Goals for Summer 2020

This summer, I hope to learn more about coral reefs, develop skills in various coding programs, and to come out the other side better prepared for the working world ahead. Coral reefs have always mildly interested me, but I’ve never considered learning about them because I was studying Earth Science. However, as I learn more about my internship, I’ve come to realize how research in the Earth Sciences, Biology, Computer Sciences, and various other topics are naturally interconnected. For example, in our first conversation, my internship mentor noted that I was interested in hurricanes and explained that coral reefs act as a buffer to lessen the destruction of tropical cyclones. Later, in his first internship informational email, he mentioned that we will learn how to use various coding programs because coding skills are necessary for translating data into useful information. I aim to learn more about the role of coral reefs in a biological and geological sense, and develop coding skills for research purposes and general use this summer.

The most important thing I hope to get out of this internship is experience in the field. This will be my first full time internship, or job, within the Earth Sciences and I’d like to have a better sense of the direction I want to take my career in. The Earth Sciences encompass a vast array of subjects alone, and combined with subjects like Biology and Computer Science, it feels like there are infinite possibilities. Along with taking this opportunity to learn more about potential careers, I’d also like to develop a better work ethic. Whenever I’m not at work or school and stuck at home all day, I’m often very unproductive because it never feels like I started the day right. Since I’ll be stuck at home all day during this internship, I’m going to experiment with different methods of being productive. For example, and in reference to the GeoInterns Guidebook, I’d like to get into the habit of having a daily routine and create spaces for different activities to make it feel like I’m physically travelling somewhere else. By the end of the summer, I hope to have at least one well tested strategy of working from home.

How Covid-19 changed my summer plans

Back in the beginning of Winter Quarter, I expected to spend my summer interning or volunteering, and hanging out with friends and family.

When Covid-19 became more impactful towards the end of Winter Quarter, I thought that I wouldn’t have an internship this summer. Many of the potential internship and volunteering opportunities I applied to fell through, and the organizations I contacted in the later months had no opportunities to offer. At that point, I had decided to take a leave of absence during Spring Quarter and began to work at a grocery store in my hometown, now expecting to continue working there, full time, until Fall Quarter. Then, as you may know, the GeoInterns offer came out of nowhere and now I’m working under a PhD student, learning how to analyze microbiome data.

In my spare time, I planned to cook and travel around with friends, but those plans also fell through. We do text a lot and I’ve found a way to socially distance with one of them by ordering take out food from restaurants and eating spaced out in an open area. It feels a lot more distant, but we’ve still found ways to communicate. On the other hand, I see my family all the time. Normally, my family would be working or travelling for work, either individually or together. We had even planned to fly to Chicago for a dragon boat race, but we’re definitely not doing that now. Even then, we still find ways out of the house through biking or hiking away from other people for our sanity.

I’ve heard about the difficulties of being productive while working at home but haven’t experienced it until now. My grocery job is relatively normal to pre-pandemic conditions besides the masks, gloves, and plastic screens between the customer. A day normally consists of my boss texting me my schedule, travelling to work, interacting with customers and coworkers, travelling back home, and then relaxing until the next day. I expected the work itself to be the most difficult part of the internship, and while the material is still brand new to me, scheduling and motivating myself has been challenging. The main challenges so far include the lack of separation between work and relaxing modes, doing work without being pressured by a boss, and the lack of coworkers, so far. Despite this, I know from the past obstacles of this summer that I’ll eventually adapt to working at home, and I’ll will continue to experiment with different methods of being productive in one space. For the rest of the summer, I plan on working full time on my internship and part time at the grocery store until Fall Quarter.

GeoScience Career Panel Reflection

Rikke’s extended career path resonated with me because it shows that college does not have to follow a single, rigid path. For me, there is a straightforward plan to get from college to a career: after high school, you go to college, find some internships, maybe go to graduate school, then get a career in your field of study. I have never seriously considered the idea of going to college abroad or spreading out my educational career. Sometimes I forget that these are challenging, yet potentially more fulfilling options that people have taken. Anything but the traditional pathway through college can feel prone to failure or wasted money. However, knowing that successful people, like Rikke, spent years in between their education makes me believe that even if I don’t have a specialization in the Earth Sciences right now, graduate school can still be an option years after my bachelor’s. In hearing Rikke’s story, I was surprised to learn that she went from an undergraduate in Denmark to around ten years in college, mostly in the United States, and eventually a job at Elkhorn Slough in California. I find it unlikely that Rikke could have imagined where she is today back when she was an undergraduate in Denmark and with the uncertainty in my own career path, Rikke’s story makes me hopeful for the future.

Final Reflection

This summer, I was able to complete the majority of my listed goals from the initial GEOPATHS Internship reflection. My first completed goal was to learn about coral reefs. Through reading academic articles on coral microbiomes and meeting scientists whose research specializes in the subject, I have a greater appreciation for the beneficial role that corals play in the ecosystem and their vulnerability to human interference. Another goal I completed was learning how to use the coding programs and computer languages QIIME2, Bash, and R. At the beginning of my internship, I also planned to learn Python, a common programming language. However, I have noticed that the general structure of coding is somewhat universal, meaning that knowing QIIME2, Bash, and R will make it easier to learn Python and other computer languages and programs in the future.

I have developed strategies for productivity although following a consistent schedule has proven to be more difficult. I did not develop a consistent schedule this summer mainly partially because of my cashier job and an erratic sleep schedule. Despite these shortcomings, having an inconsistent schedule has allowed me to gain insight into my energy levels throughout the day. One of my recently implemented strategies has been working and napping around this schedule. Another effective strategy has been to leave the bed immediately upon awakening. In my experience, getting out of bed as soon as possible results in having both additional energy and a more positive mood throughout the day. Lastly, moving workspaces every hour or so makes for a short break from work and helps me stay focused as long as I do not become distracted with another task along the way.

The goals of being better prepared for the working world and narrowing down my career choices have yielded mixed results. I am definitely more experienced in the research world, however the unique circumstances of this year forced my working experience to be sitting in front of a computer all day. I can spend long periods of time in front of a computer if necessary, but I would enjoy spending a similar amount of time out in the field. As a result of this internship, I am more comfortable working on a computer, but I do not feel more prepared for any sort of field work.

This internship has not narrowed down my potential career paths in the ways I expected. As I mentioned in the previous reflection, the Earth Science field already encompassed a vast array of subjects and coupled with Biology, Computer, and other sciences, the possibilities are endless. I expected to cross out and narrow down my options, but I have instead added to the list and not completely crossed out anything. I am not currently pursuing a career in coral microbiomes, but I can see myself applying for opportunities with either corals or microbiome analysis coupled with another subject. While I still don’t know exactly what I want in a future career like I had hoped, I have developed skills that will be useful in many fields and learned a lot about myself and my interests.

Expanded AGU Abstract:

In the internship, I first learned how to use the programs and computer languages R, Bash, and QIIME2 to eventually analyze microbial sequences from the V4 region of the 16s rRNA gene. Bash, a command language, was first learned to combine pair-end sequence reads before they were imported into QIIME2, which also requires the same language to operate. QIIME2 was used instead of QIIME, the program mentioned in the abstract, because QIIME2 is the most recent version of the microbiome bioinformatics program. The majority of the internship work was done on this program, including performing quality control, clustering similar features or denoising with the Deblur method, assigning taxonomy to these features by comparing them to outside databases like Silva and Greengenes, and finally performing diversity analyses to compare similarities and differences between the samples. Although I previously mentioned clustering similar features into OTUs, QIIME2 clusters into ASVs, a newer, similar, and more effective method than OTUs as described on the website.

After assigning taxonomy and researching the identified species, the diseased coral samples were found to have more microbial diversity and higher counts of harmful bacteria than the healthy corals. The latter observation agrees with the findings of the academic article “Responses of Coral-Associated Bacterial Communities to Local and Global Stressors”. In this article, bacteria within the order Flavobacteriales are often associated with corals diagnosed with white-band disease. (McDevitt-Irwin, 2017) In the UCSC samples, the order Flavobacteriales is found in large numbers in all of the diseased samples while being present in only one of the three healthy samples. Lastly, I learned R, a software environment for statistical computing and graphics, and used it to convert the final QIIME tables from a wide format to a long format for more effective visual communication.

References:

• McDevitt-Irwin, J., Baum, J., Garren, M., Vega Turber, R. (2017, August 15). Responses of Coral-Associated Bacterial Communities to Local and Global Stressors. Frontiers in Marine Science. https://www.frontiersin.org/articles/10.3389/fmars.2017.00262/full