Here's to the Troubleshooters!

This week has been a pretty tough one for me.  Like many researcher who study animals in the ocean, I use a lot of technology.  Technology is very important for a lot of ocean research - humans are not adapted to live underwater, and technology allows us to sea the ocean in ways our puny physiology would never allow. 

The problem with technology is that it usually involves electricity, and the problem with electricity is that it does not play well with salt water.  This means if you use any kind of wired technology to do you underwater research, you've got to make sure they never get anywhere NEAR each other.

We keep salt water from getting anywhere near our electricity by separating them with a barrier of plastic or rubber.  Unfortunately, sometimes this barrier gets broken, and salt water comes through the break like Orcs through a hole in the walls of Gondor.

When things go wrong with research equipment, it can derail an entire research project.  Ocean researchers can spend from thousands to millions of dollars to get to a location to do their research, and if the equipment fails when they get there, everything is wasted.  Case in point: the $125 million mars rover satellite that failed in 1999 due to a math mistake in the thruster software.

Fortunately, my equipment isn't 35 million light years away.  Last Monday, on my way to Kauai, my hydrophone cable hit something in the water which sliced a tiny little hole in the cable.  The hole was smaller than the tip of my pinky nail, but since the break occurred quite early in the trip, I didn't discover it until we got to Kauai and it had been dragging through the water for about 14 hours.  This gave the water quite enough time to work its way up into the hydrophone and most of the cable.  Since my research project depends on collecting data at regular intervals, I needed to get this fixed FAST.

One of the largest benefits (as well as the greatest challenges) of working at my research lab is that we don't have some of the resources that bigger mainland labs do.  For example, the Scripps whale lab employs several engineers, who can design and make electrical recording equipment.  We don't have engineers who make our equipment - we make it ourselves (my advisor has a PhD in electrical engineering, so he gives direction).  This can be very frustrating at times.  For students like me, who have a degree in Biology, there is a steep learning curve to understanding electronics.

Climbing the electronics learning curve.

Anyway, I spent the week fixing my hydrophone and hydrophone cable.  So the blog post this week is a time-lapse video of me doing that. 'Cuz sometimes you just gotta BRING IT, and there's not as much time for the fun stuff (e.g. blogging).

But here's the thing that I think is really important, and which is the reason that I decided to make this video.  Without the technical, hands on, practical, getting sh*t done, there would be nothing to blog about.  This type of work is the very makeup of most science, but it doesn't really get the recognition it deserves.  It's hard work (you may notice I get progressively tireder looking throughout the week), and I just want to give it some props.

Here's to you, equipment-fixers and the trouble-shooters.  Blessings be upon you and many thanks!

(BEAR is my jokey-term for my equipment.  I use a modified Ecological Acoustic Recorder 

(EAR), which I tow off a Barge.  I guess I could call it a Towed EAR (TEAR) or a Mobile 

EAR (MEAR), but for some reason I think that it's hilarious that you can add one letter to 

Ear and get Bear.  So I'm calling it a Bear (for now).  Hopefully Steven Colbert doesn't hear 

about this, or I'll be put on Notice.

Here's a breakdown of what happens in the video:

Monday


Hydrophone Breaks, but I'm on the tug, so I don't know until...


Tuesday


I download my data, and find... nothing after the first 20 minutes.  I check the hydrophone cable and find a break.  I fly back from Kauai to Oahu to start fixing things


Wednesday


Use a hacksaw to cut into the epoxy of the hydrophone and try to expose the wires, cutting my hand in the process.  I start soaking the epoxy in acetone, which will dissolve it if it's in there long enough (acetone dissolves plastic, which is why you buy it in a metal container!)


Thursday


Give a talk about my research at our department symposium, then run around town buying things I need to fix my equipment (cable, aquarium sealant, zip-ties, etc).  Remove cable from the tow-rope.


Friday


Attach new cable onto the tow rope, then go help out at the symposium banquet (where I got a flat tire).


Saturday


Attach plug to end of cable.  Dremmel into the hydrophone epoxy to get to the wires inside it.  Test the hydrophone and pre-amp (still working).  Do a happy dance.  Attach new wires to the hydrophone.  Attach the cable to the hydrophone. Set up a mold and pour epoxy around the hydrophone and cable.


Sunday


Pour a second mold because my mold is tiny.


Monday


Remove hydrophone from mold, clean up and sand.  Re-test (it still works!).  Take hydrophone to car and drive to tug boat to try again (I'm leaving in an hour). 
Tuesday
Update: 3/20/2012 at 8:56 am. Just got to Kauai, downloaded the data, and my fix worked! Woohoooo!



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Turning Whalesong into Rainbows: 1000 Numbers to 1000 words

Art by Casey Roberts

Two weeks ago I wrote about how sound gets from a whale, and into your computer.  At the end of that post, I included a pretty rainbow-colored picture of some dolphin whistles.  But I didn't ever explain how all that digital data got translated from zeros and ones into a nice pretty picture.


Why are pretty pictures important to science?  Awards are given out every year by several prestigious groups for the best images in science and biology.  These images are not only beautiful, but they often help us understand complex concepts that are difficult to understand using words alone.  For instance, I can tell you that dolphins have fat deposits in their jaw bones that help transfer sound into their ears, but the following picture by Darlene Ketton's lab at Woods Hole really shows you how the auditory fats (orange) connect up with the inner ear bones (red) to help the dolphin hear.  This picture does a better job of communicating the concept than I could do in 1000 words, AND you're not bored to death, either.

A 3-D image generated from a CT scan highlights selected

 tissue groups of a bottlenose dolphin's head. 

 (Courtesy of Darlene Ketten, WHOI)

Humans process most of their information visually, so we often need to translate acoustic information into visual information.

The acoustic data that I collect in my research is stored as binary data, which means that it is stored as a bunch of ones and zeroes, like this: 


01001000 01100101 01101100 01101100 01101111 


Each of these sets of ones and zeros corresponds to a letter or a number (the code I just used says "Hello"). Unfortunately, I can't look at binary code and understand what it means, because I'm not Neo from the Matrix.  Alas!

However, my computer understands the language of binary, and it translates all of these ones and zeros into slightly shorter strings of numbers, which look something like this (except a whole lot longer):

0.000113379 0.000136054 0.00015873 0.000181406 0.000204082 0.000226757

Not really a whole lot better, is it?  

2-D

Fortunately, I know that these random-looking numbers are the pressure values for a sound wave that has been measured 80,000 times every second. This means that the first number has a time value of 0, followed by 1/80000, 2/80000, etc.  Now that I know what the time values are, I can make graph with time on the x axis and the value for pressure on the y axis, like so: 

This is better: I can see that the sounds get louder and softer over time.  If the sound is louder, it will make bigger bumps on the graph, and if it is quieter, the bumps will be smaller.  It's still pretty hard for me to pick out the different sound frequencies, or pitches.

I can kind of see what is going on here, but it is like looking at only one line of pixels from an image of Marilyn Monroe; I don't really know what is going on [A]:

Fortunately for me, a French mathematician named Jean Baptiste Joseph Fourier (1768-1830) figured out a way to represent a continuous periodic signal (like a sound wave) as the sum of a bunch of sine waves.  This means that I can break up the signal above into a lot of simple sine waves.  I can also do the opposite, by adding up a bunch of simple sine waves to create a complicated one [B]:

Adding two sine waves together.

The top four waves combined (light blue) create the more complex wave at the bottom (dark blue) 

Even REALLY complicated waves, like this one, can be created by combining fourteen simpler waves:

2-D Again - Frequency

Once we break the sound up into its component frequencies, we can create a different picture.  This picture looks at how much of the sound is made up of each frequency.  For example, in this picture we are looking at the relative contributions of different frequencies to a sound recording.  You can see that there are more low sounds than high sounds, and that there are two small "peaks" between the frequencies of 1250 Hz and 1500 Hz.  (Hertz measures the frequency of a sound.  You can hear between 20 and 20000 Hz, depending on your age.) These two small peaks are actually the two frequencies at which the humpback whale is singing at this particular moment in time.

Now, it's like I'm looking at that picture of Marilyn vertically, but still only one row at a time.

Let's recap: To make a picture of a whale song, the computer breaks up the original sound recording into hundreds or thousands of individual segments.  For each of these segments, it does a Fourier Transform, which breaks the sound wave up into its component frequencies and creates the graph shown above.  

Next, the sound values are assigned a color.  Loud sounds are generally shown as red, and quiet sounds are blue.  If we stack these values next to each other, we start to see more of the picture:  

As more and more Fourier transforms are combined, they create the picture below, which shows the whistles of two common dolphins recorded in the Irish Sea. This picture allows us to see several important parts of the sound at once - how long it is, how loud it is, and how shrill or low the noise is.  I guess it's no lady in a red dress, but it's a whole lot more useful to me!

[A] Of course, this is not a perfect analogy, because a sound waveform is a combination of all the different frequency parts.  

[B] The explanations in this post about Fourier transform are grossly, extremely simplified, and skip over most of the math.  If you want a more thorough explanation, please see The Scientist and Engineer's Guide to Digital Signal Processing.  If you have any comments on my over-simplification, please leave them on the post or shoot me an email. 



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Whales and other mythical creatures: A gallery of Modern Art

           So long, and thanks for all the fish!                        

Can I just start out by saying I was REALLY surprised by how many page-views there were for the post on piezoelectricity?  I thought piezoelectrics and analog-to-digital converting would be beyond most people's interest, but either it wasn't, or people were suckered in by the naked hippie pictures.  Note to self: whenever possible, relate research to naked people.

This week I am taking some time off of in-depth blogging to work on another project (A guest post for Scientific American).  I didn't want to go a week without a blog post, so I'm going to share something that my friends have been forced to look at for years.  It is much in the same vein of silly pictures of naked hippies playing the cello to whales, except minus the naked hippies and the chello.  I'm talking about my collection of silly, whimsical cetacean art.  While I don't want to promote the idea that whale and dolphin scientists aren't serious, there's always a place for fun.  Some of these are available as prints online (someday, I envision my university office festooned with them), and some were emailed to me by friends.  Please share any information you have about the artists, or any additional artistic masterworks you may find.

A sly reference to the unicorns in the waves from The Last Unicorn.
 My absolute favorite, and I can't figure out who the artist was
or where on earth to buy it.

Artist's commentary: Here, raw sexual aggression is symbolized by the sperm whale, while the squid acts as a thinly-disguised metaphor for the multi-armed oligarchies of Rockefeller, Hearst, and Morgan. Their battle plays against the backdrop of the sea, standing in for—what else?—the vastness of the unconscious mind.

If dolphins were equipped with robotic bodies and guns.

Is anyone else secretly turned
on by guys with blue skin?

Better than sharks with laser beams!

My guess is that this is the only way a
dolphin COULD take on a unicorn.

I think this was originally in a magazine article on the

 "10 worst jobs." Anyone who thinks collecting whale 

feces is gross should try doing a necropsy.

The dolphin looks faintly puzzled.  "I knew swimming up that
stream was the wrong idea."  From Jeremy Scheuch.

Friendship.

Dear god, WHY didn't I buy this?

"Look, baby unicorn/dragon, the mystical 

dolphin is real!" Via Dr. Dewald.

I'm the one on the left.

I have no idea what is going on here.

Hugs! by thedreamygiraffe

Family portrait by littlegreentoaster via Alison.

Dolphicorn, or Unicolphin, by LineDrawTShirts 

Why are their open mouths so hilarious?  By LegendaryTigerHero.
*cough*mybirhdayisinJuly*cough*

Braaaiiins!

 

Yes, that is a tattoo of a dolphin wrapped in Bacon.

This is an actual book that I actually own and have read,
 a dystopia about cyborg whales that people live in under the ocean.

The answer to this math problem is... whale!

My fiend michael spotted this glassy mermaid
booty-groper painting on the Big Island.

.

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Raindrops, Keep Falling!

I just have to put this up, because it's so pretty.  This is the view from my office and bedroom windows right now.  It's been raining heavily in the Koolau Mountains, and when it does that, we get choke waterfalls (choke is Hawaiian slang for many, as in "there were choke tuna under that bird pile").  This view makes up somewhat for living in a tiny little apartment, and I should take time to appreciate it more often.  How many waterfalls can you count?

Click here for larger version.

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