Bridging the Gap

Screen Shot 2016-07-29 at 12.48.44 PMContributed by Leah Shizuru


As I stood near the puka and gazed at the raw beauty of the steady flow of incoming ocean water spilling into the fishpond I listened to and appreciated the unmistakable sound of rushing water. What a thrilling experience for both the eyes and ears.

It was hard to fathom that the 80 ft gap directly in front of me would soon be closed. I pondered how the volunteers would ever complete this task when the water appeared to ebb and flow with such impressive speed. Though difficult to imagine, I was told that the enthusiastic bunch of men and women that worked daily on closing the puka, or gap, were making great progress with the help of a campaign to fund this labor-intensive project and raise awareness of the need to close the break in the wall in He’eia fishpondPani ka Puka.

Screen Shot 2016-07-29 at 12.48.12 PM

Bridging the gap would be a crucial step toward restoring this fishpond to its original state and enabling traditional aquaculture to ensue again. Ultimately, caretakers of He‘eia Fishpond would once again be able to raise enough herbivorous fish such as mullet (‘ama‘ama) and milkfish (‘awa) to provide for the community. Sustainability. Preservation. Tradition.

Bridging the gap

Benefits of traditional fishponds extend to research and education. That is how I became involved with He‘eia Fishpond. Last summer I had the opportunity  to intern at C-MORE (Center for Microbial Oceanography: Research and Education), a NSF Science and Technology Center, to work on a research project with Dr. Rosie Alegado looking at the microbial diversity in this coastal ecosystem. As part of my research, I ventured to the fishpond once a week with my two lab mates in order to gather water samples. These water samples were then taken back to the lab, filtered, and subjected to extraction of genomic DNA.

During these visits we got to know the Paepae o He’eia stewards (kia’i loko), learn about the history surrounding the fishpond and see the progress of the various other restoration

Screen Shot 2016-07-29 at 12.48.32 PM

Pictured left to right: Dr. Kiana Frank, Charles Beebe, Kyle Yoshida, and Ka’ena Lee

projects including the removal of mangrove from along the ancient fishpond wall  and invasive limu (algae) from in and around the pond. Our research aimed to complement these restoration efforts. Through a better understanding of the genetic makeup of microbes such as photosynthetic bacteria and microalgae that form the base of the food chain in the fishpond, better management policies could be implemented.

Our weekly visits to the fishpond also enabled us to see, first hand, the outreach efforts of the fishpond stewards. One evening during a 26-hour diurnal experiment in which we worked with Dr. Kiana Frank (who was analyzing microbial communities at different depths within the sediment as well as their sources of respiration and respiration rates), we interacted with a few children who were on the property.  

During the process of water filtration and processing of sediment cores we were surrounded by a group of inquisitive and eager children who wanted to help. Ka‘ena, who was 5 years old, asked, “What are you doing?” as he looked at the filtration apparatus, bewildered. My co-workers and I told him that we were filtering water that we had just collected in order to study the microbes in the fishpond. Ka‘ena looked puzzled and we could see from the confused, yet still-interested look on his face that we needed to add to our answer and perhaps simplify it. I quickly began to think of a way to re-explain this so that he could understand it. Thankfully, my labmate, Mikela, interjected, “Oh, ok! So you know when you’re finished cooking spaghetti noodles and you have to drain out the water?” Ka‘ena nodded. “How do you get rid of the water that you cook your pasta in,” Mikela asked. He described a strainer and Mikela replied in an encouraging tone, “Yes, exactly, a strainer. So what this is [as she pointed to the filtration apparatus with the filter membrane] is like the strainer and the microbes are like the spaghetti noodles that we want to keep.” What a perfect analogy to give to this young child! Ka‘ena beamed at Mikela and responded, “Oh, I see!” We followed Mikela’s lead and continued to answer the other children’s questions in a simplistic, analogous manner. What a treat it was to be able to answer their thought-provoking questions.


Illustration of Oahu fishponds by Robert Dampier, 1825. (Wikipedia Commons)

It was in that moment that I realized how this summer had come full circle: I was working for an organization that, in its very title, seeks to educate. I gleaned from the knowledge of Dr. Alegado and Dr. Frank and in turn was able to pass on that knowledge to these young kids. Not only had I learned more science this summer, but I had formed a deeper appreciation for my culture, for the faithful caretakers at He‘eia fishpond, and for the brilliant scientists (like those at C-MORE) who seek to better understand the environment in which we live. I saw the value of perpetuating knowledge from one generation to the next.

It was then that I understood the necessity of bridging the gap.

Hawaiian fishponds, also known as loko i‘a, were traditional forms of aquaculture that served as a dependable protein source for ancient Hawaiians. The oldest fishpond in Hawai‘i was built about 1200 years ago. By the 1900s there were only 99 of the 360 built in the islands that were operable. 

Leah Shizuru attends the University of Hawaiʻi at Mānoa and will earn a B.S. in Microbiology Spring 2017. As a part-time lifeguard with Ocean Safety, she enjoys spending her free-time outside with her friends and family— surfing, hiking, swimming, paddling, and bodyboarding are just a few of her favorite hobbies. 

Leah would like to thank Yoshimi Rii, Hi’ilei Kawelo, Keli’i Kotubetey, and Dr. Rosie Alegado for their oversight and feedback on this blog post and would also like to thank Dr. Alegado for the opportunity she has to work in her lab.           

Would you like a side of plastic with your fish?

J.Wong-Ala_picContributed by Jennifer Wong-Ala

The aroma of freshly defrosted Alepisaurus ferox (Longnose Lancetfish)  stomach begins to fill the lab as I place my first stomach of the day on the dissection tray. I look at the unopened stomach and begin to see an odd shaped object protruding from the inside. I make my first cut to expose the stomach contents and see the culprit responsible. A white piece of plastic that closely resembles the material paint buckets are made of emerges along with a degraded piece of a black trash bag intertwined with fishing wire. I begin to shake my head and continue to document the rest the of stomach contents.

Plastic pollution has been known to affect large, much-adored marine animals such as sea turtles, monk seals and seabirds. These animals can be strangled, suffocated, or even killed when they ingest plastic debris. Even microscopic organisms such as copepods have been seen to eat microplastics because they closely resemble phytoplankton – microscopic plants in the ocean. Now teams of scientist from the Monterey Bay Aquarium Research Institute (MBARI) and the University of Hawai‘i at Mānoa (UHM) are finding more trash at deeper depths (2000 – 4000 m), where commercially important fish are mistaking plastic debris as food.

But how does plastic even get that deep in the ocean? Aren’t most plastic debris buoyant and stay on the surface? Scientists at MBARI analyzed 1149 video recordings of marine debris from 22 years, looking at videos from remotely operate vehicles (ROVs) in the Monterey Canyon, and found that the largest proportion of the debris observed in the videos was plastic (33%) and metal (23%). Plastic debris was most abundant in undersea canyons at depths of 2000 to 4000 meters. It is thought to have reached those depths by these canyons’ natural sediment transport processes, which exert forces great enough to carry research equipment to the bottoms of these canyons.

Plastic debris can also be passed through the food web in the ocean when deep-sea animals eat other organisms that can live at many depths. For example, plastic debris has been found in the stomachs of the lancetfish which occupy a broad depth range  (0 to 1,000 meters). Lancetfish have been found to ingest plastic from the surface and then travel to deeper depths where it becomes prey to other species such as Opah, Albacore and Yellowfin tuna. The plastic from the Lancetfish has now been passed through the food web and potentially to our dinner plates.


Lancetfish habitat extends to depths where plastic accumulates.

Big steps are already being made in regards to one type of plastic debris called microbeads. This year President Obama signed the Microbead-Free Waters Act of 2015 that will ban the use and sale of products containing microbeads by 2018 and 2019. This was a big step in making a positive impact for our environment, but there is so much more to do.


The author working in the field

Jennifer Wong-Ala transferred from Kapi‘olani Community College to the University of Hawai‘i at Mānoa (UHM) in Fall 2015 as a Junior in the Global Environmental Science Program. She is a NOAA Hollings Scholar, C-MORE Scholar in Dr. Neuheimer’s Lab, Laboratory Technician in Dr. Drazen’s Lab, and is also part of the SOEST Maile Mentoring Bridge. Jenn is interested in computer modeling/analysis of how ocean processes interact with organisms in the ocean and how to best preserve these natural resources. In the future she plans to bring these skills and interests together to conserve marine life in Hawaii. This post was originally written for OCN 320 (Aquatic Pollution), a writing intensive requirement for the GES major.           

Mining, Metals and Megafauna in the Pacific Deep-Sea

DivaAmon Contributed by Diva Amon

I’m a deep-sea biologist with an ethical conundrum: I get to work in one of the most poorly-known habitats on the planet but the only reason I have that privilege is because it will likely be exploited and irreparably altered within the next decade.

We rarely think about where the never-ending stream of resources that we consume comes from. Take for instance the iPhone 6S you upgraded to when nothing was wrong with iPhone 5, or that zero-emission electric car you just bought: do you know where the materials used to make those came from? The demand for metals is increasing worldwide resulting in resources being harvested in ever more remote places, and the next frontier of mining will likely take place in the deep ocean.


Figure 1. Polymetallic nodules of various sizes. Image credit: Diva Amon.

My research takes place in the Clarion-Clipperton Zone (CCZ), an abyssal region (3500-5500 m) in the tropical Pacific Ocean that stretches from Hawaii to Mexico. The CCZ has dense beds of polymetallic nodules: lumps of metallic ore laden with cobalt, copper, nickel and other rare metals that sit like cobbles on a street. It is thought that they form in a similar way to a pearl (accretion) at a rate of a few millimeters per million years. As this entire region is in international waters, it falls under the mandate of the International Seabed Authority (ISA) and so far, there have been 15 mining exploration areas allocated, each up to 75,000 km2 or roughly the size of Panama.

ISA map

Figure 2. Exploration claim areas in the CCZ. Downloaded from the ISA website.

Let’s be honest, nodule mining is going to do some damage. Nodules will be harvested, destroying all animals that rely on this habitat and leaving no possibility for the re-establishment of this community in the future. Machines will also likely disturb and compact large swathes of sediment >5 m wide and 5-20 cm deep, squashing air out of the sediment (removing crucial living space for animals) as well as directly killing any animals residing in or on the sediment. Huge sediment plumes will also be kicked up, which will travel for kilometers before depositing elsewhere, potentially stifling animals and blocking filter-feeding apparatuses. Further entombment of the seafloor will likely occur when tailings are discharged into the water column. Not to mention other possible impacts that include light and noise pollution from machinery, and major changes to the geochemistry of the sediment, food webs (with repercussions for fisheries), and carbon sequestration. The cumulative impacts of these operations aren’t yet understood but will likely be long-standing and ocean-wide.

Oebius mining method

Figure 3. The polymetallic-nodule mining concept taken from Oebius et al 2001.

Despite this looming threat, the CCZ is critically underexplored. We literally do not even know what lives there. The ISA has made it mandatory that contractors undertake a baseline study of the biology living at the seafloor before EIAs and mining can begin.  The ABYSSLINE Project, which I work on, is doing just that in the claim area leased to UK Seabed Resources Ltd (UKSRL). My task is to find out what megafauna (the awesome charismatic animals over 2cm in size) live in the UKSRL claim, how abundant and diverse they are, and what ranges they occupy, not only within the claim but also across the entire CCZ. It’s also crucial to find out whether variations in the megafauna community correlate with nodule presence and other environmental parameters.

Although it is still early days for the project and there are still many more years of work to do, preliminary results show that the UKSRL claim area is rich not only in metals but also in life. Our first expedition sampled a 30 x 30 km area of the UKSRL claim using a remotely operated vehicle and various other pieces of equipment. There was life everywhere: tiny white corals, pink and purple sea cucumbers, bright red shrimp and strange unicellular animals that create sedimented homes the size of your fist.  In this relatively small area, we saw 170 megafauna morphotypes and it’s likely that’s an underestimate! These levels of biodiversity are the highest in the CCZ and are comparable to many other abyssal regions worldwide. We also collected 12 megafauna morphotypes and half of those were new to science including some of the most commonly seen, reiterating how little we know of the abyssal life in this region.


Figure 4. Some of the rare and unique megafauna that call the CCZ home. Image credit: Diva Amon and Craig Smith, University of Hawaii at Manoa. Collage created by Amanda Ziegler.

We’ve seen so many incredible animals in the CCZ and it can suck when you think about what will likely happen in the future. But when I feel that sinking feeling inside, I find the strength to continue by remembering why we are doing this work. We can’t manage what we don’t understand and we can’t protect what we don’t know. If deep-sea mining is to go ahead in the CCZ, high-quality scientific work needs to be done to establish the full extent to which animals will be impacted and how best to mitigate these effects and balance the needs of both society and nature.

Diva Amon is a postdoctoral scholar in the Smith Lab at the Department of Oceanography at the University of Hawaii at Manoa. She is a deep-sea ecologist with a special interest in chemosynthetic habitats and anthropogenic impacts in the deep sea. Her current research is focused on understanding what megafauna inhabit the largely unknown deep sea of the Clarion-Clipperton Zone in the Pacific Ocean, in advance of the mining of this region for polymetallic nodules. She considers herself to be a ‘tropical species’ having been born and raised in Trinidad and Tobago and so has adjusted to life in Hawai’i quickly. You can find her on Twitter as @DivaAmon.  

The art in microbial oceanography – why data visualizations and art are two sides of the same coin

Contributed by Mpvj0vEct_400x400arkus Lindh

When I visited the Museum of Modern Art in New York City this December, I was struck by the similarities between the Jackson Pollock collection and data visualizations of microbial oceanography. It may seem surprising, but the processes of science and art are very similar, if not identical. Some of the major cornerstones of both involve observation, collaboration, research and creativity. Here’s how art can help us appreciate the infinite depth and beauty of biological complexity in the ocean.

In our field of microbial oceanography, we are trying to understand the distribution and function of the smallest plankton in the ocean. Marine microbes have high diversity, short generation times and rapid turnover, and despite their small size, these numerous microorganisms regulate fluxes of energy and chemicals in the ecosystem by processing organic matter. Microbial oceanographers often employ artistic renditions to depict how the very small interact with each other and the environment. For example, in her excellent text on why microbes matter Alice Vislova showed an image by professor Roman Stocker, which illustrates microbial life and organic matter fluxes within a drop of seawater. In particular, illustrations based on ideas by professor Farooq Azam have provided us with a concept of how microbially driven ecosystems work. Azam once drew an illustration on a napkin to convey his ideas to fellow colleagues. This illustration (shown in A, below) has since been used in thousands of classrooms and lectures and is widely known to the oceanography community via his 1998 Science paper ”Microbial control of oceanic carbon flux: The plot thickens” (Science 280: 694-696).


Illustration of the microbial loop, from Azam (1998) “Microbial control of oceanic carbon flux: The plot thickens,” Science 280:694-696 (left), and Jackson Pollock’s No. 31 (right).

Let’s compare Azam’s illustration with Jackson Pollock’s No. 31 (B, above). Ok, now you are probably wondering what Pollock’s drip technique type of painting has to do with a conceptual scientific idea about biological complexity. First, let me quote Pollock when he was explaining the process of his new technique:

New needs need new techniques. And the modern artists have found new ways and means of making their statements… Each age finds it’s own technique. On the floor I’m more at ease…I feel nearer, more part of the painting since this way I can walk around it, work from the four sides and literally be in the painting.

In essence, the process of painting can be analogous to the process of science since we, like artists, use different techniques for different purposes that develop over time. Further, we the scientists are often trying to conceptualize data that are abstract and complex. For example, microbial oceanography deals with multidimensional variation, resulting from differences in ocean circulation, hydrology, and environmental disturbances, and also biological variation.


Jackson Pollock in the process of painting with his “drip” technique.

One of the major challenges for microbial oceanographers today is to understand and predict the consequences of changes in climate for microbially driven ecosystem processes like biogeochemical cycling of elements that are essential to all living organisms. It’s safe to say that the technique of the current age is performed by collecting “big data” from high-throughput sequencing of genes and/or genomes in the ocean. Samples are taken, water is filtered and biomass collected. From the vast complexity of billions of microbes in a liter of seawater, we retrieve gigabytes to terabytes of data. There are several different approaches ranging from amplicon sequencing focusing on specific genes, to annotating microbes taxonomically, to transcriptomics that addresses the expression of particular functional genes. Still, all techniques have the same common tool for understanding results – data visualization. We are working with an ocean canvas that helps us conceptualize microbial dynamics. There are a million ways to visualize data but in the creative process of choosing visualizations, we are constantly learning. In a sense, this is where the science occurs. Hypothesis are born from this artistic process of data visualization. Alternatively, it is in the visualizations that hypotheses are answered. Therefore, regardless of whether your particular field of interest is hypothesis-driven or hypothesis-generating, the art of science is invaluable.

So how do we visualize science? Using computer programs such as R, MATLAB, Excel, or by hand? If you are an ecologist and a deft R programmer, you have probably encountered the Vegan package in R. Vegan is a fantastic resource for microbial ecologists and includes many of the essential analyses to describe alpha and beta diversity as well as population dynamics. I often couple such analyses with the graphical tool ggplot2 , also in R. This tool is very versatile and allows users build essentially any type of plot imaginable. Actually, one of R’s greatest advantages is that it can be used to bring to life virtually any idea for data visualization. Moreover, although ‘help’ functions in R work poorly and are often incomprehensible, there are thousands of online communities with people who are probably doing something similar, from which you can draw inspiration and solutions. Typically I render the art in R and make the finishing touches in Adobe Illustrator. However, often times the process of art begins even before even collecting samples or conducting experiments. By making drawings with a pen and paper, I can take the first step towards a particular analysis I want to make. In the end, few ideas for data visualization are kept, but that does not mean that the process of making the many others was in vain. Rather, it is in this selection process of trial and error that we may learn the most. In fact, I believe that it is in this moment that we as scientists endeavor to push the limits of human knowledge.


Bacterial populations distributed in time and space. Figure by Markus Lindh

 Once the data have been visualized, another process begins: the process of writing. But that, as they say, is a completely different story…

Markus Lindh received his doctoral degree in Ecology at Linneaus University in Sweden. He is interested in how projected climate change could influence the dynamics of particular bacterioplankton populations. He’s also curious about the use of marine bacteria as bio-indicators of environmental change to determine the health status of the sea. He is currently a post-doctoral researcher at the Center for Microbial Oceanography Research and Education at UH Manoa.                                                                                   

Thinking Small: Part I

It isn’t easy to study life forms we can’t see. It’s not easy to talk about them, either. This is the first installment in a series about why and how we (try to) do it anyways.

rsz_11535797_10205060585775774_6958456103789566742_nContributed by Alice Vislova

You can imagine that microbes make tricky research subjects, being invisible to the naked eye, and all. I’m a microbial oceanographer, and, speaking of eyes, I can make people’s eyes glaze over at a party by the mere mention of my research topic by name: microbial metatranscriptomics. No don’t walk away – it only sounds boring because it’s so cutting-edge (wink). We can’t observe the behavior of microbes in the ocean by snorkeling around, but we can get a clue by sequencing RNA in seawater to learn which genes are being expressed. More on that later. For now, I want to discuss why we go to such technological lengths to microbes despite their small size.

The Illumina DNA sequencer is super cool, I promise.

The Illumina DNA sequencer is super cool, I promise.

People are surprised that as an ocean biologist, I study microbes and not something more…visible, like dolphins. It’s true – dolphins are pretty great. But their impact on the planet is nowhere near that of, say, Prochlorococcus – a genus of marine photosynthetic bacteria (cyanobacteria) responsible for at least a quarter of global oxygen production. Microbes can make a big impact despite their individual size because there are so many of them.

But first…what is a microbe, anyway?

Before I got into microbial oceanography as a grad student, I associated microbes mostly with disease. I didn’t know they were such a big deal. In fact, I didn’t even know what they were exactly. So, just to get everybody on the same page: microbes are simply organisms invisible to the naked eye. The vast majority of microbes are single-celled. This diverse group spans all three domains, making up the majority of life on Earth. 

A Bottlenose Dolphin surfs the wake of a research boat. These majestic creatures just can't compete with microbes when it comes to global biogeochemical impact Photo credit: NASA

A Bottlenose Dolphin surfs the wake of a research boat. These majestic creatures just can’t compete with microbes when it comes to global biogeochemical impact
Photo credit: NASA

Microbes – they’re kind of a big deal

Microbes are everywhere. Take a look in the mirror. You’re looking at an aggregate of human and microbial cells – 10 microbial cells to every human cell! We eat, breathe and poop microbes. That dolphin to the left is an aggregate of dolphin and microbial cells! There are a million microbes in a teaspoon of seawater and a billon in that amount of soil. With the water cycle, they rise from oceans and lakes and rain down again. And they’re not just along for the ride. In their vast numbers, microbes seriously impact the environment and organisms they live on, in and around. My aim here is to explain why microbes might matter to us.

s each individual strives to obtain the energy and 

Microbial metabolism affects the chemical composition of the earth.

A great example of both unusual microbial metabolism and symbiosis: 6-foot-tall giant tube worms living on hydrothermal vent fields are mostly bacteria-filled gonads on the inside, processing no mouths or stomachs because they depend exclusively on sulfate-reducing bacteria for energy. Photo credit: NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011

Great example of both unusual microbial metabolism and symbiosis: 6-foot-tall giant tube worms living on hydrothermal vent fields are mostly bacteria-filled gonads on the inside. Possessing no mouths or stomachs, they depend exclusively on sulfate-reducing bacteria for energy.
Photo credit: NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011

Like all living things, ourselves included, microbes are chemical factories. Certain molecules go in, enzymes mediate reactions, different molecules come out; this affects the chemistry of the environment. As with the example of photosynthesis by cyanobacteria, although the amount of a certain chemical (oxygen in this case) produced by an individual microbe over time may be small, microbes’ collective impact can have major consequences. In fact, a couple billion years ago in what has been called the Great Oxidation Event, photosynthesis by microbes raised the oxygen concentration in the atmosphere to the point that allowed for something called oxygenic respiration (a.k.a. breathing), while simultaneously wiping out the majority of anaerobic life that had populated the planet at that time.

Furthermore, microbes possess a much more diverse metabolic repertoire than multi-celled organisms. One such example of exotic metabolism is nitrogen fixation. Where animals like ourselves can only obtain nitrogen by eating other living things, diazotrophs possess the ability to incorporate inorganic nitrogen from water or air. Another example: unlike plants and cyanobacteria which obtain energy from sunlight, or the many organisms that get energy from eating those lower on the food chain, some microbes get energy by reducing sulfate emitted from hydrothermal vents. The bottom line – microbial metabolism is diverse and has considerable impacts on our planet.

Microbes are part of a network of interactions between all living things.

The samples I collect in the field just look like water with nothing in it. But in reality, each drop contains a rich hidden world that looks something like this illustration published in Science magazine, an image that has really stuck with me:

From cover of Science, 5 February 2010, used with permission from R. Stocker, J. R. Seymour, G. Gorick

Image from cover of Science, 5 February 2010, used with permission from R. Stocker.

As each individual strives to obtain the energy and particular nutrients it requires, a complex web of ecological relationships is formed. Competition is rampant, especially in the nutrient-poor open ocean around Hawaii, where my research takes place. But collaboration can be found too. For example, take our old friends the diazotrophs. In environments where nitrogen is particularly low, we find nitrogen-fixing bacteria living on or inside diatoms’ silicate shells. This is an example of mutualism, or perhaps commensalism. The bacteria provide a source of organic nitrogen to diatoms, and the diatoms provide protection, or perhaps something else.

Photomicrographs of bacterial symbionts (denoted by arrows) with rectangular host diatoms. Scale bars: 50 μm. Credit: Hilton, J. A., Foster, R. A., Tripp, J., Carter, B. J., Zehr, J. P., and Villareal, T. A. Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature Communications. 4, April 2013.

Photomicrographs of bacterial symbionts (denoted by arrows) with rectangular host diatoms. Scale bars: 50 μm.
Source: (Hilton et al., 2013)

In fact, it seems that many species of environmental microbes depend on their neighbors for survival. Perhaps this is the reason for the ‘Great Plate Anomaly’ in microbiology – the longstanding mystery of why, despite effort by many researchers, only a fraction of microbes from the environment have been successfully isolated in culture.

Favia pallida (hard coral) with signs of bleaching. Source: Nick Hobgood

Favia pallida (hard coral) with signs of bleaching. Source: Nick Hobgood

The lives of microbes are interdependent not just with one another but also with multi-celled organisms. For example, coral bleaching, the process caused by rising water temperatures and acidification that is decimating reefs around the world, is the loss of single-celled photosynthetic algae that live in and feed the coral. Just last month, NOAA declared a third major global coral bleaching event underway.

So…if you weren’t an avid microbe fan already, hopefully I’ve convinced you that microbes matter. In further installments of the Thinking Small series, we’ll explore some tools we use to study microbes, and what they’ve allowed us to discover.

Stay curious

Alice Vislova is a graduate student at UH Manoa’s Center for Microbial Oceanography Research and Education. She is interested in feedbacks between ecology and evolution. Her current focus is using molecular tools (mostly DNA and RNA sequencing) to study circadian patterns in microbial behavior and life cycles. She’s also the editor of this blog. She welcomes questions and comments at                                                                                                                                   

Works Cited:

Hilton, J. A., Foster, R. A., Tripp, J., Carter, B. J., Zehr, J. P., and Villareal, T. A. Genomic deletions      disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont. Nature         Communications, 4 (2013), p. 1767.

Inspiring community college students to pursue a career in ocean and earth sciences


Contributed by Johanna Wren

Ever wonder what questions community college STEM (Science, Technology, Engineering and Mathematics) students ask when taken on a tour of a research vessel?

“Are all beds the same size?”, posed a five-foot tall student standing next to a 6-foot fellow student, as they inspected the state rooms in the R/V Ka‘imikai-O-Kanaloa.

Or, one of my personal favorites: “Can I drive the boat!?”

Each summer, a score of Kapi‘olani Community College (KCC) students meet every day for six weeks to immerse themselves in math and other STEM subjects as part of the KCC STEM Summer Bridge program, HāKilo II. For the past three summers, C-MORE and SOEST from the University of Hawai‘i at Mānoa have been invited to spend one week with these students, introducing them to ocean and earth science careers through hands-on experiences.

HāKilo II students on a field trip to R/V KOK at Snug Harbor. Photo credit: Heidi Needham.

HāKilo II students on a field trip to R/V KOK at Snug Harbor. Photo credit: Heidi Needham.

The theme throughout the week is Learning by Doing, so we embark on field trips, engage in career exercises, and interact with graduate students and professionals in STEM fields. Our goal is to help the students discover their passions, and urge them to follow those passions in their professional careers. I first got involved with HaKilo II’s SOEST week as a graduate research assistant with the C-MORE Education office in 2013. I have since helped to organize and lead the event each summer, as the intensive week of career exploration has become one of my favorite summer events.

Learning By Doing: Field trips!

“Bet you didn’t know you got a mouthful of critters every time you get in the ocean!” said peer-mentor Dan to a student while looking at what they caught in a plankton tow.

Learning by Doing is done best outside of a classroom, so we take the students on multiple fieldtrips. For example, during these field trips, students figure out how the Hawaiian Islands were formed, and why hillsides and surrounding ocean look the way they do. Seeing first hand – and trying to figure out why – there is coral wedged between layers of basalt high above sea level, turns sea level rise from an abstract concept into a tangible one. Learning by doing, seeing and feeling is so much more powerful than being told how the world works.

Student and instructor during a geology field trip, talking about the formation of O‘ahu and sea level change at Lāna‘i lookout. Photo credit: Johanna Wren

Student and instructor during a geology field trip, talking about the formation of O‘ahu and sea level change at Lāna‘i lookout. Photo credit: Johanna Wren

Even though we have visited some of the same sites every year, there are always new things to discover, and students never fail to impress and surprise me with their curiosity and insightfulness. I really enjoy showing students what lives in the clear and seemingly empty waters near the beach. After conducting a plankton tow, while looking at the copepods and other animals in the water, students often wonder if they swallow all of those animals when they go swimming. It’s really nice to see even the most intractable student, who wouldn’t part from her smartphone for more than a minute, get excited about the land and sea around her.

Learning By Doing: Experience as a near-peer mentor

“Let’s ask Daren, he knows everything.” – A commonly overheard statement by a group of students when they ran into a problem they couldn’t solve.

Spending a summer studying subjects that often take students outside of their comfort zone can be intimidating and scary to many. At the same time, there is nothing more inspiring than connecting with an individual you identify with, who shares your background or interest. This is where the near-peer mentors like Dan and Daren come in. Each year, a handful of senior KCC students, many of whom participated in HāKilo II in previous years, act as peer-mentors and play a pivotal role in inspiring and engaging students. Students can identify with a mentor who went through the program just last year, and who comes from a similar cultural and/or academic background. The students are less reserved with their questions, and the peer-mentors themselves develop into teachers with enthusiasm and confidence.

Students in HāKilo II learning about seagliders, and how to combine an interest in engineering with a love for the ocean, from Sarah Searson. Photo credit: Johanna Wren

Students in HāKilo II learning about seagliders, and how to combine an interest in engineering with a love for the ocean, from Sarah Searson, a sea-going marine technician. Photo credit: Johanna Wren

I especially like witnessing the progression from student one year to peer-mentor the following year. Watching them go from shy and unsure students to outgoing, empowered, and confident in their new role as peer-mentor is motivating. And what I always find remarkable is how humble the peer-mentors are: they all have an ‘if I can do it, you can do it’ attitude. Peer-mentors take on the roles of a leader, educator, and mentor, and they not only inspire the students, they inspire me as well.

Learning by Doing: Networking with people paid to pursue their passion

“Man, that’s the closest I’ve been to an astronaut!” said one student after talking to a geology professor working on the Curiosity Mission with NASA.

Instead of reciting statistics and course requirements, which often become overwhelming, we introduce the students to career professionals in a variety of fields, from surf forecasters to ocean engineers. Students “talk story” with 20 different professionals, hearing – and often seeing – firsthand what that career entails and what kind of education they need to get there.

HāKilo II students talking with a career professional, Kimball Millikan, about wave buoys and ocean engineering. Photo credit: Johanna Wren.

HāKilo II students talking with a career professional, Kimball Millikan, about wave buoys and ocean engineering. Photo credit: Johanna Wren.

Once students realize that many of the professionals they talked to get paid to surf, dive or hike (common hobbies among the students), their enthusiasm skyrockets. The type of questions they ask changes from general (e.g. “What kind of degree do you have?”) to specific (e.g. “What subject would you recommend that I focus on to get your job?”). The dedication that the professionals show not only to their profession but also to sharing their passion with young scientists is profound. At the end of the week, we ask the professionals to give one take home message to the students, and it is universally: “You work too much not to love what you do.”

The best part about this program for me each year is when students discover that their interests don’t have to stay hobbies, but that they can become their careers. A few weeks ago, I ran into one of the students who participated in HāKilo II two years ago and was a peer-mentor last year. When I first met her in 2013 she intended to major in Nursing. Since then, she has changed her focus, transferred to UH Mānoa’s Dept. of Oceanography Global Environmental Sciences program, and participated in marine biology and oceanography summer research experiences both in the U.S. and abroad. She is a true inspiration and role model, and I’m so honored to have had a small part in helping her find her passion.

Johanna Wren is a PhD candidate in the Department of Oceanography in the Toonen-Bowen (ToBo) Lab at Hawai‘i Institute of Marine Biology (HIMB) at the University of Hawai‘i at Mānoa. Her research focuses on larval dispersal and population connectivity of reef fish using a biophysical modeling approach. She is interested in identifying biophysical drivers around the Hawaiian Islands that shape the connectivity patterns seen in reef fish communities today.


Climate Science for Marshallese High School Teachers



Contributed by Michelle Tigchelaar

As a climate modeler, I mostly experience climate change through graphs and figures, scientific papers and the long-term projections of the Intergovernmental Panel on Climate Change report. At times the reality of climate change becomes more tangible, like when we went on a field trip to Mauna Loa and were presented with a 400 ppm CO2 air sample — the Keeling curve in action! But it wasn’t until I visited the Marshall Islands this June to contribute to the 2015 Climate Science Teaching Institute, that the painful truth of a changing climate truly hit home.

Majuro Atoll from above. Photo credit: M. Tigchelaar

Majuro Atoll from above. Photo credit: M. Tigchelaar

At an average elevation of 2 m above sea level, the narrow atoll islands of the Republic of the Marshall Islands (RMI) and its population of 68,000 are at risk of near-constant inundation by the end of this century. Not much further down the road, the islands could disappear entirely. The injustice of this is enormous. Not only did the Marshallese do very little to contribute to the leading causes of climate change, they also do not have the resources that richer (i.e., more polluting) countries have to deal with its consequences. Recently, the RMI Ministry of Education added climate change education to the mandatory curriculum, so that its citizens will be better informed about what is happening to their islands and the world around them. In this context, COSEE Island Earth – with support from PREL and NSF Ocean Sciences – organized a workshop for high school teachers so that they will be equipped with knowledge and activities to use in their classrooms. I had the honor of teaching the physical climate science part of this workshop.

Teaching at this workshop proved to be challenging, for unexpected reasons. For starters, it was difficult to figure out what material to present on. How was I to  condense all the complexities of the climate system and climate change science into a few lectures that are understandable, relevant and comprehensive? Many of the attendants of our workshop were general science or biology teachers, so they had little prior knowledge of how the climate system works. Furthermore, while English is an official language of the Marshall Islands, most teachers were more comfortable in their own language — which was often, but not always, Marshallese (many teachers in the RMI come from other Pacific Islands such as Fiji, Micronesia or the Philippines). We also encountered cultural differences between teachers in the US and the Marshall Islands, with the latter seeming less vocal when questions arose. By starting with the material at the very beginning, building slowly, repeating key points and leaving ample room for questions, I hoped I was able to adequately convey the material.

Teaching about sea level rise projections at the College of the Marshall Islands. Photo credit: Dr. Judy Lemus.

Teaching about sea level rise projections at the College of the Marshall Islands. Photo credit: Dr. Judy Lemus.

In the US, decades of research and coordination have resulted in the availability of a wealth of papers, reports and websites that present scientists and the general public with detailed information about past climate measurements and future climate projections (think for instance of the National Climate Assessment or NOAA’s El Niño Portal). By comparison, a lot less is known about climate variability and change in Pacific Island nations, so I had a hard time finding easily digestible information to share with the teachers. Fortunately, the international research community is slowly starting to pay more attention to this region of the globe. I was thankful for the help of Drs. Mark Merrifield and Phil Thompson from the UH Sea Level Center, who shared and explained their work on sea level rise in the Pacific Islands. More importantly, some great local organizations were able to present at the workshop as well. By involving local organizations, we were able to facilitate the creation of (hopefully) lasting connections, so that exchange of climate knowledge can also happen outside of this workshop and in years to come.

SeaGrant’s Karl Fellenius showing the class instrumentation from the Pacific Islands Ocean Observing System (PacIOOS) that is moored in the harbor of Majuro. Photo credit: M. Tigchelaar

SeaGrant’s Karl Fellenius showing the class instrumentation from the Pacific Islands Ocean Observing System (PacIOOS) that is moored in the harbor of Majuro. Photo credit: M. Tigchelaar

During the workshop, one of our aims was to come up with activities that teachers can easily reproduce in their classrooms. On my end, I demonstrated: 1. how to create El Niño in a tank (with food coloring and a blow dryer); 2. why sea level rises due to thermal expansion and the melting of land-, but not sea-, ice (with water, clay, ice and a heat lamp); 3. where and by how much sea level is expected to rise in the future (using the online NOAA sea level rise viewer); 4. how moon phases work (with styrofoam balls and a lamp); and 5. how to measure humidity and demonstrate convection (again using ice and food coloring and thermometers). We thought we had done a pretty decent job at coming up with accessible activities, until we learned that some schools do not have the resources we expected them to have. For instance, some schools on the more remote islands of the nation only have one computer, or no steady electricity source. One teacher told us that they don’t usually have access to ice, except for when a fishing boat stops in port! Luckily we had brought supplies with us to hand out to the teachers, so that they could at least do some of the activities.

Demonstrating why we see different phases of the moon. Photo credit: M. Tigchelaar

Demonstrating why we see different phases of the moon. Photo credit: M. Tigchelaar

All these challenges aside, I left the workshop with many positive impressions. One would think that the prospect of a disappearing homeland and the terrible injustices of climate change and socio-economic inequality would leave a community despondent and angry. Perhaps a lesser people would be. But I found the Marshallese teachers to be eager to learn and open-hearted. Many of them went to great lengths to attend this workshop, and all appeared to be incredibly thankful for the opportunity and excited to teach the material to their students — with whatever resources they have. I was particularly inspired by one teacher, an older gentleman from Januit. He truly grasped that dealing with climate change in these remote islands is not only an issue for international politicians, but also an opportunity for islanders to increase resiliency and battle poverty by taking better care of reefs, land and people. When these kinds of insights enter into school curricula, that is the power of education. So in the end, while I hope that the Marshallese high school teachers were able to learn from me and my knowledge of climate change, I am also grateful for all that they taught me.

Michelle Tigchelaar is a PhD candidate in the Department of Oceanography at the University of Hawai’i at Mānoa. Her research focuses on modeling the response of the climate system to long-term forcing over the past 800,000 years. She also enjoys putting science to good use and being a student activist. 


To Jargon or not to Jargon


Contributed by Elisha Wood-Charlson

Jargon, as defined by Google, consists of “special words or expressions that are used by a particular profession or group and are difficult for others to understand.” So, you can imagine why jargon is a natural target for science communication training and workshops. Hey, science jargon even has its own April Fool’s spoof article.

Well, as it turns out, defining jargon and identifying jargon create a bit of inherent irony. A word is only considered ‘jargon’ when it isn’t well understood, so when are science words ‘jargon’ and when are they not? Google’s definition suggests that jargon can be specific to a group, and not necessarily restricted to a technical field. In addition, Google gives the entertaining synonym of “slang”, which begs the question – are scientists actually speaking our own form of “Science Jive”?

One of the most challenging parts of science communication is understanding your audience well enough to choose vocabulary that will communicate your science accurately while still getting your message across. Therefore, we need to start thinking about our “Science Jive” in layers. How far removed is our target audience from our science field?

The Russian Doll of Science Jive
Nesting Dolls (Photo Credit: James Lee)

Nesting Dolls (Photo Credit: James Lee)

As with all science communication efforts, you must first understand your audience(s) before you determine how much jargon you can layer on. The smallest, innermost ring is your peer group (you are the doll in the center). Your peer audience will include members of your lab group, your collaborators, and even your fellow participants in a domain-specific session at a conference. Almost everything in this ring may be considered jargon to a general audience, who resides in the largest, outermost doll layer. And, although some of the jargon translations from the far inner ring to the far outer ring may be the most challenging (discussed later), the dolls in the middle are where things get really interesting. How well do you know your audience two rings removed? For example, I recently attended the 2015 AAAS conference in San Jose, CA. Having never attended an AAAS conference before, I was surprised at the breadth of science topics presented. They ranged from looking at the effect of epigenetics on the brain to 3-D printing of 4-D mathematical models to microbial oceanography, my personal ring of Science Jive. So, how do you know when to jargon and when not to jargon?

The best way to figure out your audience is to understand where they exist in the science communication space. Do they read popular science articles, like those in Scientific American or Discover? If so, getting familiar with those journals (if you aren’t already) will help you determine which jargon level you should speak to. For example, in situations where “addition of viral concentrates resulted in decreased photosynthetic activity” might not work, something like “after adding more viruses, the cultures started dying” might be perfect. From another perspective, if you are writing something for a government office, you might consider getting in touch with whomever is in charge of science-related issues. Depending on their background, they may only be one or two jargon rings away. Or, if their background isn’t in the sciences, they may comfortably reside in the far outer general public ring.

Communicating Science Jive to the Outer Doll

Have you tried explaining your research to a family member? Megumi Chikamoto had a great post (4 Feb 2015) on Real Science at SOEST! blog about jargon, relating to her 7 year old son and making her message more understandable to a broader audience.

Translating jargon takes a bit of trial and error. Pick a prominent jargon word in your specialization and start trying out alternative vocabulary with the lab down the hall, fellow students at a departmental seminar, or with other science departments that meet up for pick-up soccer games after work. In the end, you may still end up with a word(s) that can’t be captured at the level of accuracy you require. Another strategy is to develop an analogy for your research. Can you capture the dispersal model or biogeochemical flux pathway in a metaphor or image? For example, Donn Viviani, a graduate student in C-MORE, is able to transform his research into the simple process of making a cup of tea!

In the end, only you can decide when to jargon and when not to jargon, and it will take practice. However, there should also be a collective effort by every science specialization to establish some translated terms that are acceptable replacements for their domain. In some areas, such as climate change, this is already happening. But we shouldn’t wait for a social movement to motivate us! Scientists are people too, and we should be making an effort to communicate using language that can be understood by our audiences.


Other resources
Scientific Jargon, Thompson Writing Program handout by Jordana Rosenberg 2012
Terms that have different meanings for scientists and the public, log post by Andrew David Thaler at Southern Fried Science
Words Matter, AGU blog post by Callan Bentley

Elisha M. Wood-Charlson has a PhD in marine science, and has worked in a variety of research areas including coral symbioses, marine viruses, and viruses in corals. She is currently testing out life as a science communicator and is finding the creative latitude enjoyable. She works for the Center for Microbial Oceanography: Research and Education (C-MORE) as an educator, designing #scicomm training for graduate students, postdocs, and early career researchers (check out the new Science Communication Portfolio training guide on the SOEST website!). She is also managing the EarthCube Oceanography and Geobiology Environmental ‘Omics (ECOGEO) Research Coordination Network (RCN), which demands structured communication between the scientists asking the difficult ‘omics questions and the bioinformaticians making the tools to help answer them.

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.

What drives me to be a scientist?: Impacting society through science

“Originally, I was driven by the type of job that I didn’t want to have, but am now driven by the potential impact that I can have while solving marine environmental problems.”

Read on to find out more about what led Stu to his career!

goldberg pic


Contributed by Stuart Goldberg

If you put a label on me, I am a microbial oceanographer. I study the function of microscopic bacteria and phytoplankton in marine food webs. I do so because these organisms support healthy ecosystems and fisheries by transferring energy and nutrients to organisms at higher levels of the food chain. But how did I get to studying microbes in the ocean? Well, thinking back, what drives me to be a scientist has changed over the years. Originally, I was driven by the type of job that I didn’t want to have, but am now driven by the potential impact that I can have while solving marine environmental problems.

One of the first jobs I had was working for Pepsi Cola of the Hudson Valley, NY during summers and holiday breaks in high school and college. My co-workers were great – their good-natured humor help to make the days more enjoyable – but it was back-breaking work. Every day, I went to supermarket after supermarket, stocking shelves with soda and building gigantic soda displays, like the pyramids you regularly see. It was also tough to earn respect from store managers that I interacted with because I was so young. This wasn’t where I wanted to be, or end up.

Once I started college at the University of Maine, I pursued a degree that would help me find a job working outside, preferably on environmental issues. I started freshman year as a forestry major with the hopes of working on conserving New England’s forests for future generations. I quickly discovered that the majority of UMaine forestry graduates went on to work in the paper industry. What really turned me off to this career path was that the paper industry contributes significantly to air and water pollution. Every day, paper mills emit tons of gases into the air, causing acid rain and global warming. They also have discharged pollutants into freshwater ecosystems that can bioaccumulate in fish, contributing to some of the state-issued consumption warnings due to possible health side effects. Although there were other forest conservation career opportunities working for state and federal agencies, I felt the urge to change majors to marine science to live a life near the ocean studying how its processes support our lives.

Being by the sea had always provided a sense of comfort and ease while growing up, so the idea of a career on the water or understanding more about marine ecosystems was enticing. Fortunately, UMaine had just initiated an undergraduate major in marine science. After learning about ocean food web dynamics and nutrient upwelling in my first oceanography class, I knew that this topic area was the right fit because I was very interested in how nutrients are recycled to support productive ecosystems and fisheries. From there, it was up to me to discover a career path in this field. I embarked on undergraduate research experiences in Maine and Bermuda, and eventually began graduate school at UC Santa Barbara where I earned my PhD studying the marine carbon cycle. Soon thereafter, I moved on to post-graduate school research studying a variety of topics including aquatic nutrient cycling and ocean acidification. At this point in my career, I was motivated by the desire to eventually become a professor. As time went by, however, my career interests began to change. I wasn’t enjoying the long hours writing grants and papers, or staying up late at night working in the lab, and a change was needed.

A few years after earning my PhD, my spouse accepted a marine policy fellowship in Washington D.C. I was looking forward to a fresh start in a new place, but I would have to eventually find a job. Although being unemployed for a few months was stressful, it was during this time that I found new motivation for being a scientist at an unexpected event. Every year, the nation’s shellfish farmers come to D.C. to talk to their congressional representatives about their relevant concerns, some of which are focused on things that can improve the productivity of their farms and shellfish sales. For example, the proper training and equipment to monitor changes in salinity, temperature, and ocean acidity can help prevent juvenile oysters from dying, thus enhancing harvests and profitability. On the last evening of their visit, I was invited to an elegant party that was hosted by U.S. shellfish growers associations from around the country. While mingling, I began a conversation with a shellfish farmer from Northern California. Upon hearing about my background in oceanography and ocean acidification, he asked if I could help him predict upwelling events that would bring acidic waters over his oysters. Acidic seawater is harmful to juvenile oysters because it kills them by dissolving their shells. In this instance, I realized that my scientific skills and expertise could be used to help solve real-world problems while informing decisions about marine natural resources.

My newfound drive to work on applied scientific problems to assist everyday people helped me to land a policy fellowship at a non-profit in D.C. My first task was to build trust and collaborations with shellfish farmers, and then talk to federal agency leaders and congressional representatives about ways to help these farmers adapt to the negative impacts of ocean acidification on their shellfish harvests. As a policy fellow, I began to network with other ocean non-profits to advocate to congress and federal agencies on behalf of U.S. shellfish farmers for more resources to purchase and implement ocean acidification monitoring instrumentation at oyster hatcheries. As part of this outreach effort, I organized, facilitated and led a stakeholder meeting between ~20 shellfish farmers from all over the U.S. and representatives from the USDA to provide a forum for farmers to clearly state their concerns about ocean acidification’s impacts on their industry, including discussion about what that the agency could do to assist them in adapting to these changes in ocean chemistry. One of the shellfish farmers and I also met with his congressional district representative from Oregon and her staff to further discuss these issues. The experience as a fellow helped me learn how to better translate my scientific knowledge to a variety of audiences and has helped me become a more confident scientist and person.

Whereas I was initially driven by the type of career that I didn’t want, I now realized that there are endless opportunities for scientists to make an impact on society by learning to use our expertise to help solve real-world environmental problems. In the future, I see my career moving along this trajectory.

Stuart Goldberg is a postdoctoral scholar in the Nelson lab at the Department of Oceanography at the University of Hawaii at Manoa. His research examines the role that microbes play in recycling nutrients in marine and aquatic environments. Recently, he has become more interested in the cycling of nutrients in coral reef and coastal environments. 

Click here to read more articles on what drives our bloggers to conduct their research everyday.
Want to submit your own article? Check out submission guidelines and email us today.


Why did I become an ecologist?

gold-medal-conCongratulations to Carolyn Faithfull for being the winner of our 1st SOESTblog Writing Contest “What drives you?”! Thank you to all of the readers and supporters of SOESTblog and congrats to everyone who entered our contest!



C FaithfullContributed by Carolyn Faithfull

I grew up next to a lake. You could always feel its presence, even though you couldn’t see it from our house. It made our farm the wettest in the district, miring us down in cattle-churned mud in the winter. Flocks of swans would fly towards it, flapping, honking and pooping. And in summer you could smell it, an occasional waft of rotten lettuce on the hay-filled breeze.

As you may have guessed, rotten lettuce is not the aroma of a healthy lake. Nope, this lake was big and shallow and totally unable to deal with the excess fertiliser being drip-fed from the surrounding farms. A regular pattern started occurring. It began with the stealthy overtaking of the entire lake by oxygen weed. Previously the weed had been safely far below us in our little boat. But by the end of the summer, rowing our little boat was like trying to row through a wet meadow. The lake was so clogged that on windy days it still looked calm, the water barely able to move between the thick weedy fronds. The swans loved it. Hundreds and then thousands came, honking and flapping and pooping.

Then the weed died. Choked by its own abundance, massive rolls of weed washed up, burying the swan nests and forming a stinking border around the lake edge. Free from the weed, the shallow sediments coloured the lake brown. Not for long though. The next summer the lake became a sickly green soup. We were not allowed to swim. Not that you would want to. The algal bloom became so dense that bacteria consuming the dead algal cells used up the oxygen in the water. Dead fish and mussels floated to the shore. The swans left. But, oxygen weed is a very hardy plant. It is an invasive species, and the small remaining fragments were slowly covering the bottom under the algal soup. Gradually, sediments were stabilized, the water became clearer and nutrients were absorbed by the rapidly growing weed.

My 14-year-old self wondered what was wrong: as the density of swans built up again, so did the oxygen weed – so was it the swans’ fault? Did all that pooping make the oxygen weed crash and the algae grow? My science fair project that year was particularly involved: I examined the effects of swan poop on algae in two types of jars, with and without oxygen weed.

Although somewhat misguided, the science fair project reflected something about me: I wanted to know. I knew the cycles happening to the lake were not how a healthy lake behaved and I wanted to know why.

Now I know that the flipping between weed and turbid algal-dominated states I observed in the lake is common in New Zealand. “Flipping” has been observed in 37 lakes and is associated with both the presence of oxygen weed and high farming pressure in the catchment area.

With my science fair project, I had wanted to know what was causing the flipping, but I also wanted to fix the lake. I remembered Grandpa’s stories about catching 70-pound eels and jet boat races; I wanted the lake to be like it once was, safe enough to drink, clean enough to swim in. Perhaps subconsciously I also knew it was partly my family’s fault, and I felt responsible for the mess we had helped create.

A calm early morning beside the lake. This picture was taken in 2003 before native plants were planted along the edge.

A calm early morning beside the lake. This picture was taken in 2003 before native plants were planted along the edge.

Last year, my family, several other landowners and a horde of volunteers, planted native plants around the edge of the lake. Wetland restoration is underway and farmers have been given advice on how to manage fertiliser application to reduce nutrient runoff. The future of the lake is starting to look a little bit clearer. Who knows, perhaps one day I will swim to the other side. I will have to watch out for those 70-pound eels though.

So I confess, I didn’t become an aquatic ecologist because I wanted to swim with dolphins, explore the arctic tundra or investigate the deepest trenches of the oceans (although those are all nice perks). My desire to know the how, what and why of things that lie beneath the water’s surface was inspired by a smelly, unstable, fascinating lake.


Liked Carolyn’s article? Share her post today!



Carolyn Faithfull is a postdoctoral scholar in the Goetze lab at the Department of Oceanography at the University of Hawaii at Manoa. Her research involves examining how tiny aquatic critters respond to different types of stress in their environment, such as excess nutrients, less light, or higher temperatures. Recently she has been very interested in what these tiny aquatic critters have for breakfast. Are they eating the equivalent of cornflakes every day, or a fruit bowl? The answer might just lie in a future blog post.



Inspiring future discoveries and changing the world

Here is our second entry of our 1st SOESTblog Writing Contest “What drives you?”! Each week, contestants will share what drives them to do their research day in and day out. Each article will be posted for 1 week and winners will be determined by the most # of reads on the site! Help Michelle this week by sharing her article!


Screen Shot 2015-04-10 at 9.28.17 AMContributed by Michelle Jungbluth


What is it that scientists really do? And what drives them to do it?

The life of a scientist is not as straightforward as you might think. To the left is a list of 18 things I am expected to do as a graduate student scientist— in addition to the necessary daily human activities such as grocery shopping, maintaining personal relationships, and keeping my apartment clean.

Given that outrageous list, I sometimes feel that there aren’t enough hours in the day  So what keeps me going?

By being endlessly curious!

I love being out on the waves, feeling the sets roll in, seeing the blue-green of the water. What makes it even better is to know what caused those waves and what shapes them, how the smell and color of the sea is related to recent rainfall in the area, that the little moving specks in the water are actually living, breathing plankton that fuel healthy ocean ecosystems.

I would not be happy working in the office all day, every day, crunching numbers or making phone calls. I would not be fulfilled as a veterinarian, neutering animals half of the week and seeing sick animals the other half of the week. I would not be satisfied working with laboratory animals, born to a life in a cage living far from their natural habitats. I know these things because I have experience with them and decided that I wanted more. It is only through experience that you can truly decide if a career path is right for you, and I am thankful, and have deep respect for everyone who has been a part of these prior experiences.

The moment I decided to move to Hawaii with my scientist husband, Sean Jungbluth was life-changing. That is when I discovered my love for oceanography (and copepods!). Some of what drives me is the diversity in that long list of responsibilities I just gave. The inherent challenges in that list keep me feeling fulfilled, most of the time.

The less tangible outcomes of my work are also what drive me to keep at it. As a scientist, the work I do now and in the future could impact the world in so many ways:

  • Inspire future generations to be scientists; despite that long list of challenging work, my science includes a lot of fun; sometimes I get to cross the equator on a British Antarctic icebreaker, and chase storms for my research
  • Be the basis for future discoveries!
  • I could, if I’m very lucky and work hard enough, make a discovery that illuminates or changes our relationship to the world around us!

When I feel discouraged, or when an experiment does not go as planned, these are the things that inspire me to push onward.

Me at the 2013 SOEST Open House, where I helped create an exhibit teaching schoolchildren and families about zooplankton, hoping to inspire future generations!

Me at the 2013 SOEST Open House, where I helped create an exhibit teaching schoolchildren and families about zooplankton, hoping to inspire future generations!

I am thankful for the hundreds of people who have been my teachers or mentors throughout my life so far. From my parents and grandparents, to all my teachers in the 20+ years of K-12, college, and graduate education, my employers over the years, and the past and present scientists who inspire me. It is due to your inspiration that I am driven to be who I am, and do what I do every day.


Liked Michelle’s article? Share her post today!



Michelle Jungbluth is a PhD candidate in the Department of Oceanography at the University of Hawaii at Manoa. She uses traditional and novel molecular techniques to study plankton food web interactions and the importance of highly abundant larval copepods in marine ecosystems. She is also a co-founder of the Science Communicators ‘Ohana and a Teaching Assistant for Introductory Oceanography OCN 201 at UH Manoa.


What drives me: Giving more, taking less

Here is the first entry of our 1st SOESTblog Writing Contest “What drives you?”! Each week, contestants will share what drives them to do their research day in and day out. Each article will be posted for 1 week and winners will be determined by the most # of reads on the site! Help Chantel this week by sharing her article!


FaceCrop_CChangContributed by Chantel Chang

I remind myself daily about why I subject myself to the challenges of graduate school (e.g., lack of sleep, free time, and money, feelings of incompetence, etc.) in order to answer questions from myself and others like, “Why am I back in school at the age of 30 while most of my peers own homes, are starting families, and get free weekends?”

The initial driver was that I knew what I did not want. I could not stand to stay in my previous career as an occupational therapist because it was missing something for me on a personal level. I believe everyone has a natural strength – a gift, and I recognized from grade school that mine was in mathematics and analysis. Today I realize how important it is for me to use mathematics, and to keep learning and growing. I chose to study oceanography because of the complexity and dynamic nature of the ocean. With an interest in biophysical modeling, I create computer models to assist with answering questions like, “What are the major physical, biological, and behavioral drivers that impact genetic or larval connectivity in the ocean?” Or “How might computer models be used to assess and improve placement of marine protected area boundaries?” I could study oceanography for a lifetime and still have more questions.

However, my primary driver goes beyond mathematics and my interests. My primary driver is that I strive to give back to Hawai‘i. As a fifth generation child of Hawai‘i, my favorite memories were of surfing and bodyboarding with my family in the crystal-clear blue ocean, while taking lunch breaks to feast on spam musubi and Hawaiian Sun juice. I’ve fished for ‘ahi and mahimahi, snorkeled and dove the Hawaiian coral reefs, and hiked the tall mountains of O‘ahu. Hawai‘i has provided a tremendously beautiful home and I hope to give back to the islands more than what has been given to me. I hope that many future generations will be able to enjoy Hawai‘i as I have. I’m not quite sure of what my specific contribution will be, but I believe that a deeper understanding of the ocean and environment is a good starting point.

During those moments of exhaustion, which are common in graduate school, I remind myself of how lucky I am to be allowed to live here in Hawai‘i of all the places in the world (less than 1%, about 2 in 10,000 people in the current world population, live in Hawai‘i) and to be in a situation where I am able to return to school for a career change. I focus on what I am grateful for, the give-take relationship between the land and humans, and I realize that the stresses of graduate school are temporary and trivial compared to those that Hawai‘i is under. Imagine the burden of Hawai‘i – the rise of industrialization, an increasing population and pollution have put tremendous stress on the islands, corals and marine life over the years. It’s common to hear stories of the ‘old days’ from my father’s generation when fish were plentiful and marine life was thriving. But now, “there’s not as many fish” in those same places where they used to be abundant. Even in my lifetime, I can remember what it was like to see open land instead of condominium upon condominium.

With everything back in perspective, I continue on with a renewed spirit and the mantra “give more, take less.” What can I do for Hawai‘i?

Liked Chantel’s article? Share this article today!

Bedtime Science Stories

Contributed by Megumi Chikamoto

Every night, while sitting beside my 7-year-old son’s bedside, I ask him one question.

“What did you do today?”
“Work,” he replies, briefly. Sometimes he says, “math,” or “recess.” Some days, he turns to ask me the same question.
“Mommy, what did you do today?”

To answer his question, I try to explain one of my current research projects in detail. When I talk about the basic theory or hypothesis of my scientific topics, my son is really interested. Specifically, I have succeeded in catching his attention by talking about the drastic changes in marine plankton species that occurred around 15,000 years ago. After listening to my explanation, he comes up with his own hypothesis, which he tells me excitedly. This conversation with my son is much like brainstorming with my colleagues, and I am impressed that my son understands the big concepts of my research. But one night, I decided to take it one step further by explaining the modeling concept of my research. He fell asleep before I finished my story.

I often face this problem when I talk about modeling simulation to the general public, like my friends or relatives, not just my son. People, especially those living in Hawaii, surrounded by the ocean, tend to have a stereotypical image of oceanographers, thinking that we go out to sea for our research. I am an oceanographer; yet, I do not go out to sea. Instead, I sit down in front of a computer, peer at a screen, and write programming codes for over 6 hours everyday, 5 days a week. When I explain this to my friends and relatives, this unexpected research style seems to intrigue them, and they ask me to tell them more about my research. My research approach is using an Earth system model that is a numerical tool for calculating time evolution of the global climate system. The model calculates the atmosphere and ocean phenomena, such as wind blows, ocean currents and precipitation. Furthermore, the model includes components of marine ecosystems such as tiny plankton. My target is to elucidate marine ecosystem processes that link to climate change. But when I describe a model in such a way, my audience, like my son, loses interest quickly. This is one of the reasons why I want to improve my skill of public speech.


Map of present-day phytoplankton biomass in chlorophyll concentration in an Earth System model. Image Credit: M. Chikamoto

One thing I realize now is how much jargon my explanation contains! Due to the specialized words, my audience might hardly understand the basic concepts and their attention is lost. Generally, people prefer to relate to a personal story, or sometimes an emotional one like in a novel; no one cares about the specialized issues (if someone is very interested in the specialized issues, he/she might be close to being the expert!). I know now that I should avoid describing my research like a scientific presentation, which is what I have done so far. Rather, I need to focus on the storytelling during an interactive conversation. Without more ado, I will try storytelling.

Why do we simulate?

Just think about this. If you take photographs in sequence with a camera and then want to know what is happening between the photos, what do you do? You might convert these intermittent images to an image sequence by taking the gaps and try to predict what happened in between in your brain. I do similar things in my research. Oceanographers monitor signals of ocean phenomena when going to sea, but getting the data is like one photo snapshot at a time. In order to display an image sequence like you do in your brain, I simulate it using a computer model instead. The model simulation in the computer calculates the time evolution of the Earth environment. By analyzing the simulated results, I can know what is going on in the environment. In fact, I use many kinds of models for today’s environment as well as for the past or the future. Through past, present and future climate simulations, I want to know mechanisms of the earth systems – how the earth systems of several different rhythms play harmony.

Trying again

One night, I decided to try explaining model simulation to my son again.

“I simulate the Earth environment using a computer and study what is going on in the atmosphere and the ocean. When I was a college student, computers were very slow and we were waiting to finish the calculation for several months. But nowadays, technology has developed tremendously and computer speed is much faster than it was in the previous era. For example, my computer can finish a 500-year-long simulation while you are sleeping at night. In this way, we can go back to the past using very long simulations, even as far back as to the Ice Age. Using a computer, I can study all of the past, the present, and the future climate.”

“That’s great!” my son said, admiringly.



Megumi O. Chikamoto is an affiliate researcher in SOEST and a postdoctoral researcher at International Pacific Research Center. After getting her Ph.D in Atmosphere and Ocean Science at Hokkaido University in Japan, she has worked at the University of Minnesota, the University of Tokyo, the Japan Agency of Marine Science and Technology, and then the current position.  Her research focuses on marine ecosystem response to climate variability and changes in the past, current, and future.

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.

Continue reading

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!


Read this original post at:

Name the Three Types of Rock: Balancing Music and Minerals

Contributed by Christine A. Waters

Phaedrus Quote

iPhoto by Christine A. Waters

Igneous Geologist Under Pressure

Graduate school is an inevitably stressful experience. I entered with a mix of feelings: optimism, adventure, skepticism, motivation, and fear. For the first two years, in an attempt to channel these emotions in a positive direction, I practiced extreme discipline which I hoped would contribute to my success as a graduate student:

  • I made my job a priority (above everything, even my health)
  • I frequently pulled all-nighters without sleep and followed a “military minimum” rule (a minimum of four consecutive hours of sleep per night).
  • Almost every single day of the year, I went to the office to work as if the stock market’s opening bell rang.

Believe it or not, there was little tangible or emotional reward as a result of this behavior. Every scholarship or honor that I received (i.e. National Science Foundation Graduate Research Fellowship, a three-month work internship, accommodations/travel to a conference) contributed to a growing pile of tasks. My discipline had created an environment progressively more challenging and harder to maintain day by day. In fact, the bullet points above, when adhered to strictly, had the effect of greatly increasing the negative stress of graduate school.

In a study recently discussed on Science Magazine’s Life and Career blog, 78.5% of graduate students in science feel overwhelmed, with 60% feeling exhausted, hopeless, sad, or depressed nearly all of the time. That seemed like a discouraging statistic to me! Hoping to not become one of the students in the study, I decided to re-balance and take control of my life. I reassessed my standard operating procedure for daily activities by making some non-work time with one of the recreational niches offered at my own institution.


I decided to return to an activity that always made me smile. I joined the UH Summer Band, a community band that rehearses at the university during the summer months. As I entered the rehearsal room for the first time, I felt like a school girl on her first day at a new campus: “Where do I sit? What do I do? How do I talk to these people who are already gathered in circles?” Admittedly, the freshman feeling was refreshing given my long comfort with academia. There were music majors in the group, and others, like me, who just wanted to play. I slowly made acquaintances and then friends. Every week, I looked forward to working with new music.

UH Fall Campus Band playing at Ala Moana

The UH Fall Campus Band, led by director, David Blon, performing at Ala Moana Center Stage, on November 26, 2013 | iPhoto by Greg Bagnaro

Kismet and Positive Stress

Kismet, to my friends, is the feeling we get when the music is just right – when it fills our body and mind. Music is my second language. I began with a Yamaha keyboard when I was in the first or second grade, picked up the flute in the fourth grade, and played the latter through my last year of high school. Music, for me, is a lifelong chase and a clandestine love. However, since the world is full of flautists with greater talent, I retired my flute to explore more sensible and less competitive career opportunities: electrical engineering, the military, and graduate school. For the past thirteen years, I dabbled on the flute for my own enjoyment when I could – playing for the 304th Signal Battalion in Korea during special events, marching with the Miners at the University of Texas at El Paso in 2006, and touring with And the Furies Say in 2007.

It is humbling to note that my stress-relieving activity actually produced some stress. The difference is that this stress was ultimately positive and inspiring! Returning to a retired pastime required much willingness to bruise my self-esteem. It was a struggle to be a born-again intermediate, to no longer be able to play with the same elegance and technique of years ago. Initially, there was frustration. Later, there was acceptance for the growing nimbleness in my fingers and awareness of my embouchure. The practice is challenging – just as it was when I first began learning to play. Quitting is sometimes reason enough to remain quit. I was deterred to begin again from fear of my growing lack of conditioning – as one might be from a sport she has left. For hobbies that required years of training, I recommend a modest relapse, as clumsy as it may be. For me, the experience has brought a harmonious (pun intended) balance to my previously work-controlled life.

Sedimentary Fill and Collateral Effects

Loosing work ties for two hours a week in one recreational niche became a gateway through which I am now able to enjoy life as a graduate student. So far, I have played with the UH Fall Campus Band, and I have also enrolled in the UH Concert Band. Music is an incredibly mindful experience, and I’ve found that playing with the university bands has been a generous and wonderful outlet for my stress. During rehearsals, I concentrate on the sound I’m producing, the combined sound of the band, the instructions given by the director, and the feel of the keys beneath my fingertips. There is something elevating and magical about being a part of a large creative force – kismet indeed. I believe that many others who have “retired” their instruments can identify with this and remember it sentimentally. I encourage my fellow students to go out and find the activity that challenges, motivates, and inspires them – outside of graduate work. And, if there are other mélomanes (music-lovers) in our science group, I’d love to hear about your own experiences below!

The UH Summer Band will be performing at Ala Moana Center Stage on July 24th at 7:00 p.m.

“Vesuvius” by the University of Hawaii Concert Band Aloha Concert on May 4, 2014, from†musicAENni†YouTube



Christine A. Waters is a veteran of the United States Army and a graduate student pursuing a M.S. in Marine Geology. She is working with advisor Dr. Henrieta Dulaiova on submarine groundwater discharges off the Kona coast of Hawai’i.

Read this original post at:

Related articles


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 (

Adapting Locally to Sea-level Rise

By: Haunani Kane

Wetlands are important to Island communities because they provide food in the form of loʻi (taro patch), and loko iʻa (fishpond), trap sediment that may otherwise enter the ocean, and provide habitat to a number of native and endangered species.  Sea-level rise, however, threatens the integrity of coastal wetlands due to increased erosion, salt-water intrusion and flooding. The greatest challenge for wetland managers/users will be to prioritize management actions at each of the areas that are predicted to be impacted.  To assist in this challenge we worked closely with wetland users to develop two strategies to manage predicted impacts.

Firstly, due to the low gradient of most coastal plain environments, the rate of sea-level rise impact will rapidly accelerate once the height of the sea surface exceeds a critical elevation.  We calculate a local sea-level rise critical elevation (similar to a tipping point) that marks the end of a slow phase of flooding and the onset of rapid flooding.  The outcome of this method provides wetland managers with maps that can be used to create an inventory of resources that may be impacted during the slow and fast phases of flooding.

Secondly, within highly managed coastal areas, vulnerability is related to site the specific goals of coastal stakeholders.  For example in response to sea-level rise a kalo farmer may prioritize management efforts at the loʻi over the nearby pond because the loʻi provides food for his/her ʻohana (family). On the other hand, a federal manager who is tasked with providing habitat for endangered species will focus sea-level rise management efforts on the pond because it is used more frequently by endangered waterbirds.  We worked closely with wetland users to develop a ranking system that models the local vulnerability as a function of 6 input parameters: type of inundation, time of inundation, habitat value, soil type, infrastructure, and coastal erosion.  Through the use of an in person survey each input parameter was ranked based upon the goals and objectives the users of that area.  Areas of the highest cumulative vulnerability were mapped and should be used to prioritize future adaptive management.

Haunani Kane is a graduate student in Geology and Geophysics, working in the Coastal Geology lab of Dr. Chip Fletcher within SOEST. Haunani is from Kailua, O‘ahu, and her research centers on better understanding past and future sea-level rise events to assist coastal risk management. She believes that by tying culture to science we may be able to inspire more young native scientists.

Storm Chasing on O‘ahu!

By: Shannon McElhinney

SMcelhinneyheadShotStorm chasing is a glorified way to describe what my MET628 (Radar Meteorology) class did for three weeks in November.  From October 21nd to November 13th 2013, the Doppler on Wheels (DOW) visited O‘ahu for the very first time.  The DOW is a mobile weather radar, an active remote sensing instrument, which emits radio waves to detect rain and clouds at different ranges.  The permanent radars typically used to monitor weather on O‘ahu are located on Moloka‘i and Kaua‘i, so this was a unique opportunity to look at O‘ahu weather- up close and personal.

Doppler on Wheels (DOW) Radar

Doppler on Wheels (DOW) Radar

The Hawaii Educational Radar Opportunity field project (HERO) was part of a National Science Foundation Educational Deployment of the DOW radar.  It was shipped all the way from Boulder, Colorado to Honolulu Harbor.  When it was finally unloaded from the ship, I drove down to the harbor with my professor and another student.  We were waiting in the hot dusty parking lot that would be its home base for the next few weeks, when it pulled up to the gate.  The giant blue semi-truck did not have a trailer on the back; instead it had an antenna, bigger than me.  It would get a lot of funny looks over the course of the project, as we drove it all around the island.

Each morning the class, as well as some undergraduates and National Weather Service employees, would meet for a forecast briefing.  If there was so much as a chance for mauka or trade showers, we deployed.  This was my first experience with hands-on fieldwork, and sitting in the operator’s chair, surrounded by all of the computers and switches, made everything feel real and exciting.  The DOW is usually chasing tornadoes in the Great Plains (it has been featured in the Discovery Channel’s Storm Chasers series).  Hawai‘i weather seems tame in comparison, but we were blessed with a variety of interesting weather.

The downsides of HERO included the very early mornings, the constant sound of the transmitter, and watching computer screens for hours on end.  There was also the frequent disappointment when a storm cell died or moved out of range.  But I can’t complain. I got my five seconds of fame when Meteorologist Jennifer Robbins interviewed me for a Hawaii News Now segment (I even got a free surfboard locker when my apartment supervisor saw me on TV!)  I had some exciting moments, like trying to launch an uncooperative weather balloon between heavy tropical downpours.  I got to see hundreds of children’s’ faces light up as they explored the DOW at a community outreach event, the SOEST Open House.

The News crew caught our balloon launch on camera

The News crew caught our balloon launch on camera

The real climax of HERO came as the final week was drawing to a close.  A cold front was forecast to pass through the islands, bringing convective and windy weather.  The forecast group noted a cold pool aloft, which meant an even greater chance for instability and thunderstorms.  The only problem was timing.  The timing of the frontal passage could have been any time from Saturday night to Sunday morning.  To be sure we caught it, three consecutive groups were assigned to work through the night.  I was happy to be in the first group because we experienced a lot of pre-frontal action at the Wahiawa site.  Parked on the side of a highway, we were able to see a large band of heavy showers approach from the north, which eventually reached the site.  Later that night there was heavy rain all around the island and even some flooding in town.

This is the main radar display during the big cold front event, showing where the heavy rains are (top) and wind speeds (bottom)

This is the main radar display during the big cold front event, showing where the heavy rains are (top) and wind speeds (bottom)

Most of that night consisted of four graduate students and the technician crammed inside the truck to keep dry.  My favorite moment was when the second team took over at 2 AM.  As I emerged from the truck, after my 8-hour shift, I was surprised to see 15 other students there, huddling under umbrellas and open car trunks.  Nobody had wanted to miss out on the excitement.  So there we stood, 15 meteorology students on the side of a road surrounded by pineapple fields at 2 AM on a Sunday morning… for fun!

Surprisingly we got no inquisitive visits from the police or locals, as we had many times before.  Our deployment sites were often at beach parks, which put us in clear view of the public.  People would approach us in the DOW or during a balloon launch to ask what we were doing.  Most showed great interest and support, although some were suspicious.  One lady even asked us not to scan her because she feared we could see through her clothes!

Weather balloon launch

Weather balloon launch

Weather radars are not a common sight here on O‘ahu, but we hope to change that.  The data allowed for a detailed and never-before-seen view of how rain forms around the islands.  I was able to watch a small trade wind cumulus cloud form and develop all the way to the end of its life cycle, completely captured by the radar.  Most importantly, this project got a bunch of students and meteorologists together to take part in hands-on weather data collection.  Through collaboration and operating the radar, I learned more in three weeks than I could have in a whole semester in the classroom.


Shannon McElhinney is a 2nd year Masters student in the Department of Meteorology at UH Manoa.  Her current research uses models and observations, including airborne Doppler radar, to study the Hurricane boundary layer.  She also enjoys teaching some meteorology fundamentals to MET101 lab students.