Life after grad school

For a while there, it seemed like I was going to be a graduate student forever…then I graduated and got a job. And then I decided to go *back* to grad school (oh, Michelle…). But then, in December 2016, I successfully defended my dissertation – Huzzah! (I like to tell my nieces I made it to grade 22, how funny/terrifying!) Then about a month and a half after wrapping up my PhD, I started working (remotely) for JASCO Applied Sciences. (oh, and a couple of months after that I had a baby.)

JASCO is a company that does consulting and research for assessing and mitigating underwater noise. They sort of do it all – they design and build super cool underwater acoustic sensors, install those sensors and collect data all around the world, often in remote and dangerous locations. They measure sounds produced by marine animals like whales, dolphins, seals, fish, crabs… basically if it makes a sound and lives underwater, JASCO is probably gonna record it at some point. They also record sounds from noise sources like ships and seismic experiments. Then once all those data are collected, JASCO scientists crunch through it – signal processing, acoustic propagation modeling, interpretation, whatever needs to be done to understand what’s happening in the world of underwater sound.

My job at JASCO is a blend of things – data analysis and visualization, but also education and outreach. Here I am at my home-office, working on a comic about marine noise, and how we can measure it:

Communicating science + baby wearing, for the win.
Communicating science + baby wearing, for the win.
Hopefully I’ll have more posts to share soon, so stay tuned!

Hydrophone arrays, FTW!

Figure 1. Photo of Amy and Emily deploying the array off the back deck of the R/V Ocean Starr.
Figure 1. Photo of Amy and Emily pulling in the array at the end of the day.

We do a lot of things out here on the CalCurCEAS cruise – we play cribbage, we eat cookies, we ride the stationary bicycle – but mostly we do these two things, A LOT:

1) Look for whales and dolphins.
2) Listen for whales and dolphins.

Part 1, the “Look” part, is within the realm of the visual team, who stand bravely in wind and cold and rain (and sometimes gorgeous, balmy sunshine) and scan the surface of the ocean for animals that might pop up to say hi and or take a quick breath of air.

Part 2, the “Listen” part, exists because, well, it’s pretty difficult to see what animals are doing once they dip down beneath the waves. And we all know that’s where the fun stuff happens (synchronized swimming practice? underwater tea parties? you never know!).

Since I’m on the acoustics team, I thought I’d give a little overview of how our operation works.  We eavesdrop on the animals using a pair of hydrophones, which are basically underwater microphones. If we just used one hydrophone, it would be okay, we could hear the animals. But adding a second allows us to not only hear them, but figure out where they are.

Figure 1.  Top: Array geometry, showing how we can tell which direction a sound is coming from. Bottom: Signals measured on each of the hydrophones.
Figure 2. Top: Array geometry, showing how we can tell which direction a sound is coming from. (The poor creature pictured is my sad attempt at a striped dolphin, if you were wondering) Bottom: Signals measured on each of the hydrophones.

The pair of hydrophones are built into the end of a cable that is spooled onto a winch on the back deck. Every morning we head out there, don our life jackets, hard hats, and boots, and reel out the cable until the hydrophones are 300 meters behind us. The hydrophones are spaced one meter apart, and once the vessel is up to speed, they are roughly at the same depth.

The upper part of Figure 2 (blue) shows a cartoon schematic of the hydrophone setup. Here’s what it all means:

H_1 and H_2 – hydrophones #1 and #2

Known quantities:

d_h – distance between H_1 and H_2. For our array this distance is 1 meter

c_w – measured sound speed in water (approximately 1500 m/s, but depends on temperature and salinity)

Measured/derived quantities:

\Delta t – time delay between when the signal arrives at H_1 and H_2

d' – distance associated with the time delay \Delta t, derived using c_w

Unknown quantity:

\theta – angle between the incoming ray path and the array baseline. This is what we’re solving for!

OK, that seems complicated. But feel free to ignore the math, of course. The basic idea is that depending on where the sound comes from, it can arrive at the hydrophones at different times. For example, in the image above, it hits hydrophone 1 first, and after some amount of time, it hits hydrophone 2. The signals from each of the hydrophones are sent upstairs to the acoustics lab (see bottom part of Figure 2). The call shows up at slightly different times on each of the hydrophone channels, and we can measure that time delay \Delta t very precisely.

Using the time delay \delta t and the measured sound speed c_w, we can obtain distance d' using:

d' = c_w * \Delta t

So now we’ve got a right triangle where we know the hypotenuse and one other side, and you know what that means – trigonometry time!! Everyone’s favorite time! We finally have what we need to solve for the angle \theta.

\theta = acos( \frac{d'}{d_h})

We now know what angle the dolphin is at relative to the array. Huzzah! But wait. There are just a couple of little details that you need to remember (see Figure 3). First: you don’t know how far away the dolphin is. Second: there’s this pesky thing called “left-right ambiguity” *.

doge_angles3

From the perspective of the array, there’s no difference between an animal calling from an angle \theta to the left and an animal calling from an angle \theta to the right.

Figure 3. Left-right and range ambiguity.
Figure 3. Left-right and range ambiguity.

These are fundamental limitations of the method, but we can (sort of) overcome them. As the vessel moves along, and we estimate angles at different locations, we end up with a location where most of the bearing lines intersect. If the vessel is traveling in a straight line, we can get a good idea of range – how far the animal is from the trackline. We just won’t know which side of the trackline it’s on. But if the vessel makes a turn, the new bearings estimated after the turn will resolve which side of the line it’s on!

Resolving_ambiguities_600px
Figure 4. Bearing estimates (red lines) taken at different locations along the track line. Probable location is where most of the lines intersect.

At this point you might be wondering, Michelle, what assumptions are you making when you do these calculations? So here they are:

Assumptions**:

  • The array is horizontal
  • The animals are calling at the surface
  • The animals are staying in approximately the same location for the duration of the measurements

So there you have it. That’s how we locate animals underwater with a towed, 2-element hydrophone array.

 

* Yin, one of the amazing visual observers on the cruise, thinks “Left-right ambiguity” would be a great name for a band, and I agree.

** assumptions are made to be broken

Doodle videos, heck yeah!

My latest project is figuring out how to make a doodle video. Or a speed drawing animation. I don’t actually know what they’re called, but you’ll get the idea if you check out the videos below. I started off attempting to use my iphone. Setting the iphone up to record was… awkward:

completely professional.

I did my video this way, posted it to youtube, and got a bunch of feedback from my awesome Facebook and Twitter friends. I tried to take that feedback into account as best I could and eventually moved on to my Nikon D5100 (dSLR).  I even set it up on an actual tripod (Thanks, Andrew Shao!).

slrvideo

Recording on my SLR was pretty easy too, once I got it adjusted. I did have some issues with focusing – not that it was hard, I just kept forgetting to check. oops. Editing for the SLR video was done in iMovie, and the audio was recorded in Hindenburg Journalist. Here’s a 30-second sample from this experiment. I hope that you agree that it has improved, at least marginally, from my first attempt!

Next, I decided to try doing the video using Camtasia. Luckily they have a free trial, so I gave that a whirl. Camtasia is for screen recording and video editing, and was really easy to jump into and start using right away. I did the drawings in Adobe Photoshop using my Wacom Intuos4 tablet/stylus. Here’s the 30-second sample using the “all-digital” method:

Dear reader, if you have been patient and kind enough to actually read all this, and more importantly, watch the two videos, please feel free to give me feedback in the comments (below) or in email or on Twitter or Facebook!

Harmful algal bloom forecasting: Chasing toxin producers

It started with “drunk” pelicans. While studying aquatic sciences at the University of Santa Barbara, Liz Tobin noticed that there was something wrong with the fish-gulping birds.  They exhibited unusual behavior, getting hit by cars, and sometimes simply falling out of the sky. The pelicans suffered from seizures induced by domoic acid poisoning, a particularly dangerous affliction when it hit mid-flight.  Biologists traced the source of the poisoning to rapid springtime growth (bloom) of Pseudo-nitzschia, a tiny, single-celled organism, distantly related to the giant kelps thriving in nearby coastal waters.  Small fish and shellfish consume these algae, and although they are not harmed, they store the toxins produced by algal cells and pass them on to their predators, including seabirds and marine mammals.

Scientists refer to these incidents as harmful algal blooms, or HABs.  They are not restricted to the waters of southern California, though.  And Pseudo-nitzschia cells are not the only culprits.  There are a number of other algal species that can cause trouble for local marine ecosystems. HABs occur in coastal waters around the globe, with larger and more frequent blooms being linked to a warming sea surface [1] and also to increased nutrient runoff from land [2], which is a common by-product of animal or plant agriculture.  Local economies suffer due to tourism losses and local residents can’t harvest shellfish from their beaches.

After wrapping up a bachelor’s degree at UCSB, Liz moved on to graduate school at the University of Washington so that she could study harmful algal species in Puget Sound.  One of the species she’s interested in is Alexandrium catanella, another single-celled marine alga that produces a suite of deadly neurotoxins causing paralytic shellfish poisoning, or PSP.  Alexandrium blooms can become so intense that they give the water a reddish-brown tinge, often called a “red tide” (although they don’t always cause water discoloration).

Oysters

If you eat a shellfish that has accumulated Alexandrium toxins, a series of unpleasant events unfolds. First, your fingers and toes will tingle and your lips will feel numb.  Next, you may become nauseous and unsteady on your feet.  If the toxins hit you at full force, your diaphragm will become paralyzed, which means that you are unable to pull oxygen into your lungs.  Without prolonged artificial respiration, a severe case of PSP can lead to death in a matter of hours.

In recent years, poisoning cases in Washington State have been rare, but they do happen. Washington Department of Health aims to prevent outbreaks by regularly testing shellfish along Puget Sound beaches.  Commercially harvested shellfish are tested exhaustively before hitting the markets. Unfortunately, it’s tough to predict the severity, location, and timing of an Alexandrium bloom ahead of time. That’s where Liz’s work fits in: she’d like to improve our ability to forecast where those blooms will happen ahead of time so that public health officials, fisheries managers, and the shellfish industry have more time to react.

LifeCycle

Alexandrium cells have a comfort zone, she explains.  They grow and divide furiously when the days are long and the surface waters are warm.  Once the spring bloom ramps up, zooplankton, fish, and shellfish feed on the algae, eventually decimating Alexandrium populations by early to mid summer.  Less Alexandrium cells means less food for their predators, and their predators begin to die off or find food elsewhere.  By late August, with newly lowered predation pressures and plenty of sunlight, a second bloom typically occurs.  As the season draws to a close, Alexandrium  algal cells feel the effects of shorter days and less sunlight.  They struggle to grow and divide and at some point cut their losses and transit down to the sediment to wait out winter.  -Settled into the muddy seafloor, they shift to survival mode, also known as the “cyst” stage.  The exact conditions that send them into their cyst stage are poorly understood, as are  the details of how they wake up and make their way to the surface come springtime.

Liz is particularly interested in how the Alexandrium cells swim, even though they are mostly at the whim of the currents.  Tides rush in and out twice each day, racing through narrows and washing languidly over mud flats.  Rivers pour into Puget Sound with irregular pulses of freshwater from rain and springtime snow melt. Alexandrium algal cells propel themselves through the water using a small whip-like appendage called a flagellum, but because of their tiny size – only about a third of the width of a single human hair – they can’t overcome even the weakest currents. However, if Liz knows their vertical swimming capabilities, she can better understand how quickly Alexandrium cells migrate from the seafloor to the surface (where blooms occur) and back again.

A lot of researchers, Liz included, study Alexandrium in the lab.  They blend solutions of water and various chemicals to imitate seawater, and observe how the cells behave and react to a variety of environmental triggers.  One of the labs she works in is a tiny bunker-like space on the second floor of the Ocean Teaching Building.  Two long black tables running along either side of the room are covered by a hodge-podge of beakers, elaborate video recording setups, and circuit boards sprouting nests of red and white wires.  At the back of the room, a giant insulated door opens to a fully programmable walk-in refrigerator, where algal cells can be subjected to controlled shifts in temperature and light.

Even at their best, however, lab experiments can’t possibly recreate the many complexities that exist in the natural world.  Liz knew that if she could monitor the emergence of the Alexandrium cells from the sediments she could combine those observations with detailed fluid flow models to better predict where the cells would eventually concentrate.  The only problem was that there were no “off-the-shelf” instruments that were capable of doing what she wanted.  So she set out to build her own.

soldering

When she starts describing the instrument she’s working on, I interrupt.  Pushing my notebook and pen across the table, I ask her to sketch her design for me.  She draws a tube a few inches in diameter, sitting upright on the seabed.  On one side of the tube a camera in waterproof housing points into a tiny window to capture any Alexandrium cells swimming past.  The end of a plankton trap sits on top, ready to catch any upward-swimming cells so they can be later compared with the video. She pauses her drawing to look up at me.  “It’s just like what we would do in the lab,” she says, “but instead of a camera looking at a tank, I have a camera looking into a chamber on the seafloor”.

As of mid-July 2013, Liz’s prototype of her seafloor camera was nearly ready to be deployed for testing.  If it works, she’ll try to capture Alexandrium cells emerging from the seafloor just prior to the late-summer bloom.  Her vision for the future, she tells me, is a network of these instruments deployed across Puget Sound, monitoring cyst emergence in real time.  Instead of only knowing about blooms once they are in full swing, they could be predicted days or weeks in advance, avoiding unnecessary closures and potentially saving lives.

[1] Climate change and harmful algal blooms, NCCOS http://www.cop.noaa.gov/stressors/extremeevents/hab/current/CC_habs.aspx

[2] Anderson, Donald M., Patricia M. Glibert, and Joann M. Burkholder. “Harmful algal blooms and eutrophication: nutrient sources, composition, and consequences.” Estuaries 25, no. 4 (2002): 704-726.
http://www.whoi.edu/fileserver.do?id=47044&pt=2&p=28251

 

Teaching and tweeting

MOR tweet

It’s been a while since I’ve been a TA in the traditional sense – you know, sitting in class, running and grading labs, answering questions from inquisitive minds (or at least referring them to smarter people than myself)… So I’m pretty excited to be back at it this quarter. Yesterday was our very first class and today is our first lab – huzzah!

I decided yesterday, somewhat on a whim, to take the class to Twitter – I’ll be tweeting class-related goodies using the hashtag #Ocean410TA, in case you want to follow along – whether you’re in the class or not. I’d be stoked to hear from people who are just curious about what we’re doing. The class is a senior level (4th year for you Canadian friends) marine geology and geophysics class – we basically learn about how the ocean basins form, and why the look like they do. Underwater earthquakes and volcanoes! The coolest.

Has anyone out there tweeted a class before? Any advice or thoughts?

And in case you’re wondering why scientists should tweet, check out this blog post on the AGU website and another one on the Deep Sea News site.

Learning to write

PickAPen

I took a writing class!  Yes I did.  I probably shouldn’t admit it, really, because now you’ll all expect me to have improved immensely, and that makes me nervous.

The class was with Stacey Solie (@StaceySolie), and it was fantastic. I learned a lot and here are a few of my favorite tips:

Freewriting: Every day, set aside a dedicated chunk of time to just write.  Don’t worry about punctuation, spelling, grammar, or anything.  It’s great for writer’s block: you don’t even need to start at the beginning or anything.  It just helps get the ball rolling and get you out of whatever funk you’re in.  I’m trying to do at least 15 minutes per day (minimum).

Read your work out loud:  Admittedly, this is one that I knew about before, but it bears repeating.  I don’t do it nearly enough and I really should because when I do, I always catch mistakes.

Stop apologizing for your work: It’s a terrible habit of mine and doesn’t really accomplish anything.  For example, when giving an essay to someone to proof-read, it’s pointless to say things like, “Oh, here you go. It’s really bad, sorry.”  It’s probably got some bad parts, and some good parts, and whoever is reading it will figure it out without you telling them.

So I’m working on building confidence in my writing…

Confidence

 

Know when to stop:  Try to recognize when you reach the point when your ongoing efforts cease to result in significant improvements. The “sweet spot”.  Stacey talked about this, and so did one of our guest speakers, Katie Arkema.  Here’s my own interpretation, in graphical form:

ListenToYourBladder2

Bonus materials!

Thanks to the terrific @realscientists followers, who pointed out a couple of important points that I missed before!

READ! Yup, to become a better writer, you have to read. A lot. I mean, you should read every day, and be critical about it, too.  Ask yourself, what is it that makes a certain piece of writing excellent or terrible? What techniques does the author use? Is there anything about their writing that could be improved upon? These observations will all eventually sink into your brain and make their way into your own writing. Hopefully not word for word though, because that’s not cool.

Practice. This sort of goes with the “free-writing” point above, but let’s give it a whole section unto itself. Because that’s how important it is. Like many skills, it’s more about hard work than innate genius. Have you read that book, Outliers, by Malcolm Gladwell? In it, he talks about what all of these wildly successful people have in common. Sure, there are loads of factors that lead to success, but the one in common between them all was that they’d put a metric butt-load of hours into their craft. Ten thousand hours, minimum, to be exact. So put in your time!

Well there you go.  You know I’m not a writing expert, I’ve just listed/regurgitated things that I thought were useful or inspiring. Hope it helped! Feel free to add to the list in the comments. 🙂

 

 

The biggest waves are the ones you can’t see!

Your weekly dose of ocean science + comics!

Name:  Andy Pickering
Job: 5th year PhD student, Physical Oceanography, University of Washington. Works with the Wave Chasers Lab at APL
Research: Ocean physics, internal waves

What lives underwater, is hundreds of meters tall, and can swipe a submarine out of its way like it’s a fly? An internal wave, that’s what! They don’t all get to be so big, but once a wave is released from the shackles of the air-sea interface, who knows what crazy things it might get up to?

Oh wait – Andy Pickering knows! He and his lab group study internal waves. Internal waves are kind of like surface waves – they need that density gradient to even exist. So in order to figure out how they propagate under water, Andy needs to know how the density varies underwater. There is often a surface mixed layer where the density is constant for tens or hundreds of meters, and after that it tends to increase with depth.

Although density is a continuous function of depth, the density gradient can be modeled as a series of very thin slices of constant density. And once you do that, internal waves are no longer confined to the interface; they can propagate vertically as well. Internal waves can travel very far, and just like waves crashing on the beach, internal waves can break as they approach the seafloor.

surfing-internal-waves-no-cite

One of the very important implications of internal waves breaking is that they can cause turbulence, which has a surprisingly significant effect on ocean circulation models. Because this kind of turbulence happens on such a small scale relative to a global ocean circulation model, it’s really tough to incorporate it properly. Especially since it is not fully understood yet.

Andy and his lab group are participating in a large project called IWISE (Internal Waves in Straits Experiment). The goal of the project is to better understand the behavior of internal waves in a strait environment by taking tons of measurements in one particular strait: The Luzon Strait.

If you were ever looking for an awesome spot to find out how tides interact with shallow ridges to produce gnarly internal waves, look no further, my friend. As the tides slosh back and forth over the two ridges that run between Taiwan and the Philippine island of Luzon, enormous internal waves are generated that roll west into the South China Sea and east into the Pacific Ocean. These waves are so massive that the perturbations that they cause at the sea surface can be seen from space!

luzon-strait

In addition to all the craziness from tides barreling over the shallow ridge, there’s also the Kuroshio current to deal with. The Kuroshio is sort of like the Gulf Stream, except in the Pacific Ocean instead. It pushes warm, tropical water Northward along the western edge of the Pacific Ocean basin. Like other ocean currents, it moves around a bit over time, and sometimes it dips further into the Luzon Strait than others.

Data for the IWISE experiment were collected in 2010 and 2011, and both moorings and ship-based instruments were used. The two most important instruments for Andy’s research are the CTD (conductivity-temperature-depth sensor) and the ADCP (acoustic Doppler current profiler). The CTD measures the density of the seawater at different depths, and the ADCP measures current speed and direction at different depths. With these key bits of data, Andy can look at how the ridges affect the generation of internal waves, and even at how this Kuroshio current adds to the mix.

internal-wave-data-collection

Andy has been looking at the data and in particular at the energy flux generated by the tides colliding with the shallow ridges. He’s seeing that the ridges are actually creating interference effects because they’re so close together. Some of that energy is dissipated away locally, but Andy is also interested in looking at how much might be escaping, and whether it could make a significant contribution to deep ocean mixing.

The amount of deep ocean mixing is critically important for constraining global ocean circulation models and also global climate models so we can better understand things like climate change and global warming. So in a way, when Andy is not wasting time doing interviews with me, he’s busy saving the planet! Awesome.

If you want to know more about Andy’s lab group, the Wave Chasers, check out this pilot put together by Wide Eye Productions:  http://vimeo.com/wideeye/wavechasers.  It’s really cool, and well-worth a couple of minutes of your time.

Why is reading so hard?

Read-O-Matic

One of the things that comes with being a grad student/scientist/engineer/etc. is that there is a TON of reading to do.  Sometimes it’s for classes, or for keeping on top of your field, or for writing the intro or background section of your thesis/paper/report/application.  And you’re not just reading for fun.  You’re reading to:

  • understand what you’re reading (okay, duh)
  • figure out how it fits in with other research
  • figure out how it fits in with your research
  • be able to explain it your own words
  • remember it later, when it inevitably becomes relevant to you again (tougher than it sounds)

I’m constantly struggling with how to do all of these things effectively, and have yet to figure out the secret, the magic bullet, the holy grail of academic journal reading.  Here are some disparate theories or thoughts that I’ve cobbled together on the subject of reading.

Writing is key

I guess different people have different learning styles:  some people are auditory learners, visual learners or tactile learners (to name a few).  I think I would fall into the category of a writing, or possibly speaking, learner.  I’ve found that if I just read and highlight the crap out of a paper, I may  think I understand it at the time, but start losing it immediately after finishing it.  It’s really annoying.  I want to just sit in my comfy chair with a highlighter in one hand, and a cup of coffee beside me.  I want it to be fun and painless.  Like watching a movie… about science… with a ton of equations… ugh.  Okay, after trying and failing the “relaxing” method too many times, I’ve finally admitted to myself that I am just wasting my time.  If I don’t invest a bit more effort into typing my little synopsis as I go, then I am going to just have to go back and re-read it anyway.  Which is an even bigger pain.

Figuring out the figures

This is a tip that has pretty much been pounded into my head since starting grad school. (curiously, I don’t remember anyone telling me this in undergrad – maybe we didn’t read many papers back then?)  Understand the figures.  In fact, go through the paper and try to understand the figures before tackling the text.

Non-linear reading

This one kind of goes with figuring out the figures.  Most people I’ve talked to do not recommend reading a paper straight through.  Read the title (obvs!), the abstract, the intro, and the conclusion to get the gist of what the paper is about.  That sort of “primes” your brain for what to look for in the paper.  Additionally, I think it’s a good idea to scan the section titles so you know the structure of the paper before reading it.  And the great thing is, depending on what you need that paper for, you might be able to get by with just reading the intro and conclusion, and looking at the figures.  Although knowing when that’s enough can be tricky.

BFM (brute force method)

As time goes on, and as I read more papers on fin whale acoustics, I’ve found that they do get easier.  I mean, incrementally.  It still takes me a minimum of two or three hours to go through a paper carefully (and often more), but I find that I get more out of it now than I used to.  Here’s the caveat though:  this is only true for baleen whale acoustics.  Once I veer away from that very specific topic, the difficulty level rises again.  I think that I really get the most out of papers where I recognize a lot of what they’re saying from other papers.  Not that it’s a big revelation, really, I think it’s basic learning theory:  if you’ve built up a sort of “architecture” about a subject, then you’re not re-learning whole body of knowledge when you read about a related topic.  You’re actually just incrementally adding to what you already know.  Not to mention you’re learning the jargon as you go – those words and phrases that are short-cuts for people in the field, but completely confusing to those that are not.

So what?  Well, I think it really means that there really is no magic bullet, at least for me.  I just have to slog through a certain number of papers until I get the gist of the subject matter.  And I have to write notes about what I’m reading.

I’m curious as to whether others have similar experiences…  although I suspect some lucky folks can skip the writing/summarizing altogether and just read it and get it.  And if that’s you:  please tell me your secret!