Screencap of Onion where some sort of scientist is announcing something in front of a Powerpoint slide of a clam
Last week, The Onion, a very serious journalistic publication, published a piece “Biologists Announce There Absolutely Nothing We Can Learn From Clams“. As a print subscriber I want to say I played a small part in this article, which I’ve actually hung on my office wall. But I want to take it a step further and write a line-by-line concurrence with everything they wrote!
WOODS HOLE, MA—Saying they saw no conceivable reason to bother with the bivalve mollusks, biologists at the Woods Hole Oceanographic Institution announced Thursday that there was absolutely nothing to be learned from clams.
Wow, I do know a researcher who studies clams at Woods Hole and actually love her work! Nina Whitney is now a prof at Western Washington University but until recently was a postdoc at WHOI studying how shells can serve as records of climate! I wonder who The Onion interviewed.
“Our studies have found that while some of their shells look pretty cool, clams really don’t have anything to teach us,” said the organization’s chief scientist, Francis Dawkins, clarifying that it wasn’t simply the case that researchers had already learned everything they could from clams, but rather that there had never been anything to learn from them and never would be.
Oh I don’t know a Francis Dawkins, but I’m sure they know their clams! It is true that their shells can look pretty cool. Bivalves include everything from Hysteroconcha dione, with its beautiful color and spines, to Tridacna gigas, which grows to 4.5 feet and weighs hundreds of pounds! And like an Onion, shells have growth layers, sometimes a new one every day, which someone could use to try to figure out how clams record what they eat and how the environment changes. But why would anyone do that?
Close-up view of a Hysteroconcha bivalve shell, showcasing its intricate ridges and coloration, and rows of long spines near the margin. Source
For me, I guess I haven’t learned anything from clams. I think I already knew in my heart that clams can live for >500 years. I already knew that mussels can filter several liters of water per hour, meaning that a colony of them can filter thousands of liters an hour. All this stuff is obvious, actually. Common sense.
“We certainly can’t teach them anything. It’s not like you can train them to run through a maze the way you would with mice. We’ve tried, and they pretty much just lie there.
It is ludicrous that clams could be taught anything or have anything approaching memory or thinking. It is only coincidence that scallops appear to clap their valves to swim, using their hundreds of eyes to navigate to a new location away from predators or toward food. It’s coincidence that they increase their feeding activity when shown a video of food particles. Some researchers have even claimed that giant clams can tell the difference between different shapes of objects! It is so dumb!
From what I’ve observed, they have a lot more in common with rocks than they do with us. They’re technically alive, I guess, if you want to call that living.
Also literally true! Their shell is a biomineral, in essence a living rock, made of calcium carbonate. They are alive in the sense they have a heart that beats, pushing hemolymph around their body. Their heart rate can increase or decrease with different stressors. Remember though, we always knew this. We didn’t learn it through something like science.
They open and close sometimes, but, I mean, so does a wallet. If you’ve used a wallet, you know more or less all there is to know about clams. Pretty boring.”
I myself have wasted time studying this. I attached sensors to giant clams to monitor their feeding activity. If I had learned anything, it might have been that they change their behavior between day and night, basking in the sun to help their photosynthetic algae in the day, and partially closing at night, with those behaviors changing based on how much chlorophyll is in the water. But remember! I didn’t learn it.
The finding follows a study conducted by marine biologists last summer that concluded clams don’t have much flavor, either, tasting pretty much the same as everything else on a fried seafood platter.
I can’t see how anyone would like to eat a bivalve. Especially not a fresh-caught scallop sauteed in butter or a plate of fried clams in New England. Never try that. Leave it to me!
Source: CDWR on Facebook. I thought about titling this post “Violence of the Clams” until I realized American Dad beat me to it, releasing an episode with that title in 2024
I legitimately admire clams. I whole-gilledly believe that they do a lot of good for the world; way more than we do! But there’s no doubt that some types of clams are up to no good, thanks to our help. One of those species is Limnoperna fortunei, the golden mussel. In late 2024, this species was observed for the first time on the North American continent, found attached to various human infrastructure in the Sacramento Delta of California. Since then, it has made its way down the California aqueduct all the way to the Southern tip of the Central Valley. Golden mussels are a notorious invasive species, and California officials immediately recognized the potential for disaster here, leading to dramatic policies of containment throughout the state that have tremendously impacted the lives of people trying to enjoy life on the water.
Map from CDFW showing the locations golden mussels have been observed as of July 2025
Since we are in uncharted waters with these mussels, there are a lot of questions about these innocuous-looking but trouble-making clams. In this blog, I will try to answer some of the most frequent questions I’ve seen over the last few weeks. I will caveat this by saying that I currently have no active research on this species, but I am a card-carrying clam scientist, and have a lot of interest in its biology and the significance its presence it will have for our state. So let’s get into it!
What are golden mussels? Where are they originally from? How did they get here?
A clump of golden mussels observed in Brazil by iNaturalist user danialdias
Golden mussels are small mussels, only reaching a bit over an inch in length, native to the Pearl River basin in China (the area around Hong Kong and Macau), but have been spread around the world over recent decades with the help of humans, hitching a ride between continents in the ballast water of our ships. Once settled in a new place, they easily move between lakes attached to boats being driven around, since they can live up to ten days out of water (talk about holding their breath!). The mussels first spread throughout Southeast Asia, then to Japan, then South America, and now for the first time, to the North American continent. While they are true mussels, in the same family (Mytilidae) as the more famous saltwater mussels you might have seen in tide pools, they can’t tolerate fully marine conditions.
Why are they a problem?
A now-infamous photo of the mussels coating the inside of a pipe at the Governor Jose Richa Power Plant in Brazil
They love to attach to heat exhangers, which can cause dams and pump stations to break down. Both are crucial to the California Aqueduct. Photo by Gustavo Darrigan
They can attach to native mollusks, smothering them. Photo by Gustavo Darrigan
Golden mussels are prolific breeders and make a living by anchoring themselves to any available hard surface using byssal threads. This is relatively uncommon among freshwater bivalves, most of which live on the bottom and don’t attach to surfaces. Golden mussels reproduce by releasing thousands of tiny larvae which spread through the area on river currents. In areas where they attach (such as dams, aqueducts, boats and other infrastructure), they form dense colonies that gum up the works, clogging pipes and and coating surfaces with thousands of their sharp little shells. They can even attach to the roots of native plants and shells of other molluscs and smother them! This causes hundreds of millions of dollars in damages and continuing expense in reservoirs and irrigation systems where they’ve taken hold, like in Japan and South America. If the mussels were to unexpectedly clog the outlet of a Californian reservoir like Lake Berryessa or Folsom Lake, it could be disastrous for people who depend on that water.
Figures from a paper about golden mussels invading Brazil, showing them coating an aquaculture cage, on a buoy, on a power plant hatch, in the entry to a dam turbine, and clogging a cooling pipe
Quagga and zebra mussels, originally from Central Asia, are invaders in the Colorado River, the Great Lakes, and reservoirs in Southern California. They have been limited from spreading into most reservoirs in Northern California by the low calcium content of lakes here (a function of our local rocks and geology). But golden mussels have lower calcium requirements than zebras/quaggas, so it is likely that they can reproduce in reservoirs up here. They are also surprisingly resistant to low temperatures, meaning that they could potentially take hold in high-altitude lakes like Lake Tahoe, which could be a disaster for efforts to keep Tahoe blue.
Why are they so successful?
A growing golden mussel colony, with an adult surrounded by younger babies. They only live about 3 years, but what a life they’ll live! Photo by Alexander Karatayev via Great Lakes Echo.
Being so prolific in their numbers allows the mussels to transform the chemistry and biology of the waters where they live. Like most bivalves, golden mussels make their living by using their gills to filter particles out of the water column, drawing them down to their mouth to eat. While individual golden mussels are pretty average in their filtering ability, together they work to much more effectively clear the water than other species, thereby depriving those native species of the plankton food they need, and potentially even directly eating the plankton larvae of other animals around them!
Figure showing how densities and size of colonies of toxic cyanobacteria Microcystis increase in the presence of golden mussels. Yum! Source
The Sacramento Delta has plenty of plankton floating around, so it’s not surprising they’ve decided this is a nice place to live. But while the water-cleaning ability of clams is a useful service they provide, there can definitely be too much of a good thing. The mussels are “ecosystem engineers”, meaning that they make the environment they want to live in. The problem is that what is good living for the mussels is not necessarily the habitat of a thriving Delta. Where they take hold, they exclude native species and generally decrease water quality by trapping dirt and boosting the populations of cyanobacteria. The Sacramento Delta already struggles with toxic cyanobacteria, and don’t need to have the problem be worse! Lower water quality means fewer fish, which is bad for people and the ecosystem.
Why have they shown up now?
A handful of Corbicula fluminea (Asian clams), a different species of invasive clams in the CA Delta. Photo source
This is actually not the CA Bay/Delta’s first rodeo with foreign clams. Invasions of Asian clams (Corbiculafluminea) and overbite clams (Potamocorbulaamurensis) in the 1980s transformed the Bay, with trillions of clams spreading out all the way south towards San Jose and eastward into the Delta after being introduced in Grizzly Bay in the mid-1980s. These clams had enormous impacts on the ecosystem, excluding other bottom-dwelling animals and eating most of the plankton food that other animals rely on. They are thought to have played a major role in the decline of some native fishes like Delta and longfin smelt.
Golden mussels have been making their way around the world over the decades. It is hard for their larvae to survive a couple weeks in the belly of a ship, be released, and successfully take hold, but with enough ships coming to California, it was only a matter of time before all of the stars aligned and a population took hold. We don’t know if the appearance of golden mussels will push out Asian clams, or if they’ll coexist. Asian clams live on the bottom rather than attaching to stuff, but golden mussels may still compete with them for food.
Are there other ways they spread?
Previous studies investigating their spread in South America and Japan determined that virtually all of their spread happens attached to the hulls of ships, in ballast water, or anywhere their larvae can travel downstream. There are rare cases where they are believed to travel upstream in the guts of fish that eat them, being pooped out alive. But those are unusual cases. That also won’t help them spread past dams without a fish ladder. The planktonic larvae have very little ability to swim against the current, so they won’t be able to swim upstream through dam turbines.
A map and timeline of their spread through Japan. Source
A map of their appearances and spread through South America. Source
Unlike pea clams, which are famous for attaching to birds by clamping their shells on their feet or feathers and traveling long distances to reach new places, it is not believed that golden mussels can create their thread attachment fast enough to hitch a ride on birds (which is a process that takes hours). So fortunately, I can assure our avian friends that we won’t need to inspect them before they use our reservoirs. At the end of the day, human vessels are the main way these mussels are getting around to far-flung places. In Japan, it took around 15 years to spread river to river through the country, while in South America, it covered most of a large area from Buenos Aires to Southern Brazil in that same period of time, which was proposed to be largely due to greater boat traffic in South American rivers.
Different life stages of larval golden mussels. They’re cute when they’re babies! The bottom right is the “plantigrade” stage when they attach to a boat, at 0.75 mm size. Imagine scanning a boat looking for one of those!
Are they good eatin’?
They don’t look exactly appetizing to me. Notice the visible byssal threads! Source: Folsom Lake Recreation Area
These mussels weigh only a little over an inch at best, with not much meat on them. Unlike Asian clams (Corbicula), which are eaten in some Asian cultures, I can’t find mention of anyone eating golden mussels. There have been attempts using them as a fertilizer calcium supplement, but that needs more research. Additionally, it’s known that the other invasive clams of the Bay/Delta are concentrators of toxins, including selenium from farm runoff, heavy metals, and also toxins from harmful algae. In places where golden mussels colonize, toxic cyanobacteria can proliferate, so they actually make themselves a bit more toxic than other clams in the same place would be!
I don’t think these will be taking over the tapas restaurants any time soon! Source
What can we do about them?
We just don’t know how L. fortunei will fare long term in the California Delta and lakes. The previous clam invasions have waxed and waned through time. It’s uncertain whether these mussels will fizzle out, as sometimes happens for invasive species, or if they’re here for the long haul. The speed of their spread throughout the state personally leads me to suspect they’re here for good. And in the meantime, the invasion has caused huge issues for anglers, boaters and dam operators throughout California this summer, who have had to institute boat inspections at every reservoir in the state. Boats have to be painstakingly checked for mussels stuck to surfaces on the hulls.
Eventually, it is possible that mussels will find their way through, despite these precautions. Some could be missed in the crevices of boats entering various reservoirs. But hopefully that will buy time for dam operators to put forth the needed upgrades and develop procedures to keep them from fouling dams and aqueducts. At that point, the objective becomes mitigation rather than prevention. It won’t be cheap, usually involving manual scraping of mussels off of surfaces, application of hot water, pesticides, and use of surfaces that discourage mussel growth.
Map from a 2015 book chapter showing their distribution at that time on top, and predicted places they could invade on the bottom panel. Just as the prophecy foretold! Source
Long-term, our invasive species management needs to be more proactive rather than reactive. California was previously recognized to be in the range of territory where golden mussels could appear (see figure above). We can’t allow future invasions to catch us by surprise. To that end, there are laws on the books in California requiring inspection of 25% of incoming ships. So far, we are only inspecting a small fraction of that number. Additionally, ships were previously required to release ballast water far offshore in the ocean, where freshwater species wouldn’t be able to get a foothold. That policy was also not adequately enforced, and requirements to sterilize ballast water with chemical treatments were ruled too expensive. The state government very recently strengthened the standards, but gave ships until 2030 to comply with a weakened version of the rules, and pushed off compliance with the final strongest version until 2040!
People frustrated about such invasive species in California should insist to their policymakers that we can and must do better. There are manymoreinvasiveclam species waiting for their chance at a ride over here to make a living in our waters. It’s not too late to stop the assembly line of species coming to displace the native creatures we all love and value!
I often get asked what pearls are and why bivalves make them. Pearls are biogenic gemstones. This means they are valuable rocks made not by inorganic crystallization within the earth, like most gemstones, but instead are produced by life! Interestingly, they are living rocks, composed of true minerals. When I talk about minerals, I mean a solid substance with a known chemical composition and crystal structure.
Pearls are specifically made mostly of a mineral called aragonite. Aragonite is a mineral made of atoms of calcium bound to an ion called carbonate. There are other minerals made from calcium carbonate, like calcite and vaterite. I’ll save those for another blog, and while those are present in small amounts in some pearls, the vast majority of the material is aragonite. The clam uses calcium carbonate to make pearls because it’s a conveniently available material: it’s also what they build their shells from!
Aragonite has a very specific geometric crystal structure at the molecular level, but zooming out slightly, it can be found in a tremendous variety of microfabrics. Like the fabric of our clothes, the shell is essentially “woven” by the bivalve with a certain texture at the cellular level. There are hundreds of types of fabrics, ranging from structures looking kind of like brickwork, to plywood, to actual long fibers of carbonate. But the most valuable pearls are made of a form of aragonite called nacre, which is also called “mother of pearl” for this reason.
The platy microstructure of nacre. See how the tablets are organized into interlocking columns! Source: Wikipedia
Nacre is a very special biomineral for many reasons. To humans, it’s precious because of its beautiful, complex iridescence and luster, which has attracted our eyes for thousands of years. But most clams aren’t making the material for its luster- they value its microfabric. Nacre is made of billions of tiny flattened tablets of aragonite, arranged in tall interlocking stacks. Each aragonite tablet also has little bridges joining it to the neighboring tablet, meaning they don’t easily slide out of place. The plated structure also aids the shell in staying together. Even when fractured, the shell can stay together as plates slide to lock into another shape!
Reviewing the various strengthening aspects of nacre, including the bridges that lock tablets together, the rough surfaces of the tablets that grip against each other, the organics that glue together tablets like mortar, and the tablets sliding into new locking orientations even if they break apart! From Zhao et al., 2018
Between the bricks of aragonite are a kind of mortar or scaffolding of protein, binding them all together. This protein scaffolding is extremely important to the overall material. Like the steel rebar in concrete, it strengthens the material, making it less brittle and therefore able to resist forces that might crush the clam’s shell, while still allowing for the material to be very thin. For us humans, those alternating layers of carbonate and protein act like thousands of layers of prisms, refracting the light into thousands of colors depending on the angle it is looked at, meaning that any light becomes a miniature rainbow when it passes through the structure of the nacre.
A snuff box made from a nacreous bivalve shell, at the Vienna Natural History Museum
This structure makes nacre a “premium” material for clams to build their shells from. It costs much more energy for a clam to make such an orderly microstructure and fill it with so much protein, up to 5% by weight, which is around 5-50 times how much organic material is found in more common forms of aragonite. Nacre is also more vulnerable to dissolving in the water surrounding the clam. For this reason, clams usually will only use nacre in the internal shell layer, isolated from the surrounding waters, using cheaper materials on the outside of the shell, or at least a protective sheath of protein on top (called periostracum).
The nacre is present in mussels, oysters and other bivalves vulnerable to crushing pressures of waves as well as crushing predators like fish and birds. Nacre is like the bulletproof vest a clam uses to give itself a bit more powerful armor. Because pearls are made inside the shell, that’s why the most valuable pearls to us are made by oysters with a nacreous inner shell layer. The tropical pearl oysters (genus Pinctada) make some of the most valuable pearls, because it’s particularly rich in organic material and thus has a bright and complex lustre. Pearl oysters have extremely thin shells, which are strengthened by having a nacreous structure.
Why do bivalves make pearls? Pearls are essentially part of the bivalve’s immune system. If a piece of sand or debris got under your skin, your body would encase the intrusive object with scar tissue. Bivalves can do better than that, because they use the material of the shell to wrap around the object. Anything can be an intrusive object- a piece of sand, an infection, or even a parasite. For example, pearlfish are parasitic fish specialized to live inside the shells of clams. If they die in the shell, the clam will dutifully set to work encasing the fish in nacre, like Han Solo in carbonite!
A pearl oyster with a pearlfish wrapped in nacre against the inner shell. From the Natural History Museum London collection
Most natural pearls are irregularly shaped, so cultured pearls often use round beads as the nucleus for the oyster to grow nacre around. The farmer wedges the oyster’s shell open, deposits the bead and leaves it for a period of time to allow the bivalve to deposit nacre. At harvest time, the oyster can be shucked to remove the pearl. Some experimental approaches even anaesthetize the oyster to remove the pearl, replace it with a new nucleus and repeat the process, potentially allowing for greater efficiency and humane harvesting, allowing the oyster stock to live for years!
So next time you see a pearl, you can understand that the craftsmanship of these wondrous objects is the result of millions of years of evolution, combined with thousands of years of human ingenuity. Moving forward, researchers are attempting to learn to imitate the structure and methods that clams use to make pearls, which could lead to all sorts of improvements in materials science! Clams again prove their skill in engineering. They have a 500 million year head start against us, but we can always learn!
You might be familiar with the concept of the present “biodiversity crisis“. There is an increasing consensus in the ecological research community that the current loss of species this planet is experiencing is not sustainable, in the sense that the loss of some species may precipitate the loss of more, in an accelerating spiral. The paleontological community has found that the pattern of species loss is unusual even at the scale of geological time, potentially placing us among the great extinctions in geologic history, or at least a notably bad extinction event. A less diverse biosphere means the loss of ecosystem services associated with all of the species we lose, and potentially a less resilient biosphere, stacking the deck against us as the climate continues to change and life is forced to adapt. Because our global civilization depends on the wealth of the biosphere for our own well-being, this is definitely very bad news for humanity (I usually tend to avoid rationalizing conservation based on ecosystems’ value to us, believing that we have a moral imperative to preserve the biosphere, and organisms have an inherent right to exist outside of their economic value, but that’s a topic for another blog).
We are only aware of the loss of species due to centuries of careful collecting, cataloging, categorization and curation undertaken by conservationists around the world, including indigenous communities, museum professionals, taxonomists, seed banks, herbaria, and other very highly specialized and educated people. I won’t refer to these biodiversity experts as “countless”, because they’re actually a pretty small group of folks entrusted with an almost incomprehensible responsibility: to quantify the biological wealth of our world. They figure out when baselines are shifting, and their work keeps us accountable as we seek to stop the current bleeding of biodiversity.
I am writing this post because biological collections are having a moment of attention, and it’s been a topic I have been thinking of for some time as an outsider. Duke University recently announced that they will be throwing out their herbarium, an archive of plant samples which is one of the leading such collections in the US. The herbarium supports a vibrant ecosystem of research on the classification of plants, and is an important archive of plant diversity. Duke University, which has an endowment of $11 billion, claiming to not have the resources to support this archive is an unacceptable dereliction of their duty to preserve and nurture knowledge. And sadly, this closure of such an important collection is not a one-off event. Worldwide, taxonomist and curator jobs are declining. These are the people who spend decades learning how to tell one species of snail from another based on their genitalia. They discover cryptic species in collections. They prevent collections from degrading due to improper preservation, and charge in to save samples from fires. They process loans and when someone like me is belated in returning samples, they write a polite email reminding me to send samples back. When these people leave science, their skills can’t be easily replaced. If collections are lost, they literally can’t be replaced.
I am a biogeochemist, and not a museum worker by any means, but so much of my work has relied on biological archives. But by my count, 3/4 of my ongoing projects have used biological collections in some way. I wanted to list out some of the ways that biological collections have enabled my research, because I don’t think I’m unusual. Biodiversity curators are the keystone species in a vast ecosystem of interconnected research that wouldn’t happen without the hard work of maintaining collections. Please do what you can to protect biodiversity collections, whether by pressuring your representatives, your alma maters, and through donations.
Projects that relied on curators:
Some of my most influential educational experiences relied on teaching collections, including at Cabrillo Marine Aquarium, USC, LA Museum of Natural History, UC Santa Cruz and elsewhere. Without collections to get my hands on in lab exercises and other educational opportunities, my skills in ecology, organism ID and more would be greatly diminished.
My second PhD chapter relied on samples of well-preserved Jurassic lithiotid bivalves which came from outcrops which mostly no longer exist, having been quarried out or already sampled. These were loaned by curators at the University of Padova and University of Verona Natural History Museums
My third and fourth PhD chapters, and one of my postdoctoral papers used shells of giant clams that were stored at the Hebrew University of Jerusalem Natural History Museum. These shells had been confiscated from poachers at the Egypt-Israel border and were loaned to me by curator Henk Mienis. I would rather these clams be still alive in the Red Sea, but at least we were able to use these for a series of papers about their ecology and physiology.
Before my PhD fieldwork in Israel, I visited the California Academy of Science collection to view shells of Red Sea giant clams and practice species ID using a taxonomic key. I would also note that one of the species I have studied, Tridacna squamosina, is named because of the work of museum curators at University of Vienna.
Another postdoctoral paper (in progress) on violet bittersweet clams from the Eastern Mediterranean made use of preserved samples collected during research cruises off the coast of Israel in the 1960s-1980s. These specimens, loaned by the Steinhardt Museum in Tel Aviv, represent some of the last observed live violet bittersweets seen off of Israel. They since have (likely) gone extinct in the region, probably due to sediment changes in the late 1980s following the construction of the Aswan Dam.
Yet another postdoctoral paper in progress resulted from study of the growth and chemistry of shells of wavy turban shells loaned from the Santa Barbara Museum of Natural History, which we were comparing to individuals that grew in the hot waters of the Biosphere 2 tropical reef ocean tank. I met the curator Vanessa Delnavaz at the Southern California Union of Malacologists 2021 meeting, which was hosted by the museum. Museums are important centers of scientific organization and networking in addition to the value of their collections!
So I hope all of these anecdotes help make clear that biological collections are absolutely vital to enable an entire universe of research, and that we often can’t possibly predict what collections are going to be useful for which scientific purposes until long after the samples were preserved. So any budgetary bean-counters (not talking about bean taxonomists) should think twice before closing any collections! This is a core responsibility of academic institutions and we cannot allow any of these collections to be lost. Fund your local biological curators! Without their hard work, we’d be flying blind in the current biodiversity crisis. They’re the heroes we need, and that our earth deserves.
Two giant clams near Eilat in the Northern Red Sea. To the left is the small giant clam, Tridacna maxima, and to the right is a mature individual of the rare endemic giant clam Tridacna squamosina, only found in the Northern Red Sea.
You are what you eat, and clams are too. We’re made of atoms, which come in “flavors” called isotopes, relating back to the mass of the atoms themselves (how many protons and neutrons they have). Nitrogen, for example, comes in two stable (non-radioactive) forms called nitrogen-14 and nitrogen-15. Much like scientists can track the composition of a person’s diet from the isotopes of their hair, researchers have used the isotopes of clams to figure out their diet.
Nitrogen isotopes provide us with a useful and detailed record of food webs. Plants and algae tend to have more of the light isotope of nitrogen in their tissues than the animals that eat them (primary consumers), and the animals that eat those animals have even higher nitrogen isotope values. We can measure the amount of “heavy” atoms of nitrogen with a unit called δ¹⁵N (“delta 15 N”). A carnivore at the top of the food chain will have a very high δ¹⁵N, while plants will be the lowest. Clams, typically being filter feeders, will usually have an intermediate value, since they’re eating a lot of phytoplankton (tiny microscopic floating algae) and zooplankton (animal plankton that eat other plankton).
But I study a special kind of clam, the giant clams, which have a cheat code enabling them to become giant: they have algae *inside* of their bodies. The algae make food using photosynthesis and share it with their hosts! In exchange, the clams provide the algae with a stable environment free of predators, plenty of fertilizer in the form of their own waste, and even channel extra light to help the symbionts grow faster. This partnership is called photosymbiosis, and is pretty rare in clams, though it is common in other animals like the corals that build the reefs where giant clams are found! Previous researchers have shown that giant clams have very low nitrogen isotopic values in their tissue, like a plant, because they get most of their nutrition from the algae, rather than filter feeding.
I am a sclerochronologist. That means I study the hard parts of animals, in this case the shells of bivalves. Like the rings of tree, bivalves make growth lines in their shells which can serve as a diary of their lives. Some of my past work has looked at using chemistry of the growth lines of giant clams to measure the temperatures they grow at, compare the growth of ancient and modern clams, and even look at how much the clams grow in a day! Today though, I’m talking about my most recent paper, which looks at how we can use the shells of giant clams as a food diary.
But when they’re babies, the symbiosis in giant clams is not yet fully developed. During this early period of their lives, giant clams actually get more of their nutrition from filter-feeding like a “normal” non-photosymbiotic clam, until they’ve had a chance to grow in surface area and become a living solar panel. Like all bivalves, the shells of giant clams are made of calcium carbonate, bound together by a protein scaffold we call the shell organic matrix. Proteins are made of amino acids, which contain nitrogen! If we can get the nitrogen out of the shell from the early part of the clam’s life, and compare it to the nitrogen at the end of the clam’s life, it might record the clam’s transition from filter feeding to its mature plant-like lifestyle! If our hypothesis holds, we should record a decrease through its life in the shell δ¹⁵N values.
A model I made of the clams’ nitrogen intake, with the left plot how they switch from filter feeding to getting most of their nitrogen from dissolved sources around 5-6 years of age. Because the nitrogen isotopes of those two sources are different, that manifests in the expected values from the clam’s body (the right plot)!
A map made by my talented partner, Dana Shultz!
So I gathered a team of talented collaborators and set out to test that hypothesis, using giant clam shells that I was able to get on loan from the Hebrew University of Jerusalem Museum. These shells had been confiscated from poachers at the Egypt-Israel border. While I would have rather known these clams were still alive in the waters of the Northern Red Sea, being able to use them for research to understand the biology of their species was the next best thing! I had originally planned on pursuing a postdoc undertaking this project with Rowan Martindale, a professor at UT Austin who has studied the nitrogen isotopes of photosymbiotic corals, but when I started up at Biosphere 2, we ended up continuing with the project anyway as a collaboration! We measured the nitrogen isotopes of the shell material in the lab of Christopher Junium, a professor at Syracuse University, who has developed an exquisitely sensitive method to measure the nitrogen from shell material by essentially burning the shell powder and then scrubbing out unwanted material to isolate the nitrogen, to measure the isotopes in a machine called a mass spectrometer. Katelyn Gray is a specialist in isotopes of biominerals and assisted with drilling out powder from the shells with a Dremel. Shibajyoti Das, now at NOAA, is a specialist in measuring the shell nitrogen isotopes of other bivalves and he was master at doing much of the mass spectrometer work, and assisting in interpretation. Adina Paytan is a professor at UC Santa Cruz. She first provided the funding and support for me to go to the Gulf of Aqaba and collect these shells as part of an NSF-funded student research expedition! She also provided environmental data which helped us to interpret what the clams were actually eating!
A figure showing the four shells we sampled from, with the sampling areas in each hinge area showing colored and matching with the corresponding isotope plot to the right (colored points). 3 of the 4 shells show declines in isotope values with age. Shaded ribbon behind the data shows the model output.
So what did our crack team of scientists find out? We found that three of the four tested giant clams did indeed measure a decline in nitrogen isotopes over the course of their lives. Their earliest growth lines in the hinge areas of their shells record elevated δ¹⁵N values similar to other filter-feeders from the region. But as they aged, their later growth lines show much lower δ¹⁵N values, more like photosymbiotic corals and plants from the region. So clams indeed recorded the transition in nutrition as they became solar-powered! This degree and directionality of change in nitrogen isotopes was much greater than has been observed in any other clams measured in this way, which made sense considering their unique physiology. The clams have another area of the shell, the outer shell layer, which is closer to the symbionts than the hinge area. In this outer shell area, we did not observe much of a consistent trend in nitrogen isotopes. It’s likely that the outer layer is highly influenced by the photosymbionts even at the earliest stages of life.
Growth lines in the hinge area of two of the shells lit from behind, with the drilled areas for this study visible as well. The outer shell layer is the opaque and was also sampled for this study.
There was one clam that differed from the others in showing low δ¹⁵N values through life in its hinge shell layer. To help explain these differences, I created an independent model of the clams’ internal chemistry based on their growth rate, which slows as they age, and also is faster in the summer. When the clams are young filter feeders, they get most of their nitrogen from plankton, debris and other material floating in the water column making up floating material we call Particulate Organic Matter (POM). Meanwhile, when they are in their photosynthetic life stage, they get most of their nitrogen from nitrate, which is essentially Miracle Gro for the symbionts. The model showed that the clams should record a flip from filter feeding to photosynthesis around 4-5 years of age, which was confirmed by three of the shells! But what about the one that didn’t show this trend? My colleague Adina had fortunately measured the isotopes of POM and nitrate in different seasons in the Gulf of Aqaba. We found that in summer, as expected, POM δ¹⁵N is lower than nitrate. In the winter, meanwhile, that relationship is flipped! So if a clam grew more in winter, it would not record the same transition as was seen by the other clams. We think the clam that was the exception to the rule might have been more of a winter grower.
The chaotic nutrient environment of the Northern Red Sea, showing how in different seasons, dissolved nitrate has higher or lower δ¹⁵N values than the Particulate Organic Matter that the clams filter-feed on.
But long story short, we were able to demonstrate for the first time that giant clams show nitrogen isotopic values in their shells in line with expectations from their diet. Other clams have been measured this way, but the fact that we were able to conduct these analyses at all is a testament to the sensitivity of the elemental analyzer in Chris’s lab. Giant clams have *very* low concentrations of organic matter in their shells, so the forward march of technology was a major factor enabling this study to be possible.
Why does it matter that we can measure the transition of the clams from filter-feeding to photosymbiotic in their shell records? Well, giant clams are not the only bivalves which have photosymbionts. There are other clams in the fossil record which have been proposed to have had symbioses with algae, but until now we’ve never had a definitive geochemical way to measure this in fossils. We hope that this approach can be applied to the organic material in fossil shells, which is often well preserved, to see if huge clams in the Cretaceous and Jurassic had a similar way of life to the modern giant clams! If we can demonstrate that was the case, we can see how such species responded to past intervals of climate change, which will help us understand how giant clams will fare in the warming, acidifying ocean of the present.
These results also help explain the lives of giant clams themselves. We hope this kind of data can be used to measure the symbiotic development of giant clams in different places, with different types of food and nitrogen available, where we’d have the potential to measure pollution. Interestingly, the time that the model shows the clams transitioning to photosynthetic maturity is right around the time that they reach reproductive maturity (5-10 years of age). We’d like to investigate whether the time of clam maturity is controlled by the development of their symbiosis, which itself might relate to nutrients in the clams’ environment. If clams can grow faster, then they can mature faster, and potentially reproduce sooner in life. Will giant clams be able to thrive in the presence of increased nitrate, which is a common pollutant in coral reef environments? Like all worthwhile research projects, we have dozens of new questions to pursue as a result of this work, so stay tuned for the next installment in this journey of clam knowledge!
Every clam is a door into the sea. If the “door” of its shell is open, the clam may be happily breathing, or eating, or doing other weirder things. If the door is closed, it may be hiding from a predator, or preventing itself from drying out at low tide, or protecting itself from some other source of stress. It turns out that by monitoring the opening and closing of a clam’s shell valves, a field called valvometry, scientists can learn a lot about the clam’s physiology, its ecology and the environment around it.
Valvometry involves attaching waterproof sensors to each shell valve of the bivalve, to measure the distance between them and their movement. Researchers have used valvometers to figure out that bivalves can be disturbed by underwater pollution like oil spills, harmful algal blooms, and more unexpected sources such as noise and light pollution.
A great video from Tom Scott discussing a Polish program to monitor water quality with valvometry
Giant clams are a group of unusually large bivalves (some species reach up to 3 feet long!) native to coral reefs of the Indo-Pacific, from Australia to Israel. They grow to such large size with the help of symbiotic algae living in their flesh, the same kind that corals partner with the corals that build the reefs. The algae photosynthesize and share the sugars they make with their host clam, and the clam gives the algae nitrogen fertilizer and other nutrients, a safe home from predation and even helps channel light to the algae using reflective cells called iridophores.
A Tridacna derasa clam in the Biosphere ocean. It has deep green flesh, covered with yellow stripes of iridophores and a blue fringe at the edge.
Previous studies have used valvometers on giant clams, but I was always perplexed by how few studies there were: only two that I know of! One study on clams in New Caledonia figured out that the clams partially close every night and bask wide open during the day. The clams’ shell opening behavior and growth was found to become more erratic at temperatures above 27 °C, and when light levels become too great. Another study showed the clams start to clam up when exposed to UV light to protect themselves from a sort of sunburn, which is a real threat in the shallow reef waters they live in.
Two clams sitting next to each other in the B2 ocean. They often moved themselves to “snuggle” next to each other this way. Safety in numbers!
There is clearly a lot of information to pick up about how clams react to their environments, which can help us understand the health of the clams and also the corals around them. Coral reefs are under global stress from climate change, overfishing and pollution. Giant clams are some of the most prolific and widespread bivalve inhabitants of reefs, and represent an appealing potential biomonitor of reef conditions. Many giant clam species are threatened by the same stressors that influence the corals which build the reefs they live on, as well as overharvesting for food and their shells. For that reason, wild examples should clearly not be bothered by applying valvometric sensors. But giant clams are increasingly grown for the aquarium trade, resulting in a wealth of cultured specimens which could serve as sentinels of reef health, if they were fitted out with sensors. All of these motivators made me more and more curious of why we don’t have more literature monitoring the behavior of these clams with valve sensors.
I wondered if one of the limiting factors preventing the use of valvometry on giant clams is expense and ease of access. Giant clams live primarily in regions bordering developing countries in the Indo-Pacific, and almost all the professional aquaculture of clams for the reef trade happens in such countries, including places like Palau, Thailand, and New Caledonia. These countries are far removed from the places where most of the proprietary valvometric systems are manufactured. These systems can cost several thousand dollars even in Europe, never mind Palau, where arranging the import of electronics can be difficult.
When I started my postdoctoral fellowship at Biosphere 2 in 2020, I set out to grow two dozen smooth giant clams (Tridacna derasa, a species which can grow to about 2 feet long) in the controlled environment of the Biosphere 2 ocean, a 700,000 gallon (over 2.6 million liter) saltwater tank used to grow corals and tropical fish and kept at a stable year-round temperature of 25 °C. We suspended a series of LED lights intended to simulate the powerful light levels these clams experience in the wild (light is a lot brighter in the tropics than it is in Arizona!). The main focus of my project involved measuring the shell chemistry of the clams, to determine how their body chemistry changed as they grew from mostly getting their energy from filtering algae food from the water like other clams, to getting most of their energy from sunlight like a plant. But as a “side project” I set about measuring the behavior of the clams with custom-built valvometers based on open-source, inexpensive hardware that would be more accessible to researchers in the developing world. That work has since been published in PLoS One!
In our design, we used Hall effect sensors. Hall effect sensors generate a voltage when a change in magnetic field is detected. They are cheap, easily obtained for less than $1.50 apiece and are common in the electronics hobby trade. You might have encountered one in a home security system door/window sensor, where they help detect if a door is open or shut. We stuck a hall sensor soldered to a long copper cable to one valve of a clam, and a small magnet to the other valve. When the clam closed, we could measure exactly how closed it was. You can see why I started off by calling clams doors into the sea: we were literally measuring them that way!
Showing the sensor soldered to the three strands of the cable.
But here the first challenge of my project appeared. The off-the-shelf Hall sensors don’t come in waterproof form, and I learned quickly that the ocean really, really loves to break my gear. After dozens of failures, I settled on coating the sensors in waterproof grease, wrapping that in heat-shrink tubing and then sealing that inside of aquarium-grade silicone. During this process, a gifted technician at Biosphere 2 named Douglas Cline helped with iterating on the first prototypes. At a certain point I taught myself to solder so I could do my part to improve the sensors.
It was also hard to figure out how to attach the sensors and magnets to the clams in a durable way. Neither of the prior studies mentioned how they attached the sensors to giant clams, and I tried and failed with literally a dozen different ways before settling on “pool putty,” a two-part adhesive often used to seal leaks in pools that can cure underwater. I found the pool putty had trouble attaching to the clams’ shells on its own, so I combined it with a special kind of cyanoacrylate superglue called “frag glue,” often used to attach pieces of corals to growth stubs. I also had to find a way to attach it to the clams without stressing them out. I determined five minutes out of the water was enough time to get the sensors attached to the clams, after which they could be returned to the water to finish curing. While giant clams are adapted to spend extended periods out of the water in their natural intertidal environment, we wanted to make sure to minimize their stress however possible, to ensure they would show natural cycles of behavior in the data.
Figure from the paper showing: A) schematic of the sensor attached to the clam, linked to an Arduino microcontroller and Raspberry pi computer. B) A sensor attached to one of the clams
We were pleased to see the cyborg clams seemed to pay no mind to the sensors. Giant clams are adapted to encourage all sorts of other critters to live on their shells as a form of natural camouflage, and I think the clams interpreted the sensors as pieces of coral or anemones sticking to the side of their shell. Whatever the case, as long as we kept the cable pointing to the side away from the clams’ flesh, they opened five minutes after being returned to the water, and their behavior and growth rates were indistinguishable from the clams that didn’t have sensors attached.
One of what became many sunsets on the Biosphere 2 ocean shore troubleshooting the clam sensors! Pardon the chaos: mad scientist at work!
So how did we measure the voltages coming from the sensors? Our design featured an Arduino microcontroller, sort of like a smart circuit board which can measure the voltages coming back over the copper cables. Arduinos are very cheap, and we chose a $25 model. Even more importantly, Arduino has a huge library of plug-ins available to keep the exact time of each observation using a clock attachment, and the data can be uploaded to SD cards or an attached computer. For the attached computer, I used a Raspberry Pi computer, which are open-source Linux-based tiny computers that are very cheap! Or rather they were very cheap before the pandemic, but fortunately there a lot of open-source alternatives that can be obtained more cheaply. We logged the data on the Raspberry Pi as it rolled over from the Arduino, and I could watch the read-out on a monitor right on the Biosphere 2 beach. We set the Arduino to record every 5 seconds.
Sensors attached to four of the clams. Notice the one on top left has closed a bit, after sensing my presence! They have eyes so they were able to detect me 😀
We ran the sensors for three months. During that time, the baby giant clams grew almost an inch! What did the sensors record them doing? During the day, the clams basked wide-open, exposing as much of their tissue as possible to light (other than the times that I disturbed them by swimming above them, of course)! This schedule of opening aligned pretty closely with the times that maximum sunlight hit their part of the Biosphere 2 ocean: the mornings, because the clams were on the east side of the building. At this time of day, the clams want to expose their symbiotic algae to as much light as possible, so they can conduct photosynthesis and make sugars that the clams use as food!
A) Plot of the valvometry data. Points higher on the plot mean the clam was more closed, up to 100% closed. The clams proceeded by opening in the early morning and then closing in the early afternoon. The big red circles represent times that the clams closed briefly, with bigger circles representing a longer time spent closed. Most of these rapid closures happened at night. B. A plot of Photosynthetically active Radiation (the amount of light the clams had to use for photosynthesis). The highest values were in the mid-morning when the clam lights were running in combination with direct sunlight hitting them from above.
Around mid-afternoon, the clams started to close partially, to about half closed. Why might that be? My hypothesis is that this posture represents a kind of “defensive crouch” to protect themselves from predators, in this case fireworms that live in the Biosphere 2 Ocean and were constantly kicking the clams’ tires. Similar nighttime behavior was observed in wild clams in a previous study, but not in a study that took place in a small predator-free terrarium tank. By remaining partially closed, the clams are prepared to rapidly close completely if they feel a predator approaching. But they only expend that energy of staying in that posture if predators are around!
One of the fireworms that proved to be my nemesis and continually attacked the clams during the experiment
And approach the fireworms did. We observed frequent closures at night lasting anywhere from a few seconds to hours, likely partially related to the activity of the worms around the clams. But the clams were engaging in another activity at night: filter feeding! Giant clams really get to have their cake and eat it too, because during the day, they act like a plant, but at night, they eat other plants in the form of plankton that they filter feed out of the water using their gills! At regular intervals, the clams need to clear uneaten material from their gills in a process sometimes called “valve-clapping”. The clams yank their shell valves together rapidly to force water out, blowing out pseudofeces: unwanted material packaged with mucus. We measured this valve-clapping mostly at night. The clams are likely scheduling this activity for the night-time so they can prioritize staying open and filter feeding during the day!
Figure comparing how often clams closed per day to measures of how high plankton numbers were in the Biosphere 2 ocean (chlorophyll is a marker of phytoplankton while phycocyanin is a measure of cyanobacteria), and how high the light levels were. Peaks in closure activity often happened shortly after rises in algae.
We observed that the frequency of valve clapping aligned closely with the rises and falls of chlorophyll concentration in the Biosphere 2 ocean, which is a measure of how much plankton is in the water column. The clams would engage in a burst of valve clapping around 4 days on average after a bloom in chlorophyll, suggesting they were filtering out plankton after they had died and settled to the bottom where the clams could eat them. We also found that the clam’s filtering activity peaked at times of highest pH. This likely is due to the fact that higher pH means the algae around the clams are being more active, and pulling CO2 in from the water to use in photosynthesis, making the water less acidic. More photosynthesis means potentially more material for the clams to filter through! This data helps quantify how giant clams help filter the water in their native environments! Coral reefs depend on very clear transparent water to allow maximum sunlight to reach the corals, and the filtering activity of giant clams likely plays a big role in helping preserve those conditions!
So we found that by adding sensors to clams, we could record their ability to feed from the sun, their feeding on plankton around them and their avoidance of predators. How can this technique be used next? We hope that by using cheap off-the-shelf resources and open-source software, we can enable more sensors to be put on clams all over the world, such as places where giant clams are farmed in Palau, New Caledonia, Thailand, Taiwan, Malaysia and more! If we can collect data on clam activity from all these places, we can compare how their feeding patterns differ in places that have more or less plankton floating by, or have more or less sunlight available, or different predators that affect the clams’ behavior. This data would have importance to the clams’ conservation, as well as our understanding of the reef overall. In future years, I hope we can develop a global network of cyborg giant clams from the Red Sea to the Great Barrier Reef, so we can better understand how these oversized and conspicuous but still mysterious bivalve work their magic!
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?
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!
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!
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.
1) Following in Charles Darwin’s wake, I still use nets to sample the plankton today. This thread is a series of 32 weekly, short videos narrated by #DavidAttenborough to introduce this remarkable world of microscopic life. RT to make this series a success.@zeiss_micropic.twitter.com/ENgRyF8ujH
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.
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.
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!
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.
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.
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!
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!
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.
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.
Clamsplaining 