Samara, Author at Animal Bioacoustics

I’ve spent a lot of time on the Henry B. Bigelow. Or at least it feels that way. The familiar chirps and beeps pinging at all hours, the frigid temperature of the dry lab, the way the marine smell lingers on the back deck on a humid day and the salty ocean air makes my skin feel dry and sticky at the same time. I know exactly what clothing to bring for the various jobs I will have, how sleep in my athwartships bunk in rough weather, and that (unless I’m really unlucky) the satellite Internet will allow me to iMessage my friends and family back on land. I’ve been enjoying boat life for years now and I find so much comfort in the little routines.

After departing another ship following a trying journey this spring, I spent a long time thinking about why I couldn’t embrace the quiet weeks at sea that I usually love. Usually spending time offshore offers perspective, fresh air and space to think through ideas and goals and potential plans, but on that trip I spent most of the time wishing I was back at home. Back home at…work? Instead of embracing the break from daily life in Oregon, I was overcome with anxiety about the progress I wasn’t making towards my degree. Perhaps the jumpy response of the ship to rough weather translated directly to my restlessness?

But when my friend and colleague asked me if I was ready to head back to sea this summer on the Bigelow, I didn’t hesitate to tell her “yes”, I was ready. How could I not be – I love sailing on the Bigelow and working as a passive acoustics observer. It is amazing to listen to the whistles, clicks, and buzzes of cetaceans around us in real-time. One of my non-acoustician friends used to describe my job as “eavesdropping on whales”, which, sounds a bit silly, but really is a pretty accurate description of what I do on the boat. The days are long, but most of them are good.

In previous years I would balance my time in the lab with breaks outside to try and spot the animals I spent so many hours listening to. But this year the cruise nears conclusion and my tube of sunscreen is still full. Furiously trying to keep up with my academic responsibilities has limited the number of dolphins I’ve seen, but will allow me some peace returning to Oregon knowing that I won’t have weeks of ignored emails to attend to.

There is a quiet isolation that develops with time spent as a graduate student in academic research. Digging deeper into our own holes of scientific obsession, our theses wouldn’t be viable projects if someone else was already working on the same questions. I am aware of this at school, but the camaraderie of being surrounded by other students takes away a little of the loneliness. But at sea, secluded in my cabin to focus on my project, it feels more pronounced. A couple days ago I was analyzing a recording and identified a useful sound clip. Excitedly I considered who I could share my news with…but quickly realized that probably no one else would be quite as thrilled to look at a spectrogram of wind noise.

The next morning I woke up before my alarm and, not wanting to disturb my sleeping roommate, I got ready quickly and went to begin the daily set-up routines for our equipment in the dry lab. Ready to go half an hour early, I stood out on the back deck to watch the sunrise. And there, unhurried and under-caffeinated but still feeling accomplished from my thesis progress the day before, I finally reconnected with the sublime peace of being at sea.

This summer has been an experiment in re-adjusting my expectations, but I think I’m figuring out how to balance and prioritize. While I spend most of my hours staring at screens, moving between my laptop and the acoustics workstation in the dry lab, I keep a walkie-talkie on the desk just in case someone spots an animal close to the ship; it’s a lot harder to see a blue whale from my office in Oregon.

As a graduate student in bioacoustics, my education is interdisciplinary. Bioacoustics is a relatively small field, and (together with my peers) I am challenged to find my way through coursework in ecology, physiology, physics, oceanography, statistics, and engineering to learn the background information that I need to develop and answer research questions. While this challenge (for all young bioacousticians) presents itself a little differently at every university, the information gap is essentially the same. Hence, just over 6 years ago, Dr. Jennifer Missis-Old and Dr. Susan Parks recognized a need to fill this gap for graduate students in bioacoustics and created SeaBASS, a BioAcoustics Summer School.

This year, for the 4th iteration of the week-long program, I was lucky to have the opportunity to attend SeaBASS. I first heard about SeaBASS as a research assistant in Dr. Sofie Van Parijs’s passive acoustics group at the Northeast Fisheries Science Center, but the workshop is limited to graduate students only so I had to wait until I was officially enrolled in grad school to apply. My ORCAA lab-mates, Niki, Selene, and Michelle are all alumni of SeaBASS (read Miche’s re-cap from 2014 here) so by the time I was preparing for my trip to upstate NY this summer to attend, I had a pretty good idea of what was to come.

As expected, the week was packed. I flew to the East Coast a few days early to visit our fearless ORCAA leader, Holger, at the Bioacoustics Research Program at the Cornell Lab of Ornithology, so I was lucky to be somewhat adjusted to EST by the time I arrived at Syracuse on Sunday afternoon. After exploring the campus, it was time for official SeaBASS programming to begin. Our first class, an “Introduction to Acoustics and Proportion”, began early on Monday morning. In the afternoon and through the rest of the week we also learned about active acoustics (creating a sound in the water and using the echo to detect animals or other things) and marine mammal physiology, echolocation, communication, and behavior. We also heard about passive acoustics (listening to existing underwater sounds), including the different types of technology being used and its application for population density estimation. On Friday afternoon, the final lecture covered the effects of noise on marine mammals.

Some SeaBASS-ers testing the hypothesis that humans are capable of echolocation.

In addition to the class lectures given by each instructor, we also heard individual opinions about “hot topics” in bioacoustics. This session was my favorite part of the week because we (the students) had the opportunity to hear from a number of accomplished scientists about what they believe are the most pressing issues in the field. Unlike a conference or seminar, these short talks introduced (or reinforced) ideas from researchers in an informal setting, and among our small group it was easy to hear impressions from other SeaBASS-ers afterward. As a student I spend a lot of my time working alone, my ORCAA labmates are focused on related projects, but we do not overlap completely. The best part of SeaBASS was sharing ideas, experiences, and general camaraderie with other students that are tackling questions very similar to my own.

Although a full week of class would be plenty to take in by itself, our evenings were also filled with activities. We (students) shared posters (this was mine) about our individual research projects, listened to advice about life as a researcher in the field, attended a Syracuse Chiefs baseball game, and at the end of each day reflected on our new knowledge and experiences over pints. So, needless to say, I returned home to Oregon completely exhausted, but also with refreshed excitement about my place in the small world of bioacoustics research.

Luckily we had beautiful weather for the baseball game!

As with many things in life, fieldwork often doesn’t go as planned. But this is easy to forget when plans are made on tight timelines – we need everyone (including mother nature) to accommodate our schedule. As a marine scientist, nearly all of my fieldwork requires coordinating with vessels to reach different parts of the ocean. Sometimes these vessels are small, such as a fishing boat not meant to head very far from shore, but more often my work takes me out to sea overnight for which larger ships must be contracted.

There are many, many moving pieces (literally and figuratively) that must be considered when organizing a voyage on a ship. Everyone on board has a job, and for the most part, I always assume that if they do their job and I do mine everything will go according to plan.

But of course that is a ridiculous thing to assume.

In late March I flew to Mississippi to join a NOAA ship on a transit to Woods Hole, MA. During the trip north, the plan was to swap out both NRS06 (in the Gulf) and NRS07 (on the East Coast of Florida). Unfortunately, from the get-go we ran into problems.

Part 1: The sewage tank delay

For the first two weeks of the trip we sat at the dock in Pascagoula because sewage holding tank needed to be patched, painted, and tested. Not only was this problematic because it meant that there was a issue with the ship and we were losing valuable days at sea, but it also meant that I was on my own in small-town Mississippi until we got underway.

At first I stayed hopeful that our departure was imminent; I was able to hitch a ride into town with the crew for most meals, and I took some time to organize my mooring gear and explore the abandoned Navy Base where the ship was docked. Turns out abandoned Navy Bases are only good for a few hours of exploring…so by day five I was desperate to get a rental car so I didn’t have to rely on everyone else’s schedule. Thankfully, after calling three offices I finally found a car and was on my own (morale improved considerably).

The next week and change consisted of me hunting down high-speed wifi and southern food. I quickly learned coffee shops are hard to come by on the Gulf Coast, but I tried to make an adventure out of it. I saw two wild alligators, ate more gulf shrimp than I can count, learned about the history of the Gulf Coast, Mardi Gras, and the damage (and subsequent rebuilding) that followed Hurricane Katrina. I avoided a flash flood, tried “cajun sushi”, and consumed more BBQ chicken than someone who considers themselves a vegetarian should admit…

So it wasn’t all misery, but still I was ready to get going. On day 14, just when I was about to give-up and fly back to Oregon, we finally got the OK to cast off from the pier and head out to sea. The next morning we arrived on the site of NRS06, and even though it took all day to complete the hydrophone swap I was thrilled. Things were finally looking up – one hydrophone in the water, one to go, and we were on our way out of the gulf!

Alas, it was too good to be true.

Part 2: The weather delay

Even when everyone on board does their job and the ship is fully functional, weather remains out of our control. A storm system was hovering right in our path north, and by the time we reached the location of NRS07 the seas were too big and choppy to complete the swap. For the safety of the ship and everyone on board, we had to get away from the storm. So we continued on our journey north, battling our way out of high wind and waves. If you’ve ever spent time on a ship before, you know that being tossed around by the sea is not very much fun. Even at top speed we could not travel quickly, and a full week into the journey we hadn’t even crossed the Mason-Dixon line.

Part 3: The ship damage

On day 22 (a full week after I was supposed to be back in Oregon already) the weather finally improved. I had come to terms with the delays and was ready to get to Woods Hole say hello to my friends and colleagues there, and then head home. But we couldn’t catch a break. In the middle of the night, there was a problem with the engine and we lost control of one of the screws (there are usually two propelling the boat). With only half power and still hundreds of miles to go, a decision was made to head to the nearest port for repairs. Then, about 4 hours later, a small smoky fire was discovered in the engine room and the ship sprung into action to control the damage. Thankfully no one was hurt, and we spent the next 24 hours slowly making our way towards Charleston, SC.

Since we already passed both NRS mooring sites, my job onboard was essentially finished. So, already over a week behind schedule to return to Oregon, I decided to cut my losses and leave the ship in Charleston. I booked the latest flight I could find for the next day.

Part 4: The pilot boat

The dock we were scheduled to tie up at in Charleston, SC was up the Cooper River, so a pilot and tug boat would have to escort the ship to the pier. Keeping with the trend of the voyage, our trip up the river was delayed by a few hours (for reasons unbeknownst to me…I didn’t even ask). These hours were the difference between me being able to fly back to Oregon that day or needing to wait for the next morning. I couldn’t take no for an answer and knowing that our pilot for the day would have to be shuttled to the ship from shore, I asked if I could hitch a ride back to land in his place. Luckily my wish was granted and a few hours later I was sitting in the Charleston airport waiting for my flight home. Ironically, my flight into Portland met tailwinds at 34,000 ft and landed almost an hour early.

My view from the pilot boat after leaving the Gunter

Part 5: Feeling thankful

As a scientist it’s easy to take for granted all of the pieces that go into a trip to sea. It is not news to me that often problems arise and plans must be change. I used to sail with a captain that would tell us, “this is the plan we will deviate from”. Although, collectively, I’ve spent over a year of my life at sea, before this trip I had not found myself in the midst of so many subsequent set-backs. I could say “well that really sucked” and close the books and be done with it. Or I could embrace the tragic comedy of Murphy’s Law and appreciate that I accomplished half of my scientific mission, made it home safely, and now only have 7 states to visit before I’ve been to all 50.

I’ll be talking about my research on the radio this Sunday (2/28/16) at 1900 PST – stream the show online at http://kbvr.com/listen!

Repost from: Inspiration Dissemination Inspiring Stories From Oregon State Graduate Students on KBVR FM

“Imagine walking around your neighborhood in a dense fog as night settles in; you may be familiar with the layout, but everything seems different. Innocuous obstacles like low-hanging tree branches and broken sidewalks become invisible right until you stumble upon them. You must be extra vigilant in order to avoid blindly injuring yourself as visibility drops.

For many humans, sight is our most valuable sense, but for marine mammals like dolphins, whales, and seals, their hearing is most precious. As sound travels better through water than air, the ocean is already a noisy place with atmospheric activity and other animals passing around, but their senses have had millions of years to evolve in such an environment. Unfortunately, because of an increased human presence in the ocean, like a fog bank rolling in, the ocean is getting noisier and putting these already threatened animals in danger.

Samara Haver, a Masters student of Holger Klinck in Wildlife Science is interested in knowing about how the noise is affecting marine life. To do this, she must first characterize the ocean soundscape with hydrophones (pictured right) situated in various parts of the globe. With these data, she hopes to understand how loud the ocean is, how much noisier it’s getting, and where the noise is coming from. Tune in on Sunday, February 28th at 7PM PST on 88.7 FM in Corvallis or stream us online at http://kbvr.com/listen to hear Samara’s journey into the sounds of science.

I spent this past week on Cape Cod coordinating the retrieval and redeployment of the Noise Reference Station mooring in Stellwagen Bank National Marine Sanctuary. Last October we deployed the hydrophone (NRS09) for the first time at our long-term site, and this year we were faced with the challenge of retrieving a 700 lb mooring without any surface expression. Luckily, we had a great weather day and the process went off without a hitch!

As soon as we brought the lander back on board we got to work cleaning on the (small amount of) biofouling that accumulated over the past year. I also needed the prepare the acoustic release for re-deployment. In order to retrieve a mooring without any surface expression, we needed a system that would allow us to pull up the lander from the ocean floor; an acoustic release is the perfect solution. To make the re-deployment process easier, NRS09 was designed to use a release that can be easily re-assembled and re-used for successive deployments. Below I am taking release mechanism out of the housing to replace the battery.

Replacing the acoustic release batteries. (Photo: Onye Ahanotu)

Once we had the lander on board we swapped out the hydrophone and prepared the lander for re-deployment. We had to be very careful to secure any pieces that could create noise (and interfere with the ocean noise we are trying to record).

Preparing the lander for re-deployment. (Photo: Onye Ahanotu)

Once the lander was cleaned, acoustic release re-assembled, and new hydrophone secured we were ready to re-deploy NRS09 in Stellwagen Bank National Marine Sanctuary for another year.

Sending NRS09 back into the ocean. (Photo: Onye Ahanotu)

Since getting back to Corvallis, the glamour of my research has decidedly declined. However, as you may know, only a small part of bioacoustics research takes place in the field – mostly it takes place in front of a computer. And that’s where I am now.

This month I’ve been looking through some recordings from three different deep-water Atlantic mooring sites to compare drivers and levels of noise. Passive acoustic archival research is different from other types of data collection because we (the researchers) are not out in the field during recording. Our instruments record all sounds and then part of the analysis process is looking and listening to see what went on. Paging through years of recordings can be a tedious process, but from time to time I find something unusual and exciting like this noise recorded on Halloween night!

I did get out of the office for an afternoon this week to talk to the Girls in Engineering and Marine Science Camp (GEMS) hosted by the Oregon Coast STEM Hub. The two-day camp was organized to expose middle school girls to STEM-related careers. I spoke to the group towards the end of the camp, and despite being exhausted from two full days of science and an aquarium sleepover, they were a great audience!

If you read my last post, I left off on the dock in Newport, RI waiting for a storm to clear. As expected, the thunderstorms (and lightning) passed us by and we cast off our lines the next day.

Blue skies heading under the Newport bridge.

But to our disappointment (but not lack of trying), we didn’t find many turtles during our first couple of days on the water.

Here is the scene from the lower observation deck.

On the big eyes! I helped out the visual team during the day when we could not tow the hydrophone array. (Photo credit: Annamaria Izzi)

But after heading north to Canadian waters our luck changed and the turtle rodeo began!

As soon as we spotted a turtle, we deployed the small boat and sent a team to bring it back to the Bigelow to be outfitted with a satellite tag.

We had to travel pretty far off-shore to find the turtles!

The fast rescue boat heading back to the Bigelow.

We transferred the turtles onboard very delicately in a special turtle “hammock” so that the sampling crew could get to work taking vitals and adhering the satellite tag.

Transferring a turtle to the Bigelow. (Permit: NOAA-NEFSC-Fisheries & Oceans Canada – DFO Research Notice: M-15-07)

Once the adhesive was dry we used the turtle hammock to release the animal back into the ocean. (Permit: NOAA-NEFSC-Fisheries & Oceans Canada – DFO Research Notice: M-15-07)

Then we were back to our lookout posts to spot the next turtle. (Photo credit: Loren Kellog)

Despite a few setbacks (there are always a few), our turtle mission was a success! At night and on bad weather days we were even able to sneak in some acoustics. In the photo below we are getting ready to deploy a HARP.

I am back in Oregon now and my summer fieldwork days are over. I am trying to motivate myself to find as much fun in writing and analysis as I did in gluing my face to binoculars in hopes of spotting the next elusive loggerhead, hearing pilot whale harmonics on the array, and enjoying the glorious show that is a sunset at sea.

Between traveling to Alaska with Michelle and wrapping up spring term, this summer snuck up on me. A week after turning in my statistics final (yay!) I was on a plane headed to Boston. After a happy and relaxing weekend spent reuniting with friends on Cape Cod, I headed to Newport, RI (so many Newports!) to board the NOAA ship Henry Bigelow for an exciting stint chasing turtles by day and recording whales by night. Of course, the best-laid plans do not always work out and while all of the other typical delays seem to be under control (the boat works and the crew is healthy), the weird weather saga of southern New England continues and multi-state tornado warnings are keeping us alongside a little bit longer.

The first reason we are headed out on the Bigelow is to tag sea turtles. Chief scientist, Dr. Heather Haas, and her colleagues are interested in finding out how accurate visual surveys are in tracking numbers of sea turtles. To find out, we the science crew will work together to find as many sea turtles as we can and bring them aboard to get outfitted with satellite tags. Hopefully, the tags will give us information about how much time sea turtles spend at the surface (versus at below it) and that information can be used to better approximate population sizes. But that isn’t really why I am onboard.

I am here as a passive acoustics monitor, operating the Northeast Fisheries Science Center acoustic group’s towed array. Our towed array is a series of 6 mid-frequency and 2 high-frequency hydrophones wired together and suspended in an oil filled watertight tube that we drag behind the boat to listen to marine mammals in real-time. Becuase there are multiple components in the array we can use it to record and localize animals as we travel along a track line. If you want to know more about hydrophone arrays, Michelle Weirathmueller has an excellent write-up on her blog, The Waveform Diary. Check it out here: Hydrophone arrays, FTW!

Our array set-up ready for deployment. The array is coiled on the wooden spool and tow cable is on the net reel.

On this cruise, my friend Annamaria and I will be working with the array at night when it is too dark to search for turtles. We are hoping to record beaked and sperm whales. Since we did not leave the dock today, we were lucky to have a stable platform to get set-up. Becuase a lot of electronics are required for us to an acoustic signal from an animal onto our computer screen, we usually spend the first day at sea troubleshooting…

One of my first projects of the day was to figure out why one of the two hydrophones I was trying to listen to wasn’t working correctly. As usual, the solution is to re-think our wiring set-up. Here I am looking for the connector I need.

I was having trouble finding the right part so I decided to take a break and eat some candy dinosaurs. On the left monitor, you can see that the top half of the screen is blank…not what I wanted to see. Luckily I was eventually able to find the part I needed to fix the problem.

Thankfully we worked out a lot of technological kinks today and hopefully the weather will clear up and we will be on our way to find the turtles and whales tomorrow morning!

Modeling my survival suit during safety drills this afternoon.

This winter, New Englanders watched record-breaking amounts of snow layer up outside their doors. Snow is not unusual in the Northeast region of the United States, but the transportation-halting, business-closing, structure-damaging amounts witnessed this past winter had more people than ever questioning, “what is going on?”

When we talk about global warming, nor’easters are not typically part of our mental imagery – but they should be! Although global warming is not entirely responsible for these dramatic weather events, increased global temperatures are a major part of the problem. And I do mean “warming”; the dramatic New England winter we observed this year is connected to an oceanic warming trend.

The oceans are getting warmer at an extraordinarily fast rate. So fast that climate scientists have a hard time publishing reports as quickly as changes are occurring. While it may not seem logical that warmer water causes more snow, this temperature increase is a major contributor to extreme weather.

Flooding in Scituate, MA. Photo: Jesse Costa/WBUR.org

Water absorbs and retains heat very well. When cool air travels over the surface of warm upper layers, the water heats the air and then evaporates. The newly warmed humid air rises and cools as it travels, forming clouds and eventually precipitation (in freezing New England this comes in the form of snow). This phenomenon, known as the “lake (or bay) effect” is part of what caused coastal New England to be slammed with blizzard conditions this winter.

Cape Cod National Seashore in early March 2015. Photo: washingtonpost.com

It is not easy to fully understand the effects and extent of increasing ocean temperatures, even for oceanographers. Under static conditions, understanding vast ocean systems is difficult; surface observations and samples from depth each only give a small glimpse as to what is going on. However, current variable conditions mean that researchers must constantly gather new data and refresh records to keep up with the effects of ocean temperature rise. Extreme weather is only one consequence of these changes; the broader results of increasing ocean temperatures are felt globally and by all species.

The trend and results of global ocean warming are widespread, but not entirely understood. However, researchers do know that as ocean temperatures increase, the myriad of associated problems will intensify; including the cycle of cold air collecting moisture from the water and dumping on land. If current patterns persist, ocean warming will continue to wreak havoc at sea – and on land.

Frozen waves on Nantucket Island, MA February 2015. Photo: J. Nimerfroh/jdnphotography.com

Saturday April 11th was Marine Science Day at Hatfield. Selene and I headed to Newport to help host the PMEL Acoustics information table, but I also had a chance to explore the event and see what other labs had on display.

In the Marine Mammal Institute room, I visited fellow Fisheries and Wildlife graduate students. Below, Amanda, Erin, and Florence explain their research projects and share audio, video, and photographs from the field.

Across the hall, I learned about sea star wasting syndrome and practiced my identification skills.

Some sea stars hanging out in the aquarium.

In the genetics lab, I extracted DNA from a strawberry! In this photo, I am adding ethanol to separate the DNA material from the water in the vial.

In the Oregon Department of Fisheries and Wildlife outside tent I learned about shellfishing regulations. Sustaining the Dungeness crab fishery requires that recreational fisherman only take males crabs that are larger than 5 3/4″ across. The second photo shows an example of two crabs – can you tell which one is legal and which is not?

In the second outside tent, a life raft and survival suits were available to try-on.

Inside the library, Marine Resource Management students Sara and Sandra showed me their “Ocean Management Game”. I had pretty bad luck and sadly had remove a lot of fish and sea stars from the ocean.

Finally, at the PMEL Acoustics table, Joe, Selene, and I showed an example of our hydrophones and explained how we use a 3D printer to create custom assembly components. We also had a microphone set-up with a real-time Ismael display. When visitors spoke, whistled, or sang into the microphone they were able to “see” their voices in the spectogram.

Animal Bioacoustics

Technology. Ecology. Noise

Author Archives: Samara

New Normal

#SeaBASS2016

Sea Trials

Adrift in a sea of noise

Fieldwork success!

Back to the lab

The Turtle Rodeo Part II

Hurry up and wait (aka fieldwork)

Global Warming = More Snow?

HMSC Marine Science Day

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