Bad Data/Good Data: How a physical study ended up giving insight into animal behavior



Contributed by Katie Smith

In oceanographic research, we plan, hypothesize, and make observations as carefully as we can, but nature can still sometimes find ways to mess with us. After all, research is about investigating scientific mysteries, so we never really know what we’re going to find. That’s not a drawback to research—it’s a feature. Sometimes, the most exciting scientific mysteries are the ones that lead in a direction we never expected, as I learned in a recent study of Māmala Bay.

Typical day for a physical oceanographer

As a physical oceanographer, I study internal waves. These are underwater waves that can be found throughout most of the ocean. Similar to how surface ocean waves travel on the interface between two fluids of different densities (those two fluids being the water and the much less dense air above it), internal waves can move through water that has different densities at different depths. In the ocean, the main properties affecting water density are temperature and salinity, so generally less dense (warmer and/or fresher) water sits on top of denser (colder and/or saltier) water. Any disturbance to this structure, such as a current forcing water up and over an underwater ridge, can create internal waves that move through the water. We don’t see these internal waves with the naked eye, but we can detect them with underwater measurements of water properties such as temperature and velocity.

View of Waikiki and Diamond Head from Mamala Bay. Photo credit: Katie Smith

View of Waikiki and Diamond Head from Mamala Bay. Photo credit: Katie Smith

For six months, I had a sensor deployed in Māmala Bay at 500 m depth to look for internal waves. This sensor, called an ADCP (acoustic Doppler current profiler), measures water velocity using sonar: it sends out a brief pulse of sound through the water column, and the sound bounces back off of tiny particles drifting in the water at different distances from the ADCP. The time it takes for the sound waves to bounce back tells the ADCP how far away each particle is, and the amount of sound that returns to the sensor (the “backscatter”) gives a relative estimate of how many particles are in the water at different depths. The Doppler shift of the sound that returns gives a reading of the velocity of the drifting particles and, thus, the velocity of the water in which they are drifting. In order to get a good velocity reading, though, there need to be a sufficient number of particles in the water for enough of the sound to bounce back and return to the sensor.

Once my ADCP was hauled out of the ocean and back to the lab, I started to look at the data it collected. I used a method that essentially highlights repeating patterns in the data and the frequencies at which the patterns repeat. This type of analysis is useful when looking for signs of internal waves, because waves are themselves a repeating pattern. When I did this analysis, it showed a lot of activity occurring at a frequency of about one cycle per day. My experience with internal waves initially led me to think that this was a strong tidal signal, since many internal waves oscillate at tidal frequencies. Interesting! I might be observing an internal wave with a diurnal tidal frequency breaking at this location! But when I looked closer at the velocity readings, I realized that things were not what they seemed to be.

Animals are messing up my data!
The ADCP is hauled back on board after 6 months of data gathering. Photo credit: Katie Smith

The ADCP is hauled back on board after 6 months of data gathering. Photo credit: Katie Smith

When I looked more closely at my data, I saw that my “interesting” velocity signal was actually a false signal—an artifact of the ADCP receiving poor data. The ADCP had recorded consistently high backscatter near the bottom during daylight hours, but low backscatter at night. This means that during the day, the sensor received a nice, strong signal because there were lots of particles in the water for the sound to bounce off of. But during the night, the water near the bottom became incredibly clear, so the ADCP couldn’t get a good velocity signal. For the most part, the ADCP marked the weak signal as missing data as it is programmed to do. But sometimes, when the signal strength was at the border between too weak and maybe just strong enough, the ADCP recorded an unreliable jumble of numbers. The nighttime jumble was what caused my apparent “interesting” signal that was occurring at a cycle of once per day.

I now knew that my hypothesis of an internal wave breaking at a diurnal tidal frequency was based on false velocity readings, but this raised a new question: Why would my velocity readings be strong during daylight hours but weak during the night? The pattern repeated itself every day. To answer this question, I had to step outside of my usual research area of physical oceanography and into the field of biological oceanography. What’s happening is that there are organisms that migrate on a daily schedule in a behavior we call “diel migration.” Tiny zooplankton, fish, squid, and shrimp feed on plankton near the surface of the water, but they are vulnerable to being eaten by larger predators when they can be seen in the light of the sun. So during the day, they hide in dark waters too deep for the light to reach. At night, they swim upwards or “migrate” into shallower water to feed under the cover of darkness, when there is a lower risk of being spotted by predators.

My ADCP was located at a deep site where these animals were hiding during the day. This is why I had a high backscatter signal during daylight hours. At night, though, the animals would all move to shallower depths to feed, leaving such a low backscatter signal that the sensor couldn’t get good velocity data near the bottom. My backscatter signal was a record of diel migration!

A new direction

It turns out that the diel migration of these small animals in Oahu’s coastal waters is an area of active research. Previous studies have observed diel migration of these organisms, but they have mostly focused on shallower waters. I am now working with biological oceanographer Christina Comfort on a manuscript to report our observations of this migrating community of organisms. These observations could be important for the planned SWAC (Seawater Air Conditioning) system being built in Mamala Bay, as the intake pipe for the cold water feeding that cooling system is near 500 m depth and could affect or be affected by the presence of a large migrating community.

This study exemplifies why oceanographic research is an exciting, versatile line of work. Things don’t always go as planned, and data won’t always reveal what you expect, but that can be a good thing! You might find that your research takes you in a completely different direction that is still interesting in its own right. Oceanography is by nature an interdisciplinary field. The physics, chemistry, and biology of the ocean all exist everywhere simultaneously. Being able to start a project looking for a purely physical signal in the ocean and ending up with a manuscript about the behavior of small nearshore animals—this is one of the reasons I love doing oceanographic research.

Katie Smith is a PhD candidate in the Department of Oceanography at UH Mānoa. Her research focuses on the behavior and effects of internal waves in nearshore systems, and she is also interested in the interactions between the physics and the biology of the ocean.

It’s Not Always Bad to Cross the Line




Contributed by Michelle Jungbluth, e-mailed via satellite while battling rough seas along the Atlantic Meridional Transect. 

Monday October 13th was an exciting day for us at sea. This is the day we crossed the equator.

Me in the control room as we officially cross the equator - 0° 00.12’ N

Me in the control room as we officially cross the equator – 0° 00.12’ N

After a restless nights sleep, I woke up at 01:30 am to continue my normal early-morning routine before the big “Crossing the Line” ceremony at noon. Most of my daily routine included picking out hundreds of ~8 different copepod species (microscopic shrimp-like insects of the sea) into cryogenic tubes until breakfast. After about 21 days at sea collecting samples, my advisor Erica Goetze and I had individually isolated over 10,000 copepods, and at this point we still had three weeks of daily sampling to go.

That morning, I received an ‘anonymous tip’ from one of the police (a double agent?) recommending that as inductees we plan effective defenses, since it would be more fun for everyone. I made the last minute decision to save a portion of our stinky morning tow plankton goop for my defenses against King Neptune’s police force! This turned out to be quite useful when all of us not-yet-inducted line crossers got together before lunch to prepare our weapons: condom-water balloons!

My weapons to fight King Neptune's police force

My weapons to fight King Neptune’s police force

Why condoms? I would chalk it up to MacGyver-esque resourcefulness. The doctor had a large stock of condoms she did not mind sharing, since she too was crossing the line that day!   Condoms work quite well as water balloons. We also decided to include extra special “treats” in the balloons… purple dye, fabric softener for strong scent, and my favorite, the stinky plankton water. We then chose our hiding places, and I chose a location with two other line crossers, Ryan and Rafael.

At the strike of 13:00 the announcement came: “King Neptune has arrived on the ship, and any non-shellbacks (those who have previously crossed the equator) are to be put on trial for their crimes against his subjects!” That was our cue to quickly get to our hiding places and be ready to defend ourselves against the police. Seasoned veterans of the ceremony were chosen as the police force, so we knew who to expect.

Us "shellbacks" in our hiding place, on the defensive against one of the King's police

Us “shellbacks” in our hiding place, on the defensive against one of the King’s police

We were found within minutes. There have been many line crossings on this ship, the RRS James Clark Ross, so there were not many hiding locations left that the police didn’t know about. 

Once we were caught, trial and punishment were simple: sit before King Neptune and his lovely wife Aphrodite (i.e. John and Colin) and be put on trial. Guilty of a charge meant you received some volume of old, cabbage ridden, vinegary kitchen slop over your head, down your shirt, in your face … etc. Then before we were deemed an official “Shellback”, we had to kneel before the king and kiss a dead fish!

Me receiving a hearty scoopful of kitchen slop over the head!

Me receiving a hearty scoopful of kitchen slop over the head!

As you can see, not even I – sweet and harmless Michelle – was safe from the wrath of King Neptune! You might be wondering, what were my “charges”? In all I received 8 charges, and here are a few of them:

  • Forcing my study subjects through a tiny mesh thus causing a slow and painful death
  • Pronouncing tomato incorrectly (according to the British dominating the science team)
  • Distracting the bridge with my day-glo t-shirts
  • Wearing a ridiculous fireman’s helmet
  • Spending all day tanning at the CTD while I say I am working (I have to sit there for hours concentrating animals from the water!)

My hair exuded the scent of vinegar for at least three days afterward, and I am still finding remnants of our ‘water balloons’ on the deck of the ship despite an attempt to clean them up that evening. In the end, it’s all in good fun, and will be one of the most fun and memorable days of this shellback’s life.

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Finding my SOEST niche: From occupational therapy to mathematics to biological oceanography

 FaceCrop_CChangContributed by Chantel Chang

I had invested in a master’s degree and four years of work experience, but I could not imagine another 40+ years of constantly being around people in pain. As I, the occupational therapist (a.k.a. the pain bearer), gazed upon the agony in the patients’ faces during therapy, I realized that my career no longer reflected ‘me.’ Furthermore, I would often see readmissions and feel discouraged because we had just completed weeks of exercises, daily living and safety training. Although I have seen some successes, the failures took too large of a toll on me. The good income and job stability were not enough to lessen my heavy heart.

“I needed a change”

After reflecting on what I enjoyed most since grade school and did best in academically, I concluded that I should return to school to study mathematics. I wasn’t sure how I would survive Calculus III without having done any math for nine years, or where a degree in math would lead me, but I needed a change.

As a second Bachelor’s student majoring in mathematics at the University of Hawai‘i (UH) at Mānoa, I took Oceanography 201: Science of the Sea to fulfill degree requirements. I have always felt a deep connection to the ocean being born and raised in ʻĀina Haina, so my mind was blown away with how much mathematics was in oceanography!  I had no idea that waves could be explained with differential equations, and I never thought about the spreadsheets of data that are available to study the ocean.  At the moment I learned about the math-oceanography connection, I knew that I wanted to be an oceanographer.

Chantel standing in front of her poster at the ASLO/AGU/TOS Ocean Sciences Meeting held in Honolulu, HI in February 2014.

Chantel standing in front of her poster at the ASLO/AGU/TOS Ocean Sciences Meeting held in Honolulu, HI in February 2014.

After completing my B.S. in Mathematics and a certificate in the Marine Option Program in December 2013, I was accepted into the Biological Oceanography Division with a graduate research assistantship. Finding myself in another transition, I was nervous about not being able to keep up with the biological and oceanographic jargon and concepts. However, having one successful transition from occupational therapy to math, I felt that if I worked hard enough and remained passionate, I could survive. However, along with my stubborn determination to succeed in my new field and my perfectionism, I found that time previously used to visit ʻohana (family) and friends, exercise, and surf was all invested into studying night and day, while drinking unhealthy quantities of coffee.

“My life balance was off”

It took me hours to read one journal article, and then I’d need to read it again… and again… and again to comprehend it.  I felt that I was more than a couple of steps behind my classmates (most of whom knew that they wanted to be marine scientists pretty much since the day they were born) – in my mind, I was miles behind. The most common thing I’d hear from ʻohana and friends was, ‘long time no see,’ and fellow graduate students asked why I didn’t attend social events like ‘Coffee hour’ or Nerd Nite. I realized (after several months of study and no play) that my life balance was off.

Near the end of the semester, I was approached by Anela Choy, a recent PhD graduate and co-founder and program manager of the Maile Mentoring Bridge Program (ʻMaileʻ for short).  Maile is a program that supports Native Hawaiian and other underrepresented minority undergraduate students interested in ocean and earth sciences by pairing them with graduate student mentors within SOEST.  Anela indicated that she was leaving Hawaiʻi at the end of the year and that she needed another local person from Hawaiʻi in the SOEST graduate program to take over her program management duties… and that I was one of about five current SOEST graduate students who were from Hawaiʻi.

I knew there weren’t many of us locals in SOEST, but I was shocked with the lack of kamaʻāina (from Hawai‘i) graduate students in SOEST.  It’s baffling that there aren’t more kamaʻāina in SOEST, when we have grown up with a beautiful ocean surrounding us and active volcanoes nearby.  Perhaps many kamaʻāina are like me; we love Hawaiʻi’s natural beauty, but just havenʻt thought about studying it for a career. I wasn’t sure if I should take Anela’s offer to be an alakaʻi (leader) for Maile because of my life balance struggles from the last semester, but I took it anyway because I thought of the possibility of helping more kamaʻāina realize that great science is being done in their backyards!

“Maile has been a blessing”

I found Maile has been a blessing in helping me to improve my time management skills and feel at home in SOEST.  My position as program manager forced me to actually take lunch and study breaks, in order to attend SOEST events where I could meet colleagues. Although every single person has been very welcoming and I enjoy meeting people from different places, it was interesting to feel almost an instant connection and comfort in meeting other kamaʻāina within SOEST.  They understand the local culture, mentality, pidgin language, and the challenge of being in a rigorous graduate program while being home which involves juggling large extended ʻohanas, friends from ʻda hanabata (childhood) days, and new friends. They recognize the importance of ʻohana, but also the importance of being a part of SOEST because of the need for diversity in creating a more comprehensive and accurate scientific perspective. Being a part of Maile and meeting well-balanced and successful kamaʻāina in the ocean and earth sciences gives me fervent hope that I, too, will be a role model for future kamaʻāina in SOEST, find my balance in graduate school, and a career that is more ‘me’.

Chantel talking to Kapi'olani Community College students at a career mixer

Chantel talking to Kapi’olani Community College students at a career mixer



Chantel Chang is a graduate student pursuing a M.S. in Biological Oceanography, working with Dr. Anna Neuheimer on a project involving biophysical modeling of holoplankton.  She is also an alakaʻi for the SOEST Maile Mentoring Bridge.  In her re-found free time, she enjoys spending time with her ʻohana, surfing, reading, and eating House of Pure Aloha shave ice. Check out Chantel’s professional website!


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HIMB30 – The Prius of Bacteria

By Jennifer Wong-Ala 

Jennifer Wong-Ala

“Ew, you work with bacteria?! Aren’t you afraid of getting sick?” This is what I usually hear whenever I talk to people who are not familiar with the different types of bacteria. When most people think of bacteria, they think of the harmful germs that get them sick. The “good” bacteria I work with are called HIMB30, from the Gammaproteobacteria class. Gammaproteobacteria are common in the marine environment, and HIMB30’s name comes from the Hawai‘i Institute of Marine Biology on the east side of ‘Oahu, where it was isolated from.

So why is this bacteria “good”? HIMB30 is not harmful to human health, and serves many functions. Think of HIMB30 as a hybrid car. A hybrid car uses gas to power its engine and has an electric battery that it can recharge. HIMB30 is heterotrophic — meaning it consumes “food,” or organic matter in this case, like the gas you put in a car, but it also has the ability to use light to create extra energy, much like the rechargeable battery. Genes for phototrophy and genes that have the ability to fix CO2 into an energy source were found in HIMB30, which is unusual in this order of bacteria. With my research, I am trying to figure out how HIMB30 uses these genes to acquire its energy.

The gene found in HIMB30 that has the ability to conduct phototrophy is called proteorhodopsin. Proteorhodopsin is related to a pigment found in your eyes called rhodopsin that allows us to see different colors. This protein is able to harvest energy from the sun and it functions as a light-driven proton pump. A proton pump can be thought of as a gate that allows protons to enter the mitochondria. Since the discovery of proteorhodopsin, many bacteria have been found to contain this gene.

Stepping away from lab work for a moment to pose for a photo with Vanessa

Stepping away from lab work for a moment to pose for a photo with Vanessa

It is estimated that in one liter of water, there is about a billion bacteria. Since there are so many bacteria in the ocean, it must be easy to bring them from the ocean to the lab to start growing and experimenting with them right? Well, it is not quite that simple. It is suggested that less than 1% of the microorganisms in nature are able to be cultivated in the lab today. This being said there are even less microorganisms that can be cultivated that contain proteorhodopsin and this makes them difficult to study. This makes HIMB30 extra special, since it has proteorhodopsin and we have it growing in culture in our lab. I have been doing experiments with the cultures in order to learn more about the metabolism of HIMB30.

Many of you may ask, why is this important?  The carbon cycle in the ocean is responsible for the cycling of nutrients. In this cycle, bacteria play a huge part of the marine food web and process more than half of all the flow of carbon-based matter. There are many different types of bacteria in the ocean. Photosynthetic bacteria use sunlight and convert it into energy. Mixotrophs can use sunlight and organic matter for energy, while heterotrophic bacteria attack other organisms. Now where does HIMB30 come into all of this? HIMB30 has characteristics showing that it may be a photolithoautotroph. This means that it can use the energy it gets from light to convert substances such as carbs, fats, and proteins into simple substances. It also uses a form of sulfur and CO2 as a source of carbon for this to occur. But the big question is how would this affect the carbon cycle in the ocean? It is still unknown how some bacteria utilize the proteorhodopsin gene and the effect it can have on the carbon cycle.

Jenn's OSM2014 poster presentation

Jenn’s OSM2014 poster presentation

In February, I presented these exciting research findings at the 2014 Ocean Sciences Meeting held in Honolulu. This was the first conference I attended and let me tell you, it was huge! At first it was overwhelming, but after a while I got the hang of planning out my day. At the end of the week, I was sad that the conference was over. I learned a lot from the vastly different sessions and I met many great people whom I plan on keeping in touch with for years to come. Science has taken me farther than I had ever imagined and I am super excited that this is only the beginning.

Jennifer Wong-Ala is an undergraduate student at Kapi‘olani Community College and is currently conducting research as a Center for Microbial Oceanography: Research and Education (C-MORE) Scholar. She plans on transferring to UH Mānoa in Fall 2015 and earning a BS in Global Environmental Sciences. She is a mentee as part of the SOEST/KCC Maile Mentoring Bridge Program (

A Bittersweet Cruise

A guest blog post contributed by Donn Viviani

I conduct my oceanographic research on a 186-foot-long ship at Station ALOHA, 60 miles from ‘Oahu and the site of the 25-year-old Hawai’i Ocean Time-series. Cruises last five days and are scheduled well in advance.  So I was surprised one evening when my advisor emailed, “we have to go sample the molasses plume right away!”  I thought he was joking: What molasses plume?

Hundreds of thousands of gallons of molasses were spilling into Honolulu Harbor, and fish were dying by the thousands.  As microbial oceanographers, we immediately wanted to know how bacteria were responding.  Were they using the molasses to grow like crazy and breathing all the oxygen in the water?  We knew the Department of Health would look at fish and potentially harmful bacteria.  We didn’t think they would be very interested in the vast majority of microbes that are not dangerous to humans, but we sure were interested!

Thirty-six hours later, seven scientists, myself included, arrived at the University of Hawai’i Marine Center with all the equipment we might possibly need.  Scientists, captain, boxes of equipment, and the CTD (conductivity-temperature-density) sensor package crowded our 20-foot-long boat.  Out in Ke’ehi Lagoon, it was evident that something was wrong. The water was an odd dark color and the air smelled sort of like bread.  Later, I saw aerial photos that really showed the discoloration of the water.


Lowering the CTD into the molasses plume.
Photo credit: Fenina Buttler

We motored down the channel to the places the Department of Health had collected water samples.  I’ve never seen so many small crafts in the harbor on any of my past 60 cruises.  There were dive flags up everywhere and guys scooping nets for dead fish.  It was surreal.

Station one, near Aloha Tower, was confusing and disorganized.  None of us had used this boat before, and we were crammed like sardines between boxes of empty sample bottles.  Two scientists lowered the CTD over the side.  To check the sensor depth readout on the laptop screen, I had to crawl along the outside of the boat.  Eventually, we figured it out, filled our bottles with samples, and moved on as more boats arrived.

Our second station stunk.  Off Pier 38, there was a strong rotten egg smell, causing some of us to say “yuck” and others to say “Wow! Smells like hydrogen sulfide!”  We suspected the water below us might be anoxic (no oxygen).  Sure enough, the CTD oxygen sensor reported almost no oxygen between the surface and just above the bottom.  Anoxic water could explain the dead fish, which would have been suffocated.  The molasses was like a huge holiday buffet for bacteria living in the harbor.  They ate up all the molasses, breathed all the oxygen, and now some of them were living anaerobically (without oxygen) and releasing hydrogen sulfide.   Water at the next two stations also contained very little oxygen. We didn’t smell any hydrogen sulfide, but  there were many dead fish floating under the docks at the final station.


Taking oxygen measurements on board our “research vessel”.
Photo credit: Fenina Buttler

Back in the lab, we analyzed our samples to calibrate our CTD sensors, and to figure out what kind of bacteria were in the harbor and how fast they were growing.  We planned a second trip, to look for changes.  After washing some bottles, looking at data, and talking to some reporters, we were ready to go back out.

Our second cruise, a week later, was like going to a totally different harbor.  I saw both Jacks (‘ulua) and flying fish (malolo); I’ve never seen either in the harbor before.  At station one, the water surface was covered with a film of zooplankton, small organisms that eat bacteria and phytoplankton.  We didn’t smell hydrogen sulfide, and none of the stations were anoxic.  It seemed like microbes and water mixing through the harbor had cleaned up the molasses, and larger organisms were moving back in.


Interviewing the “TV Star”.
Photo credit: Fenina Buttler

We’re still analyzing our measurements, but I’ve learned a few things from this experience. First, people get way more interested in my science when it affects something relevant to them, like my Aunties calling me “TV Star” because they saw me get interviewed on the news.  Second, lots of interesting science happens in my own backyard.  Third, even harbor bacteria have a massive sweet tooth!

Donn Viviani is a PhD student studying the partitioning of primary production between particulate and dissolved phases in the North Pacific Subtropical Gyre. He is looking forwarding to contributing more guest posts on spontaneous research in his backyard and beyond.


Photo credit: Fenina Buttler

Gambling on Oceanography in Hawaii: The Risk Was Worth The Reward

By Sean Jungbluth

Sean Jungbluth

To describe my path to graduate school, I begin when I first really began entertaining the idea of attending graduate school, which was in my fifth year of university-level work at University of Wisconsin at Madison. I extended my stay in college so that I could pursue Bacteriology as a second major in addition to the general Biology major that I already had obtained. I had sampled a wide variety of classroom and/or research laboratory experiences spanning many biological disciplines during my time as an undergraduate, but ultimately, I really enjoyed the hands-on work performing molecular microbiology based experiments; this sort of lab work really called to me. Inspired by top-quality professors, I knew that I wanted to perform some type of microbial genetics based research for a career.

I interviewed for several jobs within the Biochemistry and Zoology departments after graduation, but ultimately my diversity of experiences allowed me to find a job at a biotechnology business in the Madison-area where they make products for molecular biology. I really enjoyed my time working at this company and continued to expand my knowledge and technique base; however, my desire to continue my education was something that prevented me from getting too comfortable being a staff scientist at a biotechnology firm. I was working there for a few months before talking with a college friend, who happened to be moving to Hawaii. I was asked if I, and my girlfriend – now wife – wanted to take a chance and move out there with him. Not fully content with our employment situations and ready to take a big risk, we decided to take a chance and move to the middle of the Pacific Ocean.

I began looking seriously into graduate programs offered in Hawaii as soon as we made the decision to move there, and quickly decided to apply to the University of Hawaii at Manoa for graduate school. I had done my research and knew that this school had a high-rated Oceanography program, so I decided to take a big chance and apply because, like many people, I find the ocean to be an exciting frontier of exploration. I was able to narrow down a list of professors that I would enjoy working for quite quickly and did my best to contact them in hopes of identifying potential opportunities. Perhaps some of that networking paid off because when applications were reviewed, surprisingly, I was offered a graduate assistant position studying the microbial life at the bottom of the ocean. This still amazes me; I still feel like one of the luckiest people in the world to be picked to do this sort of work, so I cherish every minute of it.

Sean Jungbluth is a PhD student in the Department of Oceanography at the University of Hawaii at Manoa. His research utilizes deep-sea submersibles and molecular tools to look into the nature and diversity of microbial life living within the deep subseafloor. Besides science, he also enjoys current events, scuba diving, surfing, reading, Frisbee, and laughing.

What was your path to graduate school?

Response by John Casey

I’ve been asked this question on occasion in less formal situations and have always drawn a blank, my eyes glaze over and I rattle off some long-winded recount of a series of disparate events that I suppose led me to graduate school, inevitably leaving the person who asked the question uninterested. There was no moment of clarity, no profound advice from superiors, no obscure accident that drew me to graduate school. I was, however, blessed by a contiguous series of exceptional mentors who, for some reason, took a particular interest in my progress from early education through university and later as a technician. With some exceptions, aptitude and merit is a fairly level playing field in the applicant pool for graduate education, that is, if you are considering further study you likely meet the eligibility criteria and credentials for application. Rather it would seem that motivation and confidence are more essential attributes, and for me those attributes grew from experience working with and for my mentor and supervisor Dr. Michael Lomas as an REU fellow and technician at the Bermuda Institute of Ocean Sciences. I worked for several years for Mike and was fortunate to participate in various capacities in many research projects with many collaborators from our small field, observe the work-life (im)balance of many of my superiors, and was exposed to the rote and practical aspects vital to growing and maintaining a small research group. With that experience I suppose I was less surprised by the challenges that face all early career scientists, and which dissuade and disenfranchise many. I have few words of wisdom to encourage the prospective earth sciences applicant, but if you take anything from this blog entry it ought to be that there is no substitute for experience: find opportunities to engage with a mentor, work or volunteer in a lab, and if possible apply with your own funding. Oh and keep in mind, basic research will be a short-lived privilege for many, so enjoy it humbly!


John Casey, surfing Waimea Bay

John is a 3rd year Ph.D. candidate at UH Manoa studying central carbon metabolism and the photorespiratory pathway in marine picocyanobacteria. He is broadly interested in the role of marine microbes in mediating elemental cycles and organic matter transformations in the oligotrophic gyres. (

The One With The Peanut Butter M&M’s

By Shimi Rii

Shimi RiiIn May, I embarked on HOT-252, (possibly) my last HOT cruise for my Ph.D. project.  I say ‘possibly’ because you never know what your committee may spring on you at the last minute. Inside, however, I felt a bit giddy but already nostalgic – there were many adventures that sprung out of these trips to our most frequently visited station in the North Pacific Subtropical Gyre (NPSG).

Leaving Honolulu harbor

Leaving Honolulu Harbor for a business-as-usual HOT cruise.

I have now completed a 2-year collection of monthly DNA/RNA and primary production samples within the Hawaii Ocean Time-series (HOT) program.  The HOT program is now on its 25th year of physical and biogeochemical measurements at Station ALOHA (22° 45’ N, 158° W), an ocean station representative of the NPSG, one of the largest ecosystems on Earth.  For the last 2 years, I had a duffel bag packed with acid-stained garb that was re-washed after every cruise, a mini toiletry set, my yoga mat, and my ukulele, all neatly set aside and ready to go each month.  On May 20, I folded my clean clothes full of pukas (‘holes’ in Hawaiian) and stowed away the empty duffel, hoping not to jinx myself.

Station ALOHA, site of the Hawaii Ocean Time-series, located at 22° 45’ N, 158° W.

Station ALOHA, site of the Hawaii Ocean Time-series, located at 22° 45’ N, 158° W.

I’m looking forward to the benefits of lab life: carpal tunnel syndrome on my pipetting hand, the ability to tell which centrifuge is on by its particular drone, being able to catch up on All Songs Considered podcasts.  But I will definitely miss the monthly trips to Station ALOHA – especially the ping-pong match of playful insults I’ve grown accustomed to throwing at my shipmates, playing Dominion until the wee hours when we should be sleeping, and the constant fight against motion- or food- or microscope-induced seasickness.

In truth, my shipmates have become my sea-going family.  Each HOT cruise is marked by a random exciting event that distinguishes one from another, much like a Friends episode: “The One With All The Fish” or “The One With the Mysterious Smell (you know who you are).”  We worked like a well-oiled machine, understanding each other’s looks, knowing when a Trichodesmium bloom would occur, and enjoying moments of camaraderie at 1 a.m.

A cruise that will forever remain warm and fuzzy in my heart is HOT-242, my first birthday cruise. Though I’ve sailed on research ships for over 10 years, I somehow managed to stay land-rooted on my birthdays.  I woke up to a bouquet of balloons on my stateroom door with a gift bag full of candy and a card signed by everyone on board.  It was just another birthday, but I felt special. This year, I wasn’t going to have Facebook greetings from high school classmates that I never talk to anymore.  Never mind that I had to wake up at 3 a.m. for my CTD cast; I was with my Station ALOHA ‘ohana (family) and it was going to be an awesome birthday at sea.

Balloons from the Station ALOHA ‘ohana on stateroom door.

Balloons from the Station ALOHA ‘ohana on stateroom door.

Science on my birthday cruise was nothing out of the ordinary, with every hour being accounted for and occurring like clockwork, as per usual on a HOT cruise.  The only thing different was an assignment to track down a rogue seaglider that was deployed a week prior.  This seaglider, an autonomous profiling instrument designed to give us real-time environmental data, decided to ignore all assigned depths and commands and it fell on our crew to bring the rebel home.  Unfortunately, this resulted in a spontaneous jaunt to Kaua‘i across the 72-mile-long Ka‘ie‘ie Waho Channel.

The rogue seaglider that went off track during HOT-242.

The rogue seaglider that went off track during HOT-242.

I had been feeling great for the first 4 days of the cruise, and by the time the ship started its channel transit, I was done with my work and watching movies in the lounge with a bag of peanut butter M&M’s.  Unexpectedly, that familiar, slightly acidic taste had developed in my mouth.  “You doing alright? Ready for your birthday cake?” My colleague teased, noticing my fear-filled wide eyes.  “Are you sweating?” He kept on. I glared and waved him away weakly, overcome with sudden shivering. The M&M’s were now sloshing around in my stomach, much like the water around the boat.  It was dinner time, and the smell of sautéed shrimp, normally my favorite, didn’t help. I took deep breaths and closed my eyes, determined to make it to my birthday at sea celebration.

Finally in the mess hall, I closed my eyes to concentrate as my ‘ohana sang “Happy Birthday” and presented me with my cake.  I can do this, I told myself. This day can still be awesome. I managed a smile and stood up to cut the cake, when the room blurred and started spinning.

Gulp. “Fernando, cut this,” I blurted out, shoved the knife in his hand, and ran to the nearest head (bathroom on a ship).

Thanks to HOT-242, it will be a long time before I can eat peanut butter M&M’s again.

Sara Lee birthday cake that I never got to taste.

Sara Lee birthday cake that I never got to taste.

Shimi Rii is a 5th-year Ph.D. candidate in the Department of Oceanography at the University of Hawaii at Manoa.  Her current research looks at the diversity of tiny eukaryotic phytoplankton and their role in carbon cycling in the North and South Pacific Subtropical Gyres.  She enjoys creating things, relaying the awesome-ness of microbes to high school students, and practicing science writing. 

Chasing Plankton

By Michelle J. Jungbluth


October 23, 2011.  The day started out sunny, warm, pretty much a normal day on Oahu.  Little did I know that it was going to be my own personal ‘D-day’, the next day would be the beginning of a very busy 14 days.  I was having a great night grilling at a friend’s house in St. Louis Heights.  After taking a step out of the house to get some fresh air, I looked mauka into the sky, and noticed the clouds looked darker than usual over the windward side.  “It’s going to happen tonight…” I said, more to myself than anyone around me.  Sure enough, a couple of hours later I went home, hopped on the internet and checked the rainfall. They had already received over an inch of rain in Kaneohe, with no sign of letting up.

I had been preparing for months: e-mailing undergraduate clubs looking for any bodies willing to be ‘on call’ for helping with sampling, assembling all the supplies I would need, checking the forecasts, and generally keeping my wits about me waiting for the day to come.  Greater than 2 inches of rain in 24 hours, that was my trigger.  No less.  I started my “rain watch” in late August, after that any hint or mention of rainfall made my ears perk up, and I immediately checked the forecast.  But one of the first things I learned is that it actually can be difficult to predict severe weather on the islands more than a few days out, unless it’s a monster of a storm.

Waterfalls pouring from the Koolau mountains on the Windward side of Oahu on a particularly rainy day (photo credit: Michelle Uchida)

Waterfalls pouring from the Koolau mountains on the Windward side of Oahu on a particularly rainy day (photo credit: Michelle Uchida)

You might be wondering why I am chasing a storm. Well, I am interested in the response of the plankton community to storm events and how these storms influence the marine food web around the Hawaiian Islands.  We know that the influx of nutrients causes rapid changes in the plankton communities within short time scales, and I specifically want to know what is happening to different species of copepod nauplii (youngest life stages of copepods, the most abundant metazoan in marine ecosystems all over the world)  after these storms, as compared to calm non-storm periods.  This requires sophisticated DNA-based methods, which will be the topic of a future blog article and (hopefully) a few journal articles.

Sunny vs Showers. Contrasting conditions in the bay lead to very interesting plankton dynamics, there are mountains behind that grey haze of clouds.

Sunny vs Showers. Contrasting conditions in the bay lead to very interesting plankton dynamics, there are mountains behind that grey haze of clouds.

Once I arrived home on the night of the storm chase, I sent a flurry of e-mails: to my list of available volunteers to start assigning days to people and get the first couple of days covered, to reserve a boat  for all 14 days at HIMB, and finally, the e-mail to my advisors, subject line: “Storm chase-now!” with obvious contents.

The 14 days of sampling was a whirlwind of activity.  I drove all my supplies from UH Manoa across the Koolau Mountains to HIMB, took the shuttle boat across to Coconut Island, loaded my supplies onto the boat, drove it to my GPS-located sampling location in the center of the South Bay, collected all my samples, measured the water quality, left my supplies on HIMB (I am ever so grateful to someone who will remain anonymous, thank you for sharing your space), and drove my samples back to campus for processing, which was another hour of work.   Then rinse and repeat the same procedure for 13 more days.

Michelle deploying the plankton net

Michelle deploying the plankton net

 The dynamics of the bay tend to change rapidly, and we could see that in the clarity of my plankton samples as well as the water quality measurements.  One day the chlorophyll levels were low and stratified, the next day they were high and seemingly well-mixed.  “Oh look, the freshwater lens is coming, I better collect my zooplankton before it gets here!” to avoid clogging my fine-mesh plankton net.  Each day was an adventure.

Size-fractionated plankton samples collected in Kaneohe Bay

Size-fractionated plankton samples collected in Kaneohe Bay

Each day also presented unique challenges. One day an unmanned sailboat slowly drifted past my boat while I was anchored, and we called it in so that someone could tow it back to its origin before it drifted into the unsuspecting reef.  Another day we rescued a fellow boater whose engine failed and left them stranded not far from HIMB.  On a breezy Sunday, we were anchored at the field site, and then out of nowhere a sailing race began in the exact region of the bay we were sampling from!  I don’t think the sailors were thrilled about it but hey, there was little I could do, I had been sampling there for the past 2 years doing my time-series.  And then there were the days we got stuck in the pouring rain… I rushed to collect my samples while my wonderful volunteer intermittently bailed the boat to keep us from sinking.  However, most days were average, gorgeous Hawaiian days, and sampling could not have gone more smoothly.  Those days always remind me how lucky I am to study biological oceanography at the University of Hawaii at Manoa.   I am finally processing those samples for my PhD work and getting some really exciting data, which is a nice addition to having stories about storm chasing.

Michelle Jungbluth is a student in the Biological Oceanography department at UH Manoa characterizing the response of plankton communities to storm events in Kaneohe Bay. She is specifically looking at the response by copepod nauplii, the youngest (and more abundant) life stages of copepods, using a DNA-based method called quantitative real-time PCR to study their role in the marine food web. 

Breaking ice in Antarctica… to discover what lies beneath

by Jaclyn Mueller

Mueller headshot

In March of 2012, I had the opportunity to take part in Antarctic research for the second time in my life. As a graduate student at the University of Hawaii at Manoa, I study RNA viruses that predominantly infect phytoplankton, with a focus on communities in the Antarctic. When I heard that some help was needed on an upcoming Antarctic research cruise, I couldn’t wait to get back down to one of the coldest, windiest, most desolate and absolutely beautiful places on earth. The 40-day expedition took place on the Nathaniel B. Palmer, a research vessel and icebreaker. The cruise was part of a large, multidisciplinary study called LARISSA: Larsen Ice Shelf System, Antarctica, which is a National Science Foundation initiative funded to investigate the ecosystem impacts of a catastrophic loss of ice that took place in 2002, when a 3200 sqkm piece of ice disintegrated from the Larsen B ice shelf into the Southern Ocean on the eastern side of the Antarctic Peninsula. We had a number of scientists on board, ranging from physical oceanographers, glaciologists, and geologists, to biogeochemists, marine benthic ecologists, phytoplankton specialists, microbiologists, and virologists!

The Nathaniel B. Palmer breaking through ice in Antarctica

The Nathaniel B. Palmer breaking through ice in Antarctica

As we departed Punta Arenas, Chile, the Straights of Magellan were quite choppy from the high winds and stormy weather in the area. Many people were immediately ill and turning to Dramamine and saltine crackers for comfort. Surprisingly, as we exited the straights and made our way into the Drake Passage, the seas became incredibly calm. The Drake Passage is the stretch of water where the Pacific Ocean and Atlantic Ocean come together and the Antarctic Circumpolar Current rips through the narrow passage between the southern tip of Chile and the northern tip of the Antarctic Peninsula. It’s notoriously one of the roughest crossings in the world. When the waters are abnormally calm, the passage has been referred to as the “Drake Lake,” and we were lucky enough to experience it!

On our transit through the Admiralty Sound, the weather was absolutely gorgeous and the scenery utterly breathtaking. I truly cannot put into words how beautiful and unique the world is down there. We saw numerous whales, seals, birds, and penguins with enormous ice capped mountains erected on either side of the Sound. Everyone’s spirits were high, with the sun shining and clear blue skies for miles. After the sun went down, a new beauty took over. It was impossible to capture the calm, serenity of the night with my small point and shoot camera. But imagine pitch-black darkness for miles in the distance, with the moonlight casting shadows over an endless sea of icebergs, growlers, and bergy bits. The stars were incredible. You could literally see the entire Milky Way from the top of the ice tower on the ship! At night, the captain, mates, and ice pilot used radar and spotlights to look for icebergs. It was really pretty amazing to watch. Though this vessel was built to break ice, we still had to avoid the giant icebergs and any “fast ice,” or really thick, sturdy ice.

 Clear blue skies on the eastern side of the Antarctic Peninsula

Clear blue skies on the eastern side of the Antarctic Peninsula

Most of our sampling in the Antarctic was dependent upon sea ice conditions. We spent a lot of time breaking ice and attempting to get to stations on our planned cruise track, but often had to make on-the-fly decisions to change location. When ice conditions were really bad, the ice prevailed! If conditions worsened at night, we had to wait until sunrise for easier navigation to determine our next plan of attack. If we were unable to make a large enough hole to maintain the ability to maneuver the ship, the ice was capable of closing in on us with great enough pressure to legitimately squeeze us in! (Don’t worry; the captain wouldn’t let this happen.)

 Adelie penguins on an iceberg

Adelie penguins on an iceberg

Breaking through the ice provided a very different experience for me, as far as cruising conditions go. Usually I get used to the constant rocking of the vessel with the rolling motion of the ocean, but in the ice, conditions are often very stable whilst on station. However, when we were moving through the ice, crushing along growlers, and pushing aside ice floes, it often sounded and felt much like an earthquake. The ship would often get stuck up on an ice floe and tilt sideways, slowly and dramatically, and then crash back down to position as it collided into another one. Working at sea requires us to tie everything down, as we often run into rough seas and everything slides across decks and floors, off of counters and tables, or tips over and onto the floor. While on station, we tend to forget these things; so once we start moving again, everything goes flying!

 A minke whale and crabeater seals following in the ship’s wake

A minke whale and crabeater seals following in the ship’s wake

On the cruise, I assisted with sampling for the Smith Lab, a Benthic Ecology lab at UH that studies organisms that live within and on the seafloor. I worked the night shift from midnight to noon. Scientists usually break up the work on oceanographic cruises into two 12-hours shifts to allow for constant operations around the clock. When it costs over $100,000 a day to operate a research vessel of this size, we can’t afford any breaks! Since I was working as an assistant to one group as well as collecting samples for myself, I had my work cut out for me. If my samples came up at noon, I had to process them fully before I could get to bed, and was still expected to be back and ready for action at midnight! It’s a good thing that ship had a fancy coffee maker and an in-house barista, ready to make me mocha lattes every morning!

 Image of the seafloor showing brittle stars and Scotoplanes (sesea pigs (a species of sea cucumber). Photo credit: Craig Smith

Image of the seafloor showing brittle stars and Scotoplanes (sesea pigs (a species of sea cucumber). Photo credit: Craig Smith

The benthic (seafloor) sampling began with a camera survey of the seabed to determine whether or not the sediment was soft enough for Megacore sampling. The Megacore is a piece of equipment with 12 plastic cylinders that penetrates the seafloor to collect cores of sediment ~20-40 cm deep. When the equipment came back on deck, below freezing temperatures made it very difficult for scientists to retrieve the cores as they were often frozen in place. We then sectioned the sediments by pushing the core up through the plastic cylinder with a piston extruder to slice off 1 cm sections; which were then analyzed for chemical composition, and abundance and diversity of organisms, both large and microscopic. This whole procedure took about 2 hours for deployment and retrieval of the Megacorer, and anywhere from 3-24 hours of processing of the cores.

Megacore sampling on deck

Megacore sampling on deck

The Blake Trawl was one of the more exciting operations, though processing of the sample was very time-consuming and tiring. We basically dragged a net along the seafloor which collected a bunch of sediment and rocks, and any organisms greater than ~2 cm in it’s path. After hauling the large glob of sediments, rocks, and organisms on deck, we dumped it onto a sorting table to hose away the mud and reveal the interesting creatures! The Blake Trawl sorting photo shows scientists hosing away the sediments during one of our night shift trawls. This was the very beginning of the process where we stopped to take a photo… by the end we were covered in frozen mud and water spray from head to toe! It was so cold outside that the water literally froze to our Mustang suits (orange float coats/pants, required for on deck operations), and formed icicles along the edges of the sorting table. As we uncovered the organisms, we sorted them into buckets of filtered seawater, and saved them for identification and food web analyses.


Paulo Sumida, Buzz Scott, Jaclyn Mueller, Caroline Lavoie, and Laura Grange sorting the organisms from a Blake Trawl. Photo credit: Amber Lancaster

We unfortunately did not make it to all of the intended stations due to difficult ice conditions throughout the cruise. However, we were still able to collect a large number of samples from the Larsen A embayment for all of the scientists. We hope to put our samples from the water column and sediments into the context of climate change effects in this region, and determine the impact of large ice shelf losses on the ecosystems below. Continuing to monitor and explore these regions is crucial to understanding the implications of global warming in such a delicate, unique environment.

Jackie Mueller is a PhD student in the Oceanography Department studying marine RNA viral diversity and dynamics. She is using cultivation independent techniques to characterize the composition and structure of the RNA viral community along the Antarctic Peninsula.

Creatures Lurking in the Darkness

By Anela Choy

In clear waters to the far north-west of Hawaiʻi’s main islands is a series of submerged and partially submerged remnants of once volcanic islands and drowned coral reefs.  These land masses and the 139,797 square-miles of the surrounding Pacific Ocean comprise the Papahānaumokuākea Marine National Monument, our nation’s largest conservation area and one of the largest conserved areas of marine environment globally.  Of the Marine National Monument, the vast majority of this protected area consists of deep, offshore waters that are also the least explored.

In the summer of 2009 the good ship Hiʻialakai carried a crew of scientists throughout the Monument on a month-long journey to conduct a variety of scientific and cultural explorations.  The Drazen laboratory in the Department of Oceanography at UH Mānoa is also known informally as the Deep Sea Fish Ecology Lab and thus, our participation was focused on using baited deep-sea traps to describe the vastly unknown cast of fishy deep-sea characters.  John Yeh, who designed and built the trap, and I repeatedly threw the trap off the back of the ship at various depths (mostly in very deep waters thousands of feet below the sunlit surface) and at various locations within the Monument.  In addition to comparing the Monument’s deep-sea scavenger community to others’ around the world, we wanted to see how this community varied in both the horizontal and vertical dimensions of the Monument.

The creatures lurking in the darkness were a surprise not only to science but especially to my eyes and mind.  Bright red Heterocarpus shrimps with antennae as long as pencils, slinking and shiny eels with smooth grey skin, ugly deep-sea fish known as rattails with their eyes and stomachs blown-up…these guys were enough to give any normal person nightmares.  Most disturbing (and perhaps most fascinating!) was the giant hagfish (Eptatretus carlhubbsi) that came up in one particularly slimy haul.  We won’t talk numbers and sizes, but know that it was as big as any respectably scary boa constrictor or python.  The hagfish had a face only a mother could love, with multiple fleshy barbels dangling from a large slimy hole (i.e., nostril).  There were no real eyes to look into, only primordial eye spots that held no sign of emotion or previous life.  What stuck with me most (yes, pun intended) was the heinous amount of icky, sticky slime and mucous that oozed out of the collection of glands running along the length of its chubby, slithering body.

photo by A. Choy

photo by A. Choy

John and I spent hours burning through an entire roll of paper towels to clean the continually oozing sticky stuff from the hagfish and everything it touched, including us.  When the spineless fish was as clean as we could get it, we snapped an array of pictures as if it was a celebrity.  That month in the Monument left me awe-inspired and entertained, truly driving home the reality of Earth’s deep-sea environment being less explored than the surface of our moon.

photo by A. Choy

photo by A. Choy