Why I left academia, part 5, or: Send in the Navy!

Just as I was feeling like something in my life was going to give - my sanity, my kids’ sanity, my marriage, or someone’s health, I was offered a position at the Navy in San Diego. My husband had been collaborating with some folks there, and they had come to learn of our less-than-ideal living situation. They had a looming retirement, and saw a fleeting chance to fill that slot and an opportunity to help our family become whole again. 

There's a lot to miss about Boston

The position they offered me was to be the “relief” for a retiring scientist who ran the scientific diving program and coral reef research at SPAWAR (Space and Naval Warfare Systems) Systems Center Pacific (or SSC PAC for short). The catch was that the window was short – I had to start before the next president came into office, as it was rumored that a Federal hiring freeze was going to occur, just a few short months away. I spent as much time as I had searching my soul, talking to friends from Scripps who work at the Navy, thinking about my students, and trying to decide if I should jump ship. 

In the end, as you have guessed by now, I decided to leave at the end of the fall semester. The hardest part was telling my graduate students. One of them took it very hard. I don’t know that he’ll ever forgive me, but despite my pretty suddenly ditching him, that student completed the initial work he had started with me and wrote it up to receive a master’s degree a few weeks ago. I’m incredibly proud of his persistence. My other student is luckily less completely abandoned, since his other advisor is still in Boston; he managed to fight cancer while I was moving coasts and continues to persevere toward his degree despite logistical and other challenges thrown his way. Rock stars, both.

In the end, I left academia because I felt like I couldn’t hack it. I chalked it up to my living away from my husband, but now that we are back living together I think that even if he had moved to Boston and we had stuck it out, I would have failed. I don’t like working more than 40 hours a week. I feel like I barely get to spend quality time with my kids and husband as it is; if I were to spend weekends and evenings working, as expected and required to thrive in academia, I would shrivel up into a miserable prune. 

My new job is not without stress; but to me, at least so far, the stress is compartmentalized and manageable. The job is doable and the requirements are concrete. The people are kind and understanding. My colleagues at UMass Boston were kind, but not entirely understanding. This is nothing specifically against them - I am pretty sure that all academics live in a world in which expectations and norms are different, and that most of them are Ok with this. At my new job, no one expects after-hours or weekend work (unless for travel or fieldwork, of course). Of course some people do work longer hours, particularly just before proposals are due or other deadlines, but it is not standard and expected, which is the difference. 

Fieldwork in Pearl Harbor - a bit
different from drilling coral cores!

I do feel sometimes like I failed, and that I’m not as good a scientist as my friends who are succeeding in academia. Maybe I’ll always feel that way, and wonder if I could have hacked it, had things been different. But I know that I am not failing as a mom anymore, and this is more important to me. Ryder has a hard time believing it (Kindergarten is now school #10 or 11 for him - I've lost track; he’s lived in 7 different apartments/houses over his not-quite 6 years), but when I assure him we aren’t moving houses or schools anytime soon, his comforted smile warms my heart.

San Diego has problems - the traffic sucks, we have no water, our neighborhood is mostly white and affluent, and we have to drive to everything. But I have to admit that if they’ll let me stay, I don’t want to move anymore. I’m a government scientist and so incredibly proud of it. 

Coral Cores for Science

I spent last week in St. John, US Virgin Islands, on what my friend Lauren called a “Mama Science Vacation.” That was a great term for it – a vacation from our overwhelming house renovations, and from Southern California traffic, and spending 90% of my brain capacity calculating when Ryder might next need to eat or sleep or use the toilet, and feeling guilty I didn’t have enough enriching activities planned for him. 

This week gave me a chance to reconnect with my adult self, think deeply about science, and see wild coral reefs again in person for the first time in more than a year. It’s amazing how enriching it is to be physically immersed in the environment I’ve been studying mostly remotely for the past decade. Today I saw the most extensive stand of Acropora cervicornis,  the endangered “Staghorn coral,” that I have ever witnessed. These corals used to dominate shallow Caribbean reefs, along with their relatives Acropora palmata, or “Elkhorn coral.” But both species of Acropora all but totally died off decades ago from a disease that swept through the Caribbean. Today, we saw not only thriving large colonies of adult Acroporids but also lots of juveniles – and interestingly these were often growing on dead colonies of the same species. This recalled a study I read (which of course I can't find, now) that found coral larvae of particular species preferentially settle on dead colonies of their own kind – perhaps because of some lingering chemical cues those skeletons exude?

This doesn’t have any particular bearing that I can think of right now towards my own work, but I find it really fascinating.

So, what have we been doing here in St. John? The short of it is that I’m starting a new project in collaboration with colleagues at the University of San Diego, where I’m aiming to tie records of past water quality based on coral skeletal chemistry to data they have been collecting using sediment traps and other instruments. You might remember that corals build their skeletons from chemicals in seawater, and slowly grow larger over time—thus, their skeletons record changes in water quality. Annual changes in skeletal density also provide a lovely chronometer for these chemical records. If we can tie these recent records together, I can extend records of runoff farther into the past (perhaps a century or more) using core samples from large old corals. To see if this idea will work, the first step is to collect short cores from living corals to tie to the sedimentology datasets. Hence, this trip.

Coral cores are collected using an underwater drill by divers using SCUBA equipment. Scientists either use a hydraulic drill driven by a hydraulic engine in a boat at the surface, and long hoses that deliver the hydraulic fluid down to the drill. These rigs tend to be giant, heavy, and awkward. I helped collect cores from fossil corals on land using a hydraulic drilling system at Tabuaeran Atoll way back in the dark ages of 2005, and quickly learned that unless I was going to bring along a bevy of much stronger people as field assistants, this wasn’t something little me could handle. I opted for a pneumatic drill, driven by compressed air – these drills are much smaller though less powerful (so it takes longer to collect an equivalent core length).

The cool thing about pneumatic drills is that they can be driven by an on-ship, gasoline-powered air compressor (ideally), but if this is unfeasible, they can also be driven by SCUBA tanks. Theoretically this shouldn’t be a big problem—if you have gotten to a place set up for SCUBA, there should also be a supply of tanks available to use to drive the drill. Shipping around 200-lb air compressors is, on the other hand, rather difficult and expensive. So for this trip, I opted for the SCUBA tank option.

The trip was thrown together somewhat last-minute, though it had been in the wings of planning for more than a year. Suddenly, various logistical issues came together and made it necessary to jump and get the trip organized. I was able to gather two worthy field assistants – my friend Lauren Freeman who I knew at Scripps, and a grad student at USD named Whitney who had spent at least part of the past 7 years at the Virgin Islands Environmental Resource Station (VIERS), where we were headed.

 

We converged in St. Thomas, where we rented much-too-large of a car and drove across the island, stopped to stock up on groceries and then get WD40 at Home Depot (how civilized), took the car ferry to St. John, and again drove across that island to VIERS. There, we settled into a 2-bedroom ensuite cabin with open, screened sides, a small kitchen, and an open air shower out back. Multiple cabins sat in the jungle encircling a large open area with picnic tables and a fire pit, all connected by elevated boardwalks ready for the rainy season. We slept to the sounds of tree frogs and insects, and the intermittent heart-stopping crash of mangos falling on the corrugated metal roof.

The first day consisted of getting the ladies oriented to the coral drilling gear, getting ourselves oriented to the workings of VIERS, and identifying sites to target via snorkel. We were able to swim around most of Great and also Little Lameshur bays, looking for the right sized colonies of the right coral species at the right depth. After discussions with the folks who oversee permitting for the Virgin Islands National Park, and following preliminary scouting Whitney had completed last year, I had decided to target a coral called Siderastrea siderea, or “Massive Starlet coral,” partly because it is more abundant than the coral I’ve worked with previously, Orbicella (previously Montastraea) faveolata, and partly because it seems a bit hardier than Orbicella. Coral reefs are in bad shape around the world these days, but particularly in the Caribbean. I believe that some collection is Ok for scientific purposes that are justified – but I still would rather minimize my small collection footprint. I aimed to do this by taking samples from corals that have shown evidence they may persist into the future amongst the onslaught of human impacts (sediment and nutrient runoff, overfishing, and climate change are the biggest culprits).

The next day, we got to work. It was—how shall I put this—basically complete underwater chaos. The tanks were lighter underwater than we anticipated and kept trying to escape off into the blue, the 50 foot air hose turned into a bird’s nest and got tangled with the tanks (which we’d daisy-chained together with a rope), nobody had enough dive weights on for this kind of work and couldn’t easily stay put at the target coral, the surge didn’t help things, and we hadn’t yet worked out how to communicate efficiently underwater. Thus we wasted huge chunks of time writing long epics on our dive slates and getting confused by one another. The worst part was that the drill ate up much more air than we anticipated – each tank was only lasting about 6 minutes. Using 6 SCUBA tanks to drive the drill, we collected a measly 2.5cm diameter, 4cm long core over the course of 2 dives, which took in total about 4.5 hours (including loading and unloading the boat at the dock, motoring to the site, mooring, getting geared up, etc.). It was not looking good for my goal of collecting ten 10cm-long cores in the 3 remaining diving days we had that week.

 

That evening my friend Rich—who had done some dive-tank-driven coral coring the previous year with my gear—gave some suggestions over email for improvement. The major idea was to float the tanks at the surface: because the air metered out of the tanks wouldn’t be under additional pressure from the water, the same volume of air would be delivered at a slower pace, and each tank should drive the drill for a longer time. We also decided to make a bridle with dive weights to hang over the drill; we were using a smaller, lighter core barrel than I had previously used, and we thought that the weights might help the coring move along at a more reasonable pace. The skeleton of Siderastrea was much more dense than Orbicella, so I had expected things to go slowly – but not ten times more slowly, as they had our first day.

Floating the tanks at the surface using a lift bag worked—but it was also chaotic. One person had to corral the tanks together (they were daisy-chained with rope but the currents and waves made them each constantly try to escape) and change the regulator from one tank to the next as they emptied. This turned out to be rather exhausting and caused much skull-banging and seasickness for the tank exchanger, but we were ecstatic to see that each tank now lasted about 12 minutes. With the lead-weight bridle and the tank flotilla, we were able to collect 2 whole cores in the time we’d taken the previous day to collect half a core. Things were looking up.

Each dive, we improved. We next commandeered a small kayak to hold all of the drilling tanks, which made things much easier (except when it capsized close to the rocks). Importantly, our underwater communication improved, and Lauren and Whitney quickly figured out what tasks needed to be done and developed their own drilling techniques to combat the surge while avoiding damage to other parts of the reef.

 

We finished collecting all ten cores with a day to spare, so were able to go out with a local retiree who knows practically every inch of Coral Bay – the adjacent developed watershed in which I plan to collect future cores to contrast with the runoff history in the undeveloped watersheds of the National Park. He took us snorkeling to identify future collection sites for another trip, plus to see the secret spot where we were staggered by prolific thickets of Acropora corals.

This fall comes the next fun part: geochemical analysis of these precious and hard-won samples at my new lab at UMass Boston. I can’t wait.

Some confusing facts about corals

I love coral reefs. I also love news articles about coral reefs, especially when they mention the problems corals face today that challenge their survival: mostly pollution, overfishing, and climate change. But I hate when somewhat minor inaccuracies undermine the strength of the articles. Today I came across just such an article, on one of National Geographic TV's blogs. First, I griped about it on Twitter. A few hours later, DNLee tweeted and suggested writing up corrections to news articles and sending them to the author. So, here goes my #scisplain.

The quotes below come from the National Geographic blog post, and my gripes about them follow.

"Coral Is Smaller than a Tea Cup"

Well, yes, some coral colonies can be smaller than a tea cup. But many coral colonies are huge, the size of cars and tables. The author, Rebecca O'Connor, clarifies in the next paragraph that she means individual coral polyps are smaller than a tea cup. Well, that is often true, but some coral polyps (especially those of solitary corals, which are only composed of a single polyp), are larger. To be more accurate then, this sub-headline above should say something like Individual coral animals are often smaller than a tea cup. 

Ok, my red lines are really faint...but this is a picture of a bunch of skeletons of solitary corals (and some Tridacna clams). Some of these corals, which are comprised of single polyps, are 15 cm in diameter. Maybe your tea cups are really big?

O'Connor goes on: "The animals that make up a coral reef are called polyps and they can actually live on their own, but are primarily associated with the spectacularly diverse limestone communities or reefs, they construct."

Ack! Ok, first, many different types of animals make up a coral reef, not just corals--sponges, algae, soft corals, bivalves...etc. So, no. The animals that make up a coral reef are not called polyps. Instead, this sentence could read something like: Corals are typically colonial animals; each colony is made up of many individuals called polyps, which are usually smaller than a tea cup. I'm not sure what she means by the rest of that sentence. Does she mean that some corals are not colonial, and are just single polyps? Or does she mean that sometimes corals live relatively far away from other corals, for instance in places like São Tomé where individual corals grow on rocks?

I kind of like the "spectacularly diverse" part but why are the communities limestone? Fish, sponges, and many types of algae are not limestone, yet are part of the diversity of reefs. If nothing else, a comma is desperately needed after the word "communities."

(Also, for the record, polyp is a rather general term, and can refer to an individual anemone, hydroid, or jellyfish; saying "polyp" does not specify coral.)

The other four sub-sections are also frustrating.

"Coral Reefs Are Colorless"
Each of the other sections start with "Coral Reefs" and then say something only (mostly) about coral animals. Here, "reefs" should be removed, and the headings should read Corals blah blah blah...

The article continues: "When you think of coral reefs, you imagine their vibrant colors, but coral polyps are actually translucent animals." Yes, mostly. But some corals have their own pigments as well - for instance the coral Siderastrea siderea appears blue, not white, when bleached.

Belize, October 2005: bleached Siderastrea siderea appeared bright blue on our transects

"Reefs get their wild hues from the billions of colorful zooxanthellae (ZOH-oh-ZAN-thell-ee) algae they host." No. Reefs get their wild hues partially from the zooxanthellae hosted by corals and other organisms (for instance, Tridacna clams and anemones also host "zoox"), but other colors on the reef are thanks to other organisms: sponges, algae, etc. To be accurate, this could read Corals get their wild hues... or Reefs get their wild hues partially...

"These algae use photosynthesis to survive and then this process adds nutrients to the environment which benefits the coral..." Sort of, but photosynthesis does not create nutrients, it uses them up (nitrogen, phosphorus, etc.), and produces organic carbon (sugars). The coral benefits from organic carbon translocated from the algae to the coral fully inside the tissues, not leaked to the environment and then recaptured.

"Coral Reefs Are Carnivores"
Yes, corals are carnivores.

"The stomach cavities corals in a reef system are interconnected. Food obtained by one polyp can be passed to other polyps in the colony." That first sentence is weird...maybe it should have an "of" before "corals"? Even still, it's not accurate: the stomach cavities of corals in a particular colony are not connected, and different colonies in a reef system are definitely not connected at all. Instead, corals have connective tissue called coenosarc between each polyp. Sugars and nutrients can move between coral polyps in a colony through this interconnected tissue.

"Coral Reefs Are a Map to Climate Change"
Ok...I'm not sure what this actually means but it's not hugely weird right off the bat.

"Corals are so sensitive to changes in the world climate that scientists study coral reef fossils to construct highly detailed chronologies of prehistoric climate patterns." Well, yes, that's pretty much true. One way that we do this is by analyzing the chemistry of coral skeletons to reconstruct past environmental conditions. Another way is to actually map the locations of fossil reefs, then date them (using other geochemical techniques) and figure out where that bit of Earth's crust used to be (like by using paleomagnetism of nearby rocks). This can give hints as to what the climate was like in that location during the time those fossil reefs flourished.

"When corals experience increased water temperatures, mass coral bleaching can occur.  When coral polyps, stressed by temperature or a variety of other environment factors, they expel the symbiotic algae that live within their tissues. When the algae are expelled, the coral appears white or “bleached.”" Yes, if you can skip over the grammar issues with the middle sentence, this is on track...but it doesn't really build on that first sentence about fossil corals above. What does coral bleaching have to do with fossil corals? Well, we could use old corals to estimate the occurrence of bleaching in the past...but that would require much more explaining than the article seems to want to provide.

Some non-coral reef inhabitants: sponges (orange) and algae are also colorful and important parts of the reef.

"Coral Reefs Have Showy Sex Lives
Some species of coral reproduce by coral spawning. This means that in unison and in some cases on one particular night a year, the coral eject large quantities of eggs and sperm into the surrounding water. This always happens at night and just after the full moon. Trillions of eggs and sperm are released all at once. When this occurs, the eggs and sperm fertilize in the water and then if the larvae that grow survive, they settle back to the ocean floor, attach themselves to a hard surface and grow."

I actually like this last mini-section. Coral spawning does sound pretty amazing, from my colleague's accounts (do read that article, it is gorgeous). Of course, the article doesn't want to end on a depressing note, since it is geared towards increasing viewership of a particular Nat Geo TV program (which looks amazing). But that last sentence holds a lot of importance - if the larvae that grow survive. That critical stage is one of the most delicate, where environmental impacts that might not kill adult corals can be the most problematic. Then the baby corals have to attach--where they choose to do so can also be critical.

  

Where not to dive

Because I research how human impacts influence the ocean, I’ve been to some pretty dismal dive sites. Human impacts include things like dumping raw sewage, trash, mine tailings, fertilizer and anything else we can think of into it; removing everything edible within reach of ever-more technologically advanced gear from it; and the global effects of changing ocean temperatures and acidification due to climate change.

Plenty of dive magazines and websites will direct you to the last remaining places in the ocean that still seem healthy and beautiful. But, if you’d like a realistic/horribly depressing idea of what our underwater world looks like when we don’t care for it, here are some of my favorites. You can also feel fairly certain you won’t see sharks at any of these places—those tend to be fished out quickly.

1. Near London, Kiritimati Atoll, central Pacific. 

Also known as the “Ulva Dance Party” site. Ulva, along with some other types of fleshy macroalgae (or seaweed), is used as an indicator for nutrient pollution. Here, “nutrient” refers to inorganic compounds like nitrate and phosphate—what you might use to fertilize your house plants. Where there are excess nutrients, whether from sewage or golf course runoff or perhaps changes in the way nutrients cycle through the food chain due to fishing, these kinds of algae flourish. Also helpful in the macroalgae-domination-transition is a relatively small herbivorous (plant-eating) fish population, due to fishing them out, too.

Ulva mustache

This site was also particularly nice when we were there, because of strong surge. In order to get down underneath the ulva and identify the few remaining live corals and the relict dead coral (we’re interested in whether these two groups are different), we had to either fight the current to stay in place for a moment, or try to go with the flow and identify on-the-fly as we rocketed back and forth across the transect. A combo of the two seemed to work best—watch the video to get a feel for what you are missing.

[I can't guarantee this won't make you seasick!]

Kiritimati does present some amazing coral-ogling opportunities away from the larger towns, however. So be sure to dive elsewhere to get an idea of how things perhaps used to look.

Coral bonanza!

2. Chachahuate, Cayos Cochinos Honduras.

Unfortunately this site is probably no longer as gross as it once was—the original “long drops” at the end of short piers on this tiny, rather densely populated sand island have now been replaced by composting toilets. So diving off of this caye may not get you an instant, roaring ear infection anymore, and the coral may be recovering. When I last dove here in 2006 – good lord, has it been that long?! – many corals were being smothered by sewage-fueled macroalgae and mats of cyanobacteria were marching over the substrate. But, there was also a cool wrecked airplane, and that kind of made swimming in poop-water Ok.

Part of the wrecked airplane, with hard and soft corals

The orange stuff is a thick mat of cyanobacteria

3. Western Teraina, central Pacific.

Kind of like the degraded part of Kiritimati, but replace the ulva with cyanobacteria and sea urchins. And intensify the surge. Note that urchins like to eat into dead coral; thus the effort of trying not to get stabbed while grabbing onto a section of dead reef to stabilize oneself long enough to attempt to identify said severely bio-eroded coral puts this experience in my top ten most exhausting endeavors. If you’d like to feel as though you’ve landed on a completely hostile aquatic planet, this is the dive location for you.

There are at least 8 urchins in this photo

Our surveys include identifying live and dead corals under a transect tape laid over (in this case, tied to) the reef

4. South Molle, Whitsunday Islands, Australia.

For one thing, you get to wear a neon “stinger suit” (see below) to prevent death by poisonous jellyfish. Also, there is very little to see because the water tends to be murky, so you may not notice that the bottom is mostly blanketed by, yet again, our friend macroalgae. My photos from our kayak-camping-snorkel adventure (seriously recommended, what fun!) have been lost, so you’ll just have to imagine this one. While the outer Great Barrier Reef far from land is still quite spectacular in many of the less-trampled locations, sites close to land tend to be less coral-reefy and more algae-field-like.

So stylish! I stole this photo from somewhere online and then forgot where. Sorry, dudes

5. Bikenibeu, South Tarawa, central Pacific.

If you ask at the hospital, you can probably be directed to get as close to the main sewage outlet as possible. The best thing to do is free-dive at this site, preferably without fully clearing your ears so that you perforate an ear drum—all the better to get a most impressive ear infection that requires five types of antibiotics to conquer. Aside from the thrill of bobbing at the surface, being tossed around by large, fierce ocean swells offshore of an island in the middle of the Pacific, you can also see an interesting example of coral monoculture. Though there is fairly high coral cover (and not as much macroalgae as some of these other sites), it is mostly all one species—kind of like an underwater cornfield. Since coral reefs are usually considered the “rainforests of the sea,” with extraordinary diversity, you are correct in thinking that an underwater cornfield probably doesn’t function the same way as a more intact reef. 

Lots of Porites rus - and not much else.

Sadly, this is only a short sampling of places humans have very obviously degraded the coastal ocean. These effects are not restricted to coral reefs, either (it just so happens I know most about them). With conscious effort, the trajectory towards degradation can perhaps be reversed…but first it has to be recognized. Wherever you next stick your head under the water, give a good think about whether what you are looking at is healthy. Do you think it looks the way it has always looked? Or can you see dead ghosts – a lack of fish, large dead empty shells, old corals covered in algae? It’s hard to know what was there before, but that’s where my kind of work comes in—to use a form of environmental forensics to figure out how things have changed, and why. 

Why geochemistry is awesome

Yesterday, I had a new paper come out online in the journal Coral Reefs. I’m really excited about this paper because (1) it’s been a very, very long time in the works and (2) I think it’s pretty neat. I also think the manuscript is pretty dense, so I’m going to make a stab at explaining it simply so that you, too, think my work is neat.

Geochemistry is a science in which we collect samples of natural things – rocks, shells, feathers, bits of wood, teeth – and then measure some aspect of their chemical makeup to learn something about the world. Geochemistry can be used to learn about the organisms whose parts are being analyzed; for instance to figure out what they ate (the old adage “you are what you eat” is true here—many times a distinct chemical signature comes with eating certain food items). It can also be used to learn something about the environment in which an organism lived or a rock formed.

Requisite beautiful-coral-reef shot. Kiritimati Island

Corals are, by geochemistry-practitioner standards, awesome. For one thing, corals make their skeletons out of chemicals in seawater—as the water chemistry changes, so does the chemistry of the skeleton. Second, corals grow larger over time by adding new layers onto their skeletons, while the old skeleton often just sits there as a semi-permanent record of conditions at the time that bit of skeleton formed. This is like keeping track of daily weather on slips of paper added to a pile—you can then dig back through the pile to see how things have changed over time.

Third, corals also have a built-in time-stamp on these records: the density of the skeleton fluctuates with the seasons, leaving bands that can be seen by x-ray or CT scan in samples (see my earlier post). For coral samples collected live, these bands can be counted back in time; corals that are dead can be dated using another aspect of geochemistry: the amount of a particular radioactive element that decays at a known rate can be measured to back-calculate how long ago that coral was alive.

The fourth excellent/horrible thing about corals is this: while they sometimes act as passive recorders of water chemistry, both the density and the chemistry of the skeleton can also be affected by other things – notably how happy the coral is (corals that are heat-stressed “bleach” by expelling their colorful symbiotic algae, which screws with skeletal growth and chemical incorporation). Other aspects of coral biology such as spawning or food intake also can change the chemical signature.

If all of the different influences on the coral skeletal chemistry can be disentangled, there is fantastic potential for long reconstructions of both the environmental conditions in which the coral grew and the coral’s reactions to those conditions (over the last few100s of years, or even longer if dead corals are also used).

But that’s the hard part: disentangling. For one reason, we keep thinking that we know what controls each chemical signature (and this is the “royal we,” including me and other scientists), and then we figure out that it’s more complicated: we thought the concentration of strontium was a direct, unbiased measure of water temperature; now it seems that this is also very slightly affected by the skeletal growth rate. We also thought that the ratio of two different isotopes of oxygen in the skeleton was only controlled by water temperature and salinity (isotopes are different forms of the same element that behave the same chemically but have very slightly different weights), but then we figured out that calcification rate also matters.

Not totally happy coral

And here’s where our work comes in: faced with weird oxygen isotope data that couldn’t physically be explained by any combination of water temperature, salinity, or calcification, we knew there must another as-yet-unidentified impact at play. What we saw was a big jump in the baseline of the data after a major coral bleaching event.

Now, a quick tangent: coral bleaching is an extremely worrying phenomenon. Corals get most of their nutrition from the symbiotic algae they house in their tissues; when bleached, they can starve to death or become more susceptible to disease. With global water temperatures increasing, coral bleaching is becoming more frequent. The big question in the survival of coral reefs as we know them is therefore: can corals adapt?

One way corals might be able to adapt to warmer waters is by kicking out “weak” forms of symbiotic algae and trading them for genetic strains that are more resistant to heat stress. This is called the “adaptivebleaching hypothesis”—the idea being that by acquiring more heat-tolerant symbionts, corals can survive the onslaught of climate change (at least for a while).

 Our data might be a reflection of this very phenomenon. If the symbionts the corals housed before the bleaching event were physiologically different than those after, maybe the skeletal chemistry would be different.

There has been a lot of activity lately from scientists trying to understand the nitty-gritty workings of coral calcification. We were able to synthesize this work and put forward a potential mechanism that could cause our observations (based mostly on a change in pH at the calcification site).

We also tried to test the idea directly by collecting lots of little nubbins (possibly the best technical term ever) of live coral. We identified their symbionts using DNA methods (and here “we” means my colleague Melissa Garren), and then the corresponding oxygen isotope values. What we found was a hint of a relationship—so we didn’t disprove our hypothesis.

Our "nubbins" were essentially mini-core samples from large corals

This area of research still needs more work, but it is exciting; if this signature is real, it could be used to retrospectively test for adaptive bleaching in other corals during other bleaching events. This is important to predict the outcome of bleaching events and manage coral reefs as we face increased heat stress. If corals can adaptively change symbionts, can we help them do this? Can we more effectively manage outplanting and reseeding efforts to restock damaged reefs?

I hope that this paper stimulates new ideas and more projects to help answer these questions.

How to lose your eyesight

I’d love to be writing up my latest research for publication right now, especially since it's Academic Writing Month. But that project is currently in the waiting-for-various-things-out-of-my-control stage, so I can’t progress. Instead of biting my nails to the quick and sending inappropriately desperate emails across the globe, I have shifted focus to some lab-based tasks. What are these things? Come along and I’ll show you what fun I have! Both tasks I’m working on this week involve squinting at tiny things.

Task 1: Are the annual growth bands in my coral cores really annual?

Much of what I do involves collecting core samples from large coral heads. Much like trees, corals grow larger with time and form annual bands within their skeletons that can be visualized using x-rays or CT scans. I then measure the width and density of these bands to calculate the coral growth rate over the length of each core, and this tells me essentially how healthy the coral was over that time period.

(A) collecting a core from a nice big coral (B) the top of the core (C) what (B) it looks like once cut into a slab and (D) an x-ray showing annual density banding. If the top band in (D) is 2006, you can count years backwards as you move down the core, going back in time.

But of course this whole concept is predicated on the idea that the bands I identify are formed yearly. In some corals the banding is clear and lovely and life is happy. My most recent cores are not this type. They have painfully vague banding, and while I’d like to think that my experience means I can successfully identify the bands despite their lack of clarity, I’d like to be sure. 

This coral has nice banding. I like it.

This coral has rather shitty banding, and makes me want to poke my eyes out.

So, what to do? I first started by trying to count the number of something called “dissepiments” in the images. You can picture a coral as a tall apartment building, one that is constantly under construction; the coral adds a new floor to the top of the building once a month. Only the top floor is occupied by living coral tissue, hard at work on construction—once one level is complete, the coral seals this off and moves upstairs to start work on another. This is a decent illustration, because the coral skeleton actually looks a lot like this on magnification. The “floors” of the apartment building are equivalent to the dissepiments. All this is to say that one way to verify whether annual bands are annual is to count dissepiments—if there are about 12 of them for each of the bands identified, you are probably on the right track.

This could be easy if the corals behaved. (Nothdurft et al. 2005)

But really they look more like this and it hurts to find those little things the red arrows are pointing to.   (From Barnes and Lough 1992)

Another method is to measure the chemistry of the coral skeleton. While the coral is constantly building its skeleton, the composition of the skeleton changes ever so slightly with changes in the surrounding water—whether due to seasonal fluctuations in temperature, sediment in the water from river runoff, etc. I can use this to analyze a particular aspect of the skeletal chemistry that I know changes seasonally every millimeter down the core. This way I can put an independent time-scale on the core and then compare this with the time-scale I got by picking out my bands. In this case, I’m using the ratio of strontium to calcium, which changes due to water temperature (the skeleton is mostly made of calcium carbonate—CaCO₃—but other elements can substitute for Ca).

This is the idea. The black wiggly lines on the left show seasonal water temperature change (low in winter, high in summer), and conveniently the banding in the coral x-ray lines up with the wiggles! (From Bagnato et al. 2004)

Making these measurements is pretty straightforward but takes a lot of time:

(1) I cut the cores with a rock saw to produce a flat slab.

(2) I take the slabs to a medical facility and get them xrayed to reveal the particular convolutions of the coral growth direction in that sample.

(3) I further cut the coral slabs so that the maximum growth axis is exposed for sampling.

(4) Using an automated CNC milling machine and a lot of swearing, I grind a ledge into that exposed edge from which I’ll collect my samples.

(5) I clean out all of the powder from cutting the slab and milling the ledge that has accumulated in the coral’s pore spaces using an ultrasonic probe. This device blasts high-frequency waves through water such that tiny air bubbles form and explode, which helps clean the material, and destroy your hearing (I do wear earmuffs for this).

(6) The samples dry overnight and then I mount them on the CNC machine again and mill precise, tiny amounts of coral skeletal powder every 0.5 mm down the edge of my clean and beautiful skeletal ledge. Each of these bits of powder is caught on a square of waxed paper and then carefully transferred into a tiny plastic vial, labeled with the sample number. Too much coffee is not good for this step.

I get really excited when step 6 is over. Especially when I get to use pretty vials to spice up the lab-life.

(7) I acid-wash and dry a lot of larger plastic vials.

(8) I use a micro-balance (a very tiny and sensitive scale) to weigh out about 50 milligrams of coral powder from each of the 0.5 mm-increment samples into my clean vials. I attempt not to sneeze while doing this.

(9) I tire out my thumb using a pipette to add super-clean acid to each of the vials to dissolve the coral powder to the correct dilution.

(10) I gratefully hand the samples over to my colleague, who uses a machine called an Inductively-Coupled-Plasma-Atomic-Emission-Spectrometer to measure the Sr/Ca ratio in each of my dissolved samples.

Task 2: What’s up with the benthic foraminifera in my sand samples?

Foraminifera are single-celled marine organisms, and the “benthic” descriptor means they don’t live in the water column, but instead on the ocean bottom or on other substrates, like seagrass. Forams make complex shells, and in some areas these shells make of the majority of reef sands.

I’ve been collecting sand samples from my study sites and using a stain called Rose Bengal to dye all of the living foraminifera a lovely shade of pink. The dead shells remain white. This means that I can compare the living and the dead assemblages—the ratio of different types of foraminifera—to see if there has been a change over time (well, between “now” – alive, and “before” – dead).

Some of my pretty forams. This is from my recent paper with Sheila Walsh 

                                                                    

Benthic forams are sensitive to water quality—some types (A and B above) take over in dominance when the water is clear and low in nutrients, but this balance shifts (to critters like C-F above) if the water becomes nutrified (i.e. we dump sewage, fertilizers, etc. into it, or change the nutrient dynamics by removing the big tasty fish).

So how to quantify the assemblages? I scatter a scoop of my stained and dried sand sample onto a gridded tray, place it under my microscope, and then use a pin with a bit of surf wax stuck to the end to grab individual foram shells out of the sand and stick these onto little slides. Once I have enough, I count them. Voila! 

Unfortunately for my eyes, it takes a very long time to get enough—several hours per sample. And for science’s sake, I have a lot of samples…so…back to it!