Misadventures in undergrad research (Part II)
When I started my second research project I thought to myself, "I will be way less confused this time around. I will actually know what I am doing."
Nope. That didn't happen.
In fact, I had to deal with even more confusion! Yay. At this point, I wanted to shift from looking at the cnidae to looking at the gigantic arsenal of toxins. There was a bit of serendipity here. I wanted to study anemone toxins and my prof's lab wanted to explore this area. And then...Boom! I joined the lab and started to learn everything about protein chemistry and anemone toxins. I had to figure out a lot of stuff about anemone toxins on my own. I had to learn about the different types of toxins, how the toxin was delivered, and how the toxins worked. Of course and I had to deal with the bane of my existence, venom extraction.
It took me four months to figure out how to extract anemone venom and it turned out to be totally pointless at the end. I tried a bunch of things: poking the anemone, throwing it in an unrelenting sodium citrate solution and at one point, I just tossed the anemones in a blender. I looked at the proteomics and transcriptomics for anemone tentacle tissues. So in a nutshell, I did protein sequencing and mRNA sequencing to find new toxins for my anemones. The problem was that the proteomics approach crashed and burned faster than my hopes and dreams. The relative abundance of the toxin compared to other proteins was really low. So it was harder to sequence and find toxin peptides during MS/MS. It was also one of the most time-consuming parts of the project.
The focus of the project was too broad. I didn't have a concrete research plan from the start, I basically designed my project as I went along. The other problem is that I basically pounced into the field and collected...whatever was there. It's like going to a buffet with a blindfold on and grabbing whatever crumbs you can find. Just because you want hell-fire anemones doesn't mean that you actually will find it. When I actually found fire anemones, I basically had to transform into a ninja and quickly snip a couple of tentacle samples. In the end, I focused on two species the hell-fire anemone and an unidentified species of anemone. Which we will call 'Strawberry' because it looks like an adorable small strawberry.
Every time I managed to overcome roadblock, there was another one waiting for me. Once I actually got the data, I basically drowned in a see of amino acids sequences.
ME
ALL OF THE AMINO ACID SEQUENCES
I couldn't tell which peptide was a toxin and which was wasn't. You would think that it's a simple yes or no question. Nope! There aren't that many anemone toxins in the database to compare my sequences with. Through a combination of reading, questioning and just trusting my own instinct I did manage to find 11 toxins out of which 4 were worth studying in the future.
Even though it was a really challenging project, it was surprisingly satisfying and meaningful. I loved learning about anemone toxins. These toxins are magnificent and brilliant creations, which ruthlessly take down prey and predator. They are worth studying for potential biomedical and biotechnical applications. I am fascinated by the mechanism behind how anemone toxins bind to things and well, basically ruin things.
I felt like an idiot for most of the project because I didn't know that much. I kept comparing my research to other academic papers where they had discovered novel toxins. Why can't I find more toxins? Why isn't my data as good? Then I realized that I was comparing the work of a clueless undergrad who was still figuring things out to people who had Ph.D.'s and worked in this field for years.
If you are an undergrad who is interested in research and you are reading this post, I want you to know...it's okay to feel like an idiot. Sometimes you have to feel stupid for five minutes before you learn something new. These kinds of projects can feel like hell sometimes and other times you are high on a new discovery. It's all part of the process. The struggles in research make the breakthroughs more satisfying, because you need sorrow just as much as you need joy to lead a meaningful life.
