#PhDlife: It doesn’t always involve diving

Hey everyone,

Happy 2018 and thanks for stopping by! I hope you had a wonderful holiday! I was lucky enough to go home for the holidays and spend quality time with my family and some great friends (some of whom I haven’t seen for several years)! I spent my holiday baking (focaccia, cookies, sourdough bread), playing the violin, laughing, singing, and building legos with my young niece and nephew. My time at home was relaxing – exactly what I needed in order to replenish my energy for a season of lab work on the Cape.

This leads me to my next topic . . . I am not always in the field! I spend most of my time completing lab work, analyzing data, and writing about it (in the form of publishable units/ scientific manuscripts)!

Over the next couple months (I have given myself March 2018 as a loose deadline), I need to conduct DNA extractions on samples that I collected last summer from the U.S. Virgin Islands (see my recent instagram time-lapse video!), prepare sequencing libraries for these samples, and I also need to finish processing (eluting, drying down, and re-suspending) SPE cartridges that I collected this past November in Cuba and the U.S. Virgin Islands.

Additionally, over the next couple months (the spring semester), I need to:

  • edit and submit a manuscript
  • resume writing another manuscript
  • debug r-code and train myself how to use an r-script to analyze a new type of data (anyone know how to coerce a data.matrix or a list into a special r- object class?)
  •  prepare for another week of field work (taking inventory of the supplies we have, washing many bottles, booking flights and arranging travel)
  • schedule a dissertation committee meeting
  • hold a dissertation committee meeting
  • prepare a presentation for my department seminar (!!!)
  • take two classes

There are quite a few items on my massive PhD to-do list (which is not comprehensive and will change as time passes by) and they are representative of the responsibilities, tasks, and duties that I have upheld and completed over the course of my PhD experience.

And I want you to know that I still will have fun. I’ll be singing and dancing to music in the lab, I’ll be spending time with some great friends, I’ll be baking, I’ll be walking, and I’ll be living and learning!

Thanks for reading!

DNA extractions!



Research cruise and field work withdrawal

Hey everyone,

I am writing to you from the frozen tundra of Cape Cod. Winter has definitely arrived to the North east (and most of the East coast) since I have returned from field work in the Caribbean and I’m not going to lie, the weather has made it hard for me to transition back into the swing of things!

I wanted to take some time to write about a topic that has been on my mind since I returned from field work.

I first noticed a mournful and solemn feeling on the last day that I was on the Alucia. I was sitting in the crew mess with my sore left foot propped up on the seat in front of me and wrapped in ice (remember . . . from my bunk bed incident?) and I was alone because everyone else was preparing for the boat “demobe” (demobilization: essentially getting all of our science equipment and gear off of the boat and shipping it back to original destination).

As I sat there, I was mentally flipping through my personal cruise highlight reel, laughing and smiling to myself as I remembered all of the wonderful and specific experiences and moments that I had enjoyed for the past couple weeks. There was our initial travel down to the Alucia and our last minute errands (running around the local town the day before we left, trying to collect all the items that we needed to live and conduct research for the next month). The first moment that we boarded the vessel. Enjoying Halloween on our transit day as we steamed towards Havana. Meeting the Cuban scientists as they boarded the ship in Havana. Setting up the lab and labeling vials with Mayelin while sitting on the floor in the hallway and listening to her favorite music. Kalina’s birthday celebration. Salsa dancing (and getting salsa dancing lessons) under the moonlight and stars. Getting nudged by a shark underwater. Watching the stars on the top deck in silence. The grouper that stalked Colleen. Games of tiki toss and corn hole. Hanging off the side of the Northwind at sunset. Belting Backstreet Boys with my advisor as we filtered seawater. A specific incident involving a puddle. Just so many memories.

I am definitely missing this!

I am so grateful for these memories, but as I sat there, it dawned on me that I would never experience these specific moments again. And I was sad. And I realized that it would be some time before I could dive on these reefs again if I am so lucky. And I was sad. And I reflected that it would probably be some time before I would be able to speak with and share a dance with my new Cuban friends. And I was sad. And this is also what I am going to refer to as research cruise withdrawal.

I have experienced this feeling before, after finishing field work, but I would argue never to this degree. This was the longest I had been in the field and my first major cruise. Someone I was speaking with recently (maybe Ashlee) referred to this cruise as “science camp” and I couldn’t agree more. Everyday was filled with excitement and wonder, laughter, sunshine, time underwater, corals, delicious food, starlight, song, dance, and friendship. How could I not lament the end of this cruise?

I guess I am writing this post to record that I am feeling this bittersweet feeling, to chronicle that it is a part of my PhD journey, to emphasize that scientists are relatable, and to reach out to others who may have also experienced this. It’s likely a normal aspect of field work, but rarely discussed. I even tried to search for other posts or articles on this topic, but I couldn’t find any specifically related to field work or research.

I am using this bittersweet feeling as an anchor to help me remember how grateful and fortunate that I am to have experienced all these memories. And to motivate me to continue to seek out fun, spontaneous, and adventurous experiences no matter where I am or what I am doing. This will be especially useful to hold onto since winter is coming (who gets that reference ;)).

Thanks for reading!




Alucia: Walton Smith: Cape play by play

Hey everyone,

Guess what – I made it back safely (well- ignoring my foot issue) to the Cape after spending 35 days away (with 31 of those days spent on a research vessel on the sea)!

I have been busy since we left Havana, Cuba and transited back to Florida on the Alucia so I thought that I would use this post to give you an update!

We arrived in Florida on Friday around lunchtime (side note: it doesn’t take very long to steam from Havana to Florida, especially when you are 1) riding the gulf stream and 2) steaming on a powerful vessel) and I spent most of my Friday evening waiting at an Urgent care clinic to get my foot inspected (I fell from my top bunk and my left foot hasn’t been the same). I left the clinic with an ace bandage and knowledge that my foot doesn’t have any obvious breaks or fractures, but with no information about the source of my pain. After the clinic visit, Ashlee, Colleen, Amy, and I had a lovely dinner outside and we were serenaded by our own personal musician. After dinner we went back to the Alucia and spent our last night on the vessel.

Colleen and Ashlee during dinner on Friday night: amazing women scientists!

On Saturday morning, we dealt with some last minute packing and preparations for shipping our pile of gear back to WHOI on shipping pallets.  We departed the Alucia around mid-morning and I tried to say goodbye to as many of the Alucia crew as possible. Hopefully I will see them again! We spent Saturday afternoon getting some much needed relaxation and downtime at a hotel in Miami beach and had a lovely dinner at a happening Thai food restaurant close by.

On Sunday morning, Ashlee and I flew to St. Thomas, U.S.V.I. to meet up with the R/V Walton Smith to complete the next adventure in our field work journey. Amy wasn’t able to fly with us on Sunday because she fell ill, but she was able to recover slightly and rally, joining us on the Walton Smith two days later. Ashlee and I met Justin (another MIT-WHOI JP student who has been working on the reefs in St. John) at the airport and we took a taxi to our hotel, had dinner, and spent the night in St. Thomas.

On Monday, Ashlee, Justin, and I were picked up by the Walton Smith in St. Thomas and then we transited back to our temporary neighborhood in Great Lameshur Bay off the island of St. John, U.S.V.I. Before the pick-up, we also ran into my colleague Dr. Chris Kellogg (a scientist at USGS who studies microbial associates of tropical and deep-sea corals) who was collecting samples to assess water quality around the island of St. Thomas! It was great to see her again! Once we got to Great Lameshur Bay, we met up with the octocoral/soft coral expert Dr.  Howie Lasker (chief scientist of the cruise and professor at SUNY Buffalo) and his group of amazing scientists, divers, and people! I was especially excited to see, live, and work with Angela and Jackie again (my two friends from the past summer 2017 that I spent in St. John)!

On Monday afternoon, I frantically unpacked and located all of our water sampling equipment (all different varieties of pumps, vacuum manifolds, cryovials, data sheets), literally colonized every crevice of the spacious wet lab space on the Walton Smith, and managed to squeeze in water sampling for two of our reef sites before sunset!

Great Lameshur Bay, St. John, U.S.V.I. – the water is reflecting my favorite color!
PC: Ashlee Lillis!

The next couple days passed in a busy blur . . . many liters of water were filtered, many dives were completed, many transects were conducted, many croissants and desserts were consumed (the chef on the Walton Smith was AMAZING and he even gave me an electronic copy of a massive recipe and cookbook :)), and many sunsets were appreciated. I also got to celebrate my birthday on the Walton Smith, which was made extra special by Ashlee, Amy, and the chef! I will fill you in about the premise for this cruise in a few days and life on board the Walton Smith, but for now, know that we had a fun albeit busy and exhausting time!

On Friday, the Walton Smith took us back over to St. Thomas and all of the scientists departed with the gear and equipment. The staff at the port referred to Ashlee and I as sultans because we had so many pieces of luggage! A couple hours later, we celebrated the end of the cruise at a fun restaurant close to our hotel.

The next day, we had a nice late breakfast at Gladys’s and then we took a taxi to the St. Thomas airport (along with our 456,789 pieces of luggage). We flew back to Boston via Miami and if you want more of a description of this adventure, imagine me hobbling through the giant terminal D in the Miami airport, getting a window seat WITHOUT A WINDOW, and having a defective TV screen. This is also a reminder to myself to never fly American Airlines again!

We arrived at Logan airport at midnight, collected all of our bags, froze standing outside of the airport, and took our shuttle to the Cape and WHOI. At 2:15 am, I turned my car on for the first time in 35 days (and it turned on!), drove home, and face planted in bed.

Thanks for reading!



Updates from Day 24 on the R/V Alucia: Dinner and a conference in Havana

Hey everyone,

Today is our final full day on the R/V Alucia! We are currently steaming towards Florida on our way back from a brief visit to Havana, Cuba.

We arrived in Havana on the afternoon of the 22nd, cleared customs, and then went to shore (Havana Vieja – old Havana) for mojitos and dinner on a rooftop. It was neat to approach Havana with the Cuban scientists, many of whom had never had the experience of seeing their city from the water. We also met Fredy, Victor, Mayelin, and Viky for dinner and had a wonderful time reminiscing about our cruise while eating tostones, empanadillas, and ceviche! After dinner, we came back to the Alucia for the night. We laughed the entire boat ride from the customs back to the Alucia about a terrifying, yet hilarious event that took place earlier in the evening.

On Nov. 23rd/ American Thanksgiving, we went back to Havana Vieja in the morning to visit the permanent artisanal craft fair, to eat lunch, and to attend a small scientific conference in the afternoon. We wandered the lively and busy craft market and purchased a few gifts and momentos to remember our trip. Lunch was enjoyed outside, in the company of two street cats who decided to sit underneath our chairs. Andrew, Ashlee, and I ordered the Ropa vieja – a classic and delicious cuban dish.

After lunch, we headed to the conference venue.  The purpose of this conference was to share and review the scientific work that each of us conducted on the cruise and to teach other students within the masters and graduate programs in Cuba about our methods and techniques. We all enjoyed this experience and were happy to participate despite the lingering exhaustion from the past few weeks of busy field work! After the conclusion of the conference, we were forced to say goodbye to our Cuban family. I will truly miss living alongside of, dancing with, sharing meals with, singing with, working with, and diving with these fascinating and inspirational people. I hope to see them soon!

After the conference, we took the pilot boat back to the Alucia and then departed, leaving the glowing, mysterious, and romantic city of Havana in the distance. We also enjoyed the Alucia version of a Thanksgiving dinner (complete with homemade Pumpkin pie and whipped cream -thanks Mitch!) while watching a few movies in the crew mess.

Thanks for reading!


Updates from Day 23 on the R/V Alucia: Top 10 favorite moments of the cruise

Hey everyone,

As our cruise slowly draws to a close, I thought I would share my top 10 favorite moments with you. There were many more moments and feelings, but this list should give you a good idea!

  1. Learning from and working with brilliant, enthusiastic, and hardworking scientists.
  2. Standing off the side of the Northwind at sunset and speeding back to the Alucia.
  3. Salsa dancing lessons from Fredy, Lake, Mayelin, and Rolando.
  4. Dancing and singing with Amy in the lab during filtering.
  5. The ~35 hours that I spent underwater during this trip (including the priceless moments that I had with a shark and several grouper).
  6. Snorkeling through Acropora palmata fields.
  7. Baking chocolate chip cookies with Mitch in the Alucia kitchen.
  8. Watching birds from the bow of the ship with Tyler.
  9. Standing on the sun deck (top deck) and watching the sunrises and sunsets.
  10. Dancing in the moonlight and under the stars with new friends.

Thanks for reading!

Updates from Day 22 on the R/V Alucia: What happens when you’re clumsy at sea

Hey everyone,

We finished up our last day of “science” yesterday! We dove and conducted benthic surveys at two different reef sites and collected water samples. Colleen “DISCO’ed” (the best time yet) and Andrew assisted. Ashlee managed to conduct a 5 minute drift – it was supposed to be much longer, but due to a miscommunication with the ship, they had to cut it shorter.

Amy and I processed the samples after lunch, I entered data, and we enjoyed a beautiful sunset at the bow of the Alucia as we started heading west on our way back to Havana, Cuba and then to the states.

We will spend the next two days transiting back to Havana. I foresee a lot of packing and organizing in my future.

Okay- enough general updates. I wanted to discuss my general clumsiness at sea!

During this trip, I have managed to 1) slide/fall down the “Hell” stairs (the second time that I went down them FYI), 2) trip up the main stairwell ~5x that leads up to our rooms, 3) fall out of my bed (from the top bunk) and sprain my ankle (thank goodness this happened on the last day of the cruise), 4) struggle to get on the zodiac (small inflatable diving boat) from the water (see accompanying facebook/instagram picture), and 5) step into the depressions on the aft deck that are used to strap down equipment.

I would say that I have pretty good sea legs, but for some reason, I have been rather clumsy on this cruise. I guess I should be grateful that nothing worse has happened and that I sprained my ankle on the last “science” day.

A special shout out to all the members of the crew who have 1) physically pulled me out of the water and onto the zodiac and have helped me board and get off of the Northwind and back onto the deck of the Alucia.

Thanks for reading!


Updates from Day 19 on the R/V Alucia: A big thank you to the Alucia crew!

Hey everyone,

We had a low key and relaxing day that was much needed after a steady stream of full “science-ing.”

We went snorkeling and saw stands of Acropora palmata, the beautiful Elkhorn coral. This coral was once widespread throughout the Caribbean, but is now rare to see because it was decimated by disease in the 1970s and has not really come back in most areas.

This afternoon, Amy, Maickel, Ashlee, and I dove to recover Ashlee’s hydrophones that she had deployed on one of our reef sites.

Ashlee suggested that I write a blog post to highlight all of the cryptic/ “unseen” help and support from the crew that we have had while working and living on the Alucia. If you think about it, the crew keeps the Alucia running like all of the cryptic and unseen chemicals, microbes, and sounds that we think contribute to the health and processes that occur on coral reefs.

The crew is comprised of two chefs, stewardesses and ship managers, engineers, deck hands, the bosun, diving safety officers, an IT/technical officer, navigation and safety officers, and a captain.

When I first boarded the Alucia, I had no idea that it took so many people (20) to keep a ship like this running. Each of their contributions to the cruise is unique and important: the chefs  cook and provide food for the 40 people on board at every single meal and do so even though we haven’t been able to replenish the food supply after the first two weeks of the cruise. And they cook delicious, nutritious, and satisfying food.

The stewardesses and ship managers assist guests and other crew members with keeping the births and common living spaces clean, delegating tasks, completing paperwork for the ship, and keeping everything organized.

The engineers keep the power on and the ship moving (in addition to many other things that I am unaware of), but they also fix plumbing and lighting problems. They spend most of their time

The deck hands take care of superficial ship maintenance, drive the diving boats, help carry and pass equipment, assist during diving operations, and even dive with us as safety divers when they are needed.

The bosun is an officer of the ship who is in charge of equipment, overseeing the other deckhands, and coordinating operations on deck.

The diving safety officers oversee all diving-related operations, help inspect and fix diving equipment, and enforce diving safety before, during, and after dives.

The IT/technical officer oversees internet usage on the boat and makes sure that the satellites and wifi are working so we can communicate with the outside world.

The navigation and safety officers are in charge of getting the ship to the correct locations, enforcing on-board ship safety, and keeping the boat in a safe position (especially in shallower areas close to the shelf and the coast).

The captain oversees all operations that take place on the ship and nothing happens without his approval.

I have enjoyed getting to know and work with these amazing and talented people over the course of this cruise. They have allowed us to conduct our science and access our reef sites. They have kept us safe, taught us about life on a ship, and made us laugh. A big thank you to the amazing crew of the R/V Alucia!

Thanks for reading!





Updates from Day 18 on the R/V Alucia

Hey everyone,

Yesterday, Nov. 17, was another jam-packed day!

Amy, Maickel, Amanda (coral diversity expert), and I dove twice in the morning and Amy and I collected water samples with the help of Suzelle, Vickie, and Mitch just before lunch.

After lunch, another group of scientists (including me) went on an expedition to the beautiful mangrove system to collect more water samples, test out the DISCO, and to snorkel. We had a great time navigating through the hauntingly beautiful and ethereally gloomy underwater mangrove environment. We saw a few birds, some jellyfish and anemones (that were classified as “creepy” by some of the people on the boat), small barracuda, cool sponges, and two spotted eagle rays! Andrew enjoyed stirring up the sediment and telling us about the hydrogen sulfide that was escaping from the anoxic (no oxygen) mud and Ashlee enjoyed watching bubbles form on the outside of seagrass underwater. No one enjoyed the smell of anoxic microbial metabolism.

We also searched for crocodiles the whole time, but sadly didn’t encounter any (although I am sure my mom is fine with this!). We had to keep telling Mitch that we were looking for crocodiles, not alligators, but after the 20th time, we compromised with him and decided to call these reptiles “crocogators”.

When we got back to the Alucia, I processed water samples for three hours, had dinner, and then played a few rounds of Tiki-toss (also known as ring toss) and corn hole out on the aft deck. We had fun and I definitely improved as time progressed!

No pictures today – I was informed by the IT officer on board that I have been uploading too many photos and sucking away all of the bandwidth from other people. You will just have to wait in suspense until I get back to the States so I can share all of the cool videos and pictures I have taken while on this cruise!

Thanks for reading!

Updates from Day 17 on the R/V Alucia: Popular cruise catch phrases

Hey everyone,

Checking in with you again from somewhere south of Cuba! I realize I haven’t quite filled you in on what we have been doing the past two days! Recently, our days have involved lots of diving, surveying, and water sampling (Surprise/ bet you didn’t see that coming!?!). We are trying to make the most of the last few working “Science” days (count: 3) that we have until we turn around and head back to the US.

Today, I wanted to record a couple of phrases, sayings, and cruise mottos that have become important, motivational, and funny to the science team and the crew of the Alucia over the past few weeks.

“This science ain’t gonna science itself!” – Phrase coined by Mitch (of the Alucia crew). Usually said as we are loading up the Northwind and/or zodiac with all of our diving and science gear or as we are preparing to jump into the water before a dive.

“The pool is open!” – Scuba Steve’s (Alucia diving officer) way to inform the divers that they can jump into the water and begin the dive.

“DIIISSSCCCCOOO!” – What I say whenever I see the instrument. Also what I say whenever I am carrying the instrument and anyone is in my way (what I really mean is “This thing is heavy and I need you to move!”).

“Where’s your passport, Tyler?” – Tyler Tamasi and I have this running joke of making each other search frantically for our passports at random moments in time. We are both terrified of losing them!

“I want it that way.” – Amy and I belted out this phrase (and sang it within the Backstreet Boys song it belongs to) and danced to it during lab work one day. We will never be the same. A true bonding moment between advisor and graduate student!

“You owe me a beer.” – Crew members say this to Science members when they find something wrong with a scientist’s dive gear set-up or when he/she forgets some piece of equipment on the Alucia and we have to turn back around.

“Where’s Avalon?” – Avalon is the local dive guide group. They have been diving with us frequently, but they have the tendency to be late so we are always wondering where they are!

“What time is the transfer boat coming?”- Wondering when the boats that are bringing people back and forth from Cuba to our boat will get to the Alucia.

“How’s it going?”- Favorite phrase of a few select individuals on this boat.

“Is the internet working?” – Said with frequently with terror  by everyone on the boat.

Thanks for reading!

The pool is open!
Tyler, Kalina, and Ashlee loading up the Northwind!



Updates from Day 15 on the R/V Alucia: A-Z Alucia!

Hey everyone,

Here’s an A-Z list describing this cruise (and life on the Alucia) so far!

A: (Dr.) Andrew Babbin (Nitrogen expert and logo creator extraordinaire) (Dr.) Amy Apprill (my advisor, co-chief scientist on this cruise, Coral-microbe aficionado), Dr. Ashlee Lillis (reef whisperer)

B: Bubby (dive master on the Alucia crew)

C: (Dr.) Colleen Hansel (DISCO designer, superoxide advocate), Cuba, Coral

D: DISCO, Delicious food, Dark N’ Stormy

E: Elegant sunrises and sunsets

F: Filtering seawater, Flow cytometry (used to count the number of microbial cells within a sample)

G: Goliath Groupers

A goliath grouper goes for my sampling bags; PC: Amy Apprill

H: Helipad (location of nitrogen incubation experiments via Tyler and Andrew), Hydrophones (used to measure sound production on Reefs)

I: Ichthyology (study of fish)

J: Jardines de la Reina (Gardens of the Queen)

K: Kalina (MIT-WHOI PhD student, DISCO queen)

L: Leonardo Espinosa (fish survey expert and champion scuba diver), Living the Life aquatic

M: (Dr.) Maickel Armenteros (team leader, Meiofauna Master), Metabolomes, Moonlight

N: Natalie (talented chef on the Alucia), Nitrogen, Northwind (smaller dive boat)

The Northwind

O: Octocorals (prevalent on reefs in Jardines de la Reina)

P: Poker with skittles

Q: Quadrat (survey tool used to describe the distribution of plants and animals in the environment. Maickel uses a Quadrat to complete his surveys)

R: Reefs

S: Scuba diving, Salsa-dancing lessons, Stars, Superoxide production

T:Tyler Tamasi (MIT-WHOI Joint Program student; CRIB expert),  Taco Tuesday, Tiburones, Tiki-Toss game, Trichodesmium, Teamwork

U: Underwater

V: Very epic cruise, Vacuum pump (used for SPE)

W: Women in science

X: Xenial relationship between the American and Cuban scientists, the Alucia crew, and the media

Y: Yellowtail snapper

Z: Zooxanthellae (microalgae that live inside corals)

Thanks for reading!