There's a joke I've heard time and again. "Theory is when you know everything but nothing works. Practice is when everything works but no one knows why. In our lab, theory and practice are combined: nothing works and no one knows why." I have no idea where it originated, but I've seen it printed out and posted in at least 6 different labs that I've either worked in or visited. It's a nice play on words, but it's also eminently relatable to everyone who's worked a lab.
At the moment, I'm rotating in a cell culture lab. We grow undifferentiated cells in a culture dish until we have a large enough colony, and then differentiate them into vascular tissues. We can try a range of drugs, inhibitors, growth factors and other treatments to the cells to see how it changes the tissue growth. There are four of us doing cell culture right now: myself and one of my classmates, a post-bacc student,1 and a more senior grad student who has been teaching us techniques. In the weeks before the winter holidays, we went through the entire ~12 day process of reviving preserved cells, growing then differentiating them, immunostaining2 the developed tissues for various markers that we were interested in, and imaging them in three dimensions on a con-focal microscope.3 Everything went swimmingly. We had lots of cell growth, we ended up splitting what started as 1 plate into 8 different colonies, and each of us managed to get three different slides to image out of the colonies we maintained.
Then we all took some time off for the holidays.
We got back the beginning of this week. One of us whose family lives in the same city as our university maintained a single plate over the two week break so we wouldn't have to start from scratch. On Monday, it was my job to split that one plate into several so that we each hate a backup plate of undifferentiated cells. Undifferentiated cells grow more or less exponentially, limited only by the available resources. It's a common enough practice, it should have worked. It didn't. Two days later only 1 of the 8 plates I tried to make had enough cells to actually be viable, and no one knows why. Also Monday I started differentiating a second plate someone else had made but ended up not needing. Basic, if somewhat new to me procedure. It worked before the holidays. Two days later, most of the cells were dead. It didn't work, and no one knows why. We cracked open a new tube of frozen cells, the older grad student watched and guided me through plating them on three different plates. Two days later, none of them were viable. It should have worked, but it didn't, and no one knows why.
Some of you are probably already thinking of possible reasons for why this is happening. That's a good thing, that's what we're going to do on Monday, is sit down and brainstorm and see what, if anything, we can do differently, but remember, all of this worked before break, and nothing has really changed between then and now. It's easy to armchair analyze a problem that doesn't impact you directly. It's honestly kinda fun to do. What I need you to do, dear reader, is imagine that this problem is personally important to you, and that you need this problem to be solved, and that you are rapidly running out of time to do so. Because in academia, there is always pressure to get results, there is always a submission deadline, a grant that needs to be turned in, a progress report due to the funding agency, or a graduation deadline, a conference or journal deadline just there on the horizon. There's usually enough time to meet that deadline, just a couple more data points that we need to collect. It'll be fine, right up until the point where nothing works, and no one knows why.
I have much the same thing going on with a personal project, a cosplay prop I'm trying to 3-D print. It only works on the bigger printer at the maker space. No one else knows how to use that printer, and my first two tests both failed. No one knows where the documentation is for that printer. The convention is next weekend, and once I getting the parts printed, I'll still need a couple of days to get them assembled and painted. Nothing is working, and no one knows why.
Problem solving is fun and it's exciting. It's a part of why a lot of us got into science in the first place, to solve puzzles no one has ever answered. But when it matters, when it's important and time is running out and it SHOULD WORK, but it doesn't and no one, I mean no one, knows WHY?! That is frustrating. It is anxiety inducing. It is demoralizing. It is also an every day occurrence in grad school. This is all compounded, at least for me, by self doubt. I'm always asking myself if something went wrong just because, or if I have somehow screwed up terribly. This certainly happens often enough, and when it does, that leads to a bit of confirmation bias leading to more self doubt. I don't really know what's worse. When no one really knows what's wrong, or when part of you absolutely believe it to be your fault. All I really know is when my 3-D print finished this evening, it was too small to fit, and whether it was the machine error or my error, my cosplay isn't ready, and I have no idea how or even if I'll be able to finish it in time now.
Dovie'andi se tovya sagain,
Faxe MacAran
Twitter: @TheMacAran
1) A post-bacc or post-baccalaureate program sort of like an academic internship program. It's a 1-2 year program for students who have finished a 4 year undergrad degree but is not generally a degree granting graduate program. Often, post-bacc students intend to apply to graduate programs or medical school but either chose not to go directly from undergrad into those programs, or want to build their experience and credentials before applying. It's not an obligate part of the traditional academic path, but nor is it at all uncommon. Post-baccs can also be a good option for someone who is considering grad school, but isn't sure and wants the experience before committing.
2) Immunostaining is an imaging technique where you conjugate a stain or florescent molecule to an antibody that targets a specific protein. When you choose an antibody for proteins that are specific to a certain type of cell or tissue, this allows you to selectively stain just the specific type of tissue you are interested in. You can use more than one stain at the same time to look at where different types of cells and tissues are in relation to each other.
3) Confocal microscopy is a technique often used in conjunction with immunostaining. A confocal microscope uses lasers to stimulate the florescent tags or stains added to a tissue, and uses a set of lenses and filters to image just the fluoresced light from a very narrow two dimensional slice of the tissue. By imaging lots of these slices on one on top of the other, we can create an accurate three dimensional representation of the tissue. Here's a video if you want to learn more
At the moment, I'm rotating in a cell culture lab. We grow undifferentiated cells in a culture dish until we have a large enough colony, and then differentiate them into vascular tissues. We can try a range of drugs, inhibitors, growth factors and other treatments to the cells to see how it changes the tissue growth. There are four of us doing cell culture right now: myself and one of my classmates, a post-bacc student,1 and a more senior grad student who has been teaching us techniques. In the weeks before the winter holidays, we went through the entire ~12 day process of reviving preserved cells, growing then differentiating them, immunostaining2 the developed tissues for various markers that we were interested in, and imaging them in three dimensions on a con-focal microscope.3 Everything went swimmingly. We had lots of cell growth, we ended up splitting what started as 1 plate into 8 different colonies, and each of us managed to get three different slides to image out of the colonies we maintained.
Then we all took some time off for the holidays.
We got back the beginning of this week. One of us whose family lives in the same city as our university maintained a single plate over the two week break so we wouldn't have to start from scratch. On Monday, it was my job to split that one plate into several so that we each hate a backup plate of undifferentiated cells. Undifferentiated cells grow more or less exponentially, limited only by the available resources. It's a common enough practice, it should have worked. It didn't. Two days later only 1 of the 8 plates I tried to make had enough cells to actually be viable, and no one knows why. Also Monday I started differentiating a second plate someone else had made but ended up not needing. Basic, if somewhat new to me procedure. It worked before the holidays. Two days later, most of the cells were dead. It didn't work, and no one knows why. We cracked open a new tube of frozen cells, the older grad student watched and guided me through plating them on three different plates. Two days later, none of them were viable. It should have worked, but it didn't, and no one knows why.
Some of you are probably already thinking of possible reasons for why this is happening. That's a good thing, that's what we're going to do on Monday, is sit down and brainstorm and see what, if anything, we can do differently, but remember, all of this worked before break, and nothing has really changed between then and now. It's easy to armchair analyze a problem that doesn't impact you directly. It's honestly kinda fun to do. What I need you to do, dear reader, is imagine that this problem is personally important to you, and that you need this problem to be solved, and that you are rapidly running out of time to do so. Because in academia, there is always pressure to get results, there is always a submission deadline, a grant that needs to be turned in, a progress report due to the funding agency, or a graduation deadline, a conference or journal deadline just there on the horizon. There's usually enough time to meet that deadline, just a couple more data points that we need to collect. It'll be fine, right up until the point where nothing works, and no one knows why.
I have much the same thing going on with a personal project, a cosplay prop I'm trying to 3-D print. It only works on the bigger printer at the maker space. No one else knows how to use that printer, and my first two tests both failed. No one knows where the documentation is for that printer. The convention is next weekend, and once I getting the parts printed, I'll still need a couple of days to get them assembled and painted. Nothing is working, and no one knows why.
Problem solving is fun and it's exciting. It's a part of why a lot of us got into science in the first place, to solve puzzles no one has ever answered. But when it matters, when it's important and time is running out and it SHOULD WORK, but it doesn't and no one, I mean no one, knows WHY?! That is frustrating. It is anxiety inducing. It is demoralizing. It is also an every day occurrence in grad school. This is all compounded, at least for me, by self doubt. I'm always asking myself if something went wrong just because, or if I have somehow screwed up terribly. This certainly happens often enough, and when it does, that leads to a bit of confirmation bias leading to more self doubt. I don't really know what's worse. When no one really knows what's wrong, or when part of you absolutely believe it to be your fault. All I really know is when my 3-D print finished this evening, it was too small to fit, and whether it was the machine error or my error, my cosplay isn't ready, and I have no idea how or even if I'll be able to finish it in time now.
Dovie'andi se tovya sagain,
Faxe MacAran
Twitter: @TheMacAran
1) A post-bacc or post-baccalaureate program sort of like an academic internship program. It's a 1-2 year program for students who have finished a 4 year undergrad degree but is not generally a degree granting graduate program. Often, post-bacc students intend to apply to graduate programs or medical school but either chose not to go directly from undergrad into those programs, or want to build their experience and credentials before applying. It's not an obligate part of the traditional academic path, but nor is it at all uncommon. Post-baccs can also be a good option for someone who is considering grad school, but isn't sure and wants the experience before committing.
2) Immunostaining is an imaging technique where you conjugate a stain or florescent molecule to an antibody that targets a specific protein. When you choose an antibody for proteins that are specific to a certain type of cell or tissue, this allows you to selectively stain just the specific type of tissue you are interested in. You can use more than one stain at the same time to look at where different types of cells and tissues are in relation to each other.
3) Confocal microscopy is a technique often used in conjunction with immunostaining. A confocal microscope uses lasers to stimulate the florescent tags or stains added to a tissue, and uses a set of lenses and filters to image just the fluoresced light from a very narrow two dimensional slice of the tissue. By imaging lots of these slices on one on top of the other, we can create an accurate three dimensional representation of the tissue. Here's a video if you want to learn more
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