A Tale of Three Labs

From cracking the genetic code of brewers yeast, to preparing micro-animals for space travel and now unraveling the mystery of why underwater organisms glow in the dark, I have had quite the journey in lab research during my time at UCSB. As a CCS Biology Major, my path in college has definitely not been traditional. I actually came in as a physics major, because I liked the way physics trained my brain to think. While I had a knack for numbers and logic, my fascination has always been with biology. However, coming out of high school I thought that medical school was the only path for a degree in biology which was something I knew I wasn’t too keen on. The summer before college changed my life- I had an internship with Ginkgo Bioworks, a synthetic biology startup in Boston, coined “The Organism Company”. At Ginkgo I was able to literally hack the biosynthetic pathways of yeast to make them smell like grapes and produce other compounds found normally in plants. I was able to apply my knack for numbers and engineering while working with life.

Though I was coming in as a physics major, I knew I wanted to get right into research. I wanted to know more about why yeast are used in synthetic biology and what makes them tick. I was immediately welcomed by the Proulx Lab. During my time in the Proulx lab, I learned a textbook’s worth of information of yeast biology and evolution, while getting hands on experience in bioinformatics. This is where I learned that regardless of what Biology lab I joined, I could take an interdisciplinary approach within the lab to complete a project, while acquiring the skills I would need to do science in my future career.

After completing an URCA project and attending an incredible conference in Austin, Texas, I parted ways with the lab as both the lab’s and my interests were shifting. During this period, I finally decided to apply to the College of Creative Studies, a college within a college where structured, motivated students rely not only on coursework, but lab experience as a part of their core curriculum. As soon as I was accepted, I dove into trying to find another lab. Almost immediately I joined the Rothman lab. The Rothman lab is working on a fantastic project in collaboration with Dr. Phil Lubin’s lab; they are preparing tardigrades and nematodes to get ready for long term space travel. This work aligned with my interests at the time in genetics and astrobiology. I spent a fabulous six months there, learning at an exponential rate. However for personal reasons I felt I hadn’t quite found my niche yet. I was grateful for all of my experience, but I started to become stressed. I found myself asking the questions, “Shouldn’t I have found my place by now?” “What will my future employers think of me when they see I jumped around to multiple different labs in four years?” As I soon learned, this yearning to find my place was not a reflection of me being flaky or irresponsible. It was just a matter of finding the magical place where I felt my presence was needed to conduct scientific research.

It took me a while to come to terms with feeling like I had done something wrong by not sticking with one lab in my time at UCSB. It wasn’t until I joined the Oakley lab this past summer, studying the evolution of bioluminescence in marine ostracods, that I felt like I was finding my place and my confidence as a scientist. I joined and got to know the lab, and almost immediately dove into my own project, assisting my postdoc and PI in their larger research question. The trust and respect they placed in me fueled my fire, and has resulted in my best work yet as a scientist, with another conference attended under my belt, future ones to come as well as a potential publication! Not to mention finding the answers to their larger research questions at hand. I learned that “failure” is actually progress, as every second, and I mean every SECOND in the lab is critical to your growth as a scientist. Messing up or getting funky results the first or second or third time on a new protocol, is just another fun puzzle to solve as to why those funky results happened in the first place. I learned that no matter what research question the lab you join is addressing, you and your interests will have a place in the lab, as Biology is becoming more and more interdisciplinary every day. What truly matters is your comfort, your lab mates and eventual friends, and your drive. With those things under your belt, there limit is truly the sky, the sea or the galaxy.

Embracing Failure: When Undergraduate Research Just Doesn’t Work

It’s well known that failure is an inherent, if not integral, part of the scientific process. In many ways, a failed experiment can be just as informative and useful as a successful experiment. But for young and aspiring scientists this is often a hard fact to come to terms with. This blog is about my experience with failure, and how I transitioned from “this is terrible, I’m quitting science,” to “I love this.”

Last spring I was fortunate enough to receive the SURF grant, which provided funds to carry out an independent summer project. At the time my lab was studying the Measles virus replication machinery, known as inclusion bodies. My advisor and I had been discussing one particularly interesting and novel hypothesis about the proteins involved in the formation of inclusion bodies, and we decided that I should pursue this hypothesis for my project. This was exciting. Not only would I test an unstudied mechanism, but the methods I’d be using to do so hadn’t been tried by my lab before. The project was going to be an adventure.

The first step was to produce and purify two key Measles virus proteins. Unfortunately, producing the proteins turned out to be more difficult than I expected, yet this was supposed to be the easiest part. The genetically altered E. coli I was manipulating in order to make the proteins refused to grow at a reasonable rate, and I couldn’t figure out why. I tried warmer temperatures, cooler temperatures, and I even remade fresh growth medium in case the older stuff had gone bad. Finally, I learned there was an easy fix to my problem – just increase the size of the growth flask. Great, I thought, I can finally get on to the interesting part.

Now that I had happily growing E. coli and I had verified that they were indeed producing plenty of my desired protein, I was ready to purify. Unfortunately, this failed miserably right off the bat. Even under the guidance of another lab that had expertise in protein purification, nothing worked at all. No matter what I tinkered with, no matter what step in the process I optimized to ensure success, I couldn’t purify even a single mol of protein. I kept trying, but it was incredibly frustrating. Eventually I started to believe that I had simply no practical skills at the lab bench and my project was going to be a humiliating failure.

I remember calling my advisor and explaining to him that nothing was working and no one could figure out why. His response was calm and unphased; he gave me a list of simple steps to take in order to figure out what the problem was. The idea was to take a small sample at each step of the purification process, and then analyze those samples together to see exactly where the protein was going missing. What surprised me was that he didn’t believe the issue had anything to do with my technical skills, rather it was about some innate property of the proteins that we now had the opportunity to discover and analyze. So I wrote out a plan and a new experimental setup. Now, instead of focusing on the end goal of my project and how far away I was from achieving that, I was forced to focus my thinking on new, smaller questions.

This shift in mindset brought me both relief and a new appreciation for the process of troubleshooting. Suddenly the thinking was no longer “I need to fix my method so I can test my project’s hypothesis.” It was now “why is this protein so difficult to purify, and what can I learn about it as a result?” I found that I was just as excited about these questions as I was about the larger questions addressed by my project. And to my delight, the troubleshooting experiment was a complete success; it took less than a week for me to pinpoint exactly where the protein went missing. What was more exciting was that I could actually interpret the data and draw conclusions about the protein. Ultimately, we learned that there was nothing I could do within the limits of funding and lab equipment to successfully purify the protein. This may have been disappointing, but the experience of breaking apart my failure into a new, biologically interpretable experiment was priceless.

So my advice is this; if you’re struggling with failing experiments, try to think about it as an opportunity. Relish the chance to design a troubleshooting experiment, because what you learn might be just as interesting as what you hoped to learn from your failed experiment. Most importantly, don’t get discouraged! It’s not your failures that define you, it’s how you address them.

On the Pursuit of Science

After seven weeks undertaking a crash course in field biology last spring, I was convinced I wouldn’t be a particularly good scientist. My problem, I told myself, was passion, though this is perhaps a bit of a misleading statement. As our nomadic band of student researchers meandered up and down the coast of California, sleeping under oaks that had stood tall before the first Europeans set foot on the continent and wading through rivers gasping with fresh spring breath, I found myself completely entranced by an astronomically improbable, impossibly beautiful world. I quickly developed a reputation as the head-in-the-clouds idealist of the group, and could be found sketching out plans for a treehouse or writing poetry in the field I was supposed to be surveying for canopy cover. I thought I was a lousy scientist because for the first time in my life I felt a spiritual connection to nature and the people I was experiencing it with, and I believed that not only did this connection supersede the cool, calculated work of science, the two views were mutually exclusive.

My experience conducting research last summer changed my view of what science could be, and of what it could mean to somebody. I took a position as a research assistant on a behavioral ecology project out in rural northwest Pennsylvania. We were examining communities of praying mantises in old field ecosystems, and we wanted to know whether behaviorally diverse mantis communities– that is, communities with some mantises that are “bolder,” and some that are “shyer”— would occupy a different niche than a behavioral monoculture. Would these communities feed on different prey, live in a different physical space, and ultimately have a hand in shaping the overall ecosystem? It’s a fascinating research question, but as I drove east I was unsure of whether I would run into the same problem I had during the spring. I worried I lacked the mental discipline required to do good science.

By my city boy standards the research site was remote: a few miles from one of Pennsylvania’s “scenic byways” lined with fields of hay and copses of impossibly green foliage, an occasional community of ranch houses was the only break from the bucolic landscape. I quickly realized my environment for the next several months would be completely different from anything I had experienced growing up in California. Linesville, the closest town to our research site, offered little in the way of entertainment, so our small research team quickly grew close as we spent virtually every waking minute together. About a week into the field season, we started playing a game in the evenings to pass the time where one person would try and draw someone else without looking down at the paper. The results were often as comical as they were disturbing, and we decided to start hanging them up on a wall in our cabin, with the best portraits occupying the upper right corner. As the season passed, the wall began to resemble an evidence board from a made-for-TV crime drama, complete with crisscrossing red string that connected each person’s body of work.

The wall, midway through its development.

I was surprised by how quickly I came to regard the other research assistants as close friends, although it makes sense given the context. Ecological fieldwork is self-selecting, in that it attracts people who don’t mind sweat, dirt, travel to unfamiliar places, and oftentimes a lack of connection to the outside world. These people are adventurers: they love the thrill of discovery, large or small, and seek out novelty both at home and abroad. In other words, fieldwork self-selects for scientists; in my time in Pennsylvania I revised my definition of what that meant. If someone had told me before that trip that my time researching wouldn’t be spent poring over data, conducting heady calculations, or examining specimens in lab, I would have been incredulous. However, I spent much of my time that summer out in the sun, collecting mantises for assay (read: frolicking in a field), applying a sticky substance called tanglefoot to prevent the occupants of our experimental plots from escaping (painting), and constructing an apparatus to test mantis perch height (doing arts and crafts). Not to mention the actual poetry and art the other research assistants and I spent a lot of time creating and sharing with each other throughout the summer.

My experience made me realize emotional immersion in the system one is studying is an asset, not a detriment, to research. I loved the sound the wind made as it flowed through the field of goldenrod every afternoon and thus didn’t mind checking the plots an extra time to ensure that everything was set up correctly. A fellow research assistant’s fascination with arthropods meant we could identify insects to family onsite and get a jumpstart on the data analysis. And the picture of four kids armed with sweepnets and rubber boots laughing as they sauntered down a lonely stretch of country road caught the attention of more than one interested local and indirectly gave our research more recognition, not to mention connecting two of the most disparate demographic groups in America through the miracle of mutual curiosity. Science, and especially ecology, will never be entirely clinical, and that’s a good thing: who would want to live cut off from their playful, passionate, quixotic, human self?

I’m grateful to have had the opportunity to revise my definition of science. Science, I now believe, is a method, a way of asking and answering questions that matter. But the act of science is much more than that. It is a pursuit, an endless chase. It is a shared ordeal that brings people closer than they imagined they could get. It is the childlike wonder you feel when you’re faced with your own insignificance; it is an adventure to unknown lands. When you’re done, when the numbers are crunched and you have your results, you see your same surroundings with new eyes. It cannot be commodified; it is priceless.

Community in science -the best part

Less than a week ago, the project that I had poured two years of hard work into, was scrapped. While the plan for this project (up until this quarter) was to collect enough data on a fly behavior to find a correlation in the genome and publish it…science does not always work out the way you hope it will. The phenotype, egg-laying location, which was originally statistically robust, dissolved away once we tested the behavior in fly lines with specific recombination. This happened near the end of the first year, so I started the project over again using a new method that promised to lower the background noise in our analysis. I spent months rebuilding lines and several more months testing the behavior of these lines. Last week, I finally had enough data again to check for preliminary results by doing some analysis and the news was anything but good. Nothing looked promising or publishable – another year of work down the drain. At this point, the project had taken so much time and money that it was not worth continuing.

Hearing this news, while devastating, helped me put some things into perspective. Biology is messy, and behavior is REALLY messy. By no fault of my own (that I know of) my project failed. But, this one project has nothing to do with the reasons that I love biology or want to be a biologist – science is so much more than the project you’re working on. My love for evolutionary biology comes from the people and the ideas and the process. If it were to come from a focused drive to find an “answer”, I would have quit a long time ago.

I joined this lab because I loved evolution, several courses on the subject had inspired me with interesting ideas and perspectives and I wanted to start exploring some of these myself. It was upon joining the lab that I also started attending the weekly evolution seminar – a journal club for all the evolutionary biologists on campus to come together and discuss new findings, present their own research and dig into interesting literature together. Despite being a mere second year I was encouraged to join in on the conversation and ask questions. I immediately felt, and still feel at home in that community.

I continued to attend the seminar even after I could no longer receive units for it. I was learning new things every week and getting closer to the amazing individuals that comprise the evolution labs on campus. This weekly seminar gave me so many opportunities to grow as a researcher. I was able to present in a constructive, fun environment and even joined another lab at a SICB conference when no one from mine was attending. I started to learn each person’s expertise and was able to go to them for help when I was having trouble with my own research, or needed advice on graduate schools and interviews.

I can’t emphasize how important the evolutionary biology community here, as well as my community in the College of Creative Studies, was to me throughout my four years here. Without the camaraderie and advice I received, the obstacles of being a student researcher and making my way to a PhD program would have felt much too great to overcome. It’s because of this community that I was exposed to so many sides of a fascinating topic and I would have likely never found my true passion for the study of evolutionary development without it.

One of the most important aspects of science is the community and shared ideas it creates. Everyone I’ve met here is working towards the same goal of discovery and is always happy to help each other along the way.

Now, as my time as an undergrad has nearly drawn to a close, I’ve started to reflect heavily on these experiences. While I applied, and have been accepted to several PhD programs, I’m now considering pursuing a career outside of academia and science. Even in these moments of uncertainty, my mentors have helped me navigate my life both within and outside the realm of research. Regardless of my future path, the community I spent my time in as an undergrad has helped me grow in innumerable ways and I will always be grateful for these people and experiences.