Tuesday, November 10, 2015

Things went wrong. They weren’t our fault. We fixed them anyway.

A few months ago, I went to Alaska to help drop very expensive science to the bottom of the ocean.  Last week, I went back to Alaska to try and pick it back up.  “Try” is the operative word here, because often times, when you drop equipment into the ocean, you have no idea if you’ll ever see it again…

To catch up on some background info for this project, you can read my previous blog post.  But to summarize it really quickly, grad student Michelle Fournet (OSU) and I are looking at the effects of vessel noise on humpback whale and harbor seal vocalizations, respectively.  This project is all taking place in Glacier Bay National Park, Alaska.  At the end of May, we deployed four hydrophones to monitor the underwater soundscape. 

I flew in to Gustavus, Alaska on a Tuesday evening with Michelle and our friend/field assistant/resident electrician David.  It was a beautiful flight.

This flight is always a treat. (Photo: L. Matthews)

We spent all day Wednesday prepping for the recovery of our four little hydrophone babies.  Eight foot long hydrophone babies.  100-pound hydrophone babies.  Hydrophone babies full of five months worth of acoustic recordings.  Hydrophone babies that hold the keys to both mine and Michelle’s dissertations. 

The aforementioned hydrophone babies, pre-deployment.  (Photo: L. Matthews)

In theory, we knew exactly what was going to happen during the recovery.  Each hydrophone is snuggly situated in an aluminum cage.  Each cage is connected to an acoustic release via 500 ft. of line.  The acoustic release is key – that’s how we get our hydrophones back.  When the time comes to retrieve them, we send an acoustic signal from the boat to the release.  This acoustic signal tells the release to float to the surface.  Then, once the release is spotted, we can pull it on deck, connect the attached line to a crane, and reel up the 500 ft. of line and the accompanying hydrophone.  Michelle, David, and I talked through this recovery protocol with Chris Gabriele, a biologist in Glacier Bay National Park, at least 30 times.  We were still nervous to see how it all played out.  You see, sometimes, when you send the acoustic signal to the release, it doesn’t work.  Nothing floats to the surface.  The hydrophone remains on the ocean floor, patiently waiting. 

Schematic of hydrophone set-up in Glacier Bay (not to scale)

We met up with Paul and John Martin of the M/V Lite Weight (our recovery vessel) early on Thursday morning.  We arrived at our first hydrophone location about an hour later.  We sent the acoustic signal to the release.  And then we waited.  All eyes on deck scanned the water’s surface for any sign of our buoyant yellow friend.

It was about a minute later when the release was spotted!  Celebration commenced.  Hugs, laughter, a solitary joyful tear; we were all so pleased that it had worked.  We turned our attention back to the water only to realize that the release was gone.  GONE!  The tides had pulled it below the surface.  Well, now what?

So much water.  No releases to be seen.  (Photo: D. Culp)

Do we wait for the tides to calm down?  Do we put out grappling hooks to try and snag it?  Do we stare dismally at the water until it magically reappears?  The answer is D, all of the above. 

The release was re-spotted about 45 minutes later and pulled on deck.  We still don't know exactly why or how it returned to the surface.  It's possible that the tides let up a bit.  It's also possible that there were some issues with the line and it needed some extra time to sort itself out.  Whatever the case may be, we will definitely be taking extra precautions next year to ensure that this isn't a recurring problem.  

Acoustic release fresh from the ocean!  (Photo: L. Matthews)

The crew of the Lite Weight worked their magic and before we knew it, the hydrophone and its cage were safely on deck.  Success!

Yaaaaaaay!!!  (Video: L. Matthews)

I’ll keep this short and just tell you that despite temporarily losing 3 of our 4 releases to the whims of the tides, we had four hydrophones on the deck of the boat by 1pm.  It was an amazing feeling!  All of that science we dropped off five months ago was finally back!

The recovery team minus David (Photo: D. Culp)

The tides were a challenge – the releases weren’t supposed to disappear back underwater.  But we pulled it together and overall had a very successful recovery.  This, however, was not the end of our troubles.  There was a suite of technical issues that arose as we prepped the hydrophones to be shipped back to Oregon for data processing.  These technical issues were also challenging and unforeseen.  Luckily, the team rallied and managed to solve every challenge that came our way.  In the end, we summarized the trip by saying, “things went wrong, they weren’t our fault, but we fixed them anyway."  It was a solid week of science.

FUN SCIENCE FACT #42: The highest tides in the world can be found in the Bay of Fundy, Canada, which separates New Brunswick from Nova Scotia.  The difference between high and low tide in the Bay is upwards of 16m!  That's taller than a 3-story building!  Glad we weren't trying to recover hydrophones in that part of the ocean...

Tides in the Bay of Fundy (Photo: Steve Brown)

Saturday, June 6, 2015

Hello, Alaska!

After finishing fieldwork in California, I loaded up my kayak and headed north to Corvalis, Oregon to meet up with my friend Michelle, a PhD student in the ORCAA Lab at Oregon State University.  Michelle and I are part of a cooperative project with OSU, Syracuse, and the National Park Service to investigate the effects of vessel noise on the vocal behavior of harbor seals (that’s my job) and humpback whales (that part is Michelle’s) in Glacier Bay National Park, Alaska.  During the initial phase of planning for this project, a topnotch team of bright minded acousticians and marine mammal biologists came up with a plan to address this noise issue using a four-element underwater autonomous hydrophone array and shore-based visual observations.  This project has been in the works for quite a while (i.e., years), and last week it was finally time to put our hydrophone array in the ocean!

Glacier Bay National Park is a beautifully pristine wilderness area in Southeast Alaska that’s home to drastic mountain ranges, calm blue waters, and otherworldly glaciers.  The Park is not accessible by car, but despite this, over 400,000 people visit Glacier Bay each year.  Visitors arrive mostly by cruise ship or other private vessels – these boats make all sorts of noise, which is what prompted the research questions behind this project.

Cruise ship in Glacier Bay (Photo: L. Matthews)

The other option to get to Glacier Bay is to fly into Juneau, and then take a flight from Juneau to the small town of Gustavus (population: 500).  Gustavus is connected to the Park via one ten-mile stretch of road.  The flight from Juneau to Gustavus takes about 25 minutes, and it is by far the most beautiful flight I’ve ever taken in my entire life.

Flying into Gustavus (Photo: L. Matthews)

Michelle and I, along with our friend Samara (another member of the ORCAA lab), arrived in Gustavus on Monday morning, picked up our rental car from a man named Uncle Bud, and drove about a half mile down the road to our temporary Park housing.  The rental car was a 1999 gold Ford Minivan with approximately 199,872 miles on the odometer and a random assortment of misbehaving dashboard lights…and it ended up being the most perfect vehicle for our trip.  We then made our way over to Park headquarters to inspect the equipment that Michelle had shipped from Oregon.  This included the hydrophones and all the other pieces necessary to sink hydrophones to the bottom of the ocean.  You can read more about the shipping container here in Michelle’s blog.

Pallets full of anchors (left) and Michelle hanging out in the landers for the hydrophones (right).
(Photo: L. Matthews)

We also needed to assemble the acoustic releases.  Acoustic releases are how we’re able to retrieve the instruments off the seafloor when they’re done recording.   They’re attached to the landers via a 500ft line.  When we’re ready to retrieve the hydrophones in a few months, we’ll send an acoustic signal to the releases, and they’ll pop up to the surface.  Then, we can reel in all of our equipment and download the data.

Samara and Michelle assembling the acoustic releases (Photo: L. Matthews)

We checked everything off of our Monday to-do list and headed back to the house for a well-deserved night’s sleep.  The next day, our ragtag grad student team met up with Chris Gabriele, a Park biologist who spearheaded this project, to prep the hydrophones and landers for deployment.  We carried anchors (so many anchors), tightened bolts (so many bolts), electrical taped hydrophones (so much electrical tape), and zip-tied shackles (so many zip ties).  The electrical tape is to deal with biofouling – the accumulation of microorganisms, plants, algae, and animals – on the hydrophones.  And each hydrophone is color-coded so we know which one is recording in each location.

Loading and unloading hundreds of pounds of lead and concrete, but still smiling.
(Photo: C. Gabriele)
Securing anchors to landers.  (Photo: C. Gabriele)

All four hydrophones prepped and ready for deployment!  (Photo: L. Matthews)

Chris, me, and Michelle proudly posing with our lovely acoustic equipment.  (Photo: S. Haver)

Then it was finally Wednesday!  Deployment day!  It was an early morning and a long day – though not as long as we had anticipated – but I’ll keep this story short and just sum it up to say that all four hydrophones and their associated acoustic releases made it safely to the bottom of the ocean.  We couldn’t have done it without the help of the M/V Liteweight, Captain Paul Weltzin, and Deckhand John Michael.

Loaded up and en route to the drop site!  (Photo: L. Matthews)

It takes a village...  (Photo: L. Matthews)

Bye bye hydrophone!  See you in a few months...  (Photo: L. Matthews)

The next day we focused on preparing the base camp for our shore-based visual observations.  Samara, Michelle, and I spent most of our energies building a hunting blind.  Clearly it won’t be used for hunting anything, but it’s the perfect height for a panoramic view of the array area.  From this vantage point, the field team will be able to conduct scan surveys of whales and seals and focal follows of whales – the perfect behavioral complement to our acoustic data.

Map of hydrophone locations (yellow pins) and camp for shore-based observations (orange star).

That afternoon was spent cruising around with Chris dropping a dip hydrophone in various locations and looking/listening for whales and seals.  We spotted tons of animals in the array area, including harbor seals, humpback whales, stellar sea lions, harbor porpoises, and sea otters.  We heard a faint humpback vocalization, lots of boat noise, but no seal calls.  Not surprising though, since it’s still a little early in the season.

Harbor seal in Glacier Bay (Photo: L. Matthews)

Friday morning we talked sampling protocols over coffee and discussed Michelle’s return trip to Glacier Bay in a few weeks.  This summer, Michelle and a team of four undergraduate students will be living on the island in Glacier Bay to conduct the shore-based observations.  Unfortunately, I won’t be able to join them for the field season, but *fingers crossed* I’ll probably be able to swing a trip next summer to help out with data collection.

The view from the island.  Not a bad view.  (Photo: L. Matthews)

Another clear-skied flight back to Juneau on Friday and a lovely weekend with friends was the perfect ending to a successful deployment trip.  And now we wait!  Come October, Michelle and I will return in Glacier Bay to recover our hydrophones and download our data.  Until then, I will relish in Alaska’s overwhelming beauty and prepare for the onslaught of data that will be arriving in just a few short months.

Flying back to Juneau...  (Photo: L. Matthews)

FUN SCIENCE FACT #41:  Alaska is home to 616 officially named glaciers, but the Alaskan Almanac estimates that there are about 100,000 in the state.  Glaciers form when there is more snow fall than snow melt in an area.  This snow accumulates and transforms into ice.  The compression of new layers of snow causes the ice to re-crystallize, forming larger and larger crystals. In very old glacial ice, crystals can be up to several inches long.  And, when the glacier becomes extremely dense (large crystals, few air pockets), it results in a blue-ish tint to the ice.  (Source: NPS & NSIDC)

The blue-ish ice of the Mendenhall Glacier in Juneau (Photo: L. Matthews)

Thursday, June 4, 2015

Goodbye, California...

I recently wrapped up my first field season in California.  It definitely didn’t go as planned; but then again, fieldwork never really does go the way you think it will.

The original plan was to make recordings of individual male harbor seal calls, take pictures of the males that were surfacing near the underwater vocalizations, and then match these individuals to pictures of males on land.  The pictures on land (described in a previous blog post) allow me to estimate the size and weight of an individual seal.  Basically I was going to create a catalog of males in Elkhorn Slough that contained information on their vocal behavior, any distinguishing physical characteristics, and various body measurements.  There were lots research questions to answer with this catalog, but step number one was obtaining the data to populate said catalog.

Harbor seals in Elkhorn Slough. (Photo: L. Matthews)

After a rough start to the season – various delays, both weather and animal related – I managed to get out in my kayak and make recordings.  I didn’t know where exactly the males would be, so I decided to stop at about four or five different locations along the slough to listen.  And sure enough, I found one!  He was calling near the haulout on the south side, close to Seal Bend.  Woooooo data!

This is a map of Elkhorn Slough.  The red boxes show seal haulouts.
The red marker represents where I heard seal vocalizations

I did this for a few days.  I paddled around and around and made recordings in lots of different locations, but I could only ever find that one caller.  The same male vocalized in the same spot for all of my recording days.  Consistency was nice, but it wasn’t really what I needed to answer my research questions or construct that catalog.  I had planned for multiple recordings of multiple individuals over a two-month period, but ended the season with a one or two good recordings of one seal that I made in the last couple days of my field season.

There are a few explanations as to why I didn't get what I was expecting.  First of all, I might have started recording a little late in the season.  By the time I got out there, it was the middle to end of May, which is towards the end of the breeding season in that area.  It could be that the other males had already stopped vocalizing.  Second, maybe there was only one male calling this year.  In the past, there have been three, four, or five males vocalizing in Elkhorn Slough, but maybe this year was different.  No one has gone out to listen to them in a few years, so it's possible that things have shifted and there's only one man seal patrolling in the slough.

This is not the seal that I recorded.  This is just a random seal.
(Photo: L. Matthews)
But everything is going to be okay!!  I’ve got multiple projects going on at the moment and with the combination of this year and next year, I will easily have enough data to write up a dissertation.  More on these other projects in a future blog…still focusing on harbor seals, just harbor seals that live a little further north…

FUN SCIENCE FACT #40:  Walruses have a pretty impressive vocal repertoire.  Males make vocalizations that sound like knocks, pulses, and even bell-like sounds.  The bell sounds are my favorite.  Here's a video of a captive male walrus showing off his sweet skills.

Tuesday, May 12, 2015

When Otters Attack

I’m going to preface this blog post by mentioning that my field site, Elkhorn Slough, is home to over 100 sea otters.  Elkhorn Slough is not a huge area, and that’s quite a few otters, so basically what I’m saying is that you can look in any direction and there’s a 90% chance you’re going to see an otter.

Here's a picture of an otter on land.  Otters look weird on land.  (Photo: L. Matthews)

My first day of official data collection was last Friday.  Needless to say, I was very excited to finally get out there and record some harbor seal vocalizations!  I loaded up my kayak and headed about a mile into Elkhorn Slough.

Hydrophones? Check.  Recorder? Check.  Camera? Check.  Snacks? Double Check.

That T-shaped PVC pipe towards the back of the kayak is what holds the hydrophones.  It works like a pair of underwater ears: one hydrophone on the right and one hydrophone on the left to help the in-air listener roughly localize the underwater sound.

After positioning myself near one of the haul out sites and anchoring my kayak, I began assembling the recording apparatus.  Parts of this apparatus, like the hydrophones and the PVC pipe, are designed to go underwater – that’s how we’re able to listen to underwater sounds.  Other parts however, like the recorder and the batteries, need to stay dry.  Like, really really dry.  When paddling down the Slough, I keep these precious electronics stored in a reliably watertight Pelican case.  Then, when I’m securely anchored, I take them out to begin data collection.

The hydrophones were underwater, my headphones were on, and I pressed record.  The first recording of the season!!  Data!  Yay!

I didn’t hear anything.  Hmmm time to trouble shoot….

Everything looked fine on my end, so I decided to pull up the hydrophones to see if something had gone awry.  The next part of this story doesn’t sound real, but I swear to you that it did actually happen.  As I pulled the PVC piece out of the water, AN OTTER REACHED UP AND GRABBED IT!  Instinctually, I yanked the PVC pipe towards me, but given the hollow nature of PVC piping, this lead to an unfortunate influx of water into the kayak.  Things got wet.  The recorder got wet.  The batteries got wet.  Everything that wasn’t supposed to get wet, did.

I dried everything as best I could and headed back to the harbor for some further equipment triage.  I’m not an expert when it comes to electronics, so I opted for the “take out the batteries and stick it in a bag of rice” trick.  I decided to leave the recorder in the rice for 24 hours, just to be sure it was completely dry, and then I went back to the field on Sunday to see if my recorder was still alive.

I put in the batteries and flipped the power switch.  Moment of truth…

It's aliiiiiiive!

This field season isn’t over yet!  Time to get back out there (weather permitting) and attempt to make some more recordings.  Just have to watch out for those otters…

FUN SCIENCE FACT #39:  One of the loudest animals in the ocean is actually quite small.  Snapping shrimp (Family Alphaeidae) are small crustaceans that have asymmetrical claws and are commonly found in shallow coastal waters.  They are able to use the larger of the two claws to make a short, but very loud snapping sound.  The snap of this claw shoots out a jet of water at up to 62 mph, creating a cavitation bubble that bursts with a loud snap (around 220 dB re 1 uPa -- that's right up there with how loud sperm whales are, and sperm whales are really loud).  

Tuesday, April 28, 2015

How to measure a harbor seal without actually measuring the harbor seal

Seeing as I’m still waiting on the final confirmation from the permit office, I’ve decided to use my “spare time”* to test out as much equipment as possible and get as accustomed to my field site as possible.

*I use this phrase loosely, because really when is there ever a moment that a grad student has nothing to do…

Most of the equipment I’m using this summer is fairly basic – I’ve got the usual hydrophone/recorder set-up and a standard GPS unit and laser rangefinder. I also bought myself a GoPro, because what kind of marine research project would this be without a GoPro?!  And I just have to say, the GoPro camera is by far the least intuitive piece of equipment I have this summer. It took an embarrassing amount of time just to figure out how to open the waterproof case. It also took a bit of practice to figure out the difference between the video mode and the photo mode. I gave a great explanation of my field site to the GoPro camera on photo mode.

In-depth explanation of Elkhorn Slough given to a GoPro that was not recording.
(Photo(<-haha): L. Matthews)

While there was a definite learning curve with the GoPro, there was no real assembly required. There are a few pieces of equipment, however, with which I’ve chosen to get a little creative. Most notably is the equipment I’ve designed to collect morphometric data on hauled out harbor seals. Morphometrics is a fancy word that basically means, “let’s measure how big that thing is.” This is useful data for bioacousticians who are interested in seeing if size differences between individuals carry over into the vocal differences between individuals. I happen to be one of those bioacousticians.

After digging a bit through the literature, and after some helpful direction from my advisor (paraphrased email: “Leanna, read this very specific paper that outlines exactly what you want to do”), I landed on a paper by Webster et al**. In this paper they explain how they mounted a pair of lasers to a camera, took pictures with the camera, and used the dots from the lasers to make post-hoc measurements of Hector's dolphin dorsal fins. Basically, if you know how far apart the lasers are, and if you know how far away the animal is, then you know how far apart the laser dots are in the picture. Plug this into some photo analysis software, and you can make all sorts of measurements! I took this idea, ran with it, bought some lasers, and started taking pictures.

Using lasers to measure dorsal fins (Webster et al.)
For my set-up, I used hose clamps, zip ties, super glue, and a PVC pipe to jerry-rig a mount for my two lasers. I also placed a bolt in the middle of the lasers so I could screw it into the tripod mount of my camera. There were days of finagling with the lasers to keep them in the camera’s viewfinder, but as of now they are securely fastened to the PVC pipe and are ready to be used for photographing harbor seals! I’m planning on making as many measurements of individual seals as possible, and hopefully I’ll be able to do some weight estimation with these measurements as well. This is a great way to collect data on wild animals without disturbing them. It worked for Hector's dolphins, so now we just need to wait and see if it works for harbor seals!

The laser set-up!  (Photo: L. Matthews)

**Webster, T., S. Dawson, and E. Slooten. "A simple laser photogrammetry technique for measuring Hector's dolphins (Cephalorhynchus hectori) in the field." Marine Mammal Science 26.2 (2010): 296-308.

FUN SCIENCE FACT #38: Fleas can jump 130x their height.  I'm 5'4" and my max vertical doesn't even come close to 693', so mad props to you, little flea.  Those are quite the ups you've got there.

Saturday, April 25, 2015

A Lesson in Patience

Take a poll of a hundred marine mammal biologists and chances are that not a single one will tell you that studying marine mammals is easy.  One thing I’ve learned first hand about marine mammal research is that it takes a lot of people and a lot of paperwork to get a project going.  And one thing I’ve currently been dealing with is permitting. 

Now, let me just say that permits exist for VERY good reasons – marine mammals need these extra layers of protection when it comes to research.  And honestly, I don’t mind filling out permit modification requests and typing up protocols to send to the marine mammal head honchos for approval.  However, it appears that maybe I underestimated the timetable associated with permit modification requests and protocol approvals.  Oopsie. 

I made the trip from Syracuse to California about three weeks ago with every intention of starting data collection on April 15th.  This year, the plan was to go out to Elkhorn Slough (a narrow inlet in Monterey Bay), make underwater recordings of individual male harbor seal vocalizations, and take pictures of hauled out males to do some morphometrics.
Harbor Seals in Elkhorn Slough, CA (Photo: L. Matthews)

Luckily, over this past year, I’ve been able to team up with Jim Harvey at Moss Landing Marine Lab to be added as a co-investigator on his existing harbor seal permit.  Jim Harvey is basically THE go-to guy when it comes to west coast harbor seal research.  We thought that we’d gotten in all the necessary paperwork on time for my anticipated start date, but it turns out that there’s been a surge of permit applications, the permit office is a bit overwhelmed, and ours isn’t exactly at the top of the list.  It’s currently April 25th and I’ve yet to collect any data.  *sigh*  So much for that April 15th start date. 

In the meantime, I’ll play with my equipment and scope out my field site and make every possible preparation for data collection so that when I get the green light, I’ll be all set.  From what I’ve read and from what people have told me, the males vocalize through the end of May.  Seems like I’ve still got a good chunk of time to get a good chunk of data.  

So yeah, it’s definitely not easy – I knew this from the beginning.  But it’s definitely going to be worth it.  Can’t wait to get out there and make some recordings!  Any day now, I’m sure.  Fingers crossed. 

Cute little harbor seal face (Photo: L. Matthews)

FUN SCIENCE FACT #37:  The Challenger Deep is the lowest point on Earth.  Located in the Marianas Trench in the western Pacific, the Challenger Deep is approximately 10,916 m (35,814 ft) deep.  That's like putting Mt. Everest underwater and then still having another mile over water on top of it.  Maybe if you stacked like nine Empire State Buildings on top of each other you'd hit the surface.  

Photo: The Apricity