It’s odd to be writing my final blog entry outside of Charleston, Oregon. It makes me feel sad knowing that a chapter in my life has officially ended, but also hopeful of what is coming next. I think some of my biggest hopes for the program were that it would help refine my interests and better my academic trajectory. Coming from community college, research opportunities were few and even more scarce were labs able to provide prospective students with meaningful and rewarding opportunities. Without a shred of doubt, I can say that the OIMB REU Exploration of Marine Biology on the Oregon Coast (EMBOC) program has been the most transformative experience of my life.
Talking to several people throughout the program and even sending out some late-night emails, I realize that none of us truly know where we will end up in life. That being said, I believe that this program set me up to reach newer heights that I would not have been able to reach on my own. I am reminded of Robert F. Smith’s, “Bus No. 13,” speech and how he viewed the bus program as a vector of his success because it allowed him to leave his impoverished community to attend schools in a more affluent one that were well-equipped to educate its students. It may be a little early to say, but I believe that I will see the impacts of this program for years to come. I have matured and gained a plethora of knowledge and skills in just 9 weeks. This has been my bus, or ship, that has taken me much farther in life than I would ever reached on my own. When my parents first came to this country, they did not have the fortune of knowing English or being able to go to school. They lived a hardworking lifestyle, and that strong work ethic was transcended into my siblings and I. Unfortunately, they could not offer me much to better prepare my educational experience. I also came from an area of poorly funded schools and I feel as if though I also slipped through the cracks. Community college offered me a way to better prepare for university and I gained a wholesome education from being there. This program, however, just took the fire I had and poured gasoline on it. It met all my expectations and more.
Although the final week had turned out to be the one that went the fastest, it was also the most eventful. I got to speak to a couple of researchers that had or are actively doing research in genetics and gave me valuable insight on the field and advice going forward. Completing the poster and presenting it at the symposium was great for synthesizing my data and showcasing it to the scientific community. Admittedly, I was flustered at first, but I eventually shook out the jitters the more people came up and asked questions. It was great being able to interact with all the people I saw throughout the summer and show them exactly what I had been up to. All the REU’s posters were stunning, and it was great that we all could make it to that point together. I don’t think any of us in the beginning of the program would have imagined all that we ended up finding.
By the end of the poster session, we took a group photo with all the REUs in front of the iconic OIMB sign and soon afterwards we headed to Maya’s house for the final potluck. We all started collecting blackberries for Maya to make a pie with. Now that I think of it, it was a nice gesture to end the summer with something that we all helped make together. We all sat around, enjoyed food, listened to Svetlana tear it up on the guitar, laughed as George poked fun at me, and were bouncing around conversations.
We made our goodbyes and headed back to dorms where we got to spend the last moments together with each other and the University of Oregon students. It is amazing to think how much we all became friends and enjoyed the time we spent with each other. I don’t think any of us will forget this experience and I think we will always remember OIMB Summer 2019.
There are so many people that I would want to thank for my time here. My deepest regards to Svetlana, Christina, Megan, Nicole, and Kara, for all the advice that you gave me throughout the program especially for troubleshooting and helping me get through some of the toughest moments. A huge thanks to Caitlin, Clara, Lauren, and Dean for the advice that you gave me on my poster during those final weeks and helping me put it all together. Thanks to George, Phil, Sadie, Nina, and Christina for allowing me to bumble into the other side of the lab and sit in on the microscopy sessions and catch jellyfish. Thanks to Craig Young lab; Matt for always being up to throw the frisbee around and Kaylee for always bringing her musical spirit( I will never forget you playing backup as we all turned into water drops), and Craig for allowing me to go into your lab even though I didn’t have much reason to be in there. Thanks to the South Sloo lab for allowing me to borrow waders; thanks to Sophia for being the best orator that has ever stepped foot onto OIMB campus, Bree for giving advice on population genetics, and Renee, who was always quick to burn me and bring out the fact that I clapped during the wrong time (and who still owes me two games of foosball!). Big thanks to the Galloway lab; Hannah and Steven always had plenty of style and laughs to share for all of us, thanks to Natalie for all her sage REU advice that she gave to us newbies, an incredible thanks to Ross for his R workshop, thanks to Julie and Aaron for their talks at PubSci and OIMB. Thanks to every OIMB seminar speaker for giving some of the best talks in the marine biology field. All the University of Oregon students were great, but a big shout out to Butters, Zack, Lincoln, and Mackenzie. A humble thanking to Newt, Jesse, Lisa, Debbie, and the rest of the entire OIMB crew for keeping the entire campus and ship in great shape. Last but not least, I would like to thank Maya and Richard for being the best directors we could have hoped for and the NSF grant that could fund all of our ventures. I hope to see everyone again in the future!
Presenting at the Center for Marine Life Center (CMLC) had ended up being a hoot! The weekend brings in a lot of people into Charleston, and we were able to make the best of the bigger crowd. We got to show off all the work that we have done, and even specimens that we collected in the local area. I felt a bit nervous at first, but people were very enthusiastic of the research we were all doing. We had locals, but we also had people from around the country that just so happened to be passing through Charleston. It was great being able to interact with such a diverse crowd and be able to give and share insight. Surprisingly, a lot of the locals had been very curious about the nemerteans. Many of them routinely collect clams in the mudflats and come across the phylum but had known very little about them. It was great being able to answer many of the questions people had. It helped reinforce a lot of what I learned throughout the summer, and also added to people’s understanding of an understudied phylum.
Going into the week, we all had to have a rough draft for a poster. Afterwards everyone had to switch gears. Some of us were throwing it into high gear to collect the data needed for their project, and others went deeper into the poster-making aspect.
I went more into the poster-making aspect. Initially I would’ve thought that it would’ve been more relaxed, but I realized now it was a lot of work. Poster-making is a finicky process and comes with the challenge of having to maximize impact through language and visuals in a limited amount of space.
Leading up to the professional development session I thought my poster was half-way finished, but I ended up starting from scratch again. In the end, I felt that I could communicate my message in a much better fashion.
Thankfully the grad students have been an invaluable resource to improving the presentation and impact. I give my deepest and sincerest regards to all the grad students who have helped me in any way possible.
Alas, we are on the downswing and can count the days before the curtain falls and we’re all back to our respective homes.
Troubleshooting has been going very well. I can always appreciate when things go my way, but I have learned to have a growth mindset when it comes to the samples that give me difficulty. Was it the way I mixed the solution? Could I have possibly contaminated the sample? Was it the right temperature/primer set? What should be the next step for me? Although at first it was frustrating to not get a band that I wanted or figuring out why the reaction was not working, I learned to appreciate that it’s adding to my skillset.
Throughout this week, I have also begun to work on my poster and really think of the collective knowledge that I have been gaining from my time here. At first it felt very daunting to try to boil down everything that I have done so far, but little by little I’ve been able to piece together a solid start. It really wasn’t until that I had to write about my experiment that I began to connect the dots to make the bigger picture clearer to not only myself, but to a broader audience.
This has been particularly beneficial given that we will be presenting our research on Saturday at the Coastal Marine Life Center (CMLC). Being that a broad spectrum of people visit the CMLC it offers the challenge of being able to showcase our research in a more palatable format. One thing that may not come across many undergraduates, or at least be emphasized enough, is the obligation to be able to share our breadth of knowledge to the general mass. It’s great that what we are learning is enriching our own individual lives, but it will remain in an echo chamber unless we are able to dispense that knowledge to the community.
That is not to say that I did not have my fair share of fun this week. I was able to go jellyfishing several times, along with being able to catch a very good low tide that gave us an opportune time to venture out into some very remote areas.
Ultimately, I think what this week has really shown me is the value of being able to digest the research. Not only for our own interest (e.g., making a poster), but also to enrich the general society.
They kicked this week off with a very righteous weekend of touring the Oregon aquarium and Hatfield facilities. I was especially excited to broaden my understanding of ongoing research from a different institution and learning more about the Oregon coast. The faculty and interns gave us a very well-rounded introduction to the ongoing efforts being made in sustaining the local oyster population. Something that may escape an Angeleno like myself, is that marine life not only plays a role in the human food chain but it also plays an instrumental role in the ecosystem.
When considering how many oysters live throughout the Oregon coast and that they are a keystone species, if they were to one day extinct, the ecosystem could suffer dramatically. This knowledge helped put the research being conducted at Oregon State University in focus and highlighted the importance of the research pertaining to oyster sustainability.
Aside from the insight on the research being conducted, it was also great to go through the aquarium and learn more about the marine life across Oregon. It was great to see octopus throughout the aquarium, but it was surprising to see that puffins are also a species common in this area as well! I absolutely adore puffins. For years I would eat my Puffins cereal and think I could only see them in real life if I visited the arctic, but all I had to do was go to Oregon.
The following day we lounged by Hall lake, which is a lake situated right next to a dune! The scenery was epic.
All-and all the weekend was a good way to unwind and bring my focus back to my week’s research.
Troubleshooting had proved to have been one of the more challenging aspects of the project. With almost a week and a half dedicated to just trying to figure out the right annealing temperature and primer sets to set off my reaction I was becoming less and less sure that my samples would ever work. My persistence panned out, and I could get my PCR to work. I needed to get some new reagents to get my reaction working again.
One aspect that this research opportunity has given me is the opportunity to wrestle with my challenges instead of just setting my issues down for someone else to deal with them. I can hone in on my issues and plan out a constructive approach. When I hit a point that I am not sure of what my next step should be, I fall back on either Kara or Svetlana (maybe Nicole if I just want to throw darts). They both are much more knowledgeable and could better help me in navigating my issues and sure enough they almost always have advice to push me through the next step. It brings to light the importance of being able to network in any kind of situation—whether it’s work or school life. It was rewarding to see my efforts pan out.
Another treat this week was the R workshop hosted by Ross. I have taken computer science classes before and I have to say that he has arguably taught me more in 3 hours than I learned in most of my semester courses. He was very well-organized and really was great at explaining both the syntax and the math of the tools we were operating.
This week was an exciting that has left me even more grateful of this summer.
Avaste ye! There are sequences, ahead!
Going into the program, I would say that I was looking forward to the most was having to work with all the sequences. I had done a bit of PCR while I was at community college, but I never had the opportunity of analyzing, trimming, and comparing the sequences to those already uploaded to genetic databases. In fact, those extra few steps are what really what elevates PCR amplification of a gene into DNA bar-coding.
What’s great about this opportunity is that I get to use real samples that have been collected in the field. Being that these are samples from an understudied phylum, there is also a higher chance that I may recognize a sequence that has yet to be catalogued (i.e., discover a new species). So far, my lab partner and I have done just that!
Being giving so much autonomy I felt a lot of gratitude when I can discover a new species, but I also feel a lot (maybe a little less) gratitude just getting to where I can compare, or BLAST, the sequences that I PCR amplified. There are a lot of steps to get to that point (and so many ways it can go wrong to get there) but with enough practice you can start worrying less about mistakes you may have made along the way. Even then, there are still sequences that come out poor for whatever reason or, comically, you may have a great sequence of your sample’s dinner! Yes, you may have just PCR amplified what had been lurking in that specimen’s digestive tract! Frustrating but always funny to talk about in retrospect.
It’s been great seeing how far we’ve come by the end of week 5, but there is still a lot of work to do! Namely, starting to get ready for the poster!
The better part of this week has been consumed by mostly trimming, troubleshooting, and “BLAST-ing” sequences. There was, however, some small moments along the way adding on to the experience of doing research at this unique institution.
Yar’, I reckon that a many of us have been feeling a wee bit burned out from our research doing at the OIMB. Tis’ past weekend was a great way of resting our sea legs and wandering about at Cape Arago.
I, along with the rest of the REUs spent the weekend camping. At first I felt a bit worried that I wouldn’t have enough time to work on my proposal, but then I figured that I should just roll with it and plug out from the stress of lab work.
There were boatloads of critters we saw down at the tidepool and I would love to post each one of them, but alas this is a blog post and not a photo album. I am however, going to mention how we saw a giant pacific octopus in the tidepools as well! Unfortunately, we could not get a good picture of it as it was dwelling in its den, but its suckers were the size of the nudibranch that I am holding in the following picture. Was quite a lovely site, and I was particularly chipper after I saw it. Especially since I’ve been wanting to see an octopus since the first day I have been in Charleston, Oregon.
On our second day we had shared our campground with the UO SPUR students, and we managed to play a game of ultimate frisbee between both camps. As you could imagine, the REUs beat the SPUR students to 10! Not that it needed to be said.
On our way back we all got to enjoy ice cream that Richard had bought for all of us. Before you knew it the night-sky was upon us and we got to spend time over the bonfire. When dusk rose, we went tide-pooling one last time before we headed back to OIMB.
The following Monday we went back to humming along in our old routine. We did get to spend our Tuesday presenting our proposals (which had ended up turning out fine), and followed it up by celebrating a job well done and Christina’s going away at one of the local dive bars.
This entire time that I have been in this program, Christina has been at the helm of the Maslakova lab while Svetlana has been doing research abroad. She did a great job of making sure that the ship did not crash at the hands of two REUs and I can honestly say that I credit her for me being able to pick up PCR as well I have. In all honesty, the ship would’ve only crashed in my bumbling hands, but I can safely say it did not. I may not have perfected PCR (yet!), but I grew much, much more comfortable because of her mentorship. I could not have imagined my REU experience having gone nearly as well without her and I will be forever grateful for her patience and all her sage teachings and advice.
It’s odd to think about how much I have come to love benchwork. My prior research experience involved me doing a lot of field work and a little bit of benchwork, whereas this research has kept me tied to the bench with very little field work. Although it’s a completely different environment, I learned to love it the same. Being that lab work is in a more fixed setting, it has allowed me to work on refining my technique and approach in a more concise manner. That is not to say that bench work does not have its uncertainties. This week alone has been a never-ending trial of PCR, troubleshooting, purification, and more troubleshooting. Troubleshooting has been one of the more agonizing aspects of this experiment. Especially when you place so much effort into one step of the process and it does not pan out in your favor.
Thankfully, I get to be part of this program and not place too much emphasis on making a home run out of every pitch. I get to strike out and come right back to the plate for another swing. I don’t have to worry about grades, I can just focus on refining my skill set. I always strive to do better than the day before, but I do it knowing that this is done out of my own benefit. Whether it is trying to get a little bit faster at loading gels, being more efficient with timing procedures, or even just getting into lab a little bit earlier and making up a pot of coffee ready for everyone in lab.
Another aspect I have come to appreciate while being part of the REU program is collegiality. I have come to value the collegial environment in research settings as it provides an opportunity to have discussions pertaining to one’s research. Or, alternatively it can serve as an outlet to your frustrations. Sometimes we bond over a cup of coffee, and sometimes we bond over a game of hackie-sack. It all just depends on everyone’s availability, but there is a more-or-less a silent mutual agreement between all of us that sometimes we just need a take step away from research and enjoy some casual moments.
So as this work week went on it became progressively chaotic. It never quite felt that the results matched the efforts, but my perseverance and many cups of coffee kept me through it. On the Fourth of July I, along with the other REU interns and UO students, took the day off and enjoyed myself at the beach.
It was a break well worth pushing for.
Yarrr, I reckon that it is time for yet another blog post.
By know, yee may be asking how my voyage on the Pluteus went, and I would say that it was an eventful Saturday morning that I will remember for years to come. We all had layered up thick and sat around for a hearty breakfast before we set sail into the Northeast Pacific by the wee hours of 8 AM. The ocean waves were relentless and kept pushing hard against our vessel and left more than half our crew with seasickness. I was one of the fortunate ones that managed keep their sea legs on throughout the entire trek.
Nevertheless, once we had gone out deep enough, we would try to release our trawl to catch critters dwelling at the bottom of the ocean. Unfortunately, we kept ending up empty-handed until our boom had broken down along with our will to stay out in the ocean any longer.
On the way back, the few of us left standing were able to awe at the passing coastal scenery. Although it may not had been the most fruitful venture, it provided me with a tangible reminder that voyages, including scientific ones, don’t always go according to plan—even with the most thorough planning. You always hope for the best, but plan for the worst.
The following week, my lab mate and I were able to carry out much of our standard operating procedures that were taught to us from the earlier week. We would extract DNA from the samples collected in Panama by Dr. Maslakova and her colleagues; soon afterwards we would run these samples through PCR in order to amplify the gene of interest; troubleshoot the samples that had a weak/absent amplification; then have the sample ready for sequencing if there were no longer problems; and then begin to learn how to analyze sequences we received them back.
At first it was very intimidating having so much independence and having to deal with such sensitive samples (i.e., there was only a limited supply and could easily be contaminated). However, it was comforting knowing that I was given enough credibility to carry out these procedures without direct supervision and be able to mature at my own pace.
Admittedly I did fumble around at first and I made a lot of clumsy mistake, but I was able to realize the mistakes that I did make at each step and always did my best to correct rising issues. As I kept repeating the same procedure ad infinitum, I began to relax more and more and fall into a smoother routine. Before I knew it, a procedure that took me an entire day, only took me a morning. Words can not even begin to describe how gratifying it has been to see myself having grown so much in my time here. At first, I felt overwhelmed by all the procedures, but I have learned to appreciate each and every step. I wholeheartedly appreciate patience of my stand-in mentor Christina, and my lab mate Megan for making this a safe and welcoming environment for me to thrive in.
There have also been so much cool things look at around here! Check out this sea urchin!
Allow me to introduce myself to all yee computer goers. My name is Adrian Garcia, I just finished up my time at community college and will be attending the University of California, Davis where I will further my studies as a Genetics & Genomics major. I am absolutely thrilled to be spending my summer at the Oregon Institute of Marine Biology campus where I will have the great opportunity of being able to take part in Svetlana Maslakova’s ongoing research in assessing and describing the diversity of nermerteans of the Caribbean using DNA-barcoding. I am looking forward to gaining knee-deep exposure to a myriad of molecular techniques and occasionally getting my hands dirty in field work along the way.
Thus far, my first week has been the most welcoming week that a lad like myself could hope for. Many laughs have been had amongst my fellow REUs, its been very exciting going through each of the mentor’s laboratories, and the food has been top notch! The local area offers an unparallel opportunity in being able to explore with newly made friends, go for a morning run, or go on a nature walk with a cup of top-grade local artisanal coffee. Within a stone’s throw from the dorms are a beach volleyball court, a foosball table and a patch of grass which I, along with the rest of the REUs have made great use of. In short, the faculty, staff, campus, and fellow REU’s have made this such an enjoyable first week. I feel at ease and am able to focus in on the research and get to enjoy the trip that I am about to embark on.
As a lifelong Southern Californian, I could not imagine a much more different summer experience than the one I am experiencing now. However, I intend to make the most of my research opportunity (and cooler weather) before I head off to university.