Thursday, March 30, 2017

Dancing on strings

"Dancing on strings above the abyss, I cry
Reach for the skies"
- "Faster" by Amaranthe

My experimental set-up at the WHOI dock
Friends, today is the day! I have been waiting for barnacles to start recruiting to my monitoring plates before I could officially begin my succession study, and I'm happy to announce that my study has now begun! I saw a few barnacle recruits on the monitoring plates last week, so I knew it was time to get going. I made the final preparations, cleared my hypotheses with my advisor, and headed out to the dock with my experiment.

Working on docks is convenient because they're so accessible - literally right across the street from my office. I did run into one snag, though. My fouling panels are on large PVC sheets (see this photo), which were to hang parallel to the seafloor and upside-down, suspended from a corner of the dock by ropes on three of their four corners. However, as soon as I got the first sheet in place, I noticed that the free corner under the dock was getting caught in the current, and the sheet was getting swept up out of the water like a sail. I had to anchor the fourth corner.

Thankfully, the person responsible for the dock granted me permission to drill holes through the wooden top. I went out to the dock with a power drill, made the two openings I needed (one for each PVC sheet), and threaded the ropes through. Reaching under the dock to find the ends of the ropes was a bit tricky (I ended up taping a hammer to a broomstick and grabbing the ropes with the hammer's hook), but I made it work. With all four corners suspended by ropes from the dock, my sheets of fouling panels are in place. They can shift back and forth with the current, dancing in the water as it flows, but they'll stay suspended below the surface all summer.

I also put out a set of larval traps, and I left my monitoring plates in place. Altogether, that's 10 ropes hanging from the dock, with four apparatuses attached. I'll come back every other week to see what's on the fouling panels, collect the larval trap samples, and do any experimental manipulations I need to. It's going to be a great study!

Tuesday, March 28, 2017

The two-sided coin

I heard the lab door open and close, then three powerful footsteps headed my direction. Must be him. When I turned around, he was already in my office doorway. Man, he walks fast.

"Hi. I have ten minutes. Show me your thing."  He was polite but matter-of-fact.

I picked it up off the desk - a tube of white PVC with a cap on one end and three plastic tubes inside.

"See, I want it to sit like this," I explained, turning the PVC tube upright, "and I have to screw the lids on and off." I unscrewed the bottom cap and removed the three plastic tubes. "But it's leaking."

He held out his hands, and I handed him the sampler. He turned it over, looked inside, put the tubes inside, screwed the cap on. Unscrewed the cap, took the tubes back out, looked inside.

"I know how to fix this," he declared. "I have another meeting to go to right now, but I'll collect you afterward and take you up to my office. It's an easy solution."

I was stunned. That simple, really? "Can you tell me what the solution is?" I tentatively asked.

He smiled gleefully. "Teflon tape!"

Friends, I work in a very special place. WHOI is one of few research institutions that employs both scientists and engineers and puts them in close proximity to one another. I've certainly reaped the benefits of that proximity - the above example is the third time in as many months that my engineer friend has offered me a usable, affordable solution to a design problem I was having in ten minutes or less. He's very helpful. Sure, I could have messed around and maybe figured it out myself, but he saved me probably three days and a trip to the hardware store.

Engineering and science are two sides of the same coin, so it makes perfect sense to have them together. I'm grateful to work at an institution that has both.

Friday, March 24, 2017

Construction day: Part 3

Today was a long day. I've been on my feet for most of it, building lids to go on the larval traps I'll deploy this summer. Not many people realize how much construction science can involve, so I'll walk you through the process.

Not exactly candy: my PVC lids super glued to neoprene
For the lids, I needed a sturdy plastic that wasn't too bulky, so I pulled out some PVC sheet I had left over from an earlier project. I ordered a special hole saw (it drills giant holes) and set to work. I was actually using the hole saw for the opposite of its intended purpose, because I wasn't concerned with the holes themselves; I wanted the discs the hole saw would punch out. I headed to the shop to use the drill press, and two hours later, I had close to 90 little discs, the exact diameter of my larval traps.

Step two. The PVC alone won't be enough to seal the traps, so I needed something a bit more waterproof. I super glued neoprene to the PVC discs - actually, more accurately, I super glued the PVC discs to a sheet of neoprene, remarked to myself that they looked like candy buttons on paper, and cut them out. I drilled holes through the center of the discs, then threaded rubber bands through the holes. The rubber bands will hold the lids in place so my traps are sealed while they're being deployed, then pull the lids off after about a day. I want the lids to open once the samplers have settled into their places so they can start catching larvae.

Larval trap lid and galvanic release setup
To make sure the lids open at the right time, I'm using what's called a galvanic release. They're most commonly used by fishermen to keep floats underwater until the fisherman is ready to come back. The release is made of metal that corrodes at a known rate in seawater. The size of the release determines how long it holds together, and in my case, the releases last about a day. That's just the right amount of time for my samplers to be deployed and get settled in place before opening.

The design I'm using is modified from one my Ph.D. advisor came up with. Essentially, the trap lids are held on by tightly-stretched rubber bands, and when the galvanic release corrodes through, the rubber bands are no longer connected and the lid flies off. I actually tested the lid setup off of the dock near my lab to make sure the lids would open but stay connected to the trap housings, and it worked.

Friends, I am tired, but it's nice to see my construction projects coming together. Slowly but surely, everything will get built!

Wednesday, March 22, 2017

Like a helix

For some reason, I always have a hard time leaving the lab. My days don't just end - they taper off. I'll get to the end of one task, feel the sense of accomplishment, cross it off my list, then scan around my office and inevitably find something else that needs to be done. I'll spin around and shuffle little items off of my list until my brain is convinced I can go home.

I spent a lot of time on the computer today, analyzing a dataset from last summer. I've told you about these data before - they concern the behavior of oyster larvae in different water conditions, and I'm using a code-based statistical program called Matlab for the analysis. To be honest, one of the best parts of this particular project is getting to work together with the other scientists involved. The data were collected by my advisor, Lauren, and an intern in her lab last summer, Erin. Some of the codes for the data analysis were written by Lauren's former Ph.D. student, Jeanette, and of course, some are written by me. I've gotten to know Jeanette and Erin through the process of analyzing the data, and it's actually interesting to notice we each have our own coding style. I could probably tell you which one of us had written a particular code within 2 seconds of opening the file.
An example of helical swimming behavior in an oyster larva

Today, I was using one of Jeanette's codes to detect what's called helical swimming behavior in the larvae. Sometimes, the larvae will swim in a spiral, moving up or down and exploring their environment as they go. Look at the figure to the right here for an example. The actual track the larva took is in the left panel, in blue. In reality, the larva was swimming in a helical pattern - a spiral - but since the camera can only see in two dimensions, it looks like it's just swimming back and forth. This actually works out well because the sinusoidal patterns in its horizontal velocity and position (the right two panels) help us detect helical swimming patterns.

Helical swimming is important because it's an exploratory behavior. In some water treatments, larvae may be exploring more than in others, which means they could take longer to find a place to settle and metamorphose to become an adult.

The code worked beautifully. I am continually amazed at what code-based programs can do - the possibilities are pretty darn close to infinite - so I'm glad that I'm finally learning the skill. Got to admit, I feel a little like that larva, though, spinning around my office, finding little tasks that need to get done. Ok, time to go home.

Thursday, March 16, 2017

The cleansing wind

"The wind blows loudest when you've got your eyes closed"
- "Organs" by Of Monsters and Men

Me on the Polarstern pilot deck, 2012.
There is something about cold wind that makes me feel clean. I breathe it in, sucking icicles deep into my lungs, and somehow, everything vanishes. I feel refreshed, calm, and hollow.

I remember when I first discovered the effect that cold wind had on me. It was 2011, and I was on R/V Polarstern, at 78° N in the Arctic. Whenever I had a break from the lab, I would go outside on the pilot deck - the highest accessible point on the ship, essentially the roof of the bridge. I would face the bow, into the wind, and relish the piercing cold penetrating my lungs. It was best if we were steaming.

Today, when I went out to check my monitoring plates on the WHOI dock, I couldn't help but stop for a second and notice the wind. It's been wicked this week - we actually had a nor'easter on Tuesday - and the air is the coldest it's been all winter. I walked to the end of the dock and closed my eyes. Taking as deep a breath as I could manage, I welcomed frigid fingers of air into my lungs. I was cleansed.

It's been a full week. Between building samplers for a cruise this summer, getting feedback from colleagues on my succession study, analyzing a dataset in Matlab, and applying for grants for future projects, I have a full schedule. Don't get me wrong - I prefer to have multiple projects going at once - but it's also important to relax. To find peace in the midst of chaos. To stand on the dock for a second and listen to the wind.

Wednesday, March 15, 2017

Construction day: Part 2

Friends, I am back at it, building samplers for the cruise I'll go on this summer. No matter how simple the design, building samplers always involves a crazy number of steps. My lab actually looks like a disaster zone right now, with raw materials spread all over and two large bins waiting to be filled with the final products.

Connectors I built to attach my samplers to
oceanographic moorings.
I had an interesting challenge when it came to one connector. I've been communicating with the lead technician responsible for the moorings my samplers will go on, and he suggested we use thin PVC to connect my samplers to the mooring lines (see photo). It was all well and good until I realized I had to cut slits into the PVC for the cable ties. How in the world is one supposed to cut 1/2" (1.3 cm) slits into 2" (5 cm) segments of PVC without having an accident? Stay away from power tools, for a start.

I ended up using a soldering iron and just melting my way through the PVC. It worked wonderfully, except that the tip of the soldering iron got gummed up with the melting plastic. I kept a thick rag on hand and wiped the soldering iron every few minutes - easy enough.

Slowly but surely, my project is coming together! I just have a few more steps before the samplers are complete and ready to ship. Onward!

Tuesday, March 7, 2017

Construction day

"You see, Kirstin, the great thing about biology is that you learn a lot of random skills. For example, I'm getting pretty good at plumbing." - one of my professors in college

That is a LOT of PVC fittings!
Ask anybody, and they'll tell you they want a job in which they're not doing the same things over and over again every day. That's the dream, right? I'd be curious to see how many people actually achieve it, but I can tell you with certainty that I do not do the same things at work every day.

For example, yesterday. There was a giant box delivered to my lab, full of PVC fittings in various shapes. I was very excited to see the box arrive. The fittings are the raw materials for my latest project, constructing housings for samplers I'll use over the summer. The housings were designed by my Ph.D. advisor for deploying samplers in the deep sea. The arrival of my PVC fittings meant that I could steam ahead with construction.

In addition to the fittings, I had ordered myself 5, 10-foot poles of PVC. I actually spent the majority of the day in the Biology Department workshop, cutting the PVC into 2-inch segments on the chop saw. The short segments then served as connectors between the fittings, and voila! A useful product.

I'm proud of the skills I've amassed in the last few months, especially when it comes to construction. There is never a boring day as a biologist!