Mindy Perkins
Mindy pipetting media in the lab to start new cultures.

The microscope snapped another image. I stared at the grayscale nebula of fluorescent yeast that spangled the field of view, artfully if inconveniently out of focus at the edges, and my heart settled to the bottom of my ribcage.

The yeast were doing nothing.

The strain I was working with was light-responsive: the more light I shined on them, the more fluorescent their nuclei would become. Unfortunately, sometime during the past three hours, the yeast had stopped responding to intensities of light that I knew should have elicited a reaction.

What went wrong? The cells, nestled between a microscope slide and a silicone microchip, were bathed in a constant flow of media — basically sugar water with essential proteins — that I had replenished throughout the measurement. There was no salient bacterial contamination, and the time lapse images showed the yeast never stopped growing. In theory, I had done everything right.

But as they say, “The difference between theory and practice is that in theory, it works.” And until just a month before, all the work I’d done on these cells had been as a theorist in the Department of Electrical Engineering at Berkeley some 5,800 miles away from the laboratory in Basel, Switzerland, where I was spending the summer at the ETH Department of Biosystems Science and Engineering.

The group I was visiting comprised a team as international as it was interdisciplinary, which was more than a newcomer to both Swiss culture and cell culture could hope for. I had proposed my project and done the modeling for it; all that was left were the experiments. Beyond textbooks and papers, I had no experience studying living cells. I was prepared to ask a lot of questions.

The trouble was that I didn’t know what to ask, because I didn’t even know what I didn’t know.  I stepped into the wet lab without recognizing a pipette, much less knowing how to hold one.  In my first month I exploded two filters by plugging them into compressed air instead of vacuum.  I contaminated my media by dropping a pipette tip into it — and then fishing it out by (gloved) hand. I had spent three years as a Ph.D. student manipulating mathematical symbols, and it took me five minutes and a sheet of paper to calculate how much liquid I needed to add to three tubes. I then promptly measured the wrong amount into the first tube.

I recognized no such obvious mistakes that day in the microscope room as I stared at my unresponsive yeast. Yet during my next several experiments, the cells consistently dropped in responsiveness and often died before the end of the measurements. I organized a spreadsheet to look for patterns, hoping to accrue enough data so that I could point to a correlation and ask my collaborators what was happening.  My background as an electrical engineer had focused almost exclusively on pen, paper, and programming — nothing that prepared me to diagnose distress in microorganisms.

These yeast cells have been engineered to fluoresce red (left). They respond to blue light by concentrating that fluorescence into the nucleus (right).

Two weeks later, I was slouching at my desk when my eye caught on a bright green piece of tape I had stuck to the front of my composition book. Early in my stay I had off-handedly mentioned to one of my collaborators that I wasn’t sure where to find most of the equipment in the lab, given that the white cabinets were all identical and most of the drawers were not labeled. I came in alone that weekend to find that he had laid out everything I needed on the bench alongside a note telling me to “use this to grow” yeast.  It was this note, scrawled in thick black ink, that I had pasted onto my lab notebook.

As I read that message again, I finally internalized what it implied. It meant I had collaborators who were gracious and generous in their time and advice. It meant I needed to stop doing everything on my own just because I was afraid to bother anyone else about gaps in my knowledge I couldn’t articulate. Not all questions had to be precise to be understood or elaborated upon. Sometimes it was enough to say what I knew — or what I knew of what I didn’t know — and my collaborators could help me find words for the rest.

I was bushwhacking around the base of a long, steep learning curve, and I wouldn’t be able to summit by myself. Asking questions wasn’t enough. I needed to ask for help.

Over the coming weeks, with the guidance, patience, and support of my colleagues, I began to learn. I developed a sense for when something I could theoretically figure out on my own would take more time than I could dedicate to it. My collaborators imparted their hard-earned skills at technological and biological troubleshooting, improving my setup and experimental designs even as they buoyed my spirits before they could sink. I waded just deep enough into their field to appreciate the challenges they faced as scientists and synthetic biologists — challenges based on synthesizing large amounts of qualitative information about largely uncharacterized systems, like the electrical engineer’s “black boxes” of unknown behavior, only infinitely harder to probe.

Exactly why my yeast did nothing in the light-time is still a mystery, even to my collaborators. It could have been the equipment; it could have been too high of light intensity, or a near-invisible contaminant in my media. Too many possibilities make for an unsatisfactory answer, if a fine start to a question. It’s a small reflection of the research process: We observe something we don’t expect, we recognize our ignorance, and we learn and experiment more to figure out how to design our experiments or form our mathematical problems to provide insight into what we’ve observed.

I’m grateful for my time in Basel for reminding me how to be a beginner. After all, research takes place at the frontiers of human knowledge — and at frontiers, we are all beginners.

Mindy Perkins is a doctoral candidate in the Department of Electrical Engineering.  She completed her undergraduate degree in EE with a minor in Biology at Stanford University in 2015.  Her research focuses on developing mathematical tools to analyze pattern formation in biological systems, both real and synthetic.

Categories: Headlines, January 2019
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About Mindy Perkins