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

Friday, July 25, 2014

"This is either madness or brilliance"

Every scientific journey begins with an idea.  These ideas can go one of two ways: 1) after countless trials and brainstorms, they actually work; 2) after countless trials and brainstorms, they don’t.  I think you can guess which one happens more often. 

This summer, I've been working out in Newport, Oregon at the Hatfield Marine Science Center.  Hatfield is operated by Oregon State University and hosts groups like the Cooperative Institute for Marine Resource Studies and the Marine Mammal Institute, as well as researchers and staff from Oregon Dept. of Fish & Wildlife, US Dept. of Fish & Wildlife, and NOAA.  I'm here at Hatfield working on some of my dissertation research with the help of the ORCAA lab, Oregon State's animal bioacoustics group.  I came to the ORCAA lab as a visiting graduate student about a month ago with intentions of testing out some ideas.  Ideas that, when I posed them, were more like off-handed comments to my advisor rather than valid approaches to realistic data collection.  

Since my blogs seem to be few and far between these days, let me back up a tiny bit.  As I've mentioned before, I’m currently working on my PhD at Syracuse University with Dr. Susan Parks.  My interests are in pinniped behavior and physiology, and for my dissertation, I’m looking at the variation in male harbor seal mating behavior and its influence on reproductive success.  I’m also interested in the effects of shipping noise on harbor seals during the breeding season, but that’s another blog post for another time.  

Harbor seal (Phoca vitulina) (Photo: Ron Niebrugge)
A few months ago, as I was furiously preparing for my PhD candidacy exam (one part proposal defense, one part general knowledge exam, all parts stressful), I met with Susan to discuss how I could get the data that I wanted for the project I was proposing.  I wanted underwater movements of harbor seals during the breeding season.  I wanted to map out male territories and really figure out how and where they were spending their time when they were below the surface.  Harbor seals, along with the majority of phocids (i.e., true seals), mate underwater.  Underwater behavior of any marine mammal is difficult to obtain.  We, as researchers, are limited in our visual observations to what happens above water.  The best method we have to tracking animals subsurface is tagging.  But tagging is expensive, time consuming, and logistically difficult — it typically involves getting a boat and a team of able-bodied persons, capturing the animal, and gluing a tag to its fur.  It’s doable, but not with solely my grad student resources.  Susan and I began spitting out other ideas:

“What about how they track fish, like a tiny PIT tag?”  
“Can we localize with a fish tag?”
“They do it for salmon, no?”
“But how could we get the tag on the seal?” 
“Some sort of remote attachment, so you wouldn’t have to capture them.”
“Could we feed it to them?”
“That probably wouldn’t be a good idea…”
“I guess we could just shoot it at them in a paintball.”

And there you have it, ladies and gentleman.  The mildly sarcastic comment that snowballed into a cross-country trip to Oregon and countless hours of researching glues and paintballs. 

Vemco V6 Acoustic Tags
After a bit of post-meeting research, I came across some small high frequency acoustic transmitters (made by Vemco, pictured on the right) that are used to study fish movement.  They’re small, only about 16mm in length, and they emit 180 kHz signals about every 30 seconds.  These acoustic signals are picked up on receivers that are strategically moored in the study site.  By looking at differences in the times of arrival of specific signals, it’s possible to determine the location of the transmitter, i.e. the tag, i.e. the animal of interest.  Acoustic tags are great for looking at subsurface behavior because of how efficiently sound travels underwater (it’s much more efficient compared to air – you can read more about that here).  These tags seemed perfect!  They were small enough to fit in a paintball, they were the right kind of tag for studying underwater movement of individuals, and they emitted signals that were above the hearing threshold of harbor seals (and killer whales)*.

*Researchers have also used 69 kHz tags (instead of 180 kHz) to monitor fish populations.  The problem with these tags is that seals and sea lions can hear at 69 kHz.  Implanting a tag that emits a sound in the hearing range of the fish’s predator is basically attaching a dinner bell to the study organism.  When considering using acoustic tags on the seals, I wanted to make sure that they (and their predators) couldn’t hear the acoustic signal being emitted.  That way I could avoid any potential behavioral disturbance (or increased predation) caused by the sound coming from the tag. 

I took my PhD candidacy exam, finished the semester, and packed my bags for Oregon, where ORCAA commander in chief Holger Klinck had agreed to help me test this weird tag attachment idea. 
Current emotions: Excited.

Things we had to figure out:
  • How do we get the tag inside the paintball?
  • What kind of glue do we use? – something that doesn’t solidify inside the paintball, but cures almost immediately to the seal…hmmm does this product even exist?
  • How do we close the paintball once the tag and the glue are inside?
  • Will it actually stick to the seal? – we were going to need a real seal to test that one…

And thus began the Amazon binge-purchasing.  I bought glues.  Super glues.  Rapid cure super glues.  Super instant curing no drip super glues.  Veterinary grade surgical glues.  One-minute instant mix two-part epoxies.  Clear-dry power grip instant grab all-purpose interior adhesives.  I also bought some regular paintballs and some empty paintball shells.  And thanks to my paintballing sister, I already had the gun. 
Current emotions: Overwhelmed – who knew there were so many options for adhesives?

The next step was to get the tag into the shell and fill it with glue.  This took a bit of finagling, but I finally did it!  I was so proud!  I made three types of paintball tags.  The first were regular paintballs that I emptied, stuffed with a tag, and filled with super glue (the green ones in the picture below).  I sealed them with some glue and a sprinkle of baking soda.  It turns out that baking soda is an accelerant for cyanoacrylates (fancy name for super glue).  A tiny bit of baking soda and BOOM that super glue is SOLID.  The second type of tag ball was basically the same as the first, but I used the empty paintball shells.  Bonus – no emptying of paint required (the clear ones in the picture below).  I was most proud of the third kind.  These were half filled with super glue and half filled with baking soda.  In theory, when it hit the seal, the tag would cure instantly to the fur of the animal because of the addition of the accelerant. 
Current emotions:  Feelin’ creative and accomplished.

So many paintballs with tags!  So much super glue on my fingers!
So proud of my science! 
I’m going to keep this long post from becoming too long and just tell you that it didn’t work.  No tags stuck to anything. 
Current emotions:  Disappointed :(

Assembling the tiny crossbow
But this is science!  So what do we do?  We brainstorm more ideas!  And what do we do when those don’t work either??  We brainstorm even more ideas!  I went from my failed paintballs, to thinking about crossbows, tiny pistol crossbows, compound and recurve bows, drones (no one would buy me drones though…).  After lots of trial and error, with an emphasis on the error, I landed on the pistol crossbow.  It was small, manageable, and didn’t have too much power.  I crafted some bolts out of wooden dowels, foam floats, electrical tape, PVC end caps, fishing line, empty paintball shell halves (might as well use them if I’ve already got them, right?), and of course, duct tape.  With a little finesse and the right adhesive, I shot these homemade arrows out of my little crossbow and somehow got a tag to stick to my target.  I. was. shocked.  Did all of my brainstorming actually just pay off??
Current emotions: Chest-pounding, can-crushing, fire-breathing, unstoppable POWER.

Fancy homemade crossbow arrows and a successful tag attachment!

At this point it had been a roller coaster of successes and failures, which I thought was going to end with my, what could only be described as, legendary tagging success.  However, after some preliminary field-testing, it was revealed that in order to make these tags work in the locations I wanted them to work, I would have to outfit the study area with an impractical number of receivers.  Had all the time and research and effort and crossbow target practice all been for naught?  Probably. 
Current emotions:  Uggggghhhhh seriously??  COME ON.  I just got the tags to stick!

Back to the drawing board.  Conversations with Holger, conversations with Susan, and conversations with Holger and Susan at the same time led us all to the conclusion that the classic tagging approach would probably be the most logical way to go about getting my data.  Luckily, it’s looking like I’ll be able to collaborate with some other groups here in Newport on a tagging trip that’s already planned for next year.  My sample size will be lower, it’s not exactly the data that I thought I was going to get, it’s not even in the same field site I thought I’d be working, but thus is life.  As a scientist, you can’t be married to a certain data collection method or even to a certain location.  You have to keep the big picture in mind – what were the original scientific questions/objectives?  If you’re still able to get at these major objectives, then you’re probably still doing alright.  Any data I can get to better understand the underwater mating behavior of these seals is beneficial for conservation and even just marine mammal biological knowledge in general.  There’s still so much we don’t know about the organisms that live in our oceans (even ones like seals that spend part of their lives on land), but slowly and surely, we’re picking away at the mysteries. 

Current emotions: Back to being excited.  This scientific journey, though so far has been more madness then brilliance, is only just beginning.  New pinniped adventures await! 


FUN SCIENCE FACT #36:  Sea otters (Enhydra lutris) have the densest fur of any mammal -- up to 1 MILLION hairs per square inch!  This thick fur is essential for thermoregulating/keeping warm in cold water.  It works by trapping a layer of air near the body of the animal.  Air is much easier to heat than water, and when this air is kept warm, the otter is kept warm.  Lots of animals use this method for thermoregulation, not just otters!  (Think of a bird when it ruffles up its feathers and gets all puffy).  Because of the importance of their fur to survival, oil spills are a major concern for sea otters.  Crude oil can penetrate the fur, ruining the air layer and its insulating properties.  A decrease in core body temperature can cause long-term organ damage, vascular system failure, and even death.  Wow this fun science fact took a morbid turn.  Sorry about that...

Here's a cute picture of some sea otters.  And you can read more about sea otters here.  

Photo: Michael Baird


Saturday, May 25, 2013

The Seals and the Sea Lions. And the Otter.

The Pinniped Cognition and Sensory Systems Lab, based at the Long Marine Lab at UCSC, focuses on sensory, cognitive, and behavioral ecology of marine mammals.  Researchers work closely with the resident animals, training them with operant conditioning and positive reinforcement to voluntarily participate in various projects involving active decision making.  Some past projects include auditory masking, amphibious hearing capabilities, sound localization abilities, and short and long-term memory.  In other words, this place is awesome.  There are two big pools (22,500 gallons each), one of which can be set up to run underwater acoustic experiments.  There are also some smaller pools that house the marine mammals on the compound.  The water that fills these pools is pumped directly from Monterey Bay, and is therefore an accurate representation of nearby environmental conditions.  The lab is also equipped with soundproof acoustic chamber for in-air experiments (check out this video because the chamber is really really cool).

Aerial view of the Long Marine Lab complex.
(Photo: Pinniped Lab)

Right now there are eight marine mammals at the Pinniped Lab, including two California sea lions (Zalophus californianus), a harbor seal (Phoca vitulina), two ringed seals (Phoca hispida), two spotted seals (Phoca largha), and a southern sea otter (Enhydra lutris).

Rio and Ronan, pictured below, are the female two California sea lions.  Rio (on the left) was born in captivity in 1985.  Because Rio's mother did not exhibit normal maternal behavior, she was transferred to Long Marine Lab where she was hand-raised by trainers.  She has participated in LOTS of studies, including some on imprinting, concept formation, visual and acoustic perception, associative learning, and memory.  Rio is pretty well known in the animal behavior and psychology world, primarily because she is the first nonhuman animal to demonstrate "equivalence classification" (a cognitive ability formerly thought to be limited to humans).  You can watch a video of it here.





    
Ronan (above, right) was born near the Channel Islands in the summer of 2008.  She stranded multiple times in 2008 and 2009, and was eventually recovered by the Marine Mammal Center when she was found walking down Highway 1.  Ronan was deemed unreleasable (reasons being that she had grown accustomed to humans and was unable to forage successfully in the wild) and became a permanent resident of the Long Marine Lab in early 2010.  She is involved in both cognitive and acoustic projects, and recently ran into some youtube fame with her ability to keep the beat with music (see video below, or click here).




Sprouts, the resident male harbor seal, was born at Sea World, San Diego in 1988 and transferred to the Pinniped Lab less than a year later.  He's been involved in lots of sensory experiments, including some on hearing, vision, and vibrissae (whisker) sensitivity.  Recently, Sprouts helped with a joint project between the University of Virginia and UC Santa Cruz focusing on underwater wake detection.  Sprouts is a pretty easy going seal (allows lots of taction and has a great deal of patience with inexperienced animal trainers), so he also helps out with marine mammal education programs.  Here's a link to a video of Sprouts participating in an experiment and then getting his teeth brushed - yes some of the animals get their teeth brushed).



Sprouts participating in an in-air acoustics experiment

Natchek is the male ringed seal at the Pinniped Lab.  He was born in the wild in 1996, but was transferred to Sea World after he stranded as a pup.  Natchek has been with the lab since 2010, and is currently part of the ice seal bioacoustics project.  He's a weird little seal, but he's also pretty cute and loves to play in the kelp that sometimes hangs into his pool.





Nayak is the youngest pinniped at the lab.  She is a female ringed seal that joined the program about a year ago, after stranding as a pup and then spending some time at the Alaska Sea Life Center.  Nayak is also involved in the ice seal bioacoustics project.





Amak (left) and Tunu (right) are two male spotted seals that came to the lab in September of 2010.  Amak (the Alaskan Inuit word for "playful") was abandoned by his mother near King Salmon, Alaska, while Tunu (named after the Yup'ik village Tununak) was born after his mother was legally harvested.  Both pups were rehabilitated at the Alaska Sea Life Center and were later deemed unsuitable for release (permitting restrictions do not allow rehabilitated spotted seals to be re-released).  They are also both involved in the ice seal bioacoustics project.




Last but not least, we have Odin.  Odin is a male southern sea otter who joined the lab in 2009 after a stint at the Sea Otter Research and Conservation Program at the Monterey Bay Aquarium.  He was born in 2003 and stranded (for the first time) at just a few weeks of age.  He then re-stranded, was re-captured, and re-released several times over the next few years.  Right now Odin is working with the trainers on certain behaviors that will allow them to study specific aspects of sea otter vision.





All info via the Pinniped Lab website and daily conversations with the amazing people who work there.



FUN SCIENCE FACT #35:  The Baikal seal (Pusa sibirica) is one of the few exclusively freshwater seal species; they live only on the coast of Lake Baikal in Russia (Lake Baikal is the deepest lake in the world and is also my favorite lake).  In early autumn, before the lake freezes over, the seals shift their diet to consume primarily sculpin, a fish that inhabits silty areas.  The grit in the stomachs of these fish help to rid the seal's gastrointestinal tract of parasites.



A Baikal seal being adorable.