says, it will soon be too late. And she also sent a few great articles on identity and I'll link them on my website at alleyward.com slash ology slash systems biology that will be linked to the show notes also includes some hashtags and some articles that she recommends. So yes, gene editing on humans, not as simple an issue as just putting an Instagram filter on your vacation photos. I mean, when I say that it's very rooted in ableism in that it's a projection of like fear, I think. That's how I see it. Those people are worried about what if they had a genetic disease or what if we have a child with a genetic disease and how that would affect our lives but it's really, you know, there's, it's great.

I love being disabled. And I know that everyone doesn't and I fully respect anyone's right to say that they do or don't. But too often we don't hear the voices of people who love being disabled. So, yeah. Because we don't get to hear those voices, can you tell people what you do love about it? Yeah, I love being. I love the view that I have on life and how inherently different it is. I think that there are things that I think about all day every day as far as getting my basic needs met and how I'm going to plan my next career steps.

And like, that's the full gamut of like, you know, the most disabled thoughts are like, how am I going to pee tomorrow? Or like, do I have all the medicines I need and how am I going to get them if I can't leave my apartment to what am I going to do next year when I have to graduate? These are like the full spectrum of like, my most disabled specific thoughts to like, my most generalized every day, all of my peers have them thoughts. But I love that my view on those like, everyday questions that everybody has to answer is so tainted by my disability in a good way. It's that I'm thinking about the city's accessibility. And I'm thinking about the political climate. And I'm thinking about all of these kind of factors that I think are going to help me make a better choice, but it's because I have to think about them. It sounds like a richer experience because not only do you have to consider your needs, but it also must make you considerate of other people's needs across many different spectrums, you know?

For sure, yeah. And it's, I love the intersectionality of the disabled community. There is one of everyone and then some. And it's so easy to find someone who is the complete opposite of you and someone who shares so much with you in a way that I don't find in everyday spaces because there's just so much more to talk about. And to have an experience about. It's just so exciting to meet other disabled people and learn so much about what it's like to be them. And what about systems biology? What do you love the most? I love thinking about the scale of it.

And I've had the network project, which is very zoomed out. I look at like all proteins of the cell at once and like very generalized, yes or no, do they interact? What can we learn from that? And then I can look at just like singular interactions or a very small pathway of interactions and the details of such a zoomed in view are just so there's so many details. And you can always go smaller and there's so interconnected that on a tissue level and a whole body level, just very small changes at such a small, like micro level can cause huge differences in what our body does and how we perceive ourselves. I just love thinking about that view. Kind of the way I look thinking about space, but it makes me really afraid when I think about space. When I think about my body, at least there's like a small kind of limit that I can think about. That's funny. I found out there's a word for that called cosmic vertigo when you just start thinking about how big space is and you're like,

But as you were saying that, it was funny because I was like picturing you in this like tiny rocket ship and you're able to like go from like the outer edges of the universe to like all the way zoomed into like molecules and systems biology is essentially like the spaceship where you can just like hyperspeed and all these different perspectives are just so cool. It's very cool. You can just do whatever you want. So definitely follow Emily E. Ackerman on Twitter, although her display name I take issue with Emily Slackerman. The only bone I have to pick with you is that your handle is like Emily, it's Emily A. Ackerman, but it's Emily Slackerman Ackerman. And I was like, highly doubt the Slackerman. That's actually a very long story. Okay.

The internet troll bequeathed that to me. No. But I took it and just ran away. I was like, this is how I want to be like, I want this on my gravestone. I want to be none of this for the rest of my life. They thought they were like really burning. Actually, they gave me the greatest gift I've ever received. Emily Slackerman Ackerman.

Okay. Now I love it even more. Oh my gosh. Thank you so much for being on. I'm so excited that I now know what systems biology is and how cool it is. I hope that everybody knows now. They do. So ask systems biological people simple questions and you'll get to know your world and the

people making it better, better. And you can follow Dr. Emily E. Ackerman who is at Emily E. Ackerman, AKA Slackerman on Twitter. And her website is Emily E. Ackerman. And if you'd like to hear her on more podcasts, you can check out the Disability Visibility Project hosted by Alice Wong. And Dr. Ackerman is on episode 91 talking about disabled engineers. And I'll link that on my website too, as well as a link to Herd where we send a donation

today at Emily's kind suggestion. And we are at allergies on Twitter and Instagram. And I'm Ali Ward with 1L on both. So do be our friends. Thank you, Erin Campbell-Talbert for admitting the allergies podcast Facebook group full of very swell humans. Thanks, Bonnie Dutch and Shannon Feltas for managing merch. There are also sisters who host the podcast.

You are that, which is very funny. Thank you, Emily White of thewardery.com for making our transcripts. Those are up for free to anyone who wants or needs them. Thank you, Kayla Patton for bleeping episodes in case anyone needs those. We also have new family-friendly episodes called Smologies. And they are classroom safe. New one is due out this Thursday. Thank you, Noelle Dilworth and Susan Hale for keeping the trains running and helping with

social media posts. Thank you, Kelly Dwyer for making alleyward.com. She's available to make your website at kellyardwyer.com. Thank you to my legally wedded honk and editor, Jared Sleeper of Mind Gen Media for making these episodes into the dark of night. And of course, to Stephen Ray Morris of the podcast, C. Jurassic Wright in the podcast. Nick Thorburn wrote the theme song and is in a very good band called Islands, which has a new album out right now called Alamedia.

And if you stick around to the end of the episode, I tell you a secret. Sometimes they're embarrassing. Sometimes they're things you don't want to hear. This one's a life hack. I want you to know it. So I'm going to say it with my mouth. Okay, so take a pitcher, right? Fill it all the way up with ice.

Juice three limes into it. And then you fill it with water. For some reason, lime water is like a thousand percent more refreshing than lemon water. I don't know why. It's all the summer delicious of a margarita without being hammered or sugar crashing. So love some lime water all about it. Make yourself some canned lime juice, bottled lime juice. Get away from me with that.

It doesn't count. Just get some real limes. Get one of those citrus smasher squeezers. Whew, your life's going to change. Hello, Nightshade 3621 and Yo Gabba Gabba Yo. I read your reviews too. And one, congrats. That's amazing Nightshade.

Two, Yo Gabba Gabba. I'm a supermarket witch and I can see you. Okay, stay tuned for new smologies on Thursday. Okay, bye-bye. Oh, there it is. There it is.