Allison Lee is a biological oceanography PhD student at Scripps Institution of Oceanography, working to bring phytoplankton research to the world of Citizen Science in the Arctic and the Antarctic. In this episode we discuss her experience working in a lab setting, her inspiring blog ‘Woman Scientist’, her passion for phytoplankton research, and more.
Allison just completed a field season in Antarctica aboard the Hebridean Sky, launching her FjordPhyto Citizen Science project with willing and excited passengers. The beginning of this story was featured in the San Diego Tribune. During the 2017 – 2018 Antarctic summer, citizen scientists from multiple tour ships will be collecting samples which contribute to current climate research.
If you’re interested to learn more about the Citizen Science Project – FjordPhyto – in Antarctica, follow along on the FjordPhyto website, Instagram, and Facebook.
Allison Albritton is an ocean advocate, herself, sharing stories of positive change for the ocean. If you’d like to learn more about Allison Albritton, read the Woman Scientist interview here.
Re-posting an article I wrote for National Girls Collaborative Project, because I’ve added fun links in this version! You can read the original article published on National Girls Collaborative Project Blog (submitted by Greta Carlson on April 29, 2016 – 2:20 pm)
Contributed by Allison Lee
Growing up I never had a clear picture of what I wanted to become. Inspecting insects, creating mud-pies and gazing at the stars were childhood past times and as I grew into a teenager I embraced traveling and learning more about nature. I didn’t immediately connect all of these interests with becoming a scientist. My parents were not scientists. No one in my family had degrees beyond a high school diploma. I remember wondering if I even needed to go to college. I spent years frustrated by my lack of vision; finding the dream job I felt contained all of my passions was a struggle.
By the time I turned 30, I had traveled to all seven continents as a Biologist studying a diversity of lifeforms from microscopic algae, to songbirds, parrots, mice, squirrels, big cats, and whales. Obviously I figured something out! Life is funny that way. A hunch paired with the right blend of curiosity, odd jobs, research-focused vacations, volunteer opportunities, frugal living, and luck delivered me to my dream career.
Finding my passion
In my high school senior yearbook I wrote that I wanted to be an astronaut. I thought astronauts traveled the most of anyone on Earth. Inspired, I researched the degrees earned by NASA’s astronauts and found an overwhelming proportion had studied science. I decided to major in biology and geology at the University of Washington. It wasn’t until sophomore year when I had the epiphany that biology was my passion.
The scope of biology is broad and I wanted to learn as many disciplines as possible. Senior year, I signed up for an internship in neuroscience at the Allen Institute for Brain Science and found a part-time lab job in the Immunology Department taking care of a mouse colony. I started learning molecular techniques and computer programs, using fancy pieces of equipment, and doing those things called PCRs and Southern Blots. I wasn’t entirely sure what was going on – but I was doing SCIENCE!
Questioning my interests
After I graduated with my Bachelor of Science in Biology, I continued to work full time in the immunology lab. Two and a half years passed. Restlessness set in and I began to wonder if maybe I just didn’t like science anymore. I knew one next possible move was to go to graduate school, like many of my college peers, but I didn’t know what I wanted to commit to studying. I wasn’t inspired by my neurobiology or immunology experiences. I hated doing computer work. I felt stuck. So I did the thing you’re never supposed to do: I quit.
The next two months were spent feverishly searching job boards, institute websites, and email listservs. Because of my interest in many aspects of biology, I didn’t know where to focus my efforts. Regardless, I felt optimistic that my Dream Job was out there. A job posting for a field technician conducting songbird research caught my eye. I didn’t know much about birds, but I convinced the interviewer I could learn bird songs because I learned other languages easily and had been playing music for 15 years. It worked! Every morning I woke at 4:00 AM to get to the field site before the sun rose. I got paid to be outside tromping through the woods looking for birds. It was during these quiet twilight mornings, outside in nature, that I realized THIS was my dream job. I never wanted it to end.
But, as is the nature of seasonal fieldwork, it did. Five months later, I found myself once again unemployed. Turns out, seasonal work is the usual for field technicians. I knew that field biology wouldn’t be the most lucrative career choice, but I felt empowered to commit myself to studying the environment – whether I got paid for it or not.
The sacrifices
I went on a quest to find as many wildlife jobs as I could. Later that year, I studied forest fire treatments on threatened squirrel populations; I studied the breeding behaviors of endangered parrots in Mexico. Each time, the pay was minimal to none, so I worked side-gigs as a professional baker and bartender to pay my bills. While I was happy to gallivant around the woods for science, working for free wasn’t exactly the dream job I had in mind. I was turning into a poor disgruntled vagabond.
In an effort to gain a sustainable salary, I left fieldwork and went back into the lab to begin a project at the Institute for Systems Biology (ISB) investigating the genetic responses of algae to climate change and ocean acidification. I knew nothing about marine systems but I had skills in the lab and stellar references. Part of me thought leaving the field was a mistake but as I gained exposure to the natural world within a molecular science framework, I saw the impact of a systems approach to research and I was hooked. I still missed going out into nature every day, but I kept an open mind and a positive attitude.
Over six years have passed since I went back into the lab and the job has given me more opportunities than I could have imagined. What started off as a lab job performing controlled experiments on algae has evolved into a field job sampling algae from the natural environment. This work has led me all over the Puget Sound area of Washington, as well as to Hawaii, and even as far as Antarctica!
The best of both worlds As a field scientist working indoors, I still daydreamed about the rainforests. On the weekends, I’d flee to the mountains. With a bit of money saved up, I decided to satisfy my restless soul. I used my vacations to help conduct research on voluntourism projects, like Earthwatch. From aboard a restored rubber boom era steamship, I spent three weeks studying biodiversity in the Amazon jungle. I realized I could save my money, use my vacation time to get out in the field, and still have a paying job in science. It was the best of both worlds!
What’s in a dream? I’ve come to believe the dream job doesn’t exist for me, and I don’t think it’s beneficial to maintain that perspective. I have too many passions – too much wonder for the potential of science in the world. I find fulfillment in contributing to important work for the environment and interacting with innovative collaborative thinkers. I benefit from an extremely flexible schedule, live in the city, and travel to amazing places through work. And I’ve been lucky to have many other amazing experiences volunteering with local and international conservation organizations. I am continually seeking as many opportunities as I can find, but this time things are different; I’m no longer looking for the Dream Job, I am creating the Dream Career.
Allison Lee is a Seattle native who loves coffee, talking to people, and learning new things. When she’s not doing science you can catch her ultra-running, cycling, hiking in nature, traveling, and burning the candle at both ends. At age 32, she has finally realized the differences between working a job and building a career. This summer she will begin a Masters degree in Marine Biodiversity and Conservation at Scripps Institution of Oceanography in San Diego California with the hopes of following another curiosity: the social, economic and policy side of marine science. You can follow her and see examples of other inspirational women working in the field at Woman Scientist on Instagram, Facebook, and the Web.
**UPDATE** (April 2018): Allison graduated with her Master’s degree June 2017 and shortly after received funding from the National Science Foundation to support the Capstone project she created with Dr. Maria Vernet (watch the video here). Allison is now in the Biological Oceanography PhD program with Dr. Vernet at Scripps Institution of Oceanography leading the FjordPhyto citizen science project with tourists in Antarctica and the Arctic. She also works part time as a Senior Research Associate at Synthetic Genomics (Target CW) to advance breakthroughs in algal biofuel research.
Sure, I ate the traditional spiral ham for dinner, but I was at sea and my family was nowhere in sight.
I was with eight strangers aboard the R/V Clifford A Barnes cruising around the Puget Sound for six-days of research monitoring ocean acidification, referred to as OA for short.
In honor of the sea and the nature of the project, I feel I should have been eating oysters for Easter dinner!
What is this Ocean Acidification you keep talking about?
If you’ve never heard of this term, and want to know more about it (which you should want to), I will redirect you to the links found on the University of Washington’s College of the Environment’s host website. Spend some time here familiarizing yourself with the globally important terms and what it means to our environment’s health:
Below are some great graphics illustrating the important fluxes occurring in the environmental system. Take a good look at all the arrows and think about your personal experience with each. Images are from NOAA PMEL.
Changing Oceans, Changing Biology
It is easy to think of the ocean as a big vast body of empty water that doesn’t need much attention. Maybe you’ll think of a couple animals that live there like whales, sharks, and coral reefs. You’ll easily identify with currents and tides washing up on the beach if you’re a tide-pool lover or beach comber. The beauty of the oceans is that there is so much more than that. What most people take for granted is all of the intricate dynamic exchanges occurring between land, air, and water which perfectly tie biology, chemistry and geology together!
Currently, a lot of attention is being directed to a particular exchange: atmospheric carbon dioxide with the oceans. The carbon dioxide being released into the atmosphere (yes, predominately due to human needs for fuel) is absorbing into the oceans. This absorption into the ocean is a natural process as the gases in the ocean below like to be in equilibrium with the gases in the air above. However, once that carbon dioxide gets into the water it reacts with the water molecules setting off a whole chain of chemical reactions which lowers the ocean’s pH, termed ocean acidification. This rapid change we are seeing, which has been calculated to be escalating since the time of the Industrial Era, has us concerned about the chemistry and life in the oceans.
“If carbon dioxide continues to rise unchecked, computer models show that acidification will deplete carbonate ions in much of the ocean by 2100, turning the waters corrosive for many shell-building animals.”
From The Acid Test www.nationalgeographic.com
Why are we doing this cruise? … Because oysters.
No seriously, the reason us scientists are out here monitoring the waters comes from the birth of the Blue Ribbon Panel in 2011. This was enacted because, as in Governor Christine Gregoire’s own words, “Our shellfish industry employs thousands of people, and brings in millions of dollars to our state on an annual basis. Continued success depends on healthy ocean water.” The Blue Ribbon Panel is “a panel of science and policy experts to address the effects of ocean acidification on WA’s shellfish resources.”
Science will save the oysters!
In 2013 the Blue Ribbon Panel spawned the Washington Ocean Acidification Center (WOAC, sounds like ‘whoa-wack’) . The legislature requires the Center to execute five priority actions. The cruise I am currently on exists in response to the second bullet point listed within the actions. We are not directly dealing with oysters but monitoring the health of the Puget Sound builds upon our knowledge of the areas which are pivotal for successful oyster growth and harvesting:
Establish an expanded and sustained ocean acidification monitoring network to measure trends in local acidification conditions and related biological responses. This monitoring will allow detection of local acidification conditions and increase our scientific understanding of local species responses.
Below is a photo map of all the stations we will be visiting on this trip. The stations highlighted in pink are the specific locations my boss is interested in (more about that below). The ‘P’ indicates these are stations included in PRISM , the Puget Sound Regional Synthesis Model which sends biannual cruises within the greater Puget Sound to collect oceanographic time-series data. The network NANOOS was created as a place to hold more detailed scientific information and comprises over forty entities researching the Puget Sound as part of the ocean observing system.
All Hands on Deck – How We Sample
The contraption to the left is referred to as a CTD. This is a little package of sensors that measure Conductivity Temperature & Depth. It rides on the metal frame lined with gray Niskin bottles which we call a rosette.
The CTD comes up on deck full of sea water collected from different depths in the water column and we begin sampling for many different variables:
oxygen
dissolved inorganic carbon
nutrients
chlorophyll
RNA/DNA
Rachel is the first to crack open the Niskin and takes a sample of seawater for oxygen measurements. It is important to get the sample stored into the bottle as soon as possible to limit the amount of time the sea water from depth is exposed to the atmosphere.
These two bottles, pictured below, contain sea water from Hood Canal. Chemicals are added which grab on to the oxygen within the water and create a precipitate (the orange color). The left sample is from the surface and has more oxygen which creates more precipitate making it orange. The right sample is from depth and has less oxygen which creates less precipitate making it less orange (whitish).
Next, the plankton nets are deployed. On this cruise we run three types of tows: vertical, horizontal, & oblique.
Plankton net tows give back valuable information about the biological community of zooplankton. One species of particular interest are the pteropods, endearingly known as sea butterflies who’s shells are visibly suffering from increasing CO2 conditions:
The smooth shell of a healthy pteropod is seen at left. The pteropod in the center was exposed to elevated CO2 conditions in a laboratory, to mimic conditions researchers saw in the wild. And at right, a shell with holes and pits, also produced by laboratory conditions, corresponds to some of the most extreme damage scientists expect to see with elevated CO2. From The Seattle Times SEA CHANGE stories.
I am a research technician on this ship representing my Principal Investigator, Monica Orellana, with the Institute for Systems Biology. A portion of her research aims to understand ocean acidification effects on the phytoplankton community at a genetic level using next-generation sequencing tools. When I am not collecting my own samples, I help out collecting samples for the head technician, Rachel Vander Giessen.
On this cruise I would like to highlight the lady in charge: Rachel Vander Giessen. She is the technician for the head scientist, Jan Newton, and was on the ship running the science show. She has a bachelor’s degree in physics, spent time on chartered yachts as a naturalist, wanted to become a captain through the Maritime Academy, was a bartender and a barista, and is now a research technician in oceanography. She is the epitome of someone who is highly involved and doing cool shit without having a PhD. You have to read more about her in her interview (link coming soon).
Want more photos of the trip aboard the R/V Clifford A Barnes?
We’ve all gone swimming in the lakes and in the seas. We’ve all choked on that accidental gulp of water while swimming carefree.
But have we all looked under a microscope to see what these waters hold?
What you just saw were three plant-like organisms called diatoms, and the moving thing: a small larval crustacean called a nauplius. Makes you think differently about that next gulp of water you’ll take, doesn’t it?
I had previously never given much thought to the invisible marine world until I was employed to work on a project researching the effects of climate change on micro-algae, particularly the diatom Thalassiosira pseudonana.
What a beaut!
Who is this Thalassio-whatchamacallit and why should I care? Let me ask you a question:
Where does the earth’s oxygen come from? Humans, as the terrestrial beings we are, will easily shout out, “The trees!” But did you know the trees are only responsible for producing about 30% of that oxygen? The algae and phytoplankton living in the water are responsible for the other 50-70%! That is more than half!! In addition, these amazing silicified (glass) microorganisms make up the base of the food web and are responsible for 40% of the ocean’s primary productivity. What an incredible hidden forest.
I will never look at the ocean in the same way.
Phytoplankton can be identified by NASA satellites through their chlorophyll
Phytoplankton as Art
I learned of a man named Klaus Kemp, nicknamed The Diatomist, who also doesn’t look at the ocean in the same way. He sees magnificent beauty in the Invisible Forest and has spent his life mastering the Victorian art of creating kaleidoscope-like arrangements of diatoms.
I don’t think I could have the patience or attention span to do such painstaking technical arrangements under a microscope but don’t get me wrong, I do love a good microscope session attempting to photograph some of the world’s smallest organisms.
Capturing Invisible Things
The best way to collect a large abundance of phytoplankton is to do a tow with a net that has a good funnel-shaped collection cylinder called a cod end. Some nets are huge and require winches to lower into the water. Others are more manageable and can be done by hand, towed behind a row boat.
Phytoplankton can range in size from 2 – 1000 microns. What does that even look like? If you run sea water through a mesh filter that had a 333 micron weave, you could see Coscinodiscus wailesii by eye; It looks like tiny grains of sand. Does that help the visual reference at all?
Unannounced Changes
For three weeks, from March 17, 2015 until April 3, 2015, I worked up in the Pacific Northwest’s San Juan Islands at the University of Washington Friday Harbor Labs. My boss and Co. were running ocean acidification experiments on our lab strain diatom, Thalassiosira pseudonana, but we wanted to also collect the wild plankton living in the harbor. Weekly we would take the row boat out to do a tow. I attempted to photograph what I saw using only an iPhone through the microscope:
Week 1: We saw many different types of diatoms: Thalassiosira, Melosira, Coscinodiscus, Chaetoceros, Ditylum, Thalassionema, Skeletonema, Cylindrotheca, & Corethron
Week 2: The diatoms had mostly been replaced with dinoflagellates (Protoperidinium, Dinophysis) and zooplankton, such as the crustacean copepods.
Week 3: The waters were teeming with copepods and tiny little jellies: Cnidaria and Ctenophora.
Week 4: Ctenophores had disappeared and a diverse collection of diatoms and dinoflagellates floated amongst a gazillion copepods. (Diatoms: Thalassiosira, Coscinodiscus, Ditylum, Chaetoceros, Odeontella, Thalassionema, Skeletonema, Bacillaria, Cylindrotheca, Triceratium; Dinoflagellates: Ceratium, Protoperidinium.)
While I would not spend hours arranging any of these into beautiful mosaics, I would spend hours trying to photograph them as they are.
Lab Diatoms Go Wild
What experiments are we doing with these critters at the Friday Harbor Labs that we can’t do back at the Institute’s labs in Seattle? Mesocosm Experiments. Mesocosms are a bridge between controlled laboratory experiments (which use artificially made sea water) and the more variable and uncontrolled field environment (which use natural sea water coming from the harbor). In 2011 the University of Washington invested money from grants, and private donors to build an amazing Ocean Acidification Environmental Lab with pimped out coolers that have the ability to monitor and control experimental conditions.
The sea water in this area is naturally more acidic due to freshwater river run-off, coastal upwelling and anthropogenic practices. The pH of the average ocean is said to be around 8.1 reflecting the average atmospheric CO2 levels at 400ppm. The pH of the waters at Friday Harbor is 7.8 with a recorded dissolved carbon dioxide level of 650ppm. We are using this water with all its organic goodies to test how our lab strain of Diatom will respond genetically to future predicted decreases in pH (due to increases in dissolved carbon dioxide).
Thalassiosira pseudonana is an algae that creates a silica glass shell. Because of this, they do not have the same need for calcium as corals, oysters and other shellfish do. This means when carbon dioxide dissolves into the sea water, snatching up available calcium, this particular organism doesn’t seem to suffer. In fact, with increase CO2 this diatom is able to relax its carbon concentrating mechanisms, passively allowing CO2 to dissolve through its glass frustule. In the process of photosynthesis, the ability for the plant to sequester much of the increased CO2, is referred to as CO2 fertilization. To read the final publication on what we found in the laboratory experiments click the paper below:
Breathe
Next time you take a deep breath, thank these under-appreciated organisms which make up the Invisible Forest and give us the oxygen we need to survive.
Want more?
To see more photos of the entire spring trip to Friday Harbor, click here:
To see photos from a previous fall trip taken in September 2014, click here.
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