Sunday, November 11, 2018

The visitor

I came down the stairs to find him at the kitchen table. He looked every bit the professor, with a gray sweater over his collared shirt and glasses on his face. He leaned forward in the chair as he examined a scientific paper on his computer screen. He was deep in thought, immersed in the manuscript.

I had seen him like this countless times before, except that it had always been at his kitchen table, not mine. I smiled to myself at the memory of afternoons spent at his house in Stavanger, as we pored over my data, shaped it like clay, and turned it into a meaningful paper. I remembered how hard I had to work to keep up with him, and I reflected proudly on how far I've come since then.

My dear friend, Andrew, came to visit me this weekend. He was my advisor when I lived in Norway, and more than anyone else, he's the one who taught me how to think like a scientist. He played a huge role in my intellectual and personal development during my PhD, and he served on my committee. Since my defense, my relationship with Andrew has shifted, and I refer to him now not as my advisor but as my mentor. Sometimes I add the words "surrogate big brother."

Andrew used to work with the group I'm currently in, the Mullineaux lab, at WHOI, so he was able to reconnect with old colleagues during his visit. We went on walks around town and to the beach. We attended an orchestra concert. We talked about science for hours on end and agreed we needed to write a grant proposal to work together again.

It was so good for me to spend time with Andrew. He constantly reminds me to slow down, take time off, and be a human. In fact, this weekend with him felt like the first true mental break I've had in months. Just being around him makes me relax, and I could listen to him talk about science for days on end. Andrew is in my mind an innovative scientist who is unafraid to challenge old, entrenched ideas. Beyond that, he is an honest, loyal, and caring person who builds me up. I am so grateful for his friendship and glad that we got to spend a fulfilling weekend together.

"You have my permission to use all three of those photos on your blog." - Andrew K. Sweetman

Tuesday, November 6, 2018

Test run

Today was a productive day! I spent most of it upstairs in a laboratory for molecular biology, learning DNA extraction methods from Hanny. Since our return from Palau, she defended her thesis and received her PhD (congratulations, Dr. Rivera!). Now that the dust has settled, it's time we start processing all of the coral samples we collected.

Our first step was to test out two different methods for DNA extraction. Hanny's advisor graciously offered us some DNA extraction kits that were surplus in her lab, but the kits were a bit old and may have lost their effectiveness. We ran an experiment: using old samples from Hanny's PhD work, we extracted DNA using two different types of kits and then used a technique called electrophoresis to see if the extractions had worked (more on that later). It's highly convenient that several companies make standardized kits for DNA extraction, but I had to laugh at the instruction manuals. One of the extraction kits was meant for soils, while the other was meant to be used with animal tissue and had specific instructions for extracting DNA from rodent tails! Most of biology research is done using model organisms like fruit flies or mice, so the DNA kit market is driven by their demands. Obviously, the invertebrate animals I work with are not standardized models and probably never will be. There is no DNA extraction kit designed for corals, so the closest we can rodent tails.

Most of our day was spent standing at the lab bench transferring reagants between vials with a micropipette. We then spun the vials in a centrifuge, a machine that uses centrifugal force to separate substances with different densities. Pipette, centrifuge, siphon off the liquid, repeat. Molecular biology is hard because it involves numerous monotonous steps, and you don't know if you've succeeded until the very end.

The results of our DNA extraction experiment
Once we had completed the DNA extraction protocol, it came time to evaluate our success using electrophoresis. This technique uses an electrical current to separate strands of DNA by size. A sample of DNA is loaded into a gel with a certain pore size, and as the strands migrate through the gel, small pieces migrate faster and large ones migrate slower. For our purposes, we were hoping to see a single, dark band of DNA, indicating a large piece - the whole genome - and a successful extraction.

You can see the results to the right here. The two rows of whitish rectangles are the wells where we loaded our samples, and the black stripes are the DNA. The tiger stripes on the very left are a DNA ladder, a series of fragments of known size that can be used as a standard. We used the ladder as a positive control - we knew there was DNA in the ladder, so if it didn't show up, something was wrong with the electrophoresis.

As you move across the picture, each column represents a different sample. On the top row, you see four dark bands. The bands are very close to their respective wells, indicating they didn't travel very far - that means they hold large pieces of DNA. That's what we were looking for! The four samples on the top were extracted using the animal tissue kit, so that kit still works! On the bottom row, you see only very, very faint bands close to the wells. Faint DNA means an ineffective extraction. The kit we used for these bottom samples was really designed for soils, so it's not surprising that it didn't work.

Moving forward, we will use the animal tissue extraction kit (rodent tails!), and we're very grateful to Hanny's advisor for offering her surplus. I'm excited to get started with the analysis!

Friday, November 2, 2018

In print

Dear friends, I am proud to announce that another one of my scientific papers was published today. This manuscript concerns oyster larvae swimming behavior, focusing specifically on why and when larvae swim in helices. The lead author is a former Mullineaux lab intern, Meghan. During the summer of 2017, she conducted two experiments on how oysters behave when exposed to different concentrations of food or a chemical settlement cue, and this paper presents her results from those experiments.

This is the first time that a student I have helped advise produced a paper of her own, so I am very proud of Meghan! It's a huge accomplishment for an undergraduate to publish a paper and even more so as lead author. She did a great job!

You can find the paper here, in the Journal of Experimental Marine Biology and Ecology:

Sunday, October 28, 2018

Clear blue

I lay on my stomach, put my face in the water, and paddled forward with my feet. One bright pink fin was attached to each of them. With the zipper of my wetsuit open, I could feel a refreshing stream of water along my back, but my arms and legs were protected by the tight, clingy neoprene. On the ocean surface were plentiful clumps of Sargassum, a tuft-like brown alga that floats. I spread my fingers wide and felt the rough, weedy web scrape against my palms. I noticed how much more abundant the Sargassum seemed from below - hundreds of clumps floating on the glassy mirror of the ocean surface.

With my body prone and my eyes directed downward, I could see all the way to the seafloor. Dark brown and black formations dotted the rock, which coalesced into a reef about a hundred yards in front of me. I knew the corals were more colorful than they seemed from up here, having just swum past them at the end of my dive, but I still marveled that I could see them from the surface. The water was the clearest I have ever experienced. Thick, columnar rays of sunlight converged on a point beneath me, penetrating all the way to the seafloor at 50 feet deep.

I bent my knees and lifted my head. The water column was an intense blue - not bright or dark, but concentrated. Blue blue. At the edge of the reef, it grew dimmer as the seafloor dropped away and metamorphosed into the Grand Cayman Wall. About halfway to the ledge was a single yellow rope extending through the water column, book-ended by an anchor bolt in the rock and a spherical white buoy on the surface. Two divers held onto the rope with one hand each. They were positively covered in gear, with complicated, tube-infested rebreathers on their backs and a total of six additional tanks clipped onto the metallic frames. They watched their dive computers with undivided focus, like watchmakers observing their handiwork. I wanted to get their attention but restrained myself, unwilling to interrupt the last moments of what I was sure had been very intense training.

And so I floated on, having earned my own technical diving certification just an hour earlier. My week of hard work had paid off in the form of a decompression diving qualification. The class stretched me, but with my newly-honed skills, my scientific studies will be less restricted - I can dive deeper, stay longer, and explore further.

I had earned my moment of serenity, paddling through the Sargassum, watching the love of my life hang in the water column just 20 feet below me. Life is good.

Thursday, October 18, 2018

Anything-can-happen Thursday

I love the American comedy The Big Bang Theory. It's about physicists at Caltech, and as you may expect, it's a very nerdy show. One of the main characters, Sheldon, is on the Autism spectrum and is notoriously rigid. In one episode, his friends try to shake up his routine by declaring "Anything-can-happen Thursday" and replacing Sheldon's typical Thursday pizza dinner with Thai food. It does not go over well.

Friends, I'm hope you're not eating pizza, because today is Anything-can-happen Thursday.

Heart-shaped bivalve larvae, magnified 50x
I'm working on processing the samples I recovered from the Josephine Marie wreck as part of my shipwreck project this summer. You know - the one where I went diving on shipwrecks in Stellwagen Bank National Marine Sanctuary to see whether they could serve as stepping stones for invasive species. At each wreck, I deployed fouling panels and larval traps and collected samples of the adults that were living there. I recovered the fouling panels and larval traps from two of my sites in August this year, but the weather was never calm enough for me to make it to the third site.

Well, I'm currently processing the larval samples from the Josephine Marie wreck, and I had a very Anything-can-happen-Thursday moment.

As I looked through the larval sample, I kept seeing heart-shaped shells. They were bivalves like clams or mussels, because they had two symmetrical shells attached at an umbo - a very standard morphology. I assumed they must have been a species that lived buried in the sediment because I didn't remember seeing bivalves on the shipwreck. I sorted them without thinking much of it.

Juvenile "limpets" from my trap, magnified 50x
But then I noticed something else in the larval sample: a juvenile limpet. It's not uncommon for small juveniles to get washed off of their substratum and into a trap, but what actually caught my eye was the larval shell embedded in the juveniles. When shelled animals like snails, limpets, and clams settle, they grow their new shell as an extension of the old one, so the shell they had as a larva remains. The more I looked at the limpet, the more the larval shell looked heart-shaped, just like the larvae I had seen.

But bivalves don't just transform into limpets. They're two separate things. Bivalves are things like clams, and limpets are more like snails. One does not simply become the other.

I took a closer look at the juvenile "limpet." I turned it over. I zoomed in using the microscope. I adjusted the light. And I started to notice something I hadn't seen before - a thin shell on the underside of the "limpet." It had a small hole in it. This wasn't a limpet at all, I realized, but rather a bivalve with a two very different shells.

A larger juvenile jingle from my fouling panels. The larval
shell is the small yellow spot on the apex.
I pulled out a reference book from my advisor's collection. Marine invertebrates of southern New England and New York. I flipped through the pages until I reached the bivalves. I scanned for one that had two different shells, one hearty and translucent, the other clear and with a small hole. And there it was. Anomia sp., commonly known as a jingle. They're bivalves that live attached to a surface with their translucent upper shell exposed to the water and their thin lower shell facing the substratum. The small hole in the lower shell allows threads to pass through that anchor them to the substratum.

And then it dawned on me. The jingles in my larval trap were not the only jingles I had captured. Larger juveniles had colonized my fouling panels, but I had incorrectly identified them as the limpet Crepidula sp. Now I know that they are jingles.

Altogether, I had 469 heart-shaped jingle larvae in my sample, and another 21 small juveniles. They were the single most common species. Even though I don't remember seeing them on the wreck, I wasn't focused on looking for small bivalves at the time, so I may have missed them. It's an interesting species to be aware of for future studies - maybe they could be a good model species for some of my scientific questions!


"I would like to die on Mars. Just not on impact."
- Elon Musk

I love fall in New England. The air is crisp, the leaves are crunchy, and the sunshine feels comforting instead of hot.

I’m back at home now, and I used the chance to finish up my field project from this summer. Weather prevented me from making out to my third field site, the wreck of a fishing vessel called the Patriot, to recover my samplers earlier in August and September, so I scheduled a day on the dive boat Dawn Treader to try again. Unfortunately, the weather prevented me from reaching the Patriot all over again, but I was able to use the day to explore a new site closer to shore.

We went to the wreck of the Mars in Cape Cod Bay. I had never been to this site before, and I wanted to see the wreck for myself. At first, it would seem that there’s plenty of information available about wrecks in Massachusetts, but a closer look reveals that this pre-existing information is biologically sparse. It’s easy for me to find out what year a ship was built, how many hands were on board, why it sank, and how intact it is, but other divers and shipwreck enthusiasts utterly ignore the animals living on the wreck. To find out what’s there, I have to visit the wreck myself. I packed my gear, picked up my dive buddy for the day, and went to the site of the wreck.

To be honest, the Mars was a really tough dive for me. The cold water shocked my system, which had acclimated to tropical temperatures while in Palau. It was dark and turbid, so visibility was restricted to the 5 feet in front of me. I was also disoriented by nitrogen narcosis, which is a cognitive fogginess that results from breathing the gas at high partial pressure. My brain was functioning more slowly than normal, and even though I knew I was off, I had no way to fix the problem at depth.

Metridium senile on the Patriot wreck. Photo by Jim Guertin.

We swam around a little and eventually found the wreck. The bow was still intact, standing vertically above the seafloor, and as I ascended up the metallic wall, my head began to clear – just a small change in depth made a huge difference for my narcosis. All over the bow were hundreds of plumose anemones, known scientifically as Metridium senile. There’s a picture of one here, which was taken by another diver on a different wreck. The species is really gorgeous, and it has been on every shipwreck in New England that I have visited so far. I think the anemone may be pre-adapted to thrive on shipwrecks because it can disperse long distances and form populations from just a few individuals.

Even though it was a tough dive on the Mars, this project has taught me several important lessons. I’ve gained valuable experience with deep offshore diving in cold water – a difficult set of conditions that requires regular practice to master. I’ve learned the ins and outs of WHOI regulations for diving and boat charters. I have made key observations of species distributions on shipwrecks and started formulating hypotheses to pursue in future projects. Overall, it’s been a valuable learning experience, but I am glad to finally call my field season finished. Autumn is rolling in.

Tuesday, October 9, 2018

From the mixed-up files of Mrs. Basil E. Frankweiler

Right now, I am sitting on a patch of grass in front of PICRC. The air is completely still, and it’s dark except for a few lights in the parking garage and the security guard’s station. I can hear some sort of insect clicking in the night. It is calm.

I can’t help but think about one of my favorite books as a child, From the mixed-up files of Mrs. Basil E. Frankweiler. It’s about a brother and sister who run away to the Metropolitan Museum in New York City. By day, they stow away with school groups on tours and learn everything they can. Then in the evening, they hide in the bathrooms while the security guard does his rounds, and once everyone has left for the night, they have their run of the museum. They bathe in the fountain, research in the library, and sleep in an antique bed. Elementary-school Kirstin thought this kind of life – living freely in an institution of knowledge – sounded glorious.

Got to admit, that’s the way PICRC has felt every evening this trip. When the full-time staff go home for the night, it’s been just Hanny and me. We have our run of the lab, the tank room, and the dorms. We can gawk at the corals and play our music and work at whatever pace we please. It’s felt freeing and childlike and glorious. Tonight, I relish that feeling again, as we are the only ones left at the station. With a sense of calm and completeness, we await our ride to the airport.

One of my favorite moments this trip was when we finished our sampling at our last site. We had been underwater for hours on end in our wetsuits, dragging heavy tools and long mesh bags. Once the last sample had been processed, we both had this incredible moment of relief and a strong urge to go for a swim. We stripped off our wetsuits and jumped in with only our swimsuits – no neoprene, no SCUBA tanks, no hammers, no sample bags. Just smooth, salty water on our skin.

I kicked my feet and spun around in the water. I was surrounded on all sides by steep rocky cliffs covered in greenery. Tiny triangular waves peaked and then receded on the sea surface, which was deep crystal blue in the late afternoon sun. The air was completely still except for the distant calls of unfamiliar birds. It was blissful.

I am very proud of how well this trip has gone. Hanny and I undertook a lot for just two people, and we had no major hang-ups. We have worked very hard for the past two weeks, and we have worked very well together. In fact, we both agree that we would love to work together again.

My friends, I leave you now with memories of Palau’s rock islands and the beautiful corals they hold. We are headed home. It's been a very successful trip!