Sunday, July 30, 2017

Noticing beauty: part 3

Eel Pond sunset

Eel Pond fouling fauna

Seen in Falmouth Heights

Sailboat on Vineyard Sound

Beach rocks in Falmouth Heights

Botryllus schlosseri overgrowing Botrylloides violaceus

Friday, July 28, 2017

Cathedral of the deep

"And it's peaceful in the deep
Cathedral where you cannot breathe
No need to pray, no need to speak
Now I am under all...
And the arms of the ocean are carrying me
And all this devotion is rushing out of me
And the crashes are heaven for a sinner like me
But the arms of the ocean delivered me"
- "Never let me go" by Florence and the Machine

I love diving under the WHOI pier. It's where I've done most of my training dives, and it is heaven for a benthic ecologist. The pier is supported by a series of pilings, all of which are inhabited by invertebrates. Sponges and anemones and ascidians of all kinds. It's goregous.

Benthic fauna on the side of the instrument well
We always start dives from the instrument well. It's a rectangular opening in the pier, sheltered from waves and boat wake. We jump into the water from the side of the well and then grab hold of a descent line - just a vertically-hanging rope that leads to the bottom. The line actually follows one of the pilings, so I get a full depth profile of the fauna every time I swim down or up. From the surface down to about 9 m (30 ft), the most common organisms are Styela, a club-shaped solitary ascidian, and Didemnum vexillum, a peach-colored invasive, colonial ascidian. In fact, most Styela are covered in Didemnum. You can see the peach-colored, club-shaped forms just below the water line in the photo at right. Below about 9 m, though, those two species disappear and are replaced by small red anemones and a yellow sponge. On the seafloor itself, large flounder, massive conchs, and the common sea star Asterias rubens dominate.

Once we reach the bottom of the descent line, we are free to swim under the pier. It's hollow down there, and the water is interrupted only by the pilings and a few random objects. There are guide lines connecting the pilings, so in case you get lost, you can follow the lines back to the instrument well. The random objects on the seafloor can be used for orientation, too. For example, a lobster trap and an ammunition box rest on the sand just west of the descent line, and an old cart lies to the south of it. A pipe on the seafloor marks the edge of the pier, and if you reach the fake plastic hawk, you've gone too far. Everything is covered in benthic fauna, but still the pilings are my favorite.

Pilings supporting the WHOI pier
In a way, the pier reminds me of a cathedral. The pilings are the pillars holding up the grand vaulted ceiling. Every surface is covered in elaborate designs. It is peaceful, quiet, and meditative. When diving, you actually have a reflexive response that causes you to calm down. It's called the Mammalian Diving Reflex, and everyone from humans to whales do it. When your face is underwater, your heart rate slows, your peripheral blood vessels constrict, and your breaths naturally lengthen. To me, there is nothing better than being underwater, breathing slowly, swimming gracefully, surveying benthic fauna. It is relaxing and scientific and wonderful.

Wednesday, July 26, 2017

Born in the dark

"I was born in the dark
But it wasn't last night"
- "Born in the dark" by Doug Stone

"Oh, it's just her!" Nicole called in relief, opening the door wide for me. I stepped inside WHOI's Shore Lab to find the two interns hard at work. A cart filled with computer equipment and note sheets stood in the wide entrance hall. Thick cords ran from the cart through a low opening in the wall into the cold room. As I examined the scene, Meghan emerged from the cold room, wearing shorts over her leggings and a headlamp on her head. Dressed for battle, I guess.

Meghan pipetting oyster larvae for a new replicate
Meghan's research this summer is all about oyster larvae behavior. She's building on work that had been done last year and which I am in the process of analyzing. She's looking at swimming behavior of larvae exposed to a chemical settlement cue and also trying to discern the reasons why larvae swim in helices. It's very cool work.

The experimental set-up at WHOI's Shore Lab
When it was time for a new replicate, Meghan proudly showed me her experimental set-up in the cold room. The climate-controlled room was a uniform temperature and completely dark except for Meghan's headlamp (larvae respond to directional light cues, so you have to exclude as much light as possible). A 50mL flask with a specific concentration of the chemical settlement cue sat on a small table, surrounded by cameras and lights and a vice to hold a pipet. Carefully, Meghan sucked up a pre-set number of oyster larvae into the pipet and held it over the flask. "Run!" she shouted, "Record!"

Outside in the hall, Nicole responded to Meghan's commands by starting the camera's recording software. By the time Meghan and I re-emerged from the cold room, there were tiny black dots swimming up and down on the screen - larvae.

Nicole manning the computer station at Shore Lab
I was impressed to see how well the two interns were handling the experiments. Larval biology is difficult because your study organisms are young and small and sensitive. Experiments have to be run when larvae are exactly the right age, so you have to act quickly. In Meghan's case, she needed larvae that were competent to settle, about 2 weeks old, and once they were competent, all experiments had to take place within 24 hours. Thankfully, she got everything prepared a week in advance and asked Nicole to help, so once the call came that the larvae were ready, everything ran smoothly.

I'm excited to see Meghan's data once all the experiments are finished! There should be very cool results!

Friday, July 21, 2017


It was a busy day at the pier. Both Atlantis and Neil Armstrong were in port; a plankton research group was testing out a new glider; a part of the dock was being rebuilt. Trucks and cranes and people moved about on the bustling pier. Beeping and honking and shouts and loud bangs were heard all around.

Pier panorama. Neil Armstrong is to the left, Atlantis to the right.
A ctenophore, photographed by Nicole
Pittoors at the WHOI pier. 
Even the ocean was busy. As my intern and I knelt on the floating platform, reattaching fouling panels to their PVC backing, we couldn't help but notice the activity in the water. Tiny specks littered the surface, presumably the larvae of a species that had recently spawned. A large school of green minnows rushed back and forth, picking off the larvae as they swam. Two large, pink-and-blue fish swam slowly beneath, gliding and glinting in the light.

Strings of green eelgrass and brown puffy Sargassum floated on the sea surface, and then we spotted the star of the day: ctenophores.

Also known as comb jellies, ctenophores are fascinating creatures. Their bodies are made of mostly water, and they drift in the ocean with little control over their whereabouts. They have these rows of cilia called combs, though, which are totally unique to ctenophores. The combs can ripple and break up waves of light and look iridescent - they're very beautiful animals. It was a great day at the dock and another good week for my dock study!

Saturday, July 15, 2017


Well, friends, it's been over a week since my last post, so I suppose I should catch you up on what's been happening in the lab.

The fouling panels in Eel Pond are beginning to show very promising results. (Ok, let's be honest, they've been showing good results for a while.) There are now obvious, macroscopic differences between panels with different removal treatments, and I'm getting very excited about my data. (I love when my fouling panels have significant differences!)

Check out the photo below. These are three fouling panels from three different treatments, deployed right next to each other in Eel Pond. You can see right away how different they are. The panel on the left is in the "remove nothing" treatment, and you can see that a large percentage of the panel is covered by Botryllus schlosseri - that's a black ascidian that grows in sheets. However, there are also a number of yellow tree-like bryozoan colonies on the right side of the panel. It's a good mix.

The panel in the middle shows a very different community, because this panel is in the "remove ascidians" treatment. As you can see, it is dominated by those tree-like bryozoans, but it also has some flat, encrusting bryozoans - the orange circles at the top. The panel on the right is in the "remove hydroids" treatment, and it again is very different. It has some of that black colonial ascidian, Botryllus schlosseri, in the bottom right corner, but it's mostly dominated by Ascidiella aspersa, a solitary ascidian. Those are the large, blob-like animals covering most of the panel. I have no idea why a fouling panel that had its hydroids removed would come to be dominated by a different species than a panel with nothing removed.

Three fouling panels in different experimental treatments in Eel Pond.
For the record, there are four other "remove hydroids" panels in my experiment, and not all of them are dominated by Ascidiella. I think there's an element of randomness in my experiment: some panels were just colonized by a species that grew and took over.

My results are getting ever more interesting as the summer goes on. I look forward to analyzing the data!

Saturday, July 8, 2017

Arts and crafts: part 2

(Former) fouling panel inhabitants
"Ooh, it kind of looks like pasta salad! Maybe like a Mexican salad, you know, with black beans and yellow corn. It doesn't look appetizing though."

My intern was standing over the lab bench, looking at a pile of ascidians and bryozoans I had just pulled off of a fouling panel. I gave her a sideways, confused look. Pasta salad, really?

We had been working all day, pulling invertebrates off of fouling panels, leaving only strategically-chosen individuals behind. We were setting up an experiment in Eel Pond to parallel one we set up at the WHOI pier two weeks ago. For both experiments, we want to find out how the first species to settle on a fouling panel and dominate the community influences other species that might settle. I suspect that the first dominant species inhibits other organisms from recruiting to the panels, either by consuming their larvae, outcompeting them for food, altering the flow of water over the plate, or just taking up space. To figure out if inhibition is happening and if so, which one of the above scenarios is true, we outplanted plates with live animals and with mimics - non-living structures with similar shape and texture. 

The experimental panels, randomly arranged on a PVC
backing and ready for deployment in Eel Pond. The top row is
not part of the experiment. You can see panels with live
Botryllus, some with globs of sealant, some with flat sheets
of sealant, and blank controls. 
The experiments at both sites are the same in principal, but the main difference is which species dominates. At the WHOI pier, hydroids covered the panels, but in Eel Pond, it's all about the ascidians. Botryllus schlosseri, to be more precise. It's a colonial species that forms thick, squishy mats and can easily overgrow other organisms. We removed all species except Botryllus from some fouling panels, and on others, we replaced the living animals with mimics. 

How does one mimic a colonial ascidian species? We used silicon aquarium sealant because it has the same basic texture as ascidians and can be easily smeared on the panels. We used thick globs on some panels to imitate the topography of Botryllus colonies and flat sheets of sealant on others just to take up space. It will be interesting to see if there are any differences among the treatments at the end of the summer!


"I am sorry for the trouble I suppose
My blood runs red but my body feels so cold
I guess I could swim for days in the salty sea
But in the end the waves will discolor me"
- "Organs" by Of Monsters and Men

Friends, I haven't told you this yet, but in addition to my experiments, I'm learning how to SCUBA dive this summer. It's a skill that will be highly advantageous for my research. As a diver, I'll be able to reach a whole new set of habitats, filling in the gap between shallow docks and the deep sea.

The training for scientific diving is much more intense than for recreational diving. I started by taking a course on diving physics, physiology, and basic skills. Classroom days alternated with practice in the pool, and after a month, I've finally moved up to open-water training. Last Friday, my dive buddy and I had a unique challenge. We had to disassemble and reassemble a flange underwater, to simulate a working scientific dive. The task was simple but actually quite challenging, because everything is slightly more complicated underwater. The visibility was very low, and at 25 feet (8 m) depth, it was actually pretty dark. Red and orange wavelengths don't penetrate far in the ocean, so everything looks bluish green at depth. My buddy and I also couldn't speak to one another, so nonverbal communication was key. We had to maintain position in the water column and be extra careful not to drop any pieces, because hardware sinks immediately.

I have to admit, I was pretty proud of how well we worked together. It took us the full alloted time to complete the task, but we didn't drop anything!

The video below was shot by our dive supervisor, Giorgio. It shows my dive buddy and me getting ready to remove a rubber gasket from one side of the flange. We had to rotate out the rubber disc and then secure the two metal sides with a bolt. As you can tell, everything takes longer underwater. I'm the one with the sparkly white gloves!

Thursday, July 6, 2017

The day the hydroids died

"Bye, bye Miss American Pie
Drove my Chevy to the levee but the levee was dry
Them good ol' boys was drinking whiskey and rye
Singing this'll be the day that I die
This'll be the day that I die"
- "American Pie" by Don McLean

Friends, ecology is full of surprises. I never thought that hydroids would dominate the fouling community at one of my study sites. I never thought that my experiment would start to look like it was covered in shag carpet from the 60s. I never thought that hydroids would hold the #1 position for so long. And I certainly never expected them to die all at once.

Dead, headless hydroids on a fouling panel being examined
under the microscope. Check out the clump at left, then
compare to live hydroids with pink heads.
It's not because of something I did (trust me, that was my first panicked thought). Almost overnight, all the hydroids have disappeared from the WHOI pier. Not just from my experiment, but from the walls of the instrument well, the lines from which instruments hang, my monitoring plates - everywhere. Dead. Headless. Nothing left but thin, rubbery stalks.

My best guess is that it's the temperature. The water around Woods Hole has been warming rapidly over the past few weeks, and considering that the hydroids started settling back in January, maybe they can't handle the summer heat.

The WHOI pier has actually started to look more like Eel Pond as the hydroids die off. Ascidians are recruiting to the empty space on the panels, and my "remove hydroids" plates are already almost covered by the squishy creatures. This shift again supports my temperature hypothesis because Eel Pond has been warmer all along. Maybe the WHOI pier is just now catching up, both in temperature and recruitment.

In case you're wondering, I am recording water temperatures at both sites. I have loggers out with my experiments, so I'll download the data at the end of the summer and compare patterns in water temperature to what I'm seeing in the recruitment. I'm glad that I have such clear patterns, both between sites and over time. This project just keeps getting more and more interesting!

Monday, July 3, 2017

Chainsaw carving: part 3

Every data analysis has its ups and downs. My analysis of oyster larvae behavior has been mostly up recently. But after about 6 months of work, the analysis still isn't quite finished.

In a meeting, one of my collaborators on the project pointed out some nonsensical numbers in the dataset. She asked me to take another look, and I discovered that my code was miscounting the number of larvae entering each experimental flask. You'd think that counting the larvae would be the simplest task, right? It's surprisingly difficult, because no single set of parameters applies to all experiments without error. There was no way to automatically count larvae.

So I started over and did it manually.

Friends, this is just how it goes. In fact, I don't think I can name a single scientific paper I've published for which I haven't had to start over at least once. Every analysis requires at least one trip back to Square One.

The good news is that now the data look a lot cleaner, and we're mere steps away from finishing the analysis. To continue my chainsaw metaphor, I haven't scrapped my sculpture; I've hollowed it out. I have used my chainsaw to carve large swaths of wood from the inner regions of my creation. Wood chips flying, I have sliced and dug and carved until the interior was empty. It began as a tree trunk, and my sculpture is almost done.