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Hi, I’m Elizabeth Lee, and I am an Oregon State University master’s student with Dr. Kathleen O’Malley in the State Fisheries Genetics Lab at Hatfield Marine Science Center in Newport, Oregon. My first quarter as Malouf Scholar has been quite busy, but before I dive into my Fall quarter, let me provide a little background on my research.

When you think of the Oregon Coast, what comes to mind? Maybe rocky coastlines? Tides pools? Seals? Beaches? Boats? Seafood? Dungeness crab?

Oregon Coast, Yaquina Head Lighthouse, Newport, Oregon

Oregon Coast Tide Pools
Newport, Oregon

If “Dungeness crab” didn’t come to mind, you need to spend more time along the Oregon Coast! Dungeness crab (Cancer magister) is Oregon’s most valuable single-species commercial fishery. Its cultural, historical, economical, and ecological importance along the Oregon coast is prominent.

Dungeness Crab
(Photo: Delecia Loper)

In 2017, 20.4 million pounds of Dungeness crab were landed by commercial fishing vessels in Oregon, totaling $62.7 million in ex-vessel value. These may seem like large numbers to you, but I will argue, that from the perspective of my discipline, there’s another aspect of Dungeness crab that’s even bigger. The genome of the Dungeness crab.

Dungeness Crab Pots, Newport, Oregon

Let’s take a trip back to Biology 101, remember all the ‘A’s, ‘T’s, ‘G’s, and ‘C’s that make up your DNA? These ‘A’s, ‘T’s, ‘G’s, and ‘C’s (or bases) pair-up to form the double stranded structure that holds the blueprints that makes each of us unique (or DNA). The complete DNA blueprints (or genome) of the Dungeness crab is over 2 billion base pairs long! And, every cell in its shell-encrusted body has a copy of these 2 billion base pairs. So, although we catch tens-of-millions of pounds of Dungeness crab per year in Oregon, the genetic composition that makes a Dungeness crab a Dungeness crab, is even larger!

DNA Diagram
(Figure: Wikimedia Commons)

Considering the importance of Dungeness crab along the West Coast, one would assume we know a lot about the Dungeness crab’s genome and genetics. But in fact, we do not. The O’Malley Fisheries Genetics Lab undertook one of the first large-scale genetics projects on Dungeness crab. They sampled over 7,000 adult Dungeness crab off the coasts of Washington, Oregon, and California to understand the population genetic structure, genetic connectivity, and genetic diversity of Dungeness crab within the California Current System (Jackson et al. 2017)

Dungeness Crab West Coast Range
(Figure: Rasmuson, 2013)

By determining the pattern of ‘A’s, ‘T’s, ‘G’s, and ‘C’s within the crab genome, we can study the genetic structure, genetic connectivity, and the genetic diversity of the population. These findings are informative for managers and conservationists. Defining the population genetic structure of Dungeness crab is important for determining how groups of crab in the ocean are connected and allows managers to define stocks within the fishery. Assessing the genetic diversity within and among populations provides insight into the species ability to respond to environmental changes.

Dungeness Crab
(Photo: Wikimedia Commons)

In their coast-wide population genetics study, Jackson et al. (2017) found that Dungeness crab were highly connected genetically within the California Current System. Interestingly, they found inter-annual variability in the degree of genetic connectivity. This suggests that inter-annual variations in oceanographic conditions are affecting the genetic population structure of Dungeness crab. Specifically, the strength and timing of coastal upwelling, the timing of spring transition, and the phase of the Pacific Decadal Oscillation that effects of the strength of the off-shore current systems.

So, how is it that these large-scale oceanographic conditions might be affecting the bottom-dwelling Dungeness crab? Because of the complex life cycle of Dungeness crab.

Dungeness Crab Life Cycle
(Adapted from: Wild and Tasto, 1983)

Before Dungeness crab become 6 ¼-inch-bottom-dwelling (benthic) harvestable organisms in the ocean, they spend 3-4 months as very small, floating (pelagic) larvae within the water column. The pelagic larvae are moved offshore and are dispersed for 3-4 months along the west coast by the ocean currents. The time-period the larvae spend in the ocean current systems and the strength of the ocean currents influence where the larvae finally land on the bottom at the completion of their 3-4 month ocean journey. When the Dungeness crab larvae land along our coasts, we call this process recruitment. After recruitment, the juvenile crabs grow into bottom-dwelling adult crabs.

Dungeness Crab Larval Recruits (Megalopae)
Yaquina Bay, Newport, Oregon

As a graduate student, I am studying the genetic structure and diversity of Dungeness crab larvae that are recruiting to our Oregon Coast. By combining this genetic information with information about the oceanographic conditions and ocean currents along our coast, we can better understand the inter-annual variability that is observed within the adult Dungeness crab genetic population structure. The findings of my research can inform scientists and managers about the population of Dungeness crab off our coasts. Our genetic research is one of the many research projects that can help us tackle the complex questions of ‘how’ and ‘why’ the Dungeness crab fishery and population changes from year-to-year.

I am looking forward to keeping you all updated on my Dungeness crab genomics research this year. And in the meantime, I am enjoying the start of the 2018 Dungeness crab commercial season in Newport, Oregon!



Jackson, T. M., Roegner, G. C., & O’Malley, K. G. (2017). Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister) along the California Current System. Molecular ecology.

Rasmuson, L. K. (2013). The biology, ecology and fishery of the Dungeness crab, Cancer magister. In Advances in marine biology (Vol. 65, pp. 95-148). Academic Press.

Wild, P. W., & Tasto, R. N. (Eds.). (1983). Life history, environment, and mariculture studies of the Dungeness crab, Cancer magister, with emphasis on the central California fishery resource. State of California. The Resources Agency. Department of Fish and Game.


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Being welcomed into a new workplace

Posted by: | November 6, 2017 | 1 Comment |

Over the first few months of my fellowship I have been overwhelmed with welcoming gestures.  It wasn’t until a tiny hamburger sticker came my way that I actually stopped to think about it…

The first day of a position normally starts with an introduction to your work space and people you will be working with, and I did get those introductions…along with introductions to every single person in the Salem DLCD office.  Patty Snow, the director of the Oregon Coastal Program personally introduced me to every person in the office and showed me all of the good spots!  I was blown away that a program director would take the time out of her busy day just to show a fellow around (seriously!  She does a tone.  If you don’t believe me take a look at her desk!).  Andy Lanier, my mentor and the Marine Affairs Coordinator for the Coastal Program , then sat down with me during my first week and straight out asked me “what do you want from this fellowship?” He explained it was his goal to make sure I get the experience that I was hoping for.

My desk is right near some of the Geo spacial Team desks.  All of the “GIS” people as I like to call them.  ell the GIS people all have wooden letters symbolizing the first letter of their names hanging on the front of their work space. I was truly touched when Cy, the Geo spacial team leader (from what I understand) also got me one of these letters!  I have never felt so welcomed into a work space.

It really shows that small gestures go a long way.

I’ve thought long and hard about how I want to use this blog space and I’ve decided photos are much more fun than words.  So instead of describing all of my experiences, here are some photos from them!

As part of my introduction into this project, Andy and I have been making some pit stops along the coast while on our way to other meetings.  This spot is Sea Rock!
 Far from rocky, but still beautiful – Florence Dunes
 Cape Perpetua
 Yaquina Head – What you can’t see in this photo are the 3 whales swimming around within this cove.  The wave climate was intense this day and wave sets were coming in that I couldn’t believe.  Yet the whales were not phased at all and moved around the jagged rocks like dancers.
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I sat down to write this final blog post right after I finished my final day of field sampling for the year… and what a year it has been! When Sea Grant awarded me the Malouf Scholarship I was just starting to get a grasp of what I wanted to do for my PhD. I knew I wanted to work with juvenile rockfish (because collecting them is one of the most fun things on the face of the earth) and examine the role of oceanographic conditions during rockfish development in determining rockfish growth and survival. Over the course of this past year I developed my research plans, successfully defended my dissertation proposal, and just wrapped up a successful (though at times very frustrating) rockfish collection season. While my time at OSU is focused on accomplishing my research, Sea Grant has encouraged me to branch out beyond academics and I’ve discovered the world of scientific communication and educational outreach. This last blog will be a recap of the field work and outreach the Malouf Scholarship enabled and inspired me to accomplish.


My field collections of rockfish involve a three-pronged attack, or a triple threat, to capture rockfish during their early, offshore life stage (pelagic juvenile stage), their transition from offshore to nearshore (recruit stage), and once they have settled to nearshore habitat (benthic juvenile stage). While I was only able to collect 7 pelagic juvenile yellowtail rockfish during a research cruise on a NOAA ship, I was able to team up with ODFW, the Oregon Coast Aquarium, and commercial urchin divers in Port Orford to collect 622 black and yellowtail rockfish recruits (these species look very similar at this stage and I still need to ID them all). In addition, I did some freediving (with the help of two amazing undergraduate students) and SCUBA diving to collect 120 black and 25 yellowtail benthic juveniles.

I teamed up with Professor Aaron Galloway at the Oregon Institute of Marine Biology to do some diving in Port Orford to collect rockfish. Photo credit: Aaron Galloway

I was fortunate to work with two undergraduate students this summer Zach (left) is a Sea Grant Summer Scholar working with ODFW’s Marine Reserves team and Madeline (right) is an REU student working with me on rockfish recruitment patterns.


Though collecting rockfish is an absolute blast, the oceanographic conditions this year made my field work frustrating at times. An unprecedented number of pyrosomes clogged and threatened to tear our nets on the NOAA research ship, limiting our ability to trawl for pelagic juvenile rockfish. Unexpectedly late storms in late April broke two of our moorings used for collecting recruit stage rockfish, and three more moorings (of a total of 16) disappeared for unknown reasons. Finally, quillback and copper rockfish (some of my targeted species) never really showed up this year. While highly variable survival and recruitment of rockfish is to be expected, it was quite disappointing not to see any of these guys. I had really fond memories of night time snorkel collections of them the previous summer. After several night snorkels, I learned that these rockfish sleep on Egregia menziesii (feather boa kelp) and when you shine your dive light on the kelp blades, their eyes and swim bladders reflect light and look like Christmas lights on an underwater tree (I wish I had taken some pictures to share with you!). Now that the field season is over, and all the stress of repairing/rebuilding/replacing broken moorings, scheduling boat trips, and all the other logistics that go into a collecting rockfish has washed away, I find that I am already looking forward to next spring/summer.


Collecting and learning about rockfish is my passion, however, over the course of this past year I have found that I really enjoy teaching others about rockfish. When applying for this scholarship and identifying where I wanted to focus my outreach efforts, I thought that teaching children would the most fun and effective way of teaching others about rockfish because children are so curious, excitable, and, if they were anything like me when I was younger, children can’t wait to tell their parents about everything they’ve learned. Through OSU’s Winter Wonderings program, I was able to teach 3rd-5th graders about how old rockfish can get, how scientists use their ear bones (otoliths) to age them, and tried to teach them how important this information was for fisheries scientists. I found that I got a little ambitious with the last point, but the students loved looking at otolith cross sections through a microscope. I also started volunteering for the Oregon Coast Aquarium as an interpretive diver. This was an incredible opportunity to be in the water and talking with an audience of aquarium visitors about our coastal resources. Most recently, I participated in an outreach event at Hatfield called the Sustainable Fisheries Workshop for Teachers where I taught several middle and high school teachers how to distinguish juvenile rockfish to species and how closely related species can have very different life history characteristics (life spans, reproductive capacity, and development rates). All of these outreach events have been really fun and I am excited to revamp my lesson plans to improve them for next year.

Helping teachers pick up the fine details of identifying juvenile rockfish to species. Photo credit: Su Sponaugle


Working with Oregon Sea Grant has really opened my eyes to the importance of outreach and communicating my work with the people it may affect. I now feel comfortable talking to fisherman (commercial and recreational) about rockfish populations and how they naturally change through time. As my research progresses I am looking forward to communicating how oceanographic conditions affect the survival of young rockfish and how survival of young rockfish translates into changes in the adult population. Now all I have to do is begin analyzing my data to discover this relationship! I wanted to take this opportunity to thank everyone at Oregon Sea Grant for awarding me this scholarship, and for all the encouragement and support this year. It has been an incredible experience working with you all. Thank you very much!

The Oregon Coast Aquarium provides a unique opportunity to interact with aquarium visitors while you are diving. I was able to teach these visitors about plastic pollution and about rockfish. Photo credit: Nick Brown

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Interview Participation

Posted by: | September 11, 2017 | 1 Comment |

Participation in the interview process for a Sea Grant Fellow position was one of the most valuable parts of my Fellowship. While initially it may seem like an extra task added onto an already busy schedule is actually exactly the kind of preparation Sea Grant seeks to provide its fellows in order to help them enter the work force. Just the initial read of applicant’s materials helped me see how to improve my own, and not just because they had better word choice. I started to see where I had not fully explained something and left an area open to interpretation that I actually had very specific answers too. I realized that if I cannot fully explain a subject in my cover letter that I should not bring it up at all, because the blank will be filled in by the reader and that distracts from other more important subjects. I also finally understood the value of letters of recommendation, especially from those who had clearly developed a personal working relationship with a student. Letters of recommendation that highlighted the same projects or attributes of a students cover letter demonstrated that the student was under no delusions about their strengths or even weaknesses they sought to improve. While grades where a factor and where important to complete the full picture of a student they carried far less weight than I thought. Really all they are need for is to demonstrate is that a person is capable of hard work and following through, or that they have acquired skills needed for a particular job.

Through discussion of the materials with other members of the selection committee I began to understand what parts of a cover letter we all responded to. Direct statements such as “This is my dream job, I would take it above all others.” where incredibly well received. While statements such as “I would like this job so that I can stay in Oregon” were less well received unless they were followed up with further explanation of a person’s commitment to the area or a particular issue. Sea Grant really responds to passion and commitment, they want students who are going to use this opportunity to develop further, not just as something to do while they figure out a better option. It was especially interesting to see how we all balanced the multiple parts of an application against each other, grades verse dedication to a certain area or letters of recommendation verse personal statement. Each person on the panel valued things differently and through our conversation we started to put together a whole picture of what this person would look like as a fellow. I really understand now how to make myself stand out to different kinds of interviewers.

The actual interviews helped me understand how my personality and interview style is viewed by different people. There was an incredible amount of understanding from the panel about nerves and how those are presented in different people. I learned that it was ok to be nervous as long as I addressed it if my composure slipped or I answered a question weirdly. Observing this part of the process and discussing it afterwards will definitely save me some sleep at 4 am in the future. I used to think that panel interviews were worse than one on one interviews but through this process I learned that they are actually better. Every person carries with them unavoidable biases based on their personal experiences, but its is also our experiences that help us balance them out, especially when combined with other peoples. As we discussed the differences in each candidates in person interview there were some things we all noticed and agreed on and others that surprised us and needed explaining from another person. I deeply value this experience and took away a lot more than I thought I would initially.

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So I think I’ll start off by saying that I am writing my final yet very late blog post from Kawasaki, Japan. It’s currently 6:41 in the morning and my jet lag has still not adjusted itself. I got here three days ago and it’s been quite the culture shock. After leaving Oregon, I drove and stayed in Santa Cruz for two days, then I drove back home to Redlands where I stayed for a week, until going to San Diego for a night before leaving for Japan. This rapid change in scenery and cultures that’s occurred in the last week and half has me a bit discombobulated, making my time in Oregon feel like it was a year ago rather than a week. Being here in Japan especially, where the only things I can say to anyone is “Konichiwa” and “Arigato,” really make me appreciate the fact that I was living in a place where I could actually communicate with its members of society. So this final blog post is dedicated to those members of Oregon’s South Coast that I befriended during my 10 weeks and the knowledge I gained from them about something my knowledge is a bit rusty on: relationships.

I think it’s fairly obvious that older people are full of experience and knowledge about many subjects, sometimes with wisdom, sometimes without. It’s been a while since I was in a real relationship myself so whenever I get the chance to connect with the older generation I make it a point to observe them and ask about their love life if they’re comfortable discussing it. I spent my free time with more “old” people than people my age this summer so I will tell you some of the advice they imparted upon me and what I learned through observing them with their significant other. I would prefer to give a more detailed account about the event where each person gave me advice because I think it gives the advice context and depth but in order to preserve anonymity I will just list the things that I learned from all these good ole geezers.

  • Find someone with similar interests with you. Whether it’s something like bird photography or yoga or any other niche little thing, I think having someone you can share these unique experiences and interests with is important.
  • A person who you can laugh with is truly sweet or as one person put it, “someone you can talk sh*t to.” The two people who told me about this one would just clown on each other constantly and both would just laugh about it afterwards. The world seemed lighter being around them and their banter.
  • Now this one was a bit more explicit but someone who you can link up with in bed in a cooperative and positive manner is apparently very important.
  • Be real. Don’t try to be the cool guy. Know what you’re feeling and say how you feel.
  • Find someone where you genuinely love the person that they are. 
  • “Realize that all the sh*t you think is big in your twenties is little minor sh*t when you look back on it in your thirties.” Ex: “He wants to hang out with his friends tonight. Back then I would freak out and be all upset but now I’m like pushing him out the door to do it.”
  • Get your heart broken as much as possible. As tough as it is in the moment, looking back on it you’ll realize it’s the times you grew most as a person and learned the most about yourself.
  • Don’t forget your friends in a relationship. You should never have to ask for someone’s permission to hang out with your friends, especially not your significant other.
  • “The second marriage is usually the right one.” (ain’t that encouraging?)
  • Cherish the times you have away from that person. That’s the time you have to do something for yourself, like watching TV where you’re the one in control of the remote.
  • Find someone who you want to take care of. People don’t stay healthy forever and being with someone whom you genuinely want to care for is special
  • “Acknowledge and accept that every relationship is f***ed up.” Relationships are hard and they require work from both parties in order to succeed. 




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In standard fashion, a week after finishing this internship, it is really starting to hit me how lucky I was to have been surrounded by such incredible people this summer. From prepping for the final presentations to the last minute literature review on community engagement evaluation, the last two weeks of the internship were a whirlwind with no down time. Since that time there just hasn’t seemed a time to collect my thoughts and finish off this final blog (sorry Sea Grant!) Two flights and a U-Haul trip later (more on this in a hot minute), I was right back in the swing of things. Four hours after my getting picked up from the airport I was sitting in a lecture hall in New Britain Connecticut getting briefed on the syllabus for the upcoming semester. I know I’ve got plenty more to experience, but I’d like to think I’ve done a fair share of traveling for my age. Yet of all my experiences, coming home always feels the weirdest. Feeling like your experiences have given you new perspectives on life and helped shape you more into who you really are. Then coming home to find that, while you were out there exploring and growing, life at home had just kept on going without you. Home hadn’t changed a bit. Which to be honest can be pretty nice, but at the same time makes you just want to scream. I’ve got so many stories to share, but no audience to listen to them.

This summer has been different to all the traveling that I’ve done in the past. I wasn’t backpacking my way through Europe while I should have been in class, hitch hiking through Nepal or diving in the South Pacific in the name of science. Newport Oregon was the closest to home that I’ve spent an entire summer in 3-4 years. That feels pretty odd when I write it out. But what’s even weirder, is that it I felt more out of my comfort zone this summer in my own country than I did in any of my trips in recent memory. For the longest time I couldn’t figure out why that was. The people I was surrounded by were incredibly friendly and I was in a state that I had dreamed about visiting for years, why would I be out of my comfort zone?

Until this point I had only met individual peers whose commitment and motivation just caused you to respect them. This summer I found myself living with 18 of those people all at once. Every single one of them joked around like a normal person, but get them on the topic of their field or their passion and they would blow you away. It was humbling and inspiring. Being surrounded by so many incredibly intelligent and motivated people properly intimidated me at first. What was I doing there? I was older than they were and still procrastinated so hard that my final blog post was a week late (my bad). Did I have what it would take to make it in this field? Oddly enough, at the same time that I was nervous, I was hopeful that there were so many amazing young people who hadn’t decided to chase the money. Instead they chose a career to make a difference in the world. I had found a group of people who cared more about helping the planet more than the nice things money could buy. Intimidation gave way to motivation and I wanted to do as much as I could for the environment that I loved so much. Maybe I couldn’t make it in the hard sciences, but I feel like I knew that all along. I’m a people person who loves the environment and I reckon the best way of doing my part is to work with the people.

Alright introspective monologue over. Onto more important things:


The Objective Top 3 list of the Summer at Hatfield Marine Science Center

Forward: Top 3 was a joke that originated in Angelina making fun of me for saying it constantly. It turned into a way to exclaim something that is properly epic. Saying something in the top 3 does not rank first, second or third, but rather a collective top 3. These are some of the things that stood out this summer and get the nostalgia running pretty hard.


Top 3 Modes of transportation:

  1. Hatfield marine science center foldable bikes
  2. Begging the Californian interns to drive us around
  3. U-Haul Truck: Zach and I had our flights home out of Seattle. We had originally figured we’d be able to hitch a ride with someone, but the Wednesday before the internship ended we realized that was not the case. As a semi joke a friend of ours suggested renting a U-Haul since we had to be 25 to rent a car. After having a good laugh we took a look into it. Not only was it cheaper than renting a car or taking a bus/shuttle combo, we only had to be 16 and could drop it off in any of the U-Haul drop off points in Seattle! So without further hesitation we rented a full size (the only size available) and drove this bad boy 6 hours north. Was it the most extra mode of transportation? Possibly. Was it genius? Well.. we would like to think so. Did we have a blast doing it? You betcha.

Top 3 Cinnamon Rolls (No brainer on this one):

  1. Fishtail Café
  2. Fishtail Café
  3. Fishtail Café


Top 3 Waitresses at Fishtail Café

  1. The sweet middle-aged lady that calls Zach and I baby
  2. The sweeter older lady that refers to Zach and I as her boys
  3. The 20 something lady that assumed we were there to flirt with her (We just wanted cinnamon buns)


Top 3 “Songs” of the Summer

  1. Norf Norf by Vince Staples
  2. The entire Moana Soundtrack
  3. The entirety of Funk Wave Bounce Vol. 1 by Calvin Harris

The last two albums were basically extended songs as that is all we listened to this summer.


Top 3 Movies of the summer

  1. Moana – watched it 3 times and listened to the soundtrack ~a million times
  2. Shrek – ability to quote this movie is amazing
  3. The Dark Knight – So many people hadn’t seen this movie??


Top 3 worst Lil Yachty lyrics – Lil Yachty is a terrible rapper, but his terrible lyrics are one of the things that really brings people together.

  1. “You need to stay up out them streets if you can’t take the heat. Cause it get cold like Minnesota, cold like Minnesota.” – Because he’s been to Minnesota and its “really cold there”
  2. “Almost had a lifetime sentence, but I beat it, shout out to Pat! Pat, that’s my lawyer, he got me off them charges. 8 stacks for that boy, he took care of the boy” – Hits a soft spot because we, regardless of gender, are part of the “boyssssss”
  3. “Remember that time I put those pepperoni on your face. Made you a creature. Now I think about you, every single time I eat pizza.” – Top 3 most heartfelt love lyrics of all time, FOR SURE.


Top 3 Activities to Participate in on the Hatfield Dorm Porches

  1. Cold Ones and Ice Cream Porch Nights – A time for people to come together and talk about science, our feelings, Lil Yachty, race relations in the U.S., travel stories, and anything that comes to mind. A proper judgment free zone.
  2. Beer Can Hockey w/ broom sticks– self explanatory
  3. Impromptu dancing while waiting for any of the Californian’s to drive us places.


Top 3 Exclamations

  1. YA BOYYYY – A true classic way to welcome someone into your home or welcome yourself into someone else’s home
  2. TOP 3 “insert object being pointed at”, TOP 3 “insert another object” – just a great way to display affection of whatever you’re looking at.
  3. I AM SHOOK, I TELL YOU, SHOOK. – Usually exclaimed after Game of Thrones.


Top 3 Things to get stressed about

  1. Lack of proper signage at the Marine Reserves
  2. Lateness of blog posts
  3. Game of Thrones


Top 3 things spotted while snorkeling in Newport Harbor

  1. Some kelp
  2. Rocks
  3. TWO crabs


This could go on forever, but this is already super late. So I will finish it here. Thank you everyone for a wicked summer. Especially Sea Grant staff for organizing everything and constantly being supportive of us.

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Hello Everyone,

I will not be graduating until early 2018, so this is not my last post as an Oregon Sea Grant Scholar. However, this IS my last post as a Robert E. Malouf Scholar. With that in mind, I decided I would give a taste of what I have been doing this summer, but leave the “whole shebang” for my final post.

Recall, my project is characterizing metformin, a pharmaceutical drug, as a contaminant of emerging concern (CEC) in the lower Columbia River estuary. Fully characterizing a CEC in the environment should obviously include an ecosystem component. Thanks to the Malouf scholarship, I am currently exploring the effects of metformin on the lower food web.

This summer is best described as a series of never-ending lab experiments and instrumentation. It turns out that testing the effect of metformin on phytoplankton and microbes is harder than it looks! Currently, my lab bench looks like an explosion of flasks, vials, pipettes, and sediment. Like most scientists, I spend more of my time washing and prepping experiments than I do actually collecting data – an unromantic fact of the scientific existence that the public tends to ignore. I will focus on my phytoplankton work, since the microbe experiments are currently taking an unexpected turn (more on that in the future!).

Most of my phytoplankton work has revolved around the PAM fluorometer – an awesome device that measures the kinetics of fluorescence in photosynthetic cells.

The simple beauty of PAM.

If you recall basic photobiology, photosynthesis (the production of energy from sunlight) works through an electron transport chain that takes place in the thylakoid membrane of chloroplasts in photosynthetic cells. Pigment molecules (e.g. chlorophyll b, xanthophylls, or carotenes) within a membrane photosystem (Photosystem II) absorbs photon energy from sunlight. This energy is used to excite electrons donated by oxygen in water. The excited electrons are held less strongly by the oxygen nucleus and escape into a “pigment funnel” (i.e. antenna complex), where it is passed from pigment molecule to pigment molecule toward an ultimate electron acceptor (i.e. chlorophyll a) at the reaction center of the photosystem. The chain continues after the electron is shuttled to another photosystem (Photosystem I) and a different electron acceptor. The electron will ultimately be used in the production of NADPH and a proton gradient that fuels ATP synthase to produce energy.

The concept of photosynthesis: an electron from water is excited to a higher energy state and escapes into Photosystem II where it is passed from pigment molecule to pigment molecule until it hits an ultimate electron acceptor. The electron is then passed through an intermembrane system to Photosystem I where it is funneled to another electron acceptor and eventually used to reduce NADP+ to NADPH. This forms an intermembrane proton gradient that drives ATP synthase and the production of energy.

In a nutshell, the PAM fluorometer stimulates and measures this process by delivering light pulses to a water sample containing photosynthetic cells (algae, in my case). Recall, photosynthesis is based on the idea of an excited electron losing energy. Whenever an excited electron moves to a lower energy state, it must release energy. This energy is released in the form of long wavelength fluorescence, which can be measured by a fluorometer. By measuring minimum and maximum fluorescence in response to a series of light pulses, the PAM fluorometer can measure electron transport rate and non-photosynthetic quenching processes (e.g. energy lost via heat, instead of fluorescence). In my case, this is perfect for looking at the effect of a chemical compound on photosynthetic efficiency.

My labmate jokingly dubbed the PAM fluorometer a “magic box”, however, there is a scary amount of truth to that term. The PAM fluorometer is an amazingly compact device that can measure an amazing number of photosynthetic processes. People tend to take it for granted since it appears simplistic: turn it on, insert sample, measure photosynthesis, and you’re done! WRONG.

There are so many quirks to the device. First off, the manual. Or, should I say, manuals. Part of one topic will be explained in one manual, but an important note on the same topic will be explained in the other manual. Confusing is an understatement. Let’s not mention the calibration protocol which cost me a month of fiddling.

As a result, I have learned the PAM fluorometer from the inside out. Some examples of what I have learned over the past three months: (1) there is an optimum time to “dark-adapt” samples to make sure photosystems are completely receptive to light (i.e. completely empty of electrons), (2) far-red light should also be used to fully oxidize Photosystem I and the intersystem electron transport chain to maximize electron receptivity, (3) the sample should be diluted until the fluorescence value does not exceed a maximum value, and (4) the sample cuvette has an optimum volume and should be cleaned with ethanol in between samples to prevent obscured light paths. These are just some of the many things that I had to learn by trial and error through countless failed phytoplankton experiments.

I am aware that this entire post is about the PAM fluorometer, but it has arguably been my greatest achievement this summer. I am proud that I am mastering such a deceptively complicated device. By the end of this project, I plan on having written a detailed calibration protocol and detailed illustration of the PAM fluorometer so that future lab members can easily take measurements without a similar summer of trial and error. The long process was a blessing in disguise though – I truly have a better grasp on photosynthesis and fluorometry instrumentation.

What about the results? Well, if you don’t make it to the CERF conference this year, you will have to wait for my last blog post. I am currently doing my fine-tuned toxicity experiments with Chlorella vulgaris (a basic green algae) and will be performing the same experiments with Thalassiosira weissflogii (a diatom, which tends to be more sensitive). This should give us a good idea of the effect of metformin on the photosynthetic processes of two representative organisms in the Columbia River estuary.

Stay tuned.

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The work part

It’s cliché to say (and it’s cliché to say “it’s cliché to say”), but these ten weeks really have flown by. Looking back, it’s as if the first week and a half flowed like molasses, and then the rest of the summer got dropped into a time warp that spit me out here on the second to last day of my time at Hatfield. I have to honestly say that this internship did not always follow my expectations, however it did not disappoint. First off, I expected to be interning with the US EPA, but due to issues with technicalities I ended up being taken in on a USDA project. I expected to be working in an office and finally getting some wear out of the ‘business-casual’ clothes I bought in high school. I ended up wearing t-shirts and working in a lab with eelgrass samples still caked in mud. I did not expect I’d get to go on multiple fieldwork trips to Washington and I definitely did not expect to experience a month-long power outage of a federal building. However, these are all details, and while we can form predictions of how we think such details will play out, I’ve learned that things never are completely how you expect them. My expectations of the internship that were met include the experience I gained in estuarine ecosystems, affirmation of my love for marine science and field work, and the initiation of a professional social network. I was able to present my research to experienced scientists, attend two graduate student thesis defenses, and form many friendships with young scientists like myself. Working at the Hatfield Marine Science Center has been a great experience to participate in research and learn about some of the many other research projects going on in the Pacific Northwest.

My PTU (Predation Tethering Unit) fortress- a daily activity in the field to organize PTU’s prior to deployment

The play part

I’d like to revisit the tourist in my own life concept that I discussed in my first blog post. I said Newport, OR was very different from Los Angeles and Maryland, however, I now would also like to say I’ve had the most American summer of my life here. I spent the 4th of July on the beach, had a BBQ, and watched fireworks over a river. I’ve floated in rivers and waded in creeks, gone camping and hiking many times. I watched monster trucks at a county fair and worked in the realm of agriculture (USDA). Did I mention we’ve been living in wood cabins all summer? I felt so out of my element my first day here, and I felt so at home by the end. I have always valued living in a new place for extended periods of time over traveling to many places for a week or so because you really get to experience the place rather than visit it, and I feel this experience has definitely accomplished that goal. I got to not only visit Oregon, but become a part of it for a while. I went to a local “beer and dogs” festival at a brewery, cheered on fellow interns and REUs at a state volleyball tournament, and became a regular at Fred-Myer.

I think the most rewarding part about making yourself a tourist in your own life is overcoming the tourism. It’s conquering the fears of being on your own in a new place with new people, and turning those strange places and strange people into home. At the beginning of summer, I asked myself “why do I keep putting myself in these new and uncomfortable positions?” and this summer has truly reminded me of the joy that can come out of those challenges.

Holding a crawfish during the OSG camping trip

The feels part

One thing that really made a difference to my overall quality of life this summer was the amazing group of students and interns that I have had the pleasure of living with. Having a group of adventurous, passionate, and intelligent people to see every day after work and explore Oregon with has been an extremely valuable part of this experience. It’s a little weird being back to Los Angeles where topics of daily discussion don’t include bomb calorimetry and marine reserves, and beach volleyball is not the dinnertime entertainment. Where it may not be as casual to discuss climate change as it is to discuss the latest Calvin Harris album. Every person I have befriended here is not only bright but driven. I consider myself not to be an easily inspired person (it takes more than a documentary or article), but the REU’s and Sea Grant scholars I met this summer really do inspire me to be a scientist even when we are not always listened to, to stay passionate and engaged about the state of our environment and country, and to stay open to meeting new people even though it may be challenging at first.

Some of the Sea Grants and REUs this summer– if you follow any of us on social media you’ve probably already seen this ~5 times, but dang we look good)

Thank you to Sea Grant and my mentor for the internship and thank you to all the friends I made along the way for making it unforgettable.

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And That’s That!

Posted by: | August 28, 2017 | 3 Comments |

Having perused the previous Summer Scholar’s blog posts when applying for this program, I read that not only will you learn a great deal about yourself, research, and science, you will form connections with people who will serve as role models and friends long after the program ends. At the time, I knew that this would be a great experience, but I was not aware of just how meaningful those students’ statements were until now as I write this final blog post. More on that in a moment; first I want to reflect on the final week of this program. As always, it was full of positive experiences. The final weekend consisted of presenting at the Final Symposium, celebrating the end of the program with the rest of the Scholars, and traveling to Corvallis to see the total solar eclipse. To say the least, that was the most eerie, fascinating experience. The remaining weekdays consisted of finishing up small projects, saying goodbye to the magical Bandon office, farewell dinners, learning quintessential dart games from Miles, apricot ale, making too much noise with Chris, Rowland, and Dustin at our farewell breakfast, packing up all of my belongings, turning in my keys, and driving to Portland for my last night in Oregon. That evening, I visited Powell’s bookstore with a friend from school, which takes up an entire city block. Literally a dream. This weekend, I flew to my hometown of Denver for my mom’s wedding. I didn’t take any pictures because I was too preoccupied catching up with family and friends (my mom has 7 siblings, most of which have kids, some of whom also have kids), and butchering a toast in front of all of them because I was too overcome with emotion and gratitude. But here’s a picture of my mom and her best friend that my sister managed to snap. Seeing her celebrate love with our family surrounding her was one of the most beautiful experiences. 

Now that the craziness has died down, I am finally able to sit down and reflect on this past summer in the sunny, plant filled kitchen of my sister’s home. (Yes, the obsession runs in the family). I’ve previously written a bit about how my research this summer led me to learn how to maintain a strong sense of patience and diligence in the face of discomfort. (I’ve also learned that I have an almost uncontrollable sweet tooth when stressed. A very tangible thing that I will take from Oregon is my newfound obsession with Pepperidge Farm’s chocolate hazelnut pirouettes). In addition to learning about my personal research process, studying environmental interpretation, the tourism industry, and natural resource based recreation has shown me the overall potential to strengthen natural resources through sustainable tourism when collaboration between communities and the sharing of knowledge between stakeholders are the top priorities. There is so much potential for community collaboration, economic recovery, and ecosystem restoration/enhancement in the southern region of Oregon, and I hope more people have the chance to experience the wildness that resides there in the secluded coves, uninterrupted sand dunes, geologic sentinels, and centuries-old forests. 

As for the people I had the privilege of interacting with, saying that I am grateful for them is an understatement. There are so many people that have either offered me their knowledge, time, books, stories, and/or connections with other influential people that have also proven to be invaluable.

Surrogate Oregon parents Rowland and Chris with Dustin. We got scolded for laughing too loud.

Having now completed this program, I feel more motivation, bravery, and excitement for the future. Upon my return to California in a couple of weeks, I plan to complete my last round of classes, resume my role at the Estuary Program, graduate (!!), work at the Marine Mammal Center, and bring in the conclusion of the calendar year with getting my PADI Open Water Diver certification. After that – time will only tell. Within a few years from now, I hope to apply to graduate school, my (tentative) top choice being the Bren School of Environmental Science & Management of UC Santa Barbara to double-specialize in coastal marine resources management and water resources management.

In wondering about what I will end up pursuing, I am reminded of a statement I made in the essay I wrote when applying for this program: “As I approach my graduation in December of this year, and as climatic and destructive threats confront coastal communities, I feel a sense of urgency to seize every opportunity available. My lifelong goals are simple: to always learn, and to contribute to the well-being of the planet. Whether I become a scientific explorer for the National Geographic Society, obtain doctorate degrees in various areas of study, or lead a successful public environmental agency, my ambition is to be in a challenging profession that will further the scientific discovery of the world and augment the protection of our planet’s marine and terrestrial ecosystems.” This program has reinforced those goals and has added/strengthened other passions in the mix, such as marine mammal ecology and the indescribably, critical importance of effective science communication. 

Thank you to Sea Grant; Miles, the Scholars, OSU Extension; Haley; Dustin, Dave Lacey, Anthony, and friends of South Coast Tours; Rowland and Chris Willis; Erik Urdahl; Justin Meyers; Tom Calvanese; Joy Primrose; Gary & The Whale’s Tail; Marine Discovery Tours; The Oregon State Marine Board; Capt. John Blanchard; Dean Finnerty, Frank Burris; Mark Lottis; Sarah Kolesar; Mary Pleasant; and MOTHA EARTH. This has been a beautiful experience. 


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Clichés from California

Posted by: | August 27, 2017 | 1 Comment |

My lovely move-in crew to my new home in Monterey.

It amazes me the rate at which humans are capable of adapting. In just one week, I have made the trek from a life on one central coast to the next. I write to you now in California from my new balcony in Monterey. I had a wonderful move-in crew (my family) to help me set up in this new home. In the spirit of a new beginning, I have given myself the allowance to be cliché in reflection with my final blog post.

Oh how I’ve missed the California sun.

This summer has been a challenge. Not only have I learned to engage in interdisciplinary research outside of my normal scope, but I have reformed my ideologies as a person. I am increasingly aware of the social clock, watching all of those I grew up with get engaged, married, and have children. It can be easy to look at these developments of those around you and wonder, “Am I on track?”

From my research perch, all of these things are not yet an option. I am merely focused on my tasks at hand. That being said, this summer’s experience has given me one of the greatest insights into my future ambitions. Though not directly related to my research topics, this internship has caused me to parse out what I want in life from a holistic perspective. I love my career in research. And I want to pursue it.

What a successful summer! Jumping for joy in Astoria, Oregon.

As I begin to pour over my new books, research articles, and course requirements, I feel sentiments of gratitude. Thanks to the skills that I have sharpened this summer, I feel no hesitation to learning new material. After all, if a psychology major can understand the inner workings of national economics and marine policy, then what truly may stand in our way?

I am proud of our work as summer interns. Every REU and Sea Grant scholar I met during my time in Oregon shone bright with potential. I have no doubt that I will encounter them all again, working as colleagues towards a common goal in our appointed fields.

Though I walk away with a certain degree of healthy pride in our overall accomplishments, I believe that humility was one of my own greatest lessons. In being surrounded by such an abundance of remarkable people, I hold a newly found reverence for both passion and intelligence. Even amidst a politically uncertain time, I have hope that those who truly support inquisition and learning will be heard. I walk away from this internship more certain of the importance of research as well as the humble mind that must come with an ever-questioning spirit.

Goodbye Oregon- see you again soon.

Thank you, Sea Grant, for pushing our bounds and asking us to grow. I am leaving this internship a better and more hopeful person than I came. For anyone reading this blog with anticipation, waiting to hear back for next year’s recruitment, I have yet another cliché word of advice. Enter this experience with an open mind in all aspects, whether mentally, physically, socially, or spiritually.

With that, I will leave you. Thank you for reading along with me this summer.

Sarah Ann Coffin



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