A few things I’ve learned while writing a thesis

By: Amanda Holdman, MS student, Geospatial Ecology and Marine Megafauna Lab & Oregon State Research Collective for Applied Acoustics, MMI

“Never use the passive where you can use the active.” I recently received this comment in a draft of my thesis. While this pertained to a particular edit, it has since become my motto for writing in general – to stay active in writing. I knew before beginning this process, from my peers, that it takes time to write a thesis or dissertation, and usually much longer than anticipated, resulting in late caffeinated hours. My roommates have recently moved out, making it a perfect opportunity to convert my home into a great evening office. I needed fewer distractions so I unplugged the TV and set up a desk with ideal conditions for writing. I’m in a race against time with my defense set for only a month away, and getting into good writing habits has helped me smooth out a lot of the writing stress, so I figured I could share those tips.

  1. Write sooner

The writing process can be daunting due to its size and importance. In the beginning I tended to wait until I thought I had researched enough about the topic. But, I have now learned not to wait until all the data is in and the results are clear to start writing. Some researchers might argue that results are needed before one can put the proper spin on the introduction, but spin isn’t quite needed for a first draft.  Most of the writing can be actually be done before all the data have arrived. For example, I didn’t need to know the results of my observations before writing the manuscript about them; the rationale for having done the research doesn’t change with the results, so a draft of the introduction can be written without knowing the results. The methodology also doesn’t depend on the results, nor does the analysis that will be performed on the data, so a good framework for the results section can be written before all of the statistical tests are run. And before I know it, I have almost a full draft, just with quite a few gaps.

  1. Write Continually

Productivity begets productivity, so don’t stop writing. It keeps my mind working and my project moving. I try to write a little every day or set a goal word limit. (500 words a day is easily obtainable and you feel proud at the end of the day). Writing as frequently as possible for me has helped to reveal gaps in my knowledge or understanding. Vague and disoriented writing tends to reflect a vague and disorganized thought, leading me to dig through the literature for more clarity.

  1. Figure out how you write and edit

Some people are better writers when they first put their thoughts on paper and plan to go back and fix awkward sentences, poor word choices, or illogical sentences later. My perfection has always plagued me, so I always edit as a write, with one goal only: to make sure I’ve expressed the idea in my head clearly on the page. I don’t move on until the sentence (or thought) makes sense with no ambiguity in the meaning. Clarity of thought is always the aim in writing a manuscript, yet it is very difficult to come back to a section of writing days or weeks later and sort out a mess of thought if I don’t clarify my writing while the thought is still fresh in your head. This means I am constantly re-reading and revising what I’ve written, but also hopefully means that when I submit something to my advisor or committee it only needs simple revisions, thereby saving time by getting as “close to right” as I could the first time around.

 

 

 

  1. Develop a routine

It’s important to learn when and what makes us productive. For me, writing in several short bursts is more efficient than writing in a few, long extended periods. When I try to write for long hours, I notice my concentration diminishing around the hour mark, so I try to take frequent 15 minute breaks. For me, the most productive parts of the day are the beginning the end. It’s important to build momentum early, and have a routine for ending the day too. At the end of each day, I always leave myself something easy to get started with the next day, so I wake up knowing exactly where I am going to start.

  1. Find a template

Usually, when we decide on a date and deadlines for the final draft of our thesis due, we’re so frantic and pressed for time trying to get all the content, that we forget about the time it takes to make a draft pretty. My last HUGE time-saving tip is to find a colleague who has recently turned in their thesis or dissertation and still has their final word document. You can save time by reusing their document as a template for margins, page number position and other formatting guidelines. Everything you’ve written can easily be pasted into a formatted template.

  1. Keep your motivation near

Finally, always try to keep the end result in mind. Whether it be holding a beautifully bound version of your thesis or a first author publication, keeping motivated is important. Publishing is not a requirement for completing a thesis but it is an ultimate goal for me. I know I owe it to myself, the people who I have worked with along the way, those who have supported me in some way (e.g., my committee), and to the funders that have helped pay for the research. Plus, to have a competitive edge in the next job I apply for, and to get the most leverage possible from my masters training, it is important for me to finish strong with a publication or two. Visualizing the end result helps me to take action to finish my thesis and advance my career.

Now, I think it’s about time to stop writing about writing a thesis and get back to actually writing my thesis.

 

Oceanus Day Three: Dolphin Delights

by Florence Sullivan, MSc student

Our third day aboard the Oceanus began in the misty morning fog before the sun even rose. We took the first CTD cast of the day at 0630am because the physical properties of the water column do not change much with the arrival of daylight. Our ability to visually detect marine mammals, however, is vastly improved with a little sunlight, and we wanted to make the best use of our hours at sea possible.

Randall Munroe www.XKCD.com

Our focus on day three was the Astoria canyon – a submarine feature just off the Oregon and Washington coast. Our first oceanographic station was 40 miles offshore, and 1300 meters deep, while the second was 20 miles offshore and only 170 meters deep.  See the handy infographic below to get a perspective on what those depths mean in the grand scheme of things.  From an oceanographic perspective, the neatest finding of the day was our ability to detect the freshwater plume coming from the Columbia River at both those stations despite their distance from each other, and from shore! Water density is one of the key characteristics that oceanographers use to track parcels of water as they travel through the ocean conveyor belt. Certain bodies of water (like the Mediterranean Sea, or the Atlantic or Pacific Oceans) have distinct properties that allow us to recognize them easily. In this case, it was very exciting to “sea” the two-layer system we had gotten used to observing overlain with a freshwater lens of much lower salinity, higher temperature, and lower density. This combination of freshwater, saltwater, and intriguing bathymetric features can lead to interesting foraging opportunities for marine megafauna – so, what did we find out there?

Click through link for better resolution: Randall Munroe www.XKCD.com/1040/large

Morning conditions were almost perfect for marine mammal observations – glassy calm with low swell, good, high, cloud cover to minimize glare and allow us to catch the barest hint of a blow….. it should come as no surprise then, that the first sightings of the day were seabirds and tuna!

I didn't catch any photos of the Tuna, so here's some mola mola we spotted. photo credit: Florence Sullivan
I didn’t catch any photos of the tuna, so here’s some sunfish we spotted. photo credit: Florence Sullivan

One of the best things about being at sea is the ability to look out at the horizon and have nothing but water staring back at you. It really drives home all the old seafaring superstitions about sailing off the edge of the world.  This close to shore, and in such productive waters, it is rare to find yourself truly alone, so when we spot a fishing trawler, there’s already a space to note it in the data log.  Ships at sea often have “follower” birds – avians attracted by easy meals as food scraps are dumped overboard. Fishing boats usually attract a lot of birds as fish bycatch and processing leftovers are flushed from the deck.  The birders groan, because identification and counts of individuals get more and more complicated as we approach other vessels.  The most thrilling bird sighting of the day for me were the flocks of a couple hundred fork-tailed storm petrels.

Fork-tailed storm petrels
Fork-tailed storm petrels. photo credit: Florence Sullivan

I find it remarkable that such small birds are capable of spending 80% of their life on the open ocean, returning to land only to mate and raise a chick. Their nesting strategy is pretty fascinating too – in bad foraging years, the chick is capable of surviving for several days without food by going into a state of torpor. (This slows metabolism and reduces growth until an adult returns.)

Just because the bird observers were starting to feel slightly overwhelmed, doesn’t mean that the marine mammal observers stopped their own survey.  The effort soon paid off with shouts of “Wait! What are those splashes over there?!” That’s the signal for everyone to get their binoculars up, start counting individuals, and making note of identifying features like color, shape of dorsal fin, and swimming style so that we can make an accurate species ID. The first sighting, though common in the area, was a new species for me – Pacific white sided dolphins!

Pacific white sided dolphin
A Pacific white sided dolphin leaps into view. photo credit: Florence Sullivan. Taken under NMFS permit 16111 John Calambokidis

A pod of thirty or so came to ride our bow wake for a bit, which was a real treat. But wait, it got better! Shortly afterward, we spotted more activity off the starboard bow.  It was confusing at first because we could clearly see a lot of splashes indicating many individuals, but no one had glimpsed any fins to help us figure out the species. As the pod got closer, Leigh shouted “Lissodelphis! They’re lissodelphis!”  We couldn’t see any dorsal fins, because northern right whale dolphins haven’t got one! Then the fly bridge became absolute madness as we all attempted to count how many individuals were in the pod, as well as take pictures for photo ID. It got even more complicated when some more pacific white sided dolphins showed up to join in the bow-riding fun.

Northern right whale dolphins are hard to spot! photo credit: Florence Sullivan Taken under NMFS permit 16111 John Calambokidis
Northern right whale dolphins are hard to spot! photo credit: Florence Sullivan Taken under NMFS permit 16111 John Calambokidis

All told, our best estimates counted about 200 individuals around us in that moment. The dolphins tired of us soon, and things continued to calm down as we moved further away from the fishing vessels.  We had a final encounter with an enthusiastic young humpback who was breaching and tail-slapping all over the place before ending our survey and heading towards Astoria to make our dock time.

Humpback whale breach
Humpback whale breach. photo credit: Florence Sullivan. Taken under NMFS permit 16111 John Calambokidis

As a Washington native who has always been interested in a maritime career, I grew up on stories of The Graveyard of the Pacific, and how difficult the crossing of the Columbia River Bar can be. Many harbors have dedicated captains to guide large ships into the port docks.  Did you know the same is true of the Columbia River Bar?  Conditions change so rapidly here, the shifting sands of the river mouth make it necessary for large ships to receive a local guest pilot (often via helicopter) to guide them across.  The National Motor Lifeboat School trains its students at the mouth of the river because it provides some of “the harshest maritime weather conditions in the world”.  Suffice it to say, not only was I thrilled to be able to detect the Columbia River plume in our CTD profile, I was also supremely excited to finally sail across the bar.  While a tiny part of me had hoped for a slightly more arduous crossing (to live up to all the stories you know), I am happy to report that we had glorious, calm, sunny conditions, which allowed us all to thoroughly enjoy the view from the fly bridge.

Cape Disappointment Lighthouse at the Columbia River Bar.
Cape Disappointment Lighthouse at the Columbia River Bar.

Finally, we arrived in Astoria, loaded all our gear into the ship’s RHIB (Ridged Hulled Inflatable Boat), lowered it into the river, descended the rope ladder, got settled, and motored into port. We waved goodbye to the R/V Oceanus, and hope to conduct another STEM cruise aboard her again soon.

Now if the ground would stop rolling, that would be just swell.

Last but not least, here are the videos we promised you in Oceanus Day Two – the first video shows the humpback lunge feeding behavior, while the second shows tail slapping. Follow our youtube channel for more cool videos!

 

Oceanus Day Two: All the Albatrosses

By Amanda Holdman and Florence Sullivan

Today got off to a bright and early start. As soon as daylight permitted, we had spotters out on duty looking for more marine mammals. We began to survey at the north end of Heceta bank, where we again encountered many humpback whales lunge feeding. We broke transect, and got some great video footage of a pair them – so check our youtube channel next week – we’ll upload the video as soon as we get back to better internet (dial up takes some getting used to again – the whales don’t know about highspeed yet).

Humpbacks lunge feeding at surface. photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis.
Humpbacks lunge feeding at surface. photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis.

After working with the humpbacks to capture photo-id data for about an hour, we turned south, and ran parallel to Heceta bank until we reached the southern edge. Along the way, we counted 30 humpbacks, and many California gulls, marbled murrelets, pink footed shearwaters, and sooty shearwaters.

After lunch, we conducted a CTD cast to see how conditions might be different between the southern and northern edges of the bank. Surface temperatures increased from 12.09C to 13.2C while bottom temperatures decreased from 8.7C to 7.8C.  The northern station was a textbook perfect two layer system. It had a well mixed surface layer with a steep pycnocline separating it from the colder, saltier, denser, bottom layer. The southern station still had two layers, but the pycnocline (the depth where a rapid change in density occurs, which delineates the edges of water masses) was not as steep. We are interested in these discreet measurements of ocean conditions because areas of high primary productivity (the green chlorophyll-a line) are often re-occurring hot spots of food for many levels of the food chain. Since we can’t phone the whales and ask them where to meet up, we use clues like these to anticipate the best place to start looking.

Readout of the CTD cast. The left plot has temperature in blue, and salinity in green. The right plot has density in black, chlorophyll-a in green, and oxygen in blue. observe how different variables change with depth!
Readout of the CTD cast. The left plot has temperature in blue, and salinity in green. The right plot has density in black, chlorophyll-a in green, and oxygen in blue. observe how different variables change with depth (on the y-axes)!

We next turned west to transect the continental shelf break. Here, we were hoping to observe changes in species composition as waters got deeper, and habitat changed.  The shelf break is often known as an area of upwelling and increased primary productivity, which can lead to concentrations of marine predators taking advantage of aggregations of prey. As we moved further offshore, everyone was hoping for some sperm whales, or maybe some oceanic dolphin species, and if we’re really lucky, maybe a beaked whale or two.

Black footed Albatross with immature gulls. photo credit: Leigh Torres
Black footed Albatross with immature gulls. photo credit: Leigh Torres

Today our students learned the lesson of how difficult marine mammal observation can be when our target species spend the majority of their lives underwater – where we can’t see them. While there were a couple of hours of mammal empty water in there, observers were kept busy identifying long tailed- jaegers, cassin’s auklets, murrelets, petrels, shearwaters, fulmars, and so many black-footed albatrosses, that they almost became “normal”.  That being said, we did spot a fin whale, a few groups of Dall’s porpoise, and three pacific-white-sided dolphins.  Unexpectedly, we also saw an unidentified shark, and several sunfish (mola mola)!

Humpback whale profile. photo credit: Amanda Holdman. Taken under NMFS permit 16111 John Calambokidis.
Humpback whale profile – notice the hump before the dorsal fin. photo credit: Amanda Holdman. Taken under NMFS permit 16111 John Calambokidis.
Fin Whale profile. photo credit: Amanda Holdman. Taken under NMFS permit 16111 John Calambokidis.
Fin Whale profile – notice how long the back is before the fin, and how pointed the dorsal fin is compared to the humpback. photo credit: Amanda Holdman. Taken under NMFS permit 16111 John Calambokidis.

Last but not least, we engaged in a long standing oceanographic tradition, which is to draw on Styrofoam cups, and send them down to Davy Jone’s Locker attached to the CTD.  When you bring them back up, the pressure has caused them to shrink to a fraction of their original size, which is an excellent demonstration of the crushing power of pressure (and why its harder to build a submarine than a rocket).

Shrunken cups! The first row have been sent down to 1400m, while the back row are still full size!
Shrunken cups! The first row have been sent down to 1400m, while the back row are still full size!

Now, we are steaming north toward Astoria Canyon, where we hope to make some more sightings in the morning. Stand by for news from our final day at sea.

Fin Whale. photo credit Amanda Holdman. Taken under NMFS permit 16111 John Calambokidis.
Fin Whale. photo credit Amanda Holdman. Taken under NMFS permit 16111 John Calambokidis.
Dahl's Porpoise. photo credit: Florence Sullivan. Taken under NMFS permit 16111 John Calambokidis.
Dahl’s Porpoise. photo credit: Florence Sullivan. Taken under NMFS permit 16111 John Calambokidis.

R/V Oceanus Day One: Hungry Hungry Humpbacks

By Florence Sullivan and Amanda Holdman

The GEMM lab is adventuring out into the wild blue yonder of open ocean sampling and educational outreach! Leigh is the chief scientist onboard the R/V Oceanus for the next two days as we sail through Oregon waters in search of marine megafauna. Also onboard are four local teachers and five high school students who are learning the tricks of the trade. Amanda and I are here to help teach basic oceanography and distance sampling techniques to our enthusiastic students.

Science Party musters in the dry lab for safety debrief. photo credit: Florence Sullivan
Science Party musters in the dry lab for safety debrief. photo credit: Florence Sullivan

We started the morning with safety briefings, and headed out through the Newport breakwater, direction: Stonewall Bank.  Stonewall is a local bathymetric feature where upwelling often occurs, leading to a productive ecosystem for both predators and prey. Even though our main sampling effort will be offshore this trip, we didn’t even make out of the harbor before recording our first gray whale and California sea lion sightings.

California Sea Lions on the Newport buoy. Taken under NMFS permit 16111 John Calambokidis
California Sea Lions on the Newport buoy. Taken under NMFS permit 16111 John Calambokidis

Our students (and their teachers) are eager and quick to catch on as we teach them new methodologies. Amanda and I had prepared presentations about basic oceanographic and distance sampling methods, but really the best way to learn is to jump in and go. We’ve set up a rotation schedule, and everyone is taking turns scanning the ocean for critters, deploying and recovering the CTD, logging data, and catching plankton.

a small pod of Orca. Photo credit: Florence Sullivan. Taken under NMFS permit 16111 John Calambokidis
A small pod of Orca. Photo credit: Florence Sullivan. Taken under NMFS permit 16111 John Calambokidis

So far, we have spotted gray whales, sea lions, a pod of (lightning speed) killer whales, lots of seagulls, northern fulmars, sooty shearwaters, storm petrels, and cormorants, but today’s highlight has to the last sighting of ~42 humpback whales. We found them at the Northern edge of Heceta Bank – a large rocky reef which provides structural habitat for a wide variety of marine species. As we approached the area, we spotted one whale, and then another. At first, our spotters had no trouble inputting the data, getting photo-ID shots, and distinguishing one whale from the next, but as we continued, we were soon overwhelmed. With whale blows surrounding us on all sides, it was hard to know where to look first – here a surface lunge, there, a breach, a spout, a fluke, a flipper slap! The surface activity was so dense and enthralling, it took a few moments before realizing there were some sea lions in the feeding frenzy too!

Five humpback whales surface at once. photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis
Five humpback whales surface at once. photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis

We observed the group, and tried to document as many individuals as possible as the sunset faded into night. When poor visibility put a stop to the visuals, we hurried to do a plankton tow and CTD cast to find some environmental insights for such a gathering. The CTD revealed a stratified water column, with two distinct layers, and the plankton tow brought up lots of diatoms and krill. As one of the goals of this cruise is to explore how marine mammals vary with ocean gradients, this is a pretty cool way to start.

A humpback whale lunge feeds. Photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis
A humpback whale lunge feeds. Photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis

A long day observing has left us all exhausted, but not too tired to share our excitement. Stay tuned for more updates from the briny blue!

Follow this link for real time view of our beautiful ship! : http://webcam.oregonstate.edu/oceanus

Humpback flukes for photo ID. photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis
Humpback flukes for photo ID. photo credit: Leigh Torres. Taken under NMFS permit 16111 John Calambokidis

Sonic Sea asks “can we turn down the volume before it’s too late?”

By: Amanda Holdman, MS student, Geospatial Ecology and Marine Megafauna Lab & Oregon State Research Collective for Applied Acoustics, MMI

It was March 15th, 2000; Kenneth Balcomb was drinking coffee with his new summer interns in the Bahamas when a goose-beaked whale stranded on a nearby beach. Balcomb, a whale researcher and former U.S. Navy Officer, gently pushed the whale out to sea but the beaked whale kept returning to the shore. He continued this process until a second beaked whale stranding was reported further down the beach; and then a third. Within hours, 17 cetaceans had stranded in the Bahamas trying to escape ‘something’ in the water, and Kenneth Balcomb was determined to solve the mystery of the mass stranding. The cause, he eventually learned, was extreme noise – sonar tests from Navy Warships.

The world is buzzing with the sounds of Earth’s creatures as they are living, interacting, and communicating with one another, even in the darkest depths of the oceans. Beneath the surface of our oceans lies a finely balanced, living world of sound. To whales, dolphins and other marine life, sound is survival; the key to how they navigate, find mates, hunt for food, communicate over vast distances and protect themselves against predators in waters dark and deep. Yet, this symphony of life is being disrupted and sadly destroyed, by today’s increasing noise pollution (Figure 1). Human activities in the ocean have exploded over the past 5 decades with ocean noise rising by 3db per decade (Halpern et al. 2008). People have been introducing more and more noise into the ocean from shipping, seismic surveys for oil and gas, naval sonar testing, renewable energy construction, and other activities. This increased noise has significant impacts on acoustically active and sensitive marine mammals. However, as the Discovery Chanel’s new documentary Sonic Sea points out “The biggest thing about noise in the ocean is that humans aren’t aware of the sound at all.” The increase of ocean noise has transformed the delicate ocean habitat, and has challenged the ability of whales and other marine life to prosper and survive.

June blogFigure 1: Anthropogenic sources contributing to ocean soundscapes and the impacts on marine megafauna survival (sspa.se)

Like the transformative documentary from 10 years ago, An Inconvenient Truth, which highlighted the reality and dangers of climate change, Sonic Sea aims to inform audiences of increased man-made noise in the oceans and the harm it poses to marine animals. The Hatfield Marine Science Center and Oregon Chapter of the American Cetacean Society offered a free, premier showing of the award-winning documentary followed by a scientific panel discussion. The panel featured Dave Mellinger, Joe Haxel, and Michelle Fournet of Oregon State University’s Cooperative Institute for Marine Resources Studies (CIMRS) marine bioacoustics research along with GEMM Lab leader, Leigh Torres, of the Marine Mammal Institute.

Sonic Sea introduces us to this global problem of ocean noise and offers up solutions for change. The film uncovers how better ship design, speed limits for large ships, quieter methods for under water resource exploration, and exclusion zones for sonar training can work to reduce the noise in our oceans. However, these efforts require continued innovation and regulatory involvement to bring plans to action.

Around the world the scientific community, policymakers and authorities such as The National Oceanic and Atmospheric Administration (NOAA), the European Union (EU), the International Maritime Organization (IMO) and other authorities have increasingly pressed for the reduction of noise.  NOAA, which manages and protects marine life in United States waters, is trying to reduce ocean noise through their newly released Ocean Noise Strategy Roadmap, where the challenge is dealt with as a comprehensive issue rather than a case-by-case basis. This undersea map is a 10-year plan that aims to identify areas of specific importance for cetaceans and the temporal, spatial, and frequency of man-made underwater noise. After obtaining a more comprehensive scientific understanding of the distributions and effects of noise in the ocean, these maps can help to develop better tools and strategies for the management and mitigation of ocean noise.

Sonic Sea states “we must protect what we love” but then asks “how we can love it if we don’t understand it?” Here at GEMM Lab and the Marine Mammal Institute, we are trying to understand marine species ecology, distributions and behavioral responses to anthropogenic impacts. One of the suggestions Sonic Sea makes to reduce the impact of ocean noise is to restrict activity in biologically sensitive habitats. Therefore, we must know where these important areas are. In an ideal world, we would have a good inventory of data on the marine animals present in a region and when these animals breed, birth and feed. Then we could use this information to guide marine spatial planning and management to keep noise out of important habitats. My thesis project aims to provide such baseline information on harbor porpoise distribution patterns within a proposed marine energy development site. By filling knowledge gaps about where marine animals can be found and why certain habitats are critical, conservation efforts can be more directed and effective in reducing threats, such as ocean noise, to marine mammals.

Noise in our oceans is hard to observe, but its effects are visibly traumatic and well-documented. Unlike other sources of pollution to our oceans, (climate change, acidification, plastic pollution), which may take years, decades or centuries to dissipate, reducing ocean noise is rather straight forward. “Like a summer night when the fireworks end, our oceans can quickly return to their natural soundscape.” Ocean noise is a problem we can fix. To quiet the world’s waters, we all need to raise our voices so policy makers hear of this problem. That’s what Sonic Sea is all about: increasing awareness of this growing threat and building a worldwide community of citizen advocates to help us turn down the volume on undersea noise. If we sit back and do nothing to mitigate oceanic noise pollution, the problem will likely worsen. I highly suggest watching Sonic Sea.  Then, together, we can speak up to turn down the noise that threatens our oceans — and threatens us all.

Sonic Sea airs TONIGHT (6/8) for World Ocean’s Day on Animal Planet  at 10pm ET/PT!

Exciting news for the GEMM Lab: SMM conference and a twitter feed!

By Amanda Holdman (M.S Student)

At the end of the week, the GEMM Lab will be pilling into our fuel efficient Subaru’s and start heading south to San Francisco! The 21st Biennial Conference on the Biology of Marine Mammals, hosted by the Society of Marine Mammalogy, kicks off this weekend and the GEMM Lab is all prepped and ready!

Workshops start on Saturday prior to the conference, and I will be attending the Harbor Porpoise Workshop, where I get to collaborate with several other researchers worldwide who study my favorite cryptic species. After morning introductions, we will have a series of talks, a lunch break, and then head to the Golden Gate Bridge to see the recently returned San Francisco harbor porpoise. Sounds fun right?!? But that’s just day one. A whole week of scientific fun is to be had! So let’s begin with Society’s mission:

smm-2015-logo

‘To promote the global advancement of marine mammal science and contribute to its relevance and impact in education, conservation and management’ 

And the GEMM Lab is all set to do just that! The conference will bring together approximately 2200 top marine mammal scientists and managers to investigate the theme of Marine Mammal Conservation in a Changing World. All GEMM Lab members will be presenting at this year’s conference, accompanied by other researchers from the Marine Mammal Institute, to total 34 researchers representing Oregon State University!

Here is our Lab line-up:

Our leader, Leigh will be starting us off strong with a speed talk on Moving from documentation to protection of a blue whale foraging ground in an industrial area of New Zealand

Tuesday morning I will be presenting a poster on the Spatio-temporal patterns and ecological drivers of harbor porpoises off of the central Oregon coast

Solène follows directly after me on Tuesday to give an oral presentation on the Environmental correlates of nearshore habitat distribution by the critically endangered Maui dolphin.

Florence helps us reconvene Thursday morning with a poster presentation on her work, Assessment of vessel response to foraging gray whales along the Oregon coast to promote sustainable ecotourism. 

And finally, Courtney, the most recent Master of Science, and the first graduate of the GEMM Lab will give an oral presentation to round us out on Citizen Science: Benefits and limitations for marine mammal research and education

However, while I am full of excitement and anticipation for the conference, I do regret to report that you will not be seeing a blog post from us next week. That’s because the GEMM Lab recently created a twitter feed and we will be “live tweeting” our conference experience with all of you! You can follow along the conference by searching #Marman15 and follow our Lab at @GemmLabOSU

Twitter is a great way to communicate our research, exchange ideas and network, and can be a great resource for scientific inspiration.

If you are new to twitter, like the GEMM Lab, or are considering pursuing graduate school, take some time to explore the scientific world of tweeting and following. I did and as it turns out there are tons of resources that are aimed for grad students to help other grad students.

For example:

Tweets by the thesis wisperer team (@thesiswisperer) offer advice and useful tips on writing and other grad related stuff. If you are having problems with statistics, there are lots of specialist groups such as R-package related hashtags like #rstats, or you could follow @Rbloggers and @statsforbios to name a few.

As always, thanks for following along, make sure to find us on twitter so you can follow along with the GEMM Labs scientific endeavors.

 

 

On learning to Code…

By Amanda Holdman, MSc student, Dept. Fisheries and Wildlife, OSU

I’ve never sworn so much in my life. I stared at a computer screen for hours trying to fix a bug in my script. The cause of the error escaped me, pushing me into a cycle of tension, self-loathing, and keyboard smashing.

The cause of the error? A typo in the filename.

When I finally fixed the error in my filename and my code ran perfectly – my mood quickly changed. I felt invincible; like I had just won the World Cup. I did a quick victory dance in my kitchen and high-fived my roommate, and then sat down and moved on the next task that needed to be conquered with code. Just like that, programming has quickly become a drug that makes me come back for more despite the initial pain I endure.

I had never opened a computer programming software until my first year of graduate school. Before then Matlab was just the subject of a muttered complaint by my college engineering roommate. As a biology major, I blew it off as something (thank goodness!) I would never need to use. Needless to say, that set me up for a rude awakening just one year later.

The time has finally come for me to, *gulp*, learn how to code. I honestly think I went through all 5 stages of grief before I realized I was at the point where I could no longer put it off.

By now you are familiar with the GEMM Lab updating you with photos of our charismatic study species in our beautiful study areas. However, summer is over. My field work is complete, and I’m enrolled in my last course of my master’s career. So what does this mean? Winter. And with winter comes data analysis. So, instead of spending my days out on a boat in calm seas, watching humpbacks breach, or tagging along with Florence to watch gray whales forage along the Oregon coast, I’ve reached the point of my graduate career that we don’t often tell you about: Figuring out what story our data is telling us. This stage requires lots of coffee and patience.

However, in just two short weeks of learning how to code, I feel like I’ve climbed mountains. I tackle task after task, each allowing me to learn new things, revise old knowledge, and make it just a little bit closer to my goals. One of the most striking things about learning how to code is that it teaches you how to problem solve. It forces you to think in a strategic and conceptual way, and to be honest, I think I like it.

For example, this week I mapped the percent of my harbor porpoise detections over tidal cycles. One of the most important factors explaining the distribution and behavior of coastal marine mammals are tides. Tidal forces drive a number of preliminary and secondary oceanographic processes like changes in water depth, salinity, temperature, and the speed and direction of currents. It’s often difficult to unravel which part of the tidal process is most influential to a species due to the several covariates related to the change in tides , how inter-related those covariates are, and the elusive nature of the species (like the cryptic harbor porpoise). However, while the analysis is preliminary, if we map the acoustic detections of harbor porpoise over the tidal cycle, we can already start to see some interesting trends between the number of porpoise detections and the phases of the tide. Check it out!

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Now, I won’t promise that I’ll be an excellent coder by the end of the winter, but I think I might have a good chance at being able to mark the “proficient” box next to Matlab and R on my first job application. Yet, whatever your reason for learning code – whether you are an undergraduate hoping to get ahead for graduate school, a graduate student hoping to escape the inevitable (like me), or just someone who thinks getting a code to work properly is a fun game – my advice to you is this:

Google first. If that fails, take mental breaks. Revisit the problem later. Think through all possible sources of error. Ask around for help. Then, when you finally fix the bug or get the code to work the way you would like it to, throw a mini-party. After it’s all over, take a deep breath and go again. Remember, you are not alone!

Happy coding this winter GEMM Lab readers – and I wish you lots of celebratory dancing!

An insight into what Marine Mammal Observing is really like!

By Amanda Holdman

It’s August of 2015. That means I have exactly 2.5 months left until my field season and data collection for my masters comes to a close. At the end of October, I will have collected exactly 2 years of visual data on marine mammal distributions off of the coast of Newport, Oregon.

This is a bittersweet moment for me. Currently, I am on a 7 hour flight to Scotland to do some initial data analysis on my collected observations, with the help of a workshop offered by the University of St. Andrews. My first time abroad has me pretty restless with excitement on the plane, but with a 9 hour time change, some good rest will be key to being successful at the workshop. As I try to close my eyes, and picture what the next two weeks of what I like to call “Intensive Distance Sampling Summer School” will be like, the stranger next to me inevitably begins to make small talk, beginning with

“So what do you do?”

I usually tend to answer this question in two different ways. When I’m in my science community, I have no hesitation giving my 3 minute elevator speech on what I have been researching for the past year. However, when I’m making small talk with anyone I tend to just say

“I’m a master’s student studying marine mammals”

And that’s about all you need to say to get everyone’s attention around you! With a little more detail, I explain that I run transects to collect visual observation data of marine mammals to assist with understanding their patterns in distribution and habitat use. This explanation is always followed up with:

“Man, you’ve got the coolest job ever! What’s it like doing this all the time?”

Again most of the time I get this question, I’m usually conversing with people visiting the west coast hoping to see a large gray whale on vacation; or  young children who haven’t yet figured out that marine biology isn’t just about dolphins and pretty coral reefs – but it’s still good to inspire them! Just last week even, I ran into someone on the beach that told me his daughter thinks I’m a rock star for teaching her that you can research the sounds that whales, dolphins, and seals make. (His daughter attended Marine Science Day back in April, and I showed her some recordings of sounds – but I’ll carry this compliment with me for a long time)

But when people ask me how awesome my job is, I tend to keep the morale up and I usually answer

“yep, it’s pretty awesome. I love it! ”

But to be honest, sometimes… it isn’t.

For me, there are four components that equate to a great day of fieldwork: ocean conditions, marine mammals, the boat itself, and equipment (hydrophones, GPS, CTD, camera, etc.)

So in reality…

“The flow of research season goes a lot like this: whales are present, but ocean is impossible; or ocean is calm but the whales are gone; or both whales and ocean are good but the boat breaks down; or everything is working but the rain last night brought in some fog and ruined the visibility” (From Hawaii’s Humpbacks: Unveiling the Mysteries)

AND EVEN on the rare chance that everything goes right – observing marine mammals is hard and uncomfortable – 14 hours of standing with back pain, squinting into the sun until you see one part of the water that looks a little different than the others. I mean really there isn’t much on earth that’s more enormous than the ocean.

This sounds like a lot of negativity, but I am in Scotland currently to resolve some of these minor setbacks we encountered during field collection. Using a statistics program called DISTANCE, we can take into account environmental conditions, sea state, observer bias, etc. When we combine all of these factors together we create a detection function or a ratio of the animals we saw, compared to those we missed. Eventually we end up with an abundance estimate of how many animals are in our study area.

Analyzing the results of my observations this week has provided me with the realization that my time on a boat is coming to an end. In my two years of fieldwork collection, marine mammal observing has molded me into the type of person that has what it takes to do this kind of research: dedicated, tolerant to pain, boredom, and frustration, and most importantly passionate about what I am doing.

Passion is definitely a prerequisite for the life of a GEMM student. Graduate school gives you the chance to be reflective and the time to carefully wade through information. I’ve always had a strong desire to learn, and when I get to combine that with my personal interests, it turns out graduate school can be quite the rewarding initiative.

It’s easy to be discouraged sometimes, especially in an intense and competitive environment like scientific research. I can assure you though, even on our unlucky days, when we’ve swallowed all of the truths about the difficulties of what we do and we’re frustrated enough to give up, our luck turns – usually right when we need it to.

I think the BBC Zoologist, Mark Carwardine, knows just how I feel in saying, “There are few things more rewarding than seeing the worlds’s largest animal in its natural habitat!

Thanks for reading!

Sharing the Science! Outreach at the GEMM Lab

Hello Everyone,

My name is Florence, and I’m here to update you on all the amazing outreach activities that the GEMM lab has participated in this past month!

We started on April 11, with the HMSC-wide Marine Science Day celebrations.  This year was particularly exciting because the Hatfield Marine Science Center is turning 50 years old! Along with the rest of our colleagues at the Marine Mammal Institute, we presented posters detailing our projects, had a few hands on activities such as ‘spot the whale’ – a bit of a scavenger hunt designed to give people a taste of how difficult it can be to spot marine mammals, and answered questions about our work.  It was quite a success!

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Florence representing the GEMM lab and gray whale research in Port Orford
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The Redfish Rocks Community Team table!

On April 19, I went down to Port Orford, OR to participate in “Redfish Rocks on the Docks”  an outreach event showcasing all the exciting research being done in conjunction with the Redfish Rocks Marine Reserve near Port Orford.  I presented a poster about my thesis project: Assessment of vessel disturbance to foraging gray whales on the Oregon Coast to promote sustainable ecotourism, and answered questions while leading folks through our ‘stay warm like a whale’ blubber glove activity.  It was a beautiful sunny day, but so windy that at times we joked that our tables looked more like geology presentations than marine biology due to all the rocks holding everyone’s papers, photos, and flyers down! Many of the folks who I will be collaborating with over the course of this project also had their own informational booths; South Coast Tours, Redfish Rocks Community Team, and the Oregon Marine Reserves Program. The Surfrider Foundation and CoastWatch also had interesting activities and information to share about marine debris and conservation of our oceans.  My favorite moment of the day was when I was explaining to a little girl how gray whales need to eat a lot of mysid shrimp in order to maintain their blubber to stay warm in the frigid ocean – and she intuitively made the jump from the blubber glove to the wetsuit she uses to go swimming!  It was wonderful to see her thinking critically about the different strategies for heat retention in water.

 

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The Ladies of the GEMM Lab! Courtney, Amanda, Dr. Leigh, Florence, Solène
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Solène received the Best Presentation Award!

Finally, yesterday, almost the entire lab gave presentations at the Northwest Student Society of Marine Mammals Annual Meeting.  The meeting was attended by ~80 interested students and researchers from a number of outstanding universities including; Western Washington University, University of Washington, Portland State, Stanford University and of course, Oregon State University.  The day began with an excellent introductory presentation by Dr. Ari Friedlander of our sister BTBEL Lab, and then it was on to student presentations.  Courtney and I presented in the ‘Human Dimensions’ forum on the possibilities of citizen science in marine mammal research and gray whale foraging ecology respectively.  At lunch, our valiant leader, Leigh, took part in a discussion panel and fielded questions from the audience concerning current advances in technology and possible applications to field work as well as giving professional development advice.  A few take away messages; Technology can provide wonderful insights, but one should not use a tool just to use a tool.  Rather, it is important to first ask your question, and then build your methodology and choose your tools in a manner most precisely able to answer the questions at hand.  In regards to professional development, do not discount the benefit of getting international experience – A broad perspective on possible solutions, and strong international collaborations will be necessary to solve many of the management issues facing our oceans today.  During the ‘Bioacoustics’ session, Amanda presented her work concerning harbor porpoise spatial distribution. Finally, Solène presented her work on Maui’s dolphins during the ‘Space and Time’ Session, and walked out having earned the ‘Best Presentation’ Award!!  Over the past few months that she has been visiting us, she has been a dedicated colleague and a wonderfully cheerful presence in the lab, and it was fantastic to see all her hard work being recognized in this public forum.  Overall, this NWSSMM conference was a great opportunity to see what other students in the Pacific Northwest region are working on, opened doors for future collaborations and gave us ideas for future projects.

 

Sunrise in Port Orford
Sunrise in Port Orford

Surveying Harbor Porpoises on the Oregon Coast!

Hello Gemm lab readers!

Spring has officially made it to the Oregon coast.  The smells of blooming flowers are lingering in the air at the Hatfield Marine Science Center (HMSC), the seagulls are hovering around our afternoon BBQ’s, the local whale watching tour boats are zipping through the jetty’s to catch sight of all the whales still hovering in the area, and my team and I are right behind them as the field season is upon us in full force!

My name is Amanda Holdman and I am a master’s student in the Oregon State University’s Department of Fisheries and Wildlife and Marine Mammal Institute. Our lab, the geospatial ecology of marine megafuana, or GEMM lab for short, focuseharbor-porpoises_569_600x450s on the ecology, behavior and conservation of marine megafauna including cetaceans, pinnipeds, seabirds, and sharks. My research in particular is centered around the cetacean species that inhabit Oregon’s near coastal waters. While the cetacean order includes over 80 species, 30 of which can be found in Oregon, I am specifically targeting the small and charismatic harbor porpoise! I am hoping to answer questions about seasonal and diel patterns, and the drivers of these patterns to create a better understanding of the porpoise community off the coast of Newport.

To accomplish this, I have been using a couple different survey methods! Over the last year or so I have been conducting marine mammal visual surveys with a crew of observers, binoculars, cameras and lifejackets.  We’ve been very fortunate to work alongside and partner up with a number of labs and projects taking place at HMSC — including Sarah Henkel’s Benthic Ecology Lab, Jay Peterson’s Zooplankton Ecology Project, and Rob Suryan’s Seabird Oceanography Lab — who’ve invited us to share their boat time and join in on cruises to spot marine mammals. We had some motivating cruises with last year’s field season (bow riding pacific white sided dolphins and a possible fin whale sighting!) but now that the summer season is around the corner, It’s time to recruit additional observers and get everyone up to date on their safety certifications (at sea safety, first aid, etc.)

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While we currently have about 6-8 boat trips a month, I am not only just looking  for harbor porpoises, I’m also listening for them. To complement the visual surveys, I’ve added an acoustic component to my research, with the help of the Oregon State Research Collective for Applied Acoustics lab (ORCAA). This allows me to survey for harbor porpoises even under the worst sea conditions, when boat trips are unavailable. Odontocetes, such as the harbor porpoise use echolocation to navigate and forage and can be identified acoustically by their frequency range. While a full-depth analysis of last summer’s data hasn’t yet been accomplished, I was able to take a quick peek and MAN IT LOOKS GOOD! Both harbor porpoise and killer whale vocalizations were identified – you can check out the spectrogram below! This combination of using visual and acoustic surveys will help us answer when the porpoises are in our near waters, and where there primary hang-outs are!

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Visual representation of an echolocation clicks emitted by a feeding harbor porpoise

But springtime isn’t just for fieldwork, it’s also for course work! This quarter, my lab mate Erin Picket and I have enrolled into Julia Jones “Arcaholics anonymous” class, an introductory spatial statistics and GIS course that helps us piece together all the hard work we’ve put towards data collection to look for trends of animal distributions across space and time. This is the first time for both of us that we  get to upgrade our excel spreadsheets into a visual representation of our data! There will be more updates to come soon on how our projects are unfolding, but if you can’t wait til then, feel free to follow along with our class website!