Research Explainer: How I learned to stop worrying and trust the clams

Two giant clams off the coast of Israel. Left: Tridacna maxima, the small giant clam. Right: Tridacna squamosina

Another year, another new paper is out, another clamsplainer to write! The fourth chapter from my PhD thesis was just published in Proceedings of the Royal Society B. This study represents five years of work, so it feels great to finally have it leave the nest. In this study, we investigated the comparative growth of fossil and modern giant clams in the Gulf of Aqaba, Northern Red Sea. Back in 2016 during my PhD, I knew I wanted to study giant clams because they are unique “hypercalcifying” bivalves that grow to huge sizes with the help of symbiotic algae living in their bodies. The clams are essentially solar-powered, and use the same type of algae that reef-building corals depend on! Unlike corals, which are the subject of a ton of research related to how they are threatened by climate change, habitat destruction and pollution, comparatively little is known of how giant clams will fare in the face of these environmental changes. Are they more resistant than corals, or more vulnerable?

T. squamosa on the reef off the coast of Eilat.

I had strong reason to suspect that the clams are struggling in the face of human changes to the environment. They can bleach like corals do when exposed to warm water, and have been observed to be harmed when waters are less clear since they are so reliant on bright sunlight to make their food. But I need a way to prove whether that was the case for the Red Sea. I needed to travel to a place where fossil and modern giant clams could be found side by side, so their growth could be compared using sclerochronology. We would count growth lines in their shells to figure out how fast the grandaddy clams grew before humans were around, and compare that ancient baseline to the growth rate of the clams in the present. Giant clams make growth lines every day in their shells, giving us the page numbers in their diary so we can figure out exactly how fast they grew! We can also measure the chemistry of their shells to figure out the temperatures they experienced from the oxygen isotopes, and even what they were eating from the nitrogen isotopes.

A map of the Gulf of Aqaba, where our study took place. My talented marine scientist partner Dana Shultz made this map!

It just so happened that UCSC’s Dr. Adina Paytan was leading an NSF-funded expedition to the Red Sea in summer 2016, which represented a perfect place to do this work. There are many age dated fossil reefs uplifted onto land around the Gulf of Aqaba on the coasts of Israel and Jordan, and there are three species of giant clam living in the Red Sea today: Tridacna maxima (the small giant clam), Tridacna squamosa (the fluted giant clam), and Tridacna squamosina. Tridacna squamosina is particularly special because it is only found in the Red Sea, making it an endemic species. It is extremely rare in the modern day, with likely only dozens of individuals left, making it potentially endangered.

So I set off with Adina and two other students to live for two months in in the blazing hot desert resort town of Eilat, Israel, working at the famous Interuniversity Institute. Getting a permit from the Israeli National Parks Authority, I collected dozens of empty giant clam shells (no clams were harmed in the course of this study!) from the surf zone and from ancient reefs ranging from a few thousand years to almost 180,000 years old. I also spent a week over the border in Aqaba, Jordan where I worked with Dr. Tariq Al-Najjar, my coauthor and director of the University of Jordan Marine Science Station. Tariq is a specialist in algal productivity in the Gulf and was an excellent resource in trying to understand how water quality has changed in the area through time. He pointed out that over the years, the Gulf of Aqaba has had an increased nutrient supply far above what it received in historic times. For nearly 20 years the Gulf was subjected to excess nutrients from Israeli fish farms, which caused tremendous damage to the reefs of the area with their releases of fish waste. The farms were finally forced to close after a long lobbying campaign from Israeli and Jordanian scientists and environmentalists. But even after the farm pollution stopped, there was still increased nutrient supply from runoff and even carried into the Red Sea by dust in the form of nitrate aerosols. These aerosols are produced when our cars and power plants release nitrogen oxide gases, which react in the atmosphere to form nitrate and fall during periodic dust storms that hit the Red Sea a few times per year.

All of these sources of nitrogen are fertilizer for plankton, causing what scientists call “eutrophication.” When plankton blooms, it literally causes the water to be less transparent, which could reduce the clams’ ability to gather light and lead to them growing more slowly. At least that was my hypothesis, but I had to prove if it was true or not. So during that summer and over the next few months, I cut dozens of clam shells into cross-sections, used a special blue dye called Mutvei solution to make their growth lines visible, and took pictures of those lines with a microscope. Then I counted those lines to figure out how many micrometers the clam was growing per day.

A picture showing some of the fine daily lines visible in a blue-stained shell

Here I hit my first challenge: it turned out some clams were putting down one line per day as expected, but some were putting down twice as many! But the way I was using to discern between the two was to measure the oxygen isotopes of the clams’ shells, which forms a record of temperature. By counting how many lines appear between each annual peak of temperature, we confirmed some were daily and some were twice daily. But the oxygen isotope approach is expensive would not be scalable across the dozens of shells I had collected.

Annual growth lines in the shell of a Tridacna maxima clam

Then I remembered that I could measure the lines in the inner part of the clams’ shells, which are formed annually. By counting those lines and then measuring the length of the clam, I could get an approximate measure of how much it grew per year on average. This would allow me to calibrate my band-counting and discern which records represented daily lines and which were twice daily! What a relief.

So I went through all of the shells, counting lines and gathering growth info for as many shells as I could muster. It meant many hours staring at a microscope, taking pictures and stitching the pictures together, then squinting at my computer screen highlighting and measuring the distance between each growth line. I had hoped to come up with an automated way to measure it, but the lines turned out to be faint and difficult for the computer to distinguish in a numerical way. So instead I just powered through manually. When I had the raw growth data, I then transformed them to a pair of growth constants commonly used in the fisheries literature to compare growth across populations. When I put the data together across all 55 shells, I was surprised to discover that my hypothesis was totally incorrect. The clams were growing faster!

Growth constants for all three species, comparing fossils and modern shells. We used two growth constants (phi prime and k) to help control for the fact that our clams were at different sizes from each other. You wouldn’t compare the growth rate of babies and teenagers and try to make any broader assumptions of their relative nutrition without some additional attempts to normalize the data!

Science rarely goes according to plan. The natural world is too complex for us to follow our hunches in understanding it, which is the main reason the scientific method came about! But at a human level, it can still be shocking to realize your data says you were totally wrong. So after a few days sitting and ruminating on these results and what they meant, I remembered what Tariq and other scientists had said about nitrates. The clams are essentially part plant. They use photosynthetic symbionts to gain most of their energy. And much as nitrate pollution can fertilize plankton algae growth, maybe it could do the same for the algae within the clams! It had previously been observed that captive giant clams grew faster when “fertilized” with nitrates or ammonia. But such an effect had never before been observed in the wild. We needed a way to demonstrate whether the Red Sea clams were experiencing this.

Fortunately, the clams also keep a chemical record of what they’re eating within the organic content of their shells. Shells are a biological mineral, made of crystals of a mineral called calcium carbonate. But within and between those crystals, there’s a network of proteins the clam uses like a scaffold to build its shell. Those proteins are made of amino acids that contain nitrogen. That nitrogen comes in different “flavors” called isotopes that can tell us a lot about what an animal eats and how it lives. The ratio of heavier nitrogen-13 and lighter nitrogen-12 increases as you go up the food chain. Plants and other autotrophs have the lowest nitrogen isotope values because they use nitrate directly from the environment. For every level of the animal food chain, nitrogen isotope values increase. Herbivores are lower than carnivores. If you live on only steak, your nitrogen isotope values will be higher than a vegetarian. The same will be true for clams. If the clams were taking in more nitrogen from sources like sewage or fish farms, they would show higher nitrogen isotope values in the modern day.

We found that nitrogen isotope values were lower in the modern day!

Taking bits of powder from several dozen of the shells, we worked with technician Colin Carney at the UCSC Stable Isotope Lab to measure the nitrogen isotopes of the shell material. A machine called an Elemental Analyzer literally burns the shell material to release it in a gas form. A carbon dioxide scrubber absorbs the CO2 and carbon monoxide gas, leaving only the nitrogen gas behind. That gas is measured by a mass spectrometer, which essentially separates out the different isotopes of nitrogen and tells us what fraction is nitrogen-13 or nitrogen-12. Plotting all the shell data together, I discovered that my hypothesis was…totally wrong. The nitrogen isotope values of the modern shells were lower than the fossils. The clams had moved down in the food chain, but how?

https://www.israelscienceinfo.com/wp-content/uploads/2017/09/timna-park.jpg
A dust storm rolling over the Israeli Negev Desert. Source

After ruling out a bunch of other explanations including the preservation of the shells, we propose that this represents a human-related change in the environment that the clams are recording. As I mentioned before, the Red Sea these days is regularly hit by huge dust storms which are conduits for nitrate aerosols. Our cars emit nitrogen-containing gases which, through a complex web of chemical reactions in the atmosphere, end up in the form of nitrate particles called aerosols. These nitrate aerosols bind to the dust delivered by strong windstorms called haboobs, which carry the dust long distances, with some of it being deposited several times of year. This deposition of nitrate has been found to form up to a third of the nitrate supply hitting the Red Sea, and was a source of nitrogen that wasn’t available to the clams in historic times. These nitrate aerosols are extremely low in nitrogen isotope value, and would be very likely to explain the lower nitrogen isotope value in our clams! If the clams ate the nitrate, their symbionts would grow more quickly, providing them with more sugars through photosynthesis and accelerating clam growth!

Some additional factors probably also have influenced giant clam growth in the region. The Red Sea historically had regular monsoon rains which likely slowed growth in fossil clams, as storms are known to do for giant clams in other areas, but such monsoons no longer reach the area. The Red Sea also had much higher seasonal range of temperatures in the past, with colder winters and warmer summers. Both factors (storms and extremes of temperature) have been previously shown to depress giant clam growth, and so the modern Red Sea may be a goldilocks environment for the clams: a consistent year-round not too cold or hot temperature.

However, as we discuss in the paper, these factors don’t necessarily mean that the clams are healthier. Faster giant clam growth has been found in other research to lead to more disordered microstructure in their shells, which would have uncertain effects on their survival against predators like fish, lobsters and humans. Additionally, a higher nutrient supply to reefs often causes the corals that build the reefs to lose out to competition from algae that block sunlight and crowd out coral colonies. If the reefs are harmed by the climatic changes that have potentially helped the clams, the clams will still lose. Giant clams are adapted to live only where coral reefs are found, and nowhere else. So more research will be needed in the Red Sea to determine if the health of clams and corals is hurt or harmed by these nitrate aerosols, and what that will mean for their long-term survival in the area.

Over the course of working on this research, the giant clams taught me a lot about life. They taught me that my hypotheses are often wrong, but that’s alright, because my hypotheses can still be wrong in a way that is interesting. I learned to go with the flow and trust the clams to tell me their story through the diaries they keep in their shells. I have followed their lessons wherever they led. Now I am doing follow-up work growing giant clams in a giant coral reef tank at Biosphere 2 in Arizona, to directly observe how the clams’ symbiosis develops and create new forms of chemical records of their symbiosis! The work described in my paper here has led to a suite of different ongoing projects. The clams have many more lessons to teach me. Thank you clams!

Gollum clams

Right: Gollum, Middle Earth. Photo credit: Peter Jackson, New Line Cinema. Left: Congeria kusceri. Photo credit: Helena Bilandžija

In some ways, living in a cave sounds pretty comfortable. A relatively stable year-round environment and refuge from above-ground predators/competitors make it a place that trogloditic (cave dwelling) animals can develop stable evolutionary forms which persist through long periods of time. Like the deep sea, caves are great places to look for “relict” organisms representative of groups that disappeared long ago on the surface. But living in a cave presents a lot of challenges that require specialized adaptations. The most obvious is the lack of light, the source of energy for photosynthesis supports food webs on the surface. Animals in caves must make a living eating material that flows in from the surface world, like bat gauno or debris from runoff. They can also make a living eating the microbes that directly feed off the rocks of the cave walls. Some caves also have methane or other geologically sourced gases that can serve as a food source, similar to the deep sea, where methane seeps and hydrothermal vents provide fuel for diverse and vibrant ecosystems.

A map of the 15 caves where Congeria has been found. Source: Bilandžija et al. 2013

You don’t need to watch Lord of the Rings to see that spending your life in a cave like Gollum requires serious changes to your lifestyle. But that’s exactly where we can find an unusual genus of freshwater mussels called Congeria. Congeria consists of three species found so far only in fifteen caves in the Dinaric Alps, a mountain range in Southeastern Europe stretching from Italy to Albania. These mountains are made from limestone that first formed at the bottom of a shallow tropical sea (picture the Bahamas and you get a good idea of how it would have looked) during the Mesozoic era, the time of the dinosaurs. This limestone (also called karst) was lifted up in the early Cenozoic (after the Cretaceous extinction) by tectonic activity due to the collision of the Adriatic microplate with Europe. This 645 km-long row of mountains is made of a highly soluble rock similar in chemical composition to Tums. Over millions of years, cracks in this karst have been widened by acidic rainwater dissolving away the limestone to make caves. The Dinaric Karst is chock-full of such caves which form a huge maze of interconnected systems deep into the earth (the limestone goes down for kilometers into the crust)!

Congeria kusceri shows its white, unpigmented flesh. Photo by Vedran Jalžić

So if you were to put all your cards into evolving to be a cave creature, the Dinaric Karst would be a great place to try it. All sorts of spooky trogloditic creatures are found down there, such as olm salamanders, cave-dwelling isopods (rolly-pollies), and more. But Congeria is of particular interest because it is a remnant of a group of mussels that was once much more prevalent across this area of Europe, once a huge mass of swamps and lakes called Paratethys. Many species of mussels in the same family as Congeria can be found as fossils in rocks covering an area reaching from Switzerland to Lake Aral in Central Asia. But over time, the climate and geography of the area changed and almost all of these species went extinct. It was once assumed that Congeria had itself gone extinct 5 million years ago, as it was only known from fossils.

Congeria kusceri. Photo by The Croatian Biospeleological Society

In the 1960s, a team exploring the caves of the Dinaric Karst were shocked to find examples of living Congeria in caves. In many ways, the story was very similar to the discovery of coelocanths in the deep sea, a fish assumed to have gone extinct millions of years ago which was found by accident. These species are remnant twigs of previously lush branches of the tree of life. Such species are sometimes called “relict” taxa, or sometimes “living fossils.” Many biologists prefer not to use that phrase, because while these creatures may closely resemble the forms of their distant ancestors, they often have changed in all sorts of ways not easily visible to the naked eye. Congeria was unknown to us, but spent millions of years evolving to improve its fitness in its cave environment. Such groups thought extinct only to reappear later in the fossil record are also sometimes called “Lazarus taxa.” Like Lazarus in the biblical story, Congeria was thought dead only to reappear much later.

It appears the species making up Congeria were trapped in Paratethys first by the rise and retreat of the Mediterranean Sea and then trapped in caves following the drying up of Paratethys. For the past several million years, they have lived only in the cave systems of the Dinaric Alps. But like Gollum, they were not preserved exactly as they previously lived in the Paratethys. While other freshwater mussels continue to frolic like merry hobbits through the streams of the Dinaric Alps above, Congeria has adapted in all sorts of interesting ways to its life as spelunking animals.

Like other bivalves, Congeria makes a living filter feeding. But in caves, they don’t have access to the photosynthetic plankton food that is the main dietary staple for typical bivalves. Congeria instead feeds on whatever detritus flows its way through the waters of the caves, and it can’t be picky. Bivalves use their gills to catch food when filtering, and Congeria has a particularly bulked up set of gills to supercharge its ability to grab these particles. But the palps, organs to select which particles to actually bring to the animal’s mouth, are tiny to the point of being almost absent. As with Gollum, who was known to gobble down the occasional goblin, Congeria can’t be selective. They have to try to eat whatever comes its way, unlike other bivalves such as my Biosphere 2 clams, which spit out many of the particles they catch as “pseudofeces.”

In evolution, if you don’t use a feature, you often lose it. Organisms can’t afford to be sentimental about organs; if it saves energy and doesn’t cost any survival ability to cut out a particular feature, it will be reduced or lost over the generations. Like other cave animals, Congeria has lost almost all pigmentation since such pigments have no purpose in the absence of light. It also has a highly reduced foot, which is used by other freshwater bivalves to move around and dig in the sediment. In the stable, low energy environment of caves, a muscular foot would be a waste of energy. It has lost its statocysts; balance stones similar in function to our inner ear used by most mollusks to sense which direction is up. Since it settles on any available surface and doesn’t move, it makes sense to strike that item from the energy budget.

Congeria living comfortably out of water, one with valves open! Source Glavaš et al. 2017

Most bivalves in the freshwater mussel Dreissenidae family are “r strategists“, meaning they are like guppies or mice, producing and broadcast spawning a huge number of offspring. They don’t put too much energy into each offspring, and hope a certain small percentage of them will survive each year to keep the cycle going. R strategists often don’t live very long. Such a life strategy would be tough to sustain in isolated cave systems, which are a harsh environment in many ways, particularly regarding food supply for baby Congeria. Congeria instead has evolved to be a “K strategist” like humans or elephants. It “broods” its young rather than broadcast spawning. This process, found in other bivalves from extreme environments such as polar regions, involves taking in sperm to fertilize eggs internally. The mother clam then nurtures the embryos to a certain size, first within the gills and then in special pouches in the mantle tissue. This organ is called a marsupium; these clams are like kangaroos! Brooding is much more energy-intensive than broadcast spawning, since the mother is sharing energy with her babies, but the investment ensures that each baby Congeria will reach a larger size before leaving its mother’s shell, giving each one a better chance of surviving long term. In the resource-deprived environment of a cave, a little boost to reach maturity matters! Because real estate is fairly limited in its caves, Congeria can survive in very dense aggregations with over 1,600 individuals per square meter. These mussels are surprisingly selfless and communally living for such a harsh environment.

An acetate peel of the hinge of Congeria kusceri, showing annual growth lines used to tell its age. Source: Puljas et al. 2014.

As with Gollum, Congeria has become very long-lived. Individuals have been confirmed to live almost 60 years based on growth lines in its shell, and there are suggestions that they can live much longer. In the relatively predatory-free environment of the caves, Congeria can bet on not being killed before it reaches its prime. Instead, its greatest enemy is the fickle environment of the caves, which are dependent on water flow from the surface. Their shell growth is interrupted during the summer, when the waters of its cave become much less alkaline than at other times of year, depriving them of the calcium they need to build the shell. At other times they might have to survive extended periods being emersed from the water, when levels drop during the dry season or droughts. Most bivalves can only persist for hours in such conditions, but Congeria can survive 2 months out of water! For Congeria, it makes sense to bet on being able to survive as long as it can in the spot it settled, trying to reproduce little by little over a long period of time. In this way, it is not quite like Gollum, as it has evolved to live a long time to improve its ability to reproduce and pass on its genes, rather than out of selfish worship of a ring.

Like Gollum though, Congeria is very unique and fragile. The caves in which it lives are a sensitive environment, vulnerable to overdevelopment and pollution. Manipulation of groundwater has reduced the flow of water through these caves and thus restricted Congeria‘s habitat, wiping it out from areas of some caves. Because its population is inherently restricted by the “small pond” it inhabits, it would not take a big environmental disruption to wipe Congeria off of the map. To that end, Congeria is red-listed as endangered and is protected in most of its native countries. Still, we can only hope that even now there are other populations of Congeria waiting to be discovered, hidden in unexplored caverns deep in the Dinaric Karst.

Recent Science Communication!

At Biosphere 2, our science is essentially done in public. Every time I’m in the water checking on our clams and the sensors around them, I’m in view of the public and essentially an attraction for the public to watch. This is a really unique way to do science unlike any of my past experience, when I’ve been out in the field with a collaborator, or in the lab with a laboratory technician. I was initially intimidated by the idea of doing my science with an audience, but I’ve decided to lean into it as a huge opportunity. It is rare that the public gets to see all the steps going into our science; they usually only see the end of the story and not the whole journey leading up to that point. So recently I participated in two new ways of sharing my work while it’s in progress with the public.

The first was a collaboration with Mari Clevin, a videographer with the University of Arizona who made a really nice profile of my crazy clam journey. It was a lot of fun showing her around B2, trying to capture what it’s like to work here. It was fascinating seeing how all her footage and interviews came together into a video, and how she captured the key points of our conversation into a narrative!

The other scicomm event I participated in was a “Research Show and Tell” event run by the PAGES Early Career Network. Early Career Researchers include PhD students, postdoctoral researchers like me, and early career faculty. The ECN is intended to help us band together to share opportunities and plan events relevant to our interests. Among the North American regional representatives for the ECN, we saw a real need for more informal ways to share our research to an advanced audience of our peers. We’re all burned out from Zoom webinars, and on the other side Zoom coffee hours don’t typically provide much opportunity to share scientific content, so there’s a real need for events in the middle. So I was excited to share my research with a group of my peers, touring them around the Biosphere, showing them my clams via pre-recorded video and then having a Q and A to describe the work. It was a lot of fun and you can watch the whole hour-long event below!

Biosphere 2 Update!

A view from my parking spot at work

I am now several months into my postdoctoral fellowship at Biosphere 2 in Oracle, Arizona! I am working with Professor Diane Thompson on a project measuring the shell and body chemistry of giant clams in Biosphere 2’s huge reef tank. Our goal is to find better proxies (indirect ways of measuring) the symbiosis of these clams with the algae they farm within their bodies. The controlled, closely monitored conditions of the Biosphere 2 ocean tank represent the perfect balance between the real ocean and the more controlled environment of a lab. Using trace metals and isotopes in their shells and tissue, we can trace back the ways that clams record their own internal biology. Wild giant clams make chemical records via the growth lines in their shells, similar to tree rings. These have been the subject of many cool past studies, but there are aspects of the “language” they use to write their shell “diaries” that are poorly understood. Much like researchers used the Rosetta Stone to decode heiroglyphics, we are observing clams as they grow in order to better translate the shell diaries of their prehistoric ancestors. Doing so, we can better understand how their ancestors reacted during past periods of climate change, and identify similar bivalves in the fossil record which may have harbored symbionts.

A view of the ocean tank at Biosphere 2

I started my postdoc remotely in May. The following months were spent sheltering at home in Southern California with my mom, supervising the installation of a cohort of giant clams into the 700,000 gallon ocean tank over Zoom. It felt like a science fiction movie, watching technicians Katie Morgan and Franklin Lane from hundreds of miles away on my computer screen as they nurtured and installed the little clams in their new home. I felt like Mission Control back on earth, watching a group of space colonists work with strange alien creatures.

Some of the T. derasas in the Biosphere tank

But in August I was able to finally move to Tucson to meet these clams in person! We had three species in the first batch: Tridacna derasa, T. squamosa and T. maxima. Of the three, T. derasa (the smooth giant clam) has proven to be the most successful in the Biosphere 2 ocean tank. All of the derasa clams from May have survived and thrived, attaching themselves to the bottom with byssal threads and growing their shells, both very positive signs of clam health!

Some of our newer batch of T. derasa in the quarantine tank

So we have doubled down on T. derasa and installed 11 more individuals last week, sourced from Palauan clam farms via a reef supply company in Florida called ORA. They are currently in a shallow quarantine tank where we will monitor them for disease and unwanted hitchhikers before introducing them to the broader Biosphere tank.

The workers at Biosphere 2 are very creative problem solvers. Giant clams need intense amounts of light to sustain their symbiotic algae and create food for themselves, a quantity of light higher than is available in the current Biosphere tank. To provide a light supplement, the engineering team at Biosphere 2 constructed a floating lighting rig with hanging LED lighting, right over the lagoon where we have the clams!

The lighting rig glows with a blue light as the sun goes down outside the Biosphere

To make sure the clams have enough light, we installed a Li-Cor light sensor to measure the exact amount of photons (light particles) hitting the clams over the course of a day. The light is measured in units of micromoles of photons per meters squared per second. A mole is 6.02 * 1023 particles, and other clam experts like James Fatheree have suggested that the clams need light levels of at least 200 micromoles/m2s to make enough food for themselves. That’s 120,400,000,000,000,000,000,000 light particles we need to hit every square meter of their habitat every second. The clam channels as many of those photons as it can to its algae residing within tubes in its tissue. The symbionts use it in photosynthesis to make sugars, which they share with their host. A well lit giant clam is a happy, well-fed giant clam! But because the glass dome of Biosphere eats up some of the light, and plankton and floating particles in the seawater eat up another portion, we use the lights to make sure the clams have the boost they need to maintain their symbiosis like they would in the clear, shallow waters of a tropical coral reef.

The Li-Cor sensor floats above the clams, telling us how much light they’re getting

Much like a new dad might read parenting books to get ideas for baby care, I am always poring through the literature trying to figure out how to maximize the growth of these clams. Dr. Fatheree is kind of like Dr. Lipschitz from Rugrats, except unlike the suspect childcare advice in the show, this real-life giant clam advice is very valuable. Like human babies, these clams can be a challenge! The clams sometimes decide to move around and get themselves into trouble, requiring us to rescue them if they get trapped behind a rock or under a pile of sand. So I have had to do a fair amount of clam-herding during my time here.

We are growing the clams for science, and there will be data to collect. We will be monitoring data like the trace metal chemistry of the clams’ tissue and shells, the color of their mantles, and the pH, temperature and oxygen levels of their environment, all to relate together to make the best clam record of their environment possible. So far, I have been snorkeling in the tank every couple days maintaining their setup. Next week, I will dive in the Biosphere tank for the first time to collect data on their shell chemistry! I have other projects in the works to measure their valves opening and closing using magnetic sensors, and to measure their color changes through time through computational photography.

That brings me to what I’ve found to be the coolest part about Biosphere 2: the people. Something about this place attracts creative, brilliant, can-do people who solve problems on the fly and are always jumping into the next project. It has been a privilege to learn and pick up technical skills from them in the brief time I’ve been here. This place is really like a space colony out of The Expanse or Silent Running. There are endless valves, pipes, tanks, exchangers and other hardware needed to keep Biosphere 2 running. Getting to witness the technical competence behind the whimsical solutions the staff comes up with, like the floating light rig, has been the most exciting part of this job for me. Everyone has a deeply ingrained curiosity and passion for science that is inspiring to see; they are as interested in my clams as I am in their corals, tropical plants, and geochemical experiments. I would argue that the human team behind Biosphere 2 is a bigger treasure than the unique metal-and-glass structure they work under, and I look forward to seeing the results all of the collaborations we have in the works!

Research Explainer: The chemistry across a “forest” of giant clams

T. squamosa near Eilat, Israel, 2016

Another one of my PhD chapters is published in the journal G-cubed, resulting from work I did in the summer of 2016 in Israel and Jordan around the Red Sea. This is my first geochemistry article in a journal, so it is a big deal to me! I thought I’d write up a clamsplainer about what I was looking for and how we went about achieving the paper.

A slice of giant clam shell. You can see the difference between the inner and outer layers. The inner layer has visible annual growth lines.

I study the chemistry of giant clam shells. You might already be familiar with the concept of tree rings, a field called dendrochronology. It’s like reading the diary of a tree, where every “ring” is a page in the record of its life. The related field of sclerochronology looks at rings in the hard parts of shelled organisms. We can count those rings to figure out the ages of clams, or their health, and we can measure the chemistry of those rings to understand the temperature the clam grew at, and even what it ate.

A giant clam growing on the reef flat in Eilat

Giant clams are bivalves of unusually large size which achieve a very rapid growth rate through the help of symbiotic algae in their flesh. The clams are farmers, and their crop is inside their tissue! They grow their shells very quickly (sometimes up to 5 cm a year, equivalent to if a six foot tall man grew a foot every year from birth), and live a very long time, up to 100 years (their growth slows later in life). A whole bunch of talented researchers have measured the chemistry of giant clams all around the world to reconstruct past climate and even measure historic storms!

If we want to understand the ecology of a forest, we can’t measure just one tree!

But if you come back to the analogy of tree rings, we essentially have measured the rings and chemistry of individual “trees” in a bunch of different places, but don’t have as good an idea of how the chemistry varies within a “forest” of giant clams in a particular place. In our new study, we set out to describe exactly that, focusing on the Northern Red Sea.

A map of the Northern Red Sea. The right “toe” is the Gulf of Aqaba
Sites where we sampled shells along the northernmost tip of the Gulf of Aqaba

The Gulf of Aqaba represents the northernmost toe of the Red Sea, bordered by Egypt, Israel, Jordan and Saudi Arabia. It hosts some of the northernmost coral reefs in the world, aided by tropical temperatures and clear waters due to the lack of rainfall in the surrounding deserts. Here, we can find three species of giant clams including the small giant clam Tridacna maxima, the fluted giant clam T. squamosa and the very rare T. squamosina, which is found only in the Red Sea and nowhere else (as far as we know). In summer 2016, I went all around the Gulf of Aqaba collecting shells of clams from the beaches, fossil deposits, and even were able to work with shells confiscated from smugglers at the Israel-Egypt border. We cut these shells into slices and used tiny drill bits to sample powder from the cross section of their shells, which we could then conduct geochemistry with! We sampled large areas in bulk from the inner and outer portions of the shell (more on why later) using a Dremel tool, and also sampled more finely in sequential rows with a tiny dental drill bit (same brand your dentist uses!) to see how the measured temperatures varied through seasons. By “we”, I mean my coauthor and friend Ryan Thomas, who spent every Friday morning for several weeks milling out most of the powder we needed for this study. This data became part of his senior thesis at UCSC!

Two giant clams thriving on the shallow reef near Eilat, Israel

What kind of chemistry did we measure? The shells of clams are made of calcium carbonate, the same stuff Tums is made of. Calcium carbonate contains one calcium atom, one carbon atom, and three oxygen atoms. It turns out that all of those atoms come in “flavors” that we call isotopes, relating to the weight of those atoms. When you take the shell powder and put it into a machine called a mass spectrometer, you can figure out the proportions of isotopes of different elements present in the samples

The first isotope “flavors” we were interested were carbon-12 and carbon-13. The ratio of the two is thought to relate back mostly to the action of the algae inside (its symbionts) and outside the clam’s body (the floating algae the clam filters out of the water as an additional meal). This happens because as algae take carbon from the environment and bind it into sugars through photosynthesis, they naturally weight the dice in favor of carbon-12 making it into the sugars. So carbon-13 is left out in the water, and potentially in the clam’s shell. When photosynthesis is more active, it would leave the shell with proportionally more carbon-13. At least that’s what other researchers have confirmed happens in corals, and suspect happens in clams. In the world of isotope chemistry, this phenomenon is called “fractionation,” when a process causes isotopes to form fractions separated by mass. We wanted to test if that was true for giant clams, and could do so by comparing T. squamosina and T. maxima, which have more active photosynthesis, to the less photosynthetic T. squamosa.

Comparing carbon isotopes across different species and shell layers. The results are fairly flat all the way across.

It turns out that the more symbiotic species don’t have more carbon-13 in their shells. We set out several reasons that might be the case, including that the symbionts of these clams are actually more carbon-limited than many researchers might expect. Essentially, the algae lack an excess of carbon atoms to choose from, so they can’t be picky with which isotopes they use to make sugars. Therefore, the fractionation effect weakens and becomes possibly too subtle to manifest in the shell, even in the best-case scenario of three closely related species living the same area. This represents what I’d term a “null result.” We had a hypothesis and we demonstrated that hypothesis was not the case in our data. It was important to publish this result, because other researchers will know not to try the same thing. This means that when we try to search for evidence of symbiotic algae in fossil clams, we will likely need to use other types of chemistry to figure it out. But don’t worry, as finding such a “smoking gun” for algal symbiosis in fossil bivalves is part of my life’s work! I have a few projects in the works looking for exactly that kind of evidence! 😉

A look at how temperatures measured via oxygen isotopes vary through the lives of the animals. This is how scientists can use very old shells to figure out how temperatures varied through a year in prehistoric times!

But we had additional data we collected in addition to the carbon isotopes which actually turned out to provide some interesting results. This other type of measurement regarded the oxygen isotope ratio of the shells. Previous research has shown that the ratio of oxygen-18 to oxygen-16 in carbonate skeletons directly relates to temperature, a principle that has birthed a field known as paleothermometry. There are thousands of papers which use shells of corals, clams, cephalopods, microbes and more to reconstruct temperatures in ancient times. Giant clams have proven to be effective weather stations going all the way back to the Miocene epoch, millions of years ago! Because they grow so quickly (putting down a new layer every day), live for a long time, and don’t stop growing, they form very complete, high-resolution, and long records of past climate.

But no past studies had ever compared different species of giant clams from the same place. There would be interesting new lessons to draw from such a comparison, including seeing if one species preferred to grow at warmer parts of the reef. As complex, three dimensional structures, there are many remarkably different micro-environments throughout a reef, from the hot, sun-exposed reef flat and crest to the cooler, current-swept, deeper fore-reef. Do any of the species of giant clams show a consistently higher temperature than the others, and what would that mean if they did?

T. squamosina records higher temperatures than the other species. Outer shell layers also record higher temperatures than inner shell layers. More on that later in the post 😀

It turns out that the rare T. squamosina, only found in the Red Sea, does record a higher average temperature, almost 3 degrees C higher than the other two species. This is of interest because this species had been proposed by prior researchers to only live on the sun-drenched reef crest, at the shallowest part of the reef. We believe these results corroborate that observation. The previous research on the habitat of T. squamosina was limited to a single study which only was able to find 13 live animals along the coast of the Red Sea. But by independently confirming this life habit, we can ask further questions that may be borne out by further research.

An example of T. squamosina showing signs of possible bleaching (light parts at the center of its body).

Being restricted to the shallowest waters, is T. squamosina at greater risk of harvesting by humans along the shores of the region than its counterparts? Illegal poaching of giant clams along the Red Sea is believed to be a major stressor on their population size in the area. Could this explain why T. squamosina is so rare today, despite being proposed to have been more common in the past? In addition, being restricted to the top few feet of depth in the water could leave the species more vulnerable than the others to atmospheric warming. As with corals, when giant clams overheat they will “bleach”, expelling their symbiotic algae as a stress response. While the clams can recover, it is sometimes a fatal form of stress that leads to their death.

An excellent cartoon of the different shell layers in giant clams. From a peer of mine who also studies them, Michelle Gannon!

More research is needed to answer those questions. But the last aspect of this study relates to what is happening inside of the bodies and shells of the clams themselves. Giant clam shells have two layers. The outer layer grows forward away from the hinge, increasing clam’s length. The clam also makes an internal layer, growing inward to thicken the shell and add weight. We can read the growth lines of the clam’s diary within either layer, and different studies have used one or the other to make records of climate change. But very few studies have compared the two layers of the same individual. Do they record the same temperatures? Figuring it out would be important to determine how studies with just the inner layer or outer layer can be compared to each other across time and space.

A vividly blue example of the small giant clam, T. maxima. From user arthur_chapman on iNaturalist

In our studied clams, it turns out that the outer layer records warmer temperatures on average than the inner one! After ruling out other possible explanations behind this difference (the details are complicated and hard for even shell nerds to wrap our heads around), we settled on the idea that the outside of the clam is indeed warmer on average than the inside! This means that the outer layer, recording temperatures of the outer mantle, is indeed forming at a higher temperature than inside! Why is this?

Unlike us, clams are ectothermic. They generally stay the same temperature as their surrounding environment and don’t use their metabolism to generate internal heat. But that doesn’t mean that the clam doesn’t have hotter and cooler spots in its body. It makes sense that it would be hotter at the outer part of its body, facing the sun, as the solar rays hitting its outer mantle would then radiate out again as heat. The outer mantle is also darker in color than the inner mantle, allowing it to absorb more solar energy, much as you might feel hotter wearing a darker t-shirt in the sun than a white one. Photosynthesis itself produces a warming effect, a phenomenon known as non-photochemical quenching, and so the outer mantle, which contains the vast majority of the symbiotic algae, may be partially warmed by the activity of the symbionts!

More research is needed to confirm if this is true. As of yet, no researcher has ever stuck a temperature probe in multiple parts of a clam to see if the outside of it is indeed warmer than the inside. But until that day, it is interesting to think of how this would influence comparisons of diaries from the inner and outer layers of different bivalves. The effect is on the small side, so it doesn’t really mean one layer or the other should be preferred for future shell-based studies of climate change. But it could be an additional aspect to consider in the future as a way to record temperature differences within the body of an animal, and look into how those differences influence its overall level of stress.

Examples of juvenile smooth giant clams, T. derasa, that we’re growing at Biosphere 2. Photo by Katie Morgan.

So I hope this long explanation of my paper helps you to have a better idea of the work I did during my PhD thesis. There were other aspects to the paper that are too wonkish to get into here, particularly concerning the correlation we found between carbon and oxygen isotope ratios, but if you have questions or want a copy of the PDF, please message me! I have more clam papers in the pipeline, and my new postdoc at Biosphere 2 involves growing three species of giant clams in a controlled environment, where I hope to answer some of the physiological questions I mentioned above! But until then, stay hinged and happy as a clam (as much is possible in this chaotic time), and take comfort knowing there are colorful bivalves out there all at this very moment, harvesting sunlight for food and growing huge shells.

The Mystery of the Giant Clams of the Red Sea and Indian Ocean

I have always been fascinated by scientific discoveries that are hanging right in front of our noses. Cryptic species are one such surprise. Sometimes, researchers using genetic sequencing are surprised to discover that a group of animals that all look the same from the outside are actually reproductively isolated from each other; separate twigs on the tree of life. This surprise has happened over and over in the history of natural science.

It turns out such puzzles are frequent among the giant clams. These unusual bivalves are specialists in coral reef environments, growing to large size with the help of symbiotic algae that create sugars through photosynthesis. Within the genus Tridacna there are ~10 accepted species which vary in size, shape, color and mode of life.

Tridacna squamosina (right) sitting next to the small giant clam T. maxima (left) on the Israeli Red Sea coast

I specialize in the three species known (so far) from the Red Sea, including the small giant clam Tridacna maxima and the fluted giant clam T. squamosa, which are both found worldwide, all the way from the Red Sea to down past the equator along the Great Barrier Reef. The third local species, T. squamosina is more unusual, so far being only known from the Red Sea (an endemic species). T. squamosina is an example of a cryptic species, having previously been assumed to be a local variant of T. squamosa. It looks pretty similar, with long scutes (flap-like appendages) protruding from its shell, thought to help stabilize it on the flat bottom of loose coral rubble. But unlike T. squamosa, T. squamosina lives exclusively at the top of the reef in the shallowest waters closest to the sun. It has a very angular, zig-zag pattern in its plications (the wavy shapes at the edge of the shell) and a characteristic pair of green stripes where the soft tissue meets the edges of the shell. The soft tissue is covered with warty protuberances.

Pictures of details of T. squamosina from Richter et al. 2008

It was only first described in detail in the early 2000s, when an international team of researchers figured out using genetic sequencing that it was a distinct species and named it T. costata. They noted that in their surveys all around the shores of the Red Sea, they only found 13 live specimens, making it an extremely rare and possibly endangered species. Fossil specimens on local reefs appeared to be much more common, suggesting it had a much larger population in the past. Then in 2011, another team at the Natural History Museum in Vienna discovered a shell of one had been forgotten in its collection for over 100 years. Rudolf Sturany, the researcher on the 1895 research cruise who had originally collected the clam, had called it T. squamosina.

The T. squamosina shell in the collection of the Museum of Natural History in Vienna (from Huber and Eschner, 2011)

In taxonomy (the science of naming and classifying organisms), the first team to name the species wins, so the name T. costata was synonymized (retired) in favor of the earlier name T. squamosina, which became the name of record. It must be annoying to spend so much time working to name a species and then discover you had been scooped over a century before! But such is science.

A mystery clam thought to be T. squamosina, later identified as T. elongatissima found off of Mozambique by iNaturalist user bewambay

The strange part was that there were some murmurs over the last few years that T. squamosina was not only found in the Red Sea, but also had been seen along the coast of Africa as far south as Kenya, Mozambique and Madagascar. Divers and snorkelers had taken pictures of a giant clam that did indeed look strangely like T. squamosina, with a zigzag shell opening and green stripes at the edge of its tissue. But some aspects of these individuals seemed off. In the Red Sea, T. squamosina lives freely, not embedded in the coral as these pictures showed, and the geometry of the angles of the shell seemed a bit different. It also would be difficult for T. squamosina to be connected in population from the Red Sea all the way South to Mozambique, as there are natural barriers which would prevent its planktonic larvae from riding currents to intermix between the two regions. When populations are separated by a barrier, the flow of genes between them is cut off and evolution begins to separate the populations from each other until they are separate species, a process called allopatric speciation.

A large specimen of T. elongatissima observed by iNaturalist user dawngoebbels off of Kenya

I figured that someday, researchers would collect tissue samples from these mystery clams to settle whether they were actually T. squamosina or something else. And this year, a team did just that, traveling along the coast of Mozambique, Madagascar, Kenya and other places, collecting samples of tissue to compare how all the different clams they saw were related in a family tree. They genetically sequenced these “clamples” and in the process, found that the mystery clams were a new cryptic species, which they called T. elongatissima!

Shells of T. elongatissima from the Fauvelot et al. 2020 paper
For comparison, a shell of T. squamosina collected off of Sinai, Egypt. You can see why they’re easy to mix up!

T. elongatissima closely resembles T. squamosina, and they are sister species on the bivalve family tree. It’s hard to tell them apart without training. Even a professional would probably mix some of them up if they were all placed sitting next to each other. The major differences appear to relate to shell shape, with T. elongatissima having a less symmetrical shell than T. squamosina, and a bigger opening at the rear hinge for a foot to poke through. The symmetrical shell and closing of the foot opening may represent changes that T. squamosina took on to adapt to be able to sit freely on the bottom, rather than embedding in the coral like T. elongatissima seems to prefer. If you’ve read this far, you may be thinking “Who cares? A clam’s a clam and these look practically the same. Aren’t you just splitting clams at this point?” At the end of the day, a species is a man-made concept; an organizing tool for use by us humans. Species are the characters in our reconstruction of the history of the world. What can we learn about the world by having identified this species T. elongatissima?

A giant clam family tree! Notice T. squamosina and T. elongatissima right next to each other.

The researchers behind the new paper discuss that based on statistical analyses of the genetic differences between the species, the most recent common ancestor for T. elongatissima and T. squamosina probably lived more than 1.4 million years ago! Some researchers have previously suggested that T. squamosina probably began its development as a separate species due to geographic isolation by low sea level, caused by repeated glaciations. With so much water trapped as ice on land during this period, the narrow Strait of Bab al Mandab, currently the gateway to the Red Sea, became a land barrier as sea level fell (kind of like opposite of the Bering Sea land bridge that formed allowing humans to migrate to the Americas). Ancestral clams trapped on the Northern end of this barrier were proposed to have evolved to become the rare T. squamosina.

This has occurred with a variety of species that became Red Sea endemics (meaning they are unique species that evolved in the Red Sea and are found nowhere else), including a unique crown of thorns starfish. The issue is that during this time of low sea level, the Red Sea went through periods where it was a rather unfriendly place for clams to live. All sorts of creatures went extinct in the period when the sea was repeatedly cut off, because the water became extremely salty, along with other unfriendly changes. So it’s unlikely T. squamosina would be present for us to see today if it only lived in the Red Sea throughout the entire length of time.

A map from Fauvelot et al. 2020 showing the distributions of different giant clams the researchers identified along the coasts of Africa and the Red Sea. Notice the bright red dots representing T. squamosina, only found in the Red Sea, while green dots represent T. elongatissima. Notice how the currents (arrows) seem to meet and then go offshore from Kenya. More on that in the next paragraph.

The researchers of this new paper propose that T. squamosina was more likely to have initially branched off due to the barrier of the Horn of Africa. The seas off of Kenya and Somalia harbor a meeting of southward and northward currents which then group and head offshore, away from the reefs that giant clam larvae are trying to get to. So any tiny floating planktonic clam larvae would experience a strong “headwind” preventing them from crossing that point. It would also mean that during times that the Red Sea was not a happy place to be a clam, T. squamosina may have found refuge on the coasts of places like Eritrea, Oman and possibly even as far as Pakistan. During times when sea levels rose and Red Sea conditions became friendlier, it recolonized the area.

As far as we know, the Red Sea is the only place T. squamosina is now found, but it may well be present elsewhere like Yemen or Oman. If T. squamosina was found in other regions, it would be tremendously important for its conservation. Right now, the species is thought to be extremely rare, with a very small native range. If it inhabited a broader area, that would mean more reservoirs of genetic diversity. This would reduce the odds that it will go extinct as reefs are put under stress from climate change, pollution and overharvesting. To survive as a species, it helps to not put all your eggs in one basket. If you’re only found in one small place, it increases the chances that a disaster (like climate change) will wipe you out.

The only way we will know for sure is to visit reefs in understudied places like Yemen, Oman, Pakistan, Eritrea and Somalia, to understand the richness of the giant clams present. These areas are understudied for various reasons: lack of research funding for non-Western researchers, lack of interest from the scientific community too focused on familiar places, and geopolitical situations that make it difficult to conduct research. But I hope someday to collaborate with people in these countries to better understand the giant clams present in such understudied regions of the globe. It is virtually certain that there are more species of giant clams, both alive and as fossils, waiting to be discovered.

Apps that Darwin would have loved

Was Charles Darwin first? Kind of depends – Harvard Gazette

Most people know that Charles Darwin was a cerebral, deep thinking type. He traveled the world, collecting data about those finches and other stuff on field expeditions, synthesizing big ideas over decades to form his magnum opus, On the Origin of Species, where he set out his theories on natural selection and its role in evolution. However, you might not know that on a day-to-day level, Darwin was an all-around nerd’s nerd who just wanted to learn everything he could about the world, motivated by an unending sense of curiosity.

Darwin was a man who pulled plankton nets, filtering seawater just to see what cool stuff would show up when he put the resulting sample of goo under the microscope. He fiddled for earthworms and wrote a book about them over 40 years (including an experiment where he watched their progress burying a bunch of rocks over a 30 year period). He kept a heated greenhouse where he studied orchids and carnivorous plants. I consider Darwin a role model, because it’s hard to find a topic in natural history that he didn’t write about. The dude was just an unfillable sponge of knowledge.

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A view of Darwin’s greenhouse. Source: The Darwin Correspondence Project

I think Darwin would have marveled the online information that we have easy access to today. If Darwin were a researcher today, I could imagine him hosting a forum or listserv where he’d moderate, muse over the natural world and keep correspondence with the other leading scientific minds, much as he was a prolific letter writer with other researchers of his time. He might not be huge on Twitter: a bit too fast paced for his liking I bet; but I think he’d love two apps that I have also fallen in love with over the last few years.

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The Explore page on iNaturalist, where you can see what species other people have recently observed in your area!

The first is iNaturalist (Android, iOS), a website and social network where you can upload pictures of any lifeform, attach information about its location, time of day and other info, and the machine learning powering the site will try to identify it for you, with amazingly accurate results. If the AI can’t figure it out, experts are waiting in the wings to provide an identification or confirm yours. Think of it like a Pokedex or Pokemon Go, but for “collecting” real life creatures. And like Pokemon Go, it can be insanely addictive to find out about all the species that are all around us at all times. iNaturalist also has an app called Seek that makes the process even more gamified!

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a view of my observations

I am definitely an iNaturalist addict, and have accumulated a healthy collection of observations over the past couple years. My first was a red-shouldered hawk that I saw on campus during my PhD, but then I moved onward to fungi and plants I saw walking from my car to the office, and went back through my past pictures to identify bats I saw in Belize, fish I saw diving, and of course, my beloved banana slugs. I find it’s particularly satisfying to find out how life around you changes through the year, with the seasons. When I felt like pulling my hair out during my PhD, it kept me grounded to be able to know that the first spring flowers were opening, or the fledglings of birds were leaving the nest, or the winter rains were bringing all sorts of new fungus and banana slugs to life among the undergrowth.

I think being in touch with our natural world can help us now. While we’re sheltering in place, we don’t have to be trapped within ourselves. Even in the densest cities, there are so many bugs, flowers, birds and squirrels all around us going about their lives while we are effectively on pause. It brings me relief to know that life continues, and satisfaction to be able to understand them. Knowledge really is power, and if you know the relations between all the types of life both in evolution and ecology, it makes the world make sense in a way that provides a weird zen-like peace.

To that effect, there is a #citynaturechallenge happening starting yesterday, from 4/24-4/27/20. Take pictures of living things around you and upload them to iNaturalist, Twitter and elsewhere with that hashtag! My uploads there have been of interest to researchers studying rare snails of the Negev desert, writing books about tropical bats, and researching invasive beetles. I have been following uploads of giant clams on iNaturalist for quite some time, including the newest described species, Tridacna elongatissima, which users had been observing on the Eastern coast of Africa before it was formally described in a recent paper! I bet Darwin would have been a major, influential user on iNat.

Darwin was also a big nerd regarding rocks and fossils. Evolution is the story of life, and we can only understand that story by turning to the fossil record for information. Environmental changes provide a major motivating factor pushing life to constantly change. Geology in Darwin’s day was a developing field, with the first geological maps appearing only due to the work of William Smith and others, mere decades before Darwin’s work came to be. But his work would not have happened without the growing understanding of the massive passages of time needed to deposit the rocks all around us today. Evolution typically needs time, and fossils provide proof of how life has changed during those almost incomprehensibly long intervals.

https://upload.wikimedia.org/wikipedia/commons/3/38/A_new_Geological_map_of_England_and_Wales_by_William_Smith_%281820%29.jpg
One of William Smith’s geologic maps

To find a fossil of an age we are interested in, we must know the rocks present in the area. And the second app I’ll mention today is RockD (Android, iOS), which we can use to figure out the type of rocks right under our feet, how they were made, how old they are and even what kind of fossils have previously been found within. The data in RockD is pulled from two sources that scientists have lovingly curated. Macrostrat is a database of stratigraphic (rock layer) data that scientists have aggregated into one of the most detailed and comprehensive geologic maps ever made. And the Paleobiology Database collects observations that scientists have made over the decades of almost every fossil that has ever been found and recorded.

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Of local geology when you first open RockD (my detailed coordinates obscured ;))

Rather than relying on only printed maps for his work, Darwin would have loved the ability to pull out his phone in the field and instantly know the combined work of dozens of previous researchers to understand the rock he was looking at. You can even “check in” and upload your own pictures of rocks to help researchers improve their databases, and go back in time to look at where the continent you live on was during the time of the dinosaurs!

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Geologic map of my area. Darwin would have seriously nerded out checking out the locations of faults, formations and other features

These are only two of many apps and websites that I think would have blown Darwin’s mind. We are living in a golden age of digital science, with so many new discoveries being precipitated by the availability of easily accessible, free information in the palms of our hands. But more than that, it is fun to go outside and be able to decode the mysteries of the world around you without even being an expert in natural history. In the process, you might find yourself becoming an expert!

Why eating clams sometimes makes us sick (Part 1 of 2)

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Is eating these a gamble? Science can help improve our odds!

I am often asked if I eat clams. The answer is yes: while I love to observe live clams and appreciate their abilities, I will eat a good clam chowder or plate of grilled scallops if presented with the chance. While I’m generally not a fan of super fishy-tasting foods, I eat bivalves with a clear conscience because farmed mollusks represent a super sustainable way to get protein! However, as many of us have learned the hard way, shellfish can sometimes produce unwanted results later after the meal, if the animals are contaminated with food poison. Eating such “bad” clams can produce a spectrum of food poisoning symptoms ranging from vomiting and diarrhea to memory loss to even paralysis and death.

Humans have known the hazards of eating shellfish for a very long time. It has been suggested that the ban on shellfish present in kosher and halal dietary rules arose as a preventative measure to protect from food poisoning (though eating fish, land animals and even vegetables can poison people in numerous ways as well). Studies of oysters have determined that ancient peoples of modern day Georgia from 5000 years before present selected their season of harvest based partially on knowledge of the seasons when such poisoning was most prevalent in their area.

How and why does this happen, and what can we do to prevent it? It’s a billion-dollar question, because when flare-ups of shellfish food poisoning happen, they are hugely costly to fishermen and the food industry, costing millions of dollars a year in lost business when fisheries are forced to shut down and products are recalled. Such events are increasing in frequency and severity. Which makes it all the more strange that these shellfish poisoning events are not the fault of the bivalves per se, but rather what they’re eating.

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Note: people generally get annoyed when you start to point out the body parts of the oyster they’re about to swallow whole. Source

Almost all bivalves are filter-feeders, using their gills to gather small passing food particles, which they then either ingest or discard based on the quality of the food item. Clams are cows crossed with Brita filters, and for many species of clams which we eat, the reason they do all this filtration is to find phytoplankton food. Phytoplankton are microscopic algae suspended by ocean currents that make their living from photosynthesis. They are a hugely plentiful and high-quality food item, making up a huge amount of the biomass available in the ocean. Like plant-life on land, phytoplankton are highly seasonal in their appearance, rising and falling in abundance in periodic “bloom” events.

an image of red tide in Florida
Aerial view of a red tide off the Texas coast. Source: NOAA

But as Spongebob Squarepants taught us, plankton are not always peaceful. Many types of algae produce toxic compounds which may be integrated into the body parts of bivalves that eat them. Scientists call the blooms of algae which produce toxins “Harmful Algal Blooms” (HABs), and such events are growing in frequency and cause huge harm to marine life and sicken thousands of people per year. There are many algae species which cause HABs all around the world, sometimes visible as “red tides,” but not always. When HABs occur, they can lead to mass deaths of higher animals in the food chain that feed on clams such as marine mammals and seabirds. In fact, HABs are at their most dangerous to humans when they catch us by surprise.

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Who me? I’d never!

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Microscope view of the toxic dinoflagellate Karenia. Source: NOAA

When humans eat bivalves which have been dosed with such marine toxins, many types of poisoning can occur. Brevetoxin is produced by a type of dinoflagellate phytoplankton Karenia as well as other species, and when humans are exposed, we can suffer from Neurotoxic Shellfish Poisoning, which causes vomiting, diarrhea and even neurological effects like slurred speech. Saxitoxin is produced by a variety of plankton species including dinoflagellates and freshwater cyanobacteria. When ingested in clams (such as the butter clam Saxidomus which gave it its name), fish or other animals, it can cause Paralytic Shellfish Poisoning, a sometimes fatal syndrome which shuts down nerve signaling, leading to temporary paralysis.

So we know it’s bad for humans to ingest these toxins. What is it doing to the clams? Oddly enough, some types of toxins like saxitoxin are not that harmful to the clams or other plankton eating animals, allowing them to accumulate huge amounts in their bodies with little ill effect. Its presence does not seem to influence their feeding behavior much, or their growth after exposure. Its status as a neurotoxin in mammals might be a total chemical and evolutionary coincidence, as researchers suggest that it may actually serve as a signal in some part of the algae’s mating cycle. This also may be the case for brevetoxin, which appears to be produced when Karenia is under environmental stress. But there is not much agreement in the HAB and aquaculture research fields, because there are many types of algae, which may produce their toxins for many reasons, and it is very hard for us to zoom in to the scale of the microbe and out to the scale of the ecosystem at the same time, to find any kind of universal evolutionary role of these toxins. Some researchers insist that some bivalves are influenced negatively by brevetoxin, but only at the juvenile stage during major bloom events. The effects of the toxin may only influence certain species, or only become significant if the toxin reaches the digestive tract of the bivalve. Overall, research into impact of HABs on clams is still a topic of active research, and the idea that the microbes produce these toxins to defend against bivalve predators is definitely not a slam-dunk, easily proven hypothesis. While some clams are negatively affected by the toxins, it is not consistently observed across species in a open-and-shut way, and it can be a subtle effect to observe and quantify scientifically.

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Karenia to mammals: Oops!

The more I read about this stuff, the more shocked I am at the incredible complexity of marine algae and their toxins. I only started reading about them trying how to to understand how they influence bivalves. I was hoping to find some evidence of their effects on bivalve growth that I could apply back in time in fossil shells to understand the historical occurrence of HAB events. It’s important to understand HABs because they hurt people, cost our society a lot of money and if we understand how to avoid them, we can help minimize such impacts in the future as HABs continue to become more common. In my next post, I’ll talk about some of the ways that researchers have come up with to measure and monitor HABs, so that we can eat clams as safely as possible.

A Make-Up Presentation!

Hi colleagues! Several weeks ago, I was supposed to present a talk at GSA’s annual meeting in Phoenix at the session “Advances in Ocean and Climate Reconstructions from Environmental Proxies”, but I shattered my wrist in a scooter accident the night before and was in emergency surgery during my talk time. So instead I’ve uploaded my talk with voice-over to Youtube! The whole video is about 15 minutes. You can view it above. Feel free to comment on this post or email me if you have questions!

This work is currently in the last stretch of drafting before submission, but I also discuss some ongoing research and am always open if you have your own ideas for collaborations!

Correction: we are working with geophysicists to understand the shell transport mechanism.

These are the references mentioned at the end:

Crnčević, Marija, Melita Peharda, Daria Ezgeta-Balić, and Marijana Pećarević. “Reproductive cycle of Glycymeris nummaria (Linnaeus, 1758)(Mollusca: Bivalvia) from Mali Ston Bay, Adriatic Sea, Croatia.” Scientia Marina 77, no. 2 (2013): 293.

Glycymeris nummaria (Linnaeus, 1758).” 2019. World Register of Marine Species. 2019. http://www.marinespecies.org/aphia.php?p=taxdetails&id=504509#distributions.

Grossman, Ethan L., and Teh-Lung Ku. 1986. “Oxygen and Carbon Isotope Fractionation in Biogenic Aragonite: Temperature Effects.” Chemical Geology: Isotope Geoscience Section 59: 59–74.

Gutierrez-Mas, J. M. 2011. “Glycymeris Shell Accumulations as Indicators of Recent Sea-Level Changes and High-Energy Events in Cadiz Bay (SW Spain).” Estuarine, Coastal and Shelf Science 92 (4): 546–54.

Jones, Douglas S., and Irvy R. Quitmyer. 1996. “Marking Time with Bivalve Shells: Oxygen Isotopes and Season of Annual Increment Formation.” PALAIOS 11 (4): 340–46.

Mienis, Henk, R. Zaslow, and D.E. Mayer. 2006. “Glycymeris in the Levant Sea. 1. Finds of Recent Glycymeris insubrica in the South East Corner of the Mediterranean.” Triton 13 (March): 5–9.

Najdek, Mirjana, Daria Ezgeta-Balić, Maria Blažina, Marija Crnčević, and Melita Peharda. 2016. “Potential Food Sources of Glycymeris nummaria (Mollusca: Bivalvia) during the Annual Cycle Indicated by Fatty Acid Analysis.” Scientia Marina 80 (1): 123–29.

Peharda, Melita, Marija Crnčević, Ivana Bušelić, Chris A. Richardson, and Daria Ezgeta-Balić. 2012. “Growth and Longevity of Glycymeris nummaria (Linnaeus, 1758) from the Eastern Adriatic, Croatia.” Journal of Shellfish Research 31 (4): 947–51.

Reinhardt, Eduard G, Beverly N Goodman, Joe I Boyce, Gloria Lopez, Peter van Hengstum, W Jack Rink, Yossi Mart, and Avner Raban. 2006. “The Tsunami of 13 December AD 115 and the Destruction of Herod the Great’s Harbor at Caesarea Maritima, Israel.” Geology 34 (12): 1061–64.

Royer, Clémence, Julien Thébault, Laurent Chauvaud, and Frédéric Olivier. 2013. “Structural Analysis and Paleoenvironmental Potential of Dog Cockle Shells (Glycymeris glycymeris) in Brittany, Northwest France.” Palaeogeography, Palaeoclimatology, Palaeoecology 373: 123–32.

Sivan, D., M. Potasman, A. Almogi-Labin, D. E. Bar-Yosef Mayer, E. Spanier, and E. Boaretto. 2006. “The Glycymeris Query along the Coast and Shallow Shelf of Israel, Southeast Mediterranean.” Palaeogeography, Palaeoclimatology, Palaeoecology 233 (1): 134–48.

So you want to be a postdoc overseas!

Here are three issues I wish I had thought of entering my postdoctoral fellowship. These are not intended to scare anyone away from what I have found to be a very rewarding experience working abroad, learning about a new place and taking on some very fun and exciting research, but I found there are very few resources describing these practical concerns. I learned most of this stuff the hard way. For each heading, I will describe the problem and the solution that worked best for me, which may or may not apply to you.

Acclimation is difficult

Problem: The first few weeks of your postdoc will likely be sapped by concerns related to adulting. Adulting is hard enough in the country of our birth, and those difficulties are amplified in a place where the language and cultural practices are different. I’m talking about stuff like finding an apartment, making a bank account to get checks to pay for the apartment, getting a sim card for your phone, setting up utilities and furnishing your place. These will all take an insane amount of time.

Solution: You are likely a self reliant person if you are considering a postdoc overseas. I’m not telling you to give that up, because it’s a good quality, but try to swallow your pride as much as possible. Ask your supervisor, labmates and colleagues for advice, translation and help. Find someone who can be your ally and fixer. I have been so impressed in Israel by the capacity of people to take time to help me with basic stuff, but people usually won’t volunteer. They usually need to be asked.

Also, while it may seem distasteful, consider living on campus, where logistical difficulties like utilities will be prepackaged and therefore won’t be left for you to try to arrange in a place where you don’t speak the language and don’t know how things are done.

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Hermit crabs are actually highly social animals. Postdocs are no different.

You may feel like a hermit

Problem: Loneliness is a universal and growing problem in modern life. Postdocs typically move to a new place where they don’t know anyone and have few connections. Take those issues and multiply them several times over when you move to a new country. You will feel far from your loved ones (even in our internet connected times). You won’t be acquainted with fun stuff in the area. Your mobility may be impacted by not having a car, depending on quality of public transit.

You might feel what I call “culture lag,” a general feeling of unease resulting from seemingly unimportant cultural differences of your host country. Do grocery stores shut down every week on certain days? Is the work week different? Do they have your favorite comfort food at the store? All of these small inconveniences add up and make it easy to decide to retreat and hide in your cave.

Solution: You need to make friends and say yes when they invite you to stuff. Your labmates will be a great group to start. They will be there to invite you to their holiday activities (holidays are by far the most isolating times for foreigners). They will tell you about fun coffee shops you can work at, and which local destinations are fun and which are tourist traps. They can tell you what they do when the grocery stores are closed two days every week.

Reach out to other postdocs or international students at your school, who may also be working abroad and have a lot in common with you. When you’re abroad in a country where you don’t speak the language, being able to talk in person to someone from your own culture every once in a while can feel like coming up for air after many weeks holding your breath. Do not be ashamed to seek out these reminders of home. They’ll recharge you for the times when you feel like a stranger in a strange land.

Being an overseas postdoc is expensive

Problem: As a postdoc, you will most likely be considered a contractor with few of the benefits of formal employment. Being overseas, this makes you vulnerable. You may not be entitled to the same quality of health coverage as citizens of your host countries. For me, I bought into the best available option which was is still bare-bones and only covers care in Israel. Consider for fieldwork and conference travel that you may have literally no worker’s compensation whatsoever. Look up if the medications you need are even offered in your host country, and whether your insurance will cover them.

While you may have a travel budget, it will likely not go as far as you’d like because you won’t be paying just for airfare. Relocation is expensive, visas are expensive, conference registrations are expensive. You may also still have financial obligations back home requiring you to transfer money, which usually costs around $30-45 per bank transfer. All of these expenses add up and will eat out of your stipend.

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The countries in pink may try to tax citizens abroad! Source: Wikipedia

The United States is part of a very small club of countries which tax foreign income. You will need to know if your host country is going to tax you as well, you will need to tell Uncle Sam about your foreign bank account if it is above a certain balance, and you need to know if your income is above the taxable threshold and whether the length of your residency entitles you to to claim the Foreign Earned Income Exclusion.

Solution: Budget for travel insurance for literally every trip, including going home to visit family. Make a plan for your money transfers, to spread them out as much as you can. Ensure your banks in both countries have given you all the permissions you need to easily transfer money quickly and remotely. Tax software can walk you through some of the foreigner specific tax forms, but consider also seeking advice from a preparer specializing in expat taxes. For me, all of this money and healthcare stuff makes me feel like isotope geochemistry is pretty simple in comparison. The key is to not let it sneak up on you. Ask other postdocs in your country what they did when confronted with these issues

Conclusion

Please don’t let these issues make you give up on your overseas postdoc opportunity. All of these problems have solutions. But the more preparation you do ahead of time, the more time and energy you will have for your research, and even (dare I say it) to have fun in a new country. Please reach out to me on my contact page if you have any questions!