Meet My Friend, Theo

While we all sit around finagling (I can't believe that it's a real word, but it is) with a silly program (more on it later in this post), I figured I'd write my next blog post. Another educational one, on a piece of equipment lovingly called a theodolite.

Never heard of it before? Neither had I until I started applying for internships in marine mammology. Seemingly it was originally used for surveying on land, but someone thought "why can't I track dolphins using it?"

Well... you can, I guess; but it's really really hard.

Too late, it's the thing to do now. Le sigh.

First. Climb up to the top of a high cliff. Make sure you have a clear sight to the water, no trees or tall buildings in the way.

So now you have this theodolite

Hello, Theodolite

It's sitting nice and neat in the box, but you want to use it. Take its stand

Hello, Stand

Set it up. Make sure it's level. Otherwise steps after this will be harder. Use little bubble levels to make sure it's level.

Using two hands, place the theodolite on the stand. Screw it in. So far, so good.

Now... level the theodolite. There are three levels on the theodolite.

You use the little discs to mirco-move the theodolite up and down until the theodolite (for now on being called 'theo') is completely level no matter which way you spin it. Note: there are two dials on the theo. One lets it spin on the horizontal plane, the other let's the eyepiece spin on the vertical plane.

Okay, turn it on. Spin the eyepiece around until the theo recognizes it (beep!). Then you need to set the horizontal 0 mark. You can use any reference point, but then you have to remember your reference point for the day and it'll change every time. So why not just use North? That way, you can use the same reference every single time! Genius! I wish I had come up with it.

Press the "0 set" button and you're ready to go.

Find something to track. Boat, jetski, surfer, dolphin, whale, whatever. Line them up above or below the white arrows which are set up like a sight of a gun (I had to be told that). Then look through the eyepiece and you'll see a cross hair (now I feel like a stalker/ sniper). The goal is to line up that crosshair at the exact same place on your subject every time.

Now the theo is part binocular, so you can see things in the water from so far away. So as your subject is moving, you can fine tune the eyepiece to follow it as it moves through the water.

It's hard. Like, really hard. Like, ridiculously really hard.

While watching your subject, when it does something of interest, you record the behaviour and the 'location' that is on the theodolite. Then you can use that 'location' to figure out a true location later on (which will come in another post).

That's all there is to a theodolite. In essence, it's an easy piece of equipment to work. In reality, it's a pain that takes years and years of experience to expert. But it's effective and less expensive than tagging whales.

Speak Loud!

Look at What You're Listening To

Phew! I moment to breathe! And therefore, a moment to blog.

It's been a non-stop whirlwind for the past 11 days. The station is set up, we are trying to find people with boats willing to take us out to look for whales, and in the background, a couple interns are busily trying to find whales in the midst of hundreds of thousands of sound clips.

Yupp, I said hundreds of thousands.

So young padawans, I am going to (try to) explain to you the intricacies of acoustic analysis.

Hydrophones are underwater microphones attached to recorders that are suspended in the ocean by buoys. They record noise at intervals for a specific amount of time, then are brought back to the surface. The recorded clips are downloaded onto a computer, and then analyzed by people with absolutely no time on their hands (which is why they ply interns with free accommodations and a tropical setting).

The clips, in some kind of sound file format, can be analyzed in a variety of ways. One way would be to simply listen to them. All of them. Now can anyone tell me the problem with this?

Let's do a math question: a hydrophone records for a 20 second interval every five minutes for 5-8 months. What would be the length of sound you would have to listen in order to analyze every file created?

I don't even want to do the math. Bonus points for whoever does (and comments below).

So obviously that is a bigger waste of everyone's time than watching grass grow or paint dry. Plus everyone's range of hearing is different, so who knows what one person might miss?

The solution to this is to look at the sound files and find whales.

Wait... what? What dimension are you living in? Seeing sound files?


Calm down! Let me explain...

Spectrograms are a type of image that let's you see sounds over their frequency range over an amout of time. It's a graph, x by y, but each point is so minute and there are so many that it becomes an image. An image of an empty underwater spectrogram might look like this...

Sample found here

If it looks like a lot of mess, that's because it is. The ocean makes tons of noise, and that's all it is: noise.

BUT

When something biological makes sound, it shows up crisp and clear against all the background noise. Here is an example of a humpback whale spectrogram.

Can you see the whale? Can you?

Look at the empty spectrogram. Now at the whale one. Now back at the empty one. The empty one is not the whale one, but with patience and time, it could be.

So using programs like Ishamel, RavenPro, or SASlab, you can create these spectrograms and look for whales, fish, dolphins, whatever you need. Even things like rain, thunder, boats and jet skis show up distinctly on spectrograms. And once you know what your looking for, it's pretty easy and fast to get through the ones that don't have anything on them.

For us, once we find whale or fish or anthropogenic noise on a clip, we mark it in a spreadsheet so our supervisor can do what she needs to do.

That's it. Some people's eyes start to get really tired after a couple hours, but for some reason I can do about 8 hours worth of files without my eyes going buggy. I suppose that to be a good thing because I want to study acoustics for the rest of my life (or at least my next degree).

A really funny side effect: You start being able to look at the shape of the marks on the spectrograms and be able to make the sounds of the animal. So based solely on the whale shaped marks, I am learning to sing whale. But I will ever be as good as Dory.

That's it! It's essentially what I've been doing since I got here, other than general cleanup and maintenance of the station (AKA house).

One last thing... I love that my family and friends are reading and following this blog, believe me, the support is amazing and occasionally brings me to tears (kidding... sort of). BUT if anyone out in cyberspace is reading this and doesn't actually know who I am, I would love to hear from you in the comment section! The point is to inspire and educate, and I don't know if any of my friends or family are secretly aspiring marine biologists. That's it, just giving everyone a shout out.

Speak Loud!

On a Scale of Yellow to Purple...

So I just seem to keep getting more and more South! As I've said to friends and family back home, I am not looking forward to Northern weather after spending 5 months in the tropics (add the three months of summer at home before that, and I have spent 8 months in shorts and tshirt weather)!

For those of you know don't know, I am now sitting in Guayanilla, Puerto Rico at the Marine and Coastal Ecology Research Centre, where I am going to be analyzing humpback whale acoustics for approximately 3 weeks. Tres exciting, no? Oui! Okay, enough French.

More details on the actual science once I do some more of it, and when I have a better idea of what we're doing. This post is more to turn on the alarm for another one of my little wake-up calls to aspiring Marine Biologists; and that is the whole point of this blog anyways (that, and so I can stop trying to explain what I do to my parents).

This post, my dear friends (and random readers... I know you're there, leave a comment!), is too discuss my present living and working arrangements. Which is a far, far cry from my situation back in Sarasota.

Disclaimer: This is NOT me complaining at all. This is an experience that I am more than excited to have and I think it'll make me a better scientist in the future. This is simply comparing one research site to another, and a way to look at the variation of arrangements you have to be prepared for in this field. 

Okay, so...

In Florida, I lived in an apartment that was about a 15 minute bike ride from the lab. Yes, I had to share it with 3 other girls and yes, I did have to share my room. It had a living room, a kitchen 2 bedrooms, 2 bathrooms and a little porch.

In Puerto Rico, 8 of us are in a 3 bedroom house. 2 of the rooms have bunk beds, where 4 people sleep, the master bedroom is for our supervisor and her significant other, and 2 of us (including yours truly) are sleeping in what could be considered the living room area on a couple of cots. Our kitchen does not have a stove, so we cook everything either on the propane BBQ, in the toaster oven (we've baked bread in it, guys) or in the microwave. You can't put anything in the toilet or it will clog the septic tank. This includes toilet paper. Used toilet paper goes into a little waste basket that gets cleaned out every night. There is no hot water anywhere. Kitchen sink, bathroom sink, washing machine, shower: all cold water. The internet is pretty weak, especially with 8 people on it at the same time. So no skyping, and no online TV shows or movies. And the house is also the "lab", where we all sit on our computers and do the analysis, and where all the field gear is stored.

In Florida, the lab was in the corner of the Marine Mammal Research Centre. It had half a dozen offices, an AV room, a storage room or two, a little kitchenette and a conference room.

In Puerto Rico, we sit outside at a dining room table with our laptops and do everything off of programs we've installed or downloaded. Our gear is stored in the front porch (which has to be kept locked at all times), or anywhere else we can find room for it.

In Florida, we had pretty set office hours. Sure, when we were in the field you had no idea what time you'd be home for dinner, but on lab days we came in at a certain time and for the most part left at a certain time.

In Puerto Rico, we are supposed to start work at a certain time (and we're pretty sure we'll be able to do it), and we're supposed to only work to a certain hour, but seeing as we're all around in the evenings anyways, it's easy to try to wrangle some work out of us at night as well, even if it's just easy work.

In Florida, we were assisting in a study that had been in progress for over 40 years. The science behind it was near perfect, the methods near flawless, and our supervisors knew the in's and out's of all the programs we used for our photo-ID and any other analysis done.

In Puerto Rico, this study is less than 5 years old, and the acoustic analysis is a brand new addition. So our supervisor is learning right along with us, and we are being little guinea pigs for programs and analysis methods.

There are probably a million other differences between the studies, but those are some of the biggest. We all cook and clean communally, something we didn't really do in Florida, and the team is a lot more diverse than back at Mote. These are the realities of the job. You're not always going to be working in a well situated institute. Sometimes you are going to be working somewhere without running water or something like that. So consider all the differences I've posted. If you don't think you can handle it, I might suggest reevaluating the specifics of your career choice.

The title for this post was meant that even though it is a comparison along a scale, one is not necessarily better than the other (like a scale of 1 to 10, or white to black, etc.). Both types of field/living sites are exciting and offer pros and cons, just like yellow and purple. Plus I like both those colours :)

On a completely other note, those who know me more personally know that I spent about 11 days travelling around Puerto Rico before settling into the internship. For those who don't know me personally, you know that now. I survived it, I met some amazing people, and learned a bit about travelling around Caribbean islands. This is not the forum to talk about my travels, but I'm sure if I talk to you soon, you'll hear all about it!

Speak Loud!