Author: emdillon

Waves of Denticles and my Art-Science Journey

By Vicky Chan

As a part of an Art and Sciences course I took this past spring quarter at UC Santa Barbara, I learned about THEMAS, practiced making digital art, and created a 3D sculpture made of shark denticles.

So what exactly is THEMAS? THEMAS stands for Technology, Humanities, Engineering, Mathematics, Art, and Science. Throughout the course, we explored topics ranging from how helicopters work to the thoughts of Greek philosophers. We were encouraged to make things and learn how to ‘swim’ by engaging with these works. I entered this class wondering how the Arts and Sciences were connected, and I came to realize how highly interconnected all these themes are. For the final project, we were challenged to create a mediated world encompassing THEMAS, based on a subject and artistic media of our choice.

Inspired by this final assignment, I took the initiative to learn a new tool: 3D modeling. I began by trying different programs and chose Blender, an open-source 3D modeling program. Blender is very versatile and offers basic to advanced features for modeling. However, one can start with a template shape and use the 3D grid space to place vertices in order to build any shape one can imagine.

At the same time as taking the class, I was also working with the Baseline Caribbean team on a research project involving shark dermal denticles. I realized that this would be a great opportunity to showcase shark denticles in the form of a 3D sculpture. The relationship between denticle morphology and the functional properties of shark denticles is quite fascinating. Inspired by how different groups of denticles are arranged on the skin, I decided to model several basic denticle morphotypes and create an artistic piece that would bring awareness of denticles and their intriguing diversity of forms to the public.

dd1

Learning how to work in 3D space was a challenge at first, as there were many different shortcuts to create new vertices and edges. I gradually got the hang of creating the denticle base first, then the crown.

dd2

These were the final denticle models I created. (From left to right: a drag reduction denticle, a generalized function denticle, and an abrasion strength denticle.)

I then layered these denticles in 3D space, shifting the angle of the denticles ever so slightly and recreating a motion that is similar to a wave in the ocean.

Here is the finished 3D sculpture:

dd3

dd4

This is a mediated world, as it draws from elements of both reality and fiction. I created the shark denticles based on actual denticle morphology and arrangement patterns on the skin but used fictional sizes and colors to create an artistic composition. I’m glad that this class gave me the motivation to create an informed piece like this and for revealing to me more connections between Art and Science.

3D printing a shark dermal denticle

This week, I printed a 3D model of a silky shark (Carcharhinus falciformis) dermal denticle, which was enlarged nearly 500x. It took around 6 hours to print, but it was worth every minute. Lucky for you, you can watch the whole process here in 30 seconds!

Tetiaroa: sampling a little piece of paradise

Tetiaroa is an atoll I never expected to visit. Privately owned by Marlon Brando, this island hosts an interesting mix of hotel guests (paying €3000-4000 per night to stay in luxurious beachside villas), staff, and researchers. Upon becoming enamored with the island’s beauty and later purchasing it, part of Marlon Brando’s vision was to preserve and showcase its natural resources as well as facilitate scientific investigations. As such, the Tetiaroa Society was born, and an ecostation was constructed to provide logistical support for visiting researchers like us.

But why Tetiaroa? Let me back up a bit. First off, why is the Baseline Caribbean team in the Pacific? The short answer is that we can use similar sampling techniques to answer interesting ecological questions about the histories of coral reef communities across wide gradients of reef health, oceanographic conditions, and human settlement histories. Sharks are also much more abundant on many islands in the Pacific than in the Caribbean, making it more feasible to retrieve high-resolution chronologies of predator assemblages over space and time. In other words, we can get more bang for our buck, or more denticles in smaller samples. It’s a win-win situation.

Within the Pacific, French Polynesia is an ideal study system for several reasons. Here, sharks are ecologically important, revered in Polynesian culture, and help bolster tourism. French Polynesia was also recently designated a shark sanctuary. Within French Polynesia, the islands have different human settlement histories and are known – at least anecdotally – to have varying numbers of sharks. First, we can leverage this gradient to quantify how shark abundance and diversity differ spatially across islands. Second, we can explore temporal patterns of shark abundance and diversity in parallel with the diverse human histories of each island. For this study, we decided to collect samples from Moorea, Tetiaroa, and Rangiroa, which span this gradient and are easily accessible.

Tetiaroa is geographically close to Moorea and Tahiti (Society Islands), which have high population densities and human histories stretching back at least 1000 years. Tetiaroa is a bit different. While it was discovered by the Polynesians around the same time as the other Society Islands, it did not host permanent human settlements until centuries later. In its early history, it was visited infrequently and its resources were exploited at low intensities by people inhabiting the other Society Islands. Even later, its resident population was much smaller than that on Moorea or Tahiti, and it was used as a retreat by Polynesian royalty in the 19^th century. Today, there are no permanent residents, and half of the reef and lagoon has been set aside as a marine reserve.

This brings us to the other day, when we departed Moorea to begin our journey to Tetiaroa. We were originally scheduled to take a boat from Tahiti. However, the bad weather that plagued our sampling efforts on Moorea struck again. We received an email two days before our trip informing us that the boat was cancelled but that we might be able to take a plane instead. Our plans were turned upside-down as we waited in suspense. Would we actually make it out there after so much preparation, or would our plans be thwarted?

The evening before we were supposed to depart, I received another email confirming that a flight was indeed available. The catch was that we had a luggage allowance of 10kg each total. We started scrambling to get everything packed. What would stay on Moorea until the end of the trip? What did we absolutely need in Tetiaroa? What would we leave in Tahiti and take with us to Rangiroa? I currently have personal items scattered across three islands as I write this blog post. With all our sampling gear and SCUBA equipment combined, we really only had room for a t-shirt, a bathing suit, and a toothbrush. Talk about traveling light! Even then, we were over the weight limit. Luckily, they let it slide.

Air Tetiaroa does not fly out of the regular domestic terminal at the Papeete airport. They have their own private building and security, and they serve fancy juices for free in the waiting area. We indulged in a small piece of this luxury that we could otherwise never dream of affording.

The flight was only 20 minutes, but it provided a breathtaking view of Tetiaroa. Yesterday, the wind had been too strong for the plane to land. Today, we were in luck. The Twin Otter plane was wavering back and forth as we approached the tiny runway for the final descent. Even seconds before contacting the pavement, it felt like we were undulating in the wind. Despite these rough conditions, kudos to the pilots for a solid and safe landing. We had made it!

We were greeted with strong winds and a downpour. This would be a continuing trend during our days on Tetiaroa. But more on that later.

[to be continued]

A sediment core inspired road trip

US GEOLOGICAL SURVEY MENLO PARK CAMPUS
MENLO PARK, CA

As coral reefs accrete upward, their histories become buried beneath the surface. One way to unravel this history is to visit areas where the older reef has been exposed by excavations, road cuts, or storm channels. This is what we did in Bocas del Toro, Panamá and in the Dominican Republic’s Enriquillo Basin. In most places, however, living reef or mangroves grow on top of the Holocene reef. To access the underlying history, we can insert several-meter-long sediment cores into the substrate. While this technique samples a sliver of the surface area of a reef, it has the unique advantage of looking back in time. Depending on the rate of reef accretion and sedimentation, sediment cores can travel back several hundred to several thousand years with high temporal resolution. The remnants of the animals and plants captured in these cores help paint a picture of the reef in the past and how it has changed over time.

Today, I had the good fortune of sampling a gravity core extracted from Palmyra Atoll’s lagoon by a team of USGS scientists. In addition to being home to numerous sharks, Palmyra has an interesting human history despite never being settled. The atoll was originally discovered in 1802 when an American ship was blown off course in a storm. In 1862, Palmyra was claimed by the Kingdom of Hawaii, and it later became a U.S. territory following Hawaii’s annexation and subsequent statehood. At that time, it was privately owned by the Fullard-Leo family. During WWII, the U.S. Navy took over and drastically altered the atoll for use as a naval air facility. Afterwards, it was occasionally frequented by yachters despite its remote location – a nearly 1000-nautical-mile sail southwest of Hawaii. From 2000-2001 onwards, the atoll has been under the protection of the Nature Conservancy and U.S. Fish and Wildlife Service as a National Wildlife Refuge, and a handful of scientists and donors visit each year.

The 3.2m-long sediment core that I sampled covers nearly 650 years of history on the atoll, capturing its pristine state prior to discovery in addition to the last 200 years of sparse human occupation. We will use the core to begin investigating whether shark baselines on the atoll are naturally dynamic and whether the abundance and diversity of sharks changed after the arrival of humans. Palmyra has been the location of many shark tagging and survey studies over the last 12 years since the creation of the Palmyra Atoll Research Consortium (PARC), and it is considered to be a relatively untouched, healthy reef ecosystem. This new historical time series will help us understand whether its condition has fluctuated over time before these monitoring efforts began.

This opportunity was certainly worth the 10-hour round-trip road trip from Santa Barbara to Menlo Park, which is located about 40 minutes southeast of San Francisco. In addition to picking up the core from the sample storage refrigerator on the USGS campus, my secondary aim was to use their facilities to slice it into 64 5cm-long segments, each representing about 10 years of reef history. The core was composed of very fine, silty material, so cutting through it was not difficult with the help of some metal utensils and a meter stick. Furthermore, the challenging task of cutting the core in half through the PVC piping had already been accomplished. I carefully measured and cut each section and placed them into individual labeled plastic bags. After several hours of meticulous slicing and record keeping, I had amassed quite the pile of samples and was caked in a thin layer of dry mud.

Reminiscing Klein Curaçao

28 February 2017, 0545HRS

It was still dark out when we departed the field station. Groggily, we loaded up the truck with our dive gear and SCUBA tanks while sipping coffee to try to wake up. The clock was already ticking. We had 30 minutes to get to the dock in Caracasbaai before the ferry was scheduled to leave.

This was a risky yet critical endeavor. Our aim: collecting sediments from the reefs of Klein Curaçao, a tiny, uninhabited island located approximately 15 miles off the southeast point of Curaçao. Less visited or fished than Curaçao, the reefs there would provide a more ‘pristine’ end member with which to compare our other Caribbean samples. The orientation of the island, which was nearly perpendicular to the trade winds, meant that the leeward side would be quite sheltered despite lacking any lagoonal environments. But would the sediments be fine enough to contain shark dermal denticles? This was the gamble.

We arrived at the dock just in time and confirmed that no recreational divers were joining the group. We would therefore have the flexibility to select our dive sites and use the tour group’s dingy to lift our heavy sediment samples to the surface. We decided to board the ferry.

After a rough 1.5-hour ferry ride, the island’s barren landscape came into view. A thin strip of white sand beach intersected the cerulean sea and stormy sky. A lighthouse, accompanied only by a rusting shipwreck, rose in the distance, breaking the otherwise flat horizon. ‘Paradise,’ thought the tourists. ‘Healthy reef,’ thought our team.

Descending along the reef slope, I was astonished by the vibrant reef and number and size of the fish. Large parrotfish swam by in a swirl of colors and movement, and I had a standoff with a toothy barracuda within minutes of entering the water. This reef was obviously full of life. While the staghorn coral (Acropora cervicornis) had likely died off in the 1980s like in many other places in the Caribbean, many other coral species abounded.

The fine sand on the beach was a good sign. Feeling the sediment along the reef substrate, we found that the gamble had paid off. There were patches of fine, silty carbonate sediments! I let out a sigh of relief through my regulator and signaled ‘okay’ to my dive buddy. We collected eight bulk samples in spots where sediments had accumulated on ledges or patches between corals. Here, the sand grains were often held in place by an interlocking matrix of dead staghorn coral, limiting mixing.

The day, however, was far from over. Upon arriving back at the dock on Curaçao, we loaded the samples and gear into the truck and began what should have been a 20-minute drive home. Except that it was Shrove Tuesday of Carnival and half of Willemstad was blocked off for the big parade. After desperately searching for a clear route, we stopped to get directions from a police officer, who gave us the disheartening news that we would have to drive around half of the island to get home. An hour and a half later, we finally reached the station, exhausted yet victorious. What a roller coaster of a day and a fitting end to the expedition.

DCIM100GOPRO

Fetching the pallet

Today, I got a very good workout. Our 604kg (~1300 lbs) pallet could only be delivered as far as Los Angeles, so I had to go pick it up myself. After a 354km (220 mile) road trip, a fortunately uneventful visit to the US Customs Office, and nearly 1.5 hours of unloading the crates from the truck, the samples are finally safe and sound in the lab at UC Santa Barbara.

Denticle side view

Some of the denticles that we find in the sediments are exceptionally well-preserved. Here is an example of a denticle that still possesses the basal plate that once held it to the underlying skin. In many cases, though, we only find the crown (the top part). This side view taken via scanning electron microscopy (SEM) can give you an idea of the three-dimensionality of a fully intact denticle. It almost looks like some strange sort of hat (which perhaps I will 3D-print, patent, and sell online if our funding runs out prematurely or is frozen by the government… just kidding).

9_edit

Some things you may notice about this denticle:

It has a very thick crown proportional to the crown length. While many fast swimming shark species have denticles that are thin and light, this denticle means business. Its thickness lends durability, forming a protective ‘armor’ around the shark. This type of denticle is generally found on sharks that live in close-association with the benthos.
The crown is positioned at a slight angle relative to the base. This angle can alter the way in which water flows over the denticle, thereby changing the hydrodynamics of the shark on a micro level. Some of the fastest swimming species are thought to be able to vary this angle through adjustments to the basal plate and skin tension (Raschi & Tabit 1992).

Literature cited

Raschi W, Tabit C (1992) Functional aspects of placoid scales: a review and update. Aust J Mar Freshw Res 43:123–147

Evidence of a nighttime visitor

Scanning electron microscope image of a denticle extracted from the fossil reef in Bocas del Toro, Panama. 283x magnification.

Here is a denticle that I was not expecting to find. It belongs to a shark that I only on second thought included in my denticle reference collection, one that ought not belong on a coral reef. This appears to be the denticle of a crocodile shark (Pseudocarcharias kamoharai). While denticles can normally only be identified at the family level, this one fails to resemble any other denticle in my reference collection… except one. It looks almost identical to those that I isolated from the skin of a verified crocodile shark at the Smithsonian National Museum of Natural History (image below), except that it is a little smaller and much more weathered.

Scanning electron microscope image of a denticle isolated from the body of a crocodile shark for inclusion in our reference collection. 185x magnification.

Not only are crocodile sharks unassociated with coral reefs – in fact they generally only ascend from the depths at night to feed – but this shark has not been documented in the region in which this denticle was found. What’s more amazing is that this denticle is not even modern. It was extracted from our 6,600-year-old fossil reef!

While you may have never heard of a crocodile shark, they are listed as ‘Near Threatened’ on the the International Union for Conservation of Nature (IUCN) Red List. We obviously need to learn more about this species of shark in order to better protect it.

Our finding suggests that crocodile sharks did occasionally venture onto the lagoonal reefs of Bocas del Toro, Panama in the past (and perhaps even in the present day as well). More importantly, to me, this denticle epitomizes the beauty of the technique. Extracting and analyzing dermal denticle assemblages can reveal the rare, cryptic, or ephemeral elasmobranch visitors on reefs, an otherwise very challenging task to accomplish.

Crocodile shark. Source: PIRO-NOAA Observer Program. Wikimedia commons.

Time to ring in the New Year with some coral measurements

Sometimes we do a little more than just dig in the sand. Over the New Year, Mauro and I taught the coral reef ecology unit of an undergraduate field course from the University of Wisconsin–Green Bay and St. Norbert College at the STRI field station in Bocas del Toro, Panama. While we spent a portion of our time in the lab discussing the importance of the area and looking at creatures under microscopes, we also brought the class snorkeling on the reefs with us to do some field work and explore. For some of the students, this was their first time snorkeling and seeing a coral reef in person. For me, that moment was life-changing, so I’m delighted to be able to share this magic with them. We visited a diversity of reefs during the trip, some of which were clearly healthier than others, and we discussed the differences between them and the potential underlying anthropogenic and natural drivers. For example, instead of merely reading that runoff and eutrophication are harmful for coral reefs, the students were able to glimpse algae-covered corals off the coast of the Changuinola River floodplain, the site of extensive banana plantations.

The students also got some hands-on experience doing field work. With the help of the class, we’re investigating long-term bioerosion rates on branching corals, specifically staghorn (Acropora cervicornis) and finger (Porites sp.) corals, in Almirante Bay. This study will improve our understanding of the carbonate budget on reefs in the region and, in particular, which way the seesaw between reef accretion and dissolution is tilting. This question pertains directly to the future of reefs in Bocas del Toro as well as how resilient they may be to future perturbations such as storms. Furthermore, it helps us key into one of the processes contributing to the reef substrate, which is where our lab collects bulk samples and sediment cores to reconstruct historical reef communities. Understanding whether the reef is actively contributing to this substrate through coral growth and reef accretion or whether it is stagnant or even shrinking can provide context for interpreting patterns of microfossil abundance. This study may also shed light on dates we computed for corals extracted from cores at these sites, which suggest that some of the dead corals lying on the surface are far from modern.

We started this study in December 2015 by collecting, measuring, and redeploying recently-dead pieces of coral on mesh plots. We successfully relocated the plots this past December and took our first annual measurements. Some bioeroders were even see in action on the reef! Interesting trends are already starting to emerge in the data. One of the students will be conducting an independent study to try to unravel some of these patterns, so stay tuned for her findings.

DCIM100GOPRO

Twins in time

blog-1-18-17

At first glance these two shark dermal denticles appear quite similar, right? Sure, one is a little wider than the other, but they both have distinct peaks, ridges, and intriguing honeycombed ornamentation on their crowns. What if I was to tell you that they are separated in time by about 7,000 years. Which do you think came from the fossil reef?

(more…)

The next installment of shark denticle photos is here!

Over the next several weeks, I’ll be showcasing scanning electron microscope (SEM) images of some of the denticles that we extracted from the modern and ~7,000-year-old fossil coral reefs in Bocas del Toro, Panama. While the SEM images that I released previously were from known species of sharks in my reference collection, the denticles that I’m about to show you came from sediment samples we collected and processed. Our job now is to become sleuths and figure out what types of shark shed them.

Like a portrait, these denticles can paint a picture of the sharks they came from. They are the bards of the sharks of lore, lost in the sands of time… Ok, that’s one massive cliché (and I might be a bit too obsessed with denticles), but you get the point. Denticle morphology can provide us with useful insight into the historical ecology of sharks. For example, a denticle’s thickness can reveal whether its owner lived in the crevices of a reef or up in the water column. Its ridges can tell us whether or not it was a fast swimmer, speed which it may have used to catch nimble prey or swim long distances.

Some denticles are better storytellers than others, however, so we need to figure out who is who. This is one of the more unusual denticles that I’ve found so far. What type of shark do you think it may have come from? Stay tuned for my interpretation.

15_edit

The third iteration of sediment processing

The sediment processing workshop will now resume in a new location: UC Santa Barbara. First things first, I had to transform the lab. Since the size of each sample was smaller, I could also downsize the set-up a bit and move everything indoors. This meant no more massive outdoor ‘drying bubbles’ or tent-covered mazes of 5-gal buckets for digesting sediments… at least for now. We did, however, order 100 gallons of acetic acid. What a lot of vinegar!

The funnest challenge was building the new drying oven from an old storage cabinet, several power strips, and a box full of incandescent light bulbs. Drilling through the metal cabinet to feed the cords through was by far the hardest part. Standard drill bits didn’t cut it, so I had to upgrade to a step drill bit. That worked like a charm, but it still took several hours of drilling. Once everything was installed, I turned on the power strips and basked in the glow for a moment. It was toasty – exactly as intended! When I did a test run the next morning, I was pleased to find that the sediment dried in under a day.

Now, we are just about ready to rock and roll…

My 250 pound delivery

Today was my lucky day! All of my precious samples are now here and ready to process. Hilariously, the mail distributors on campus lugged them up to the mail room on the 3rd floor, just so I could bring them all the way down again and into the building across the way where the lab is located. With the help of an old rickety cart (that fortunately did not collapse under the weight of the sediment), all of the boxes were transported in two exhausting trips. Another chapter of field work closed. May the sieving begin!

20161202_103908

Getting the samples packed up and shipped home

Now the time had come to get all of the sediment home, which proved to be a tad tricky. First, we had to get the samples to Honolulu. As plastic crates are bulky and expensive, I ended up packing the individual samples into ten sandbags. What better to use than a container designed for sand?

The charter flights off the atoll are both few and far between and weight restricted. Luggage is limited, and they sometimes swap people around in the plane for takeoff and landing. Therefore, fitting 250lbs of sediment onto one flight was not going to happen. The pilot was even grumbling about putting 1-2 bags on the plane. In fact, the sediment was shipped off the island on three separate flights over the course of about two weeks! I was still on the island (having transitioned by that point to bug counting and tree measuring), so I was able to help orchestrate this operation. Fortunately, one of the donor trips did not bring much luggage, so I was able to fit the majority of the bags on that flight. Later, I certainly breathed a sigh of relief when I had accounted for all ten sandbags at the airfield in Honolulu.

The next step, of course, was shipping the sediment samples back to the mainland. For anyone who’s shipped anything large or heavy recently, you know that it can add up fast. To partially circumvent this cost, we shoved the samples into 11 large flat rate boxes and sent them on their merry way only $200 later. This sounds simple enough, but it involved a lot of (somewhat unnecessary) running around the city. However, after this ordeal, we still had several hours to kill in Waikiki before our flight home. As a side note, the abrupt transition of living on a tiny remote island with 20 other people to arriving in the bustling tourist town of Honolulu was quite overwhelming! Particularly because it was Halloween.

The next few days were spent anxiously checking the package tracking information. Would the samples arrive in one piece?

Some pictures from today’s snorkel at North Barren Island

Today we went on the snorkel of a lifetime. Or perhaps it was just Palmyra’s way of saying goodbye, as this was also our last snorkel of the trip. I followed a couple of juvenile blacktip reef sharks around the reef, was circled by a curious turtle, and was blown away by the number and diversity of fish I observed. Despite being damaged by coral bleaching last year, this reef is incredibly resilient and is now on its way to recovery. Absolutely amazing!