Qualifying… to do what?

This Friday I’ll be going through the second of three major exams on the road to a PhD.  At Scripps we call it a ‘qualifying exam,’ which I recently realized sounds quite weird.  Especially when you use it in a sentence- “I am qualifying on Friday” or “Has so-and-so qualified yet?”  Qualified to do what exactly?

In this case, to finish your PhD.  To be honest, I think this is assessed often and you’re notified by an advisor relatively quickly if you are not qualified to do a PhD.  But the three major exams give your advisor and your committee and opportunity to make sure you are on the right track and developing the ‘correct tools to succeed.’

Exam 1 was called ‘departmentals’ and was held after my first year of classes.  For me, it was two full days of written questions, based on courses I had taken.  This is far beyond the world of ‘can I bring a calculator?’  Although most of my questions involved math, even the most advanced graphing calculator wouldn’t have done much for me.  After the written test was a one hour oral exam, given by four seated scientists to me standing in the front of the room armed with a dry erase marker and white board. I managed to put that one behind me in October 2009.

Exam 3 is your thesis defense- a public presentation of what you spent the last 5-8 years doing, a grilling by your thesis committee, and the granting of your doctoral degree.

And exam 2- qualifying- is the one I am getting ready for now. The first steps were to form a thesis committee (a set of scientists to help guide you through your research) and write a thesis proposal (an outline of what you’ll be doing for your thesis).  I sent the written proposal to my committee last week, giving them lots of time to ponder and come up with difficult questions.  On Friday, I will present my ideas and methods to them, along with results of work I’ve already done, and they will ask copious questions.  One of my advisors suggested that I prepare a talk that takes me 30 minutes uninterrupted, and to allow 3 hours of time.

It is exciting and a little scary.  But now that the grunt work (mostly writing the proposal) is done, I’m feeling good about the whole process.  Being forced to write down your ideas as a scientific proposal (you know- background, hypothesis, methods, expected results) makes you really think about them and how viable they are. So I still have all fingers crossed for Friday to go well, and I hope that my committee gives me a big thumbs up at the end so we can all go drink champagne and get the long weekend started.  I am also looking forward to it as a chance to refine my research ideas and make them better, and I’m even getting a little excited.

I won’t make you read my 17 page long proposal, but in case you’re curious here is the outline:

The Interaction of Multiple Stressors on Coral Reefs: Can We Determine Resilience to Climate Change?

Doctoral Thesis Proposal

  1. Introduction and Overview
  2. Major Research Questions
  3. Research Chapter 1: Coral Habitats- Large Spatial Scale Comparison Studies
  4. Research Chapter 2: Future Projections of Coral Reef Habitats (NCAR/SUNNY)
  5. Research Chapter 3: Island Effects on Oceanography and Larval Connectivity
  6. Research Chapter 4: Historic Ecology of Caribbean Coral Reef Fish Communities
  7. Timeline
  8. Expected Publications
  9. References

Notes from the Dominican Republic

I’m back!  Alright, I’ve been back for a month and stalled on posting this, but here it is now.

I returned safely to San Diego, with about 250 pounds of sand in tow (distributed between 6 checked bags, 2 carry on bags, and 3 people) at 1am on Monday March 28.  So in summary, the field expedition was a success!  In summary:

Trials and tribulations: to be honest, this entire thing went off pretty smoothly and I can’t complain!  Felix was crucial, in terms of driving, Spanish fluency, and complete tirelessness in the field.  I was glad to be out hiking, collecting, and sieving every day.  We collected all of the samples we wanted.  Dick only tossed me into a rock wall once.  No one came down with an infectious disease.

Highlights: This was an incredibly interesting trip, both culturally and scientifically.  The fossil reefs were incredible- everything was perfectly in place and so well preserved! Fossil clams still had their hinge- even though they were 8000 years old.  The food was adequate and the rum excellent.  I was able to email Simon three different times during the week. I made a wonderful new friend and colleague in Felix. I got to spend ‘quality time’ with one of my thesis advisers.

View from the hotel, with fishing pangas in the background
Walking through a coral reef! Felix and I in a coral canyon.
Fossil corals, up close and personal- pretty amazing when you think about them being 7000 years old!

The Longer Version:

The Dominican Republic was unlike any other Caribbean Island I’ve been to.  Poverty was more evident, and tourism not as common.  There was a clear presence of the United Nations and the Peace Corps.  The streets were more reminiscent of southeast Asia than the Caribbean, with most locals on moto scooters with their livestock, fruits, vegetables, and/or children.  Road rules were only considered loose guidelines, and horns were used as a regular means of communication.  Once we left Santo Domingo, there were long stretches of empty jungle and beach between towns.  The towns were colorful, made of clapboard houses each painted in bright hues.  On weekdays we’d spot hoards of children in uniforms walking to and from school.  In the evenings the locals lived outside- eating, visiting, and relaxing.  The houses were small and mainly intended for sleeping.  Produce and meats were sold in little stands roadside- mostly pineapples and papaya, but we also saw coconuts, mangoes, and guavas.

The French-owned hotel/restaurant served delicious crepes at lunch and dinner

We made our way to our resort at La Playa Azul, just past Barahona.  The hotel was really lovely all things considered- hot showers, spacious rooms, and a pleasant restaurant.  It was built on top of sea cliffs with stunning views of the tropical sea and waves rolling in.  Each morning we watched fishers catching their bait for the day, guided by a spotter on the cliff looking for schools of fish.  During the day, we would drive between 1-3 hours to our field sites near Lago Enriquillo– in the middle of no where near the Haitian border.  When we passed through towns everyone stared at the group of white people in a nice white car.  We were stopped countless times at border checks, and had a bit of trouble explaining that we were turistas- why on earth would turistas be in the hot, dry, Enriquillo Valley?  With the help of our Panamanian assistant Felix, we only had to bribe one officer out of the many.

An 8-10 meter high wall, composed almost entirely of a single species of coral (Acropora cervicornis), from an ancient lagoon
more fossil coral!

Our first day was spent traveling to La Playa Azul, and the next three days we were in the field.  We drove to the approximate location that we found on google earth, then proceeded to play a game of ‘guess that canyon’ while watching the GPS coordinates and driving slowly through a particular area.  We eventually found our three major sites (and one… incorrect site)- two canyons that had extensive radiocarbon dating done, and one that had been studied extensively in terms of corals and molluscs, but never in terms of fish.  At each canyon we would assess the reef, pick our specific sample sites, and hammer out 10-20 pounds of sand, coral, and shell.  Then we passed samples through the vegetable grill basket (to remove the big pieces of coral and shell).  Once all of the big pieces were gone, I sieved the sand two more times and saved the ‘coarse’ fraction (didn’t go through a 2 millimeter sieve) and the ‘fine’ fraction (did go through a 2 millimeter sieve).  The really fine stuff was discarded (as in less than 0.1 millimeters) to save space.

Collecting bulk samples. The buckets got very heavy as we filled them with sand from the canyon wall, so it was easiest for me to hold it on top of my head.
An alternate perspective- admiring a coral reef from below.
Picking through samples in the pool (it was hot!)- I am removing shells and coral to make the bags lighter to take home on the plane.

I should interject here that the fossil reefs were truly amazing- 10 meter high walls of coral!  The preservation was so good, and so many pieces were there, that it was easy to imagine the entire system underwater, sharks and fish o swimming around, an occasional ray gliding past…

The veggie grill basket! This was essential for separating large pieces of coral. Once those were removed, I passed the sand through two more sieves to sort it before packing it up to take home.

On the fourth day, we stayed at the hotel and sorted samples- doing our best to take out all of the calcium carbonate, which was effectively all of the pretty stuff.  Shells and corals were all removed.  Our discards caught the interests of some other hotel occupants, and Dick did his best to turn them into ‘junior paleontologists.’

Finally, we drove (via one more canyon stop!) to Santo Domingo for our last night. Once we safely navigated the traffic and arrived at our much plusher hotel, the samples were all weighed, sorted, and divied amongst the luggage.  (While enjoying a rum drink and watching ‘Air Force One’ in English!)  One more night, lots of airport waiting, and two long flights got us safely back to San Diego, sand in tow!

265 pound of fossil coral reef sand, bagged and ready to go.

Prepping for the field- historic ecology of fish in the Dominican Republic

Some of you may have heard me mention ‘the DR’ recently.  This is short for the Dominican Republic (you’ll learn quickly that scientists love acronyms).  I am leaving for this Caribbean nation on Sunday (in 2 days!) and have planned the majority of the field expedition in the last 10 days.

The trip is last minute because of a number of coincidences and lucky breaks, but the most important thing is that it is happening.  So all of the last minute flight purchases, revisions of my espanol skills, and purchase of field tools are worth it!  I am going with on of my co-advisors and his wife, and we will meet our Panamanian tech/assistant upon arrival.  We’ll be there for a week, and spend most of the time near Lago Enriquillo– in the bottom left corner of the DR, near (but not on) the Haitian border.  This is one of the hottest, dryest, places on the island of Hispaniola with some of the highest temperatures.  For mild relief, we’re staying in a hotel by the beach in the town of Barahona.  It was highly recommended because it has a pool and wine is available.

This is a modern coral reef in Maui, Hawaii complete with fish and a sandy patch containing fish poop, sea urchin spines, shark teeth, and other goodies.
and this is a fossil coral reef in the California desert, a much more accurate representation of what I’ll be looking at for the next week!

We are bringing things you might expect- hiking boots, shovels, zip loc bags to put samples in, sharpies to label everything; and things you may not expect- tweezers, paintbrushes, vegetable grilling baskets, and folding magnifying glasses.

So why, you may be wondering, are we going to this somewhat questionable place with a very questionable assortment of gear?

Lago Enriquillo is in the Enriquillo Valley, which has been naturally dammed from rainwater for hundreds of years. Ancient rivers once carved through this valley draining into the lake, and they exposed cross-sections of limestone.  This limestone is in fact one of the best preserved Holocene (that’s the last 10,000 years) coral reefs in the world. Corals are intact and even in life position, along with algae and shells.

Trophy fish from a summer weekend fishing trip in Key West, Florida- same operation, same fish board. From top to bottom, the photos are from 1957, 1980, and 2007. Photo credit UCSD News, Loren McClenachan

I study coral reefs, things that stress them out, and things that people might be able to do about it. The deeper you dig into history, the more you realize that people have been messing with the ocean for hundreds or even thousands of years.  To better understand what a healthy or ‘pristine’ coral reef might look like, we need to do a little detective work.  The fossil reef at Lago Enriquillo is a great opportunity to do this, because we can learn a great deal about the corals, algae, and bivalves that lived there 4000-9000 years ago.  This straddles the time when the first hunter gatherer tribes reached the Caribbean- 6000 years ago.  We are looking specifically for fish parts, most notably teeth.  These are preserved in the sand that would have been in the reef lagoon thousands of years ago. We know from work of a past Scripps student, Loren McClenachan, that fish in the Florida Keys have changed dramatically in the past 100 years.  But I want to go back even further than that, to before any humans were around.

So we will be digging out shovelfuls of sand from the lower parts of this fossil reef, running them through sieves (that’s what the vegetable grilling basket is for) to save material between about 1 centimeter and 0.1 millimeters in size.  The finer stuff will be carefully packed and labeled to ship to San Diego.  We’ll use the folding magnifying glasses, tweezers, and paintbrushes to pick through the coarser sand (2 millimeters to 1 centimeter) for anything that resembles a tooth, bone, or interesting fossil.  Then those will also be carefully packed up to ship to our lab. So just in case you thought I’d be sipping sangria next to that pool on the coast- well, you may be right, but I’ll also be carefully going through our samples to try to reduce the volume that we need to bring home and grab anything that looks interesting.  Although fish teeth are super cool, they are also pretty rare- a full gallon zip loc bag of sand only gives us a few hundred teeth. Back home in the lab, we will check out all of the sand under a microscope, pick out anything interesting, then soak it in weak acid for a week or two.  The acid dissolves most of the material- reef sand is predominately made of calcium carbonate (that include sea urchin spines, coral skeletons, shells, algae).  Teeth, however, are calcium phosphate, and they will be leftover when our dissolution is done.  From counting and identifying ALL of the teeth in all of the sand that we collect, from the oldest to the youngest part of the reef, we can reconstruct the fish community of 1000s of years ago!  I’ll update you on what we find as it happens 🙂

Welcome & Hello!

Thanks for checking out my new blog!

that's me in my favorite place, pretending to be a fish

I’m a silly, fun, ocean-lover, engaged to a kiwi, and going to graduate school at Scripps Institution of Oceanography in San Diego.  Like many of us, I fell in love with the sea the first time I laid eyes on it as a small child.  For me, not much has changed since then.  I do what I can to organize my life and work around spending time in and on the ocean. I am in graduate school and not a dive bum because at some point I realized that people were in fact changing the face of our planet and its oceans, and I wanted to better understand what was happening and try to do something about it.

I’ll be posting on here about recent ocean science news, what kinds of things I do at ‘work,’ and ideas about how to change the world to be a little bit better.  Thanks for stopping by!

love, life, and adventures of an ocean science family

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