You are Isotopes (Part III)

This is the third part of a series about isotopes and why they’re useful and interesting to scientists.

Isotopes are the flavors of elements. And because our universe is made up of atoms of elements, every object can be thought of as a delicious smoothie of flavors. Scientists like me are trying to reverse engineer those mixtures and pick out individual tastes, in order to answer questions about our world.

For example, I work with giant clams. These guys build enormous shells made of a mineral called calcium carbonate: CaCO3. That means that every molecule in a clam’s shell contains a calcium atom, a carbon and three oxygens. But as you might know from reading the previous entries in this series, not all of those atoms are the same. They are a mixture of different flavors. We have some carbon-12 and 13 in there (so named for their atomic weights), and some oxygen-16, 17 and 18. Here I’m focusing on the stable isotopes, which are not radioactive and are called “stable” because they’re not going to self-destruct. There are radioactive isotopes in there too, but I don’t use those nearly as often in my work.

Officer, this is a pile of giant clam powder, I swear!

I am measuring stable isotopes of carbon and oxygen in my shell samples. To do this, I take a sample of powder, grind it up, weigh it, and put it into tiny little cups. We only need a very small sample: about 50 micrograms of shell material. A typical pill of tylenol contains over 300 mg of active ingredient, so about 6,000 of my samples will fit in a single tylenol regular strength pill, if you suddenly decided you needed a giant clam prescription.

Simplified representation of what’s happening in a mass spec. Source

This tiny sample is one of thirty that I can measure at a time. Those samples are reacted with acid and the CO2 gas that is released as a result of the reaction can be processed by a machine called a mass spectrometer. The mass spec, which is in the Stable Isotope Laboratory in my building, ionizes the molecules in that gas (gives them a bit of electric charge) and then those ions are flung through an electromagnetic field. That beam of charged gas is flung around a curve. That curve is where the magic of making a mass spectrum happens.

Think of the atoms in the CO2 gas from my sample as a bunch of racecars exiting the straightaway and starting around the curve on the racetrack. Only these racecars vary in weights. And the race organizers have greased the track at the curve so that they fling into the sides of the track when they try to turn. As the racecars fling into the sides of the track, they will separate according to their mass. The lighter cars will be able to make it further around the curve before they meet their demise because they have less inertia forcing them forward, whereas the SUVs in the race will barrel forward straight into the sides of the track. At the end, you have a spectrum of racecars poking out of the walls of the track, with SUVs first, then the coupes, then the compact cars and then the motorcycles, which almost made it around the bend, but not quite. Atoms in the mass spectrometer act the same way, and we measure how many collisions happen along each point of the bend in order to not only “weigh” the sample of gas, but also figure out how many molecules of each weight there are!

It turns out that it is quite difficult to measure the exact number of atoms of a particular isotope in gas, however. It is much more economical and feasible for the purposes of most researchers to simply compare our mass spectrum to the results from a standard. Much like there is a literal standard kilogram and standard meter in a lab somewhere in France which is used to keep track of how much mass is actually in a kilogram, there is a standard used by all researchers like me to describe our samples of carbonate.

A collection of belemnite fossils from the Pee Dee formation, similar to the one used for the PDB standard. Source

The most common standard used is from a belemnite fossil from the Pee Dee formation in North Carolina. Belemnites are extinct squid-like creatures that formed an internal shell, and one of those internal shells was fossilized, unearthed by a researcher and ground up to become the reference for all other researchers following. Samples of the carbonate in its fossil had more carbon-13’s per unit mass than most other fossil specimens known.  Almost everything you measure will be “lighter” in terms of carbon, because carbon-12 is naturally so common on our planet.

Scientists needed a convenient way to put a number on this, so a simple formula was developed which would allow us to quickly communicate to each other how isotopically “heavy” or “light” a particular sample is in comparison to the Pee Dee Belemnite. The formula isn’t that important for our purposes but the units of its output are in parts per thousand, or “per mil” for short (same idea of how we shorten parts per hundred to “percent”).

The symbol for per mil is a percent sign with an extra little loop at the end: ‰. To make the shorthand complete, we also need to note that this is how much the carbon-13 to carbon-12 isotope ratio of a sample differs from the Pee Dee Belemnite. We do so, we use the Greek delta symbol (δ), commonly used in science and math to represent “difference or change from.” So a sample that has a carbon-13 to carbon-12 ratio which is 20 parts per thousand less than that of the Pee Dee Belemnite is written -20 ‰ δ13CPDB. There are other samples that can be used as well, including Standard Mean Ocean water (SMOW), and the Vienna Pee Dee Belemnite (VPDB). It’s important to note which you are using so that people know the scale of your measurement!

Phew, hopefully that didn’t confuse the hell out of you! Next time, I’ll talk about how different δ13C (and for oxygen isotopes, δ18O) can tell us different details about the life of an organism. Here’s a cute gif of a scallop as a chaser after all that science you read.

Local thief spotted in my backyard


The brown-headed cowbird (Molothrus ater) is a notorious thief. This is merely a young thief which I observed in my yard; it’s still in training, but when it is an adult it will look more like this:

Source: Wikipedia

It will search out a nest of an unsupecting bird, perhaps a sparrow or other songbird, and it will sneakily lay an egg when the parents are away. The egg will hatch and the other birds will raise it as their own. This practice is known as brood parasitism. The unsuspecting sap that raises the young cowbird will unfortunately feed its own young proportionately less and its fitness will suffer as a result.

Sometimes, the victim figures out that one of the eggs isn’t its own and disposes of it. If the cowbird sometimes returns to the scene of the crime and if it discovers its egg is missing, it may destroy the nest in a darkly Darwinian form of payback called “mafia behavior.” Sometimes, a cowbird egg is an offer you can’t refuse.

A hinged shell does not a clam make (QUIZ)

Bivalves are so named for their two hard shell valves made of carbonate, linked by a soft ligament acting as a hinge. They use a strong adductor muscle to close their shell, and the relaxation of the muscle allows the springy ligament to reopen (you might be familiar with adductor muscles as the edible tasty part of a scallop). In deference to the bivalves, laptops and flip-phones are called “clamshell” designs. That satisfying snap into place when you spring the ligamen… I mean, hinge of a flip phone is an example of human design imitating the ingenuity of evolution. But it turns out that plenty of other members of the tree of life have also stumbled upon the durable idea of a hinged two-valve shell. On the other hand, plenty of bivalves have given up on the classic clamshell look. In fact, the ancestor of all bivalves had a one-part shell, and the hinge evolved later.

Test your knowledge by trying to identify which which pictures are bivalves and which aren’t. Answers and picture sources at the bottom!

A. brachiopod-semenov.jpg



















A. This is not even a mollusk, never mind a clam! It’s a different benthic (bottom-dwelling) invertebrate called a brachiopod, which make up their own phylum. To put that in perspective, brachiopods are as far from bivalves on the tree of life as you are (you’re in phylum Chordata)! Yet they evolved a similar look through a process called convergent evolution. If environmental needs are the same, organisms may come to the same solution multiple times. Much like wings for flight evolved independently in insects, birds and bats, bivalves and brachiopods both evolved a hinged shell as a form of protection from predation.

B. These are indeed bivalves: rock scallops commonly found off the coast of California (picture by me of an exhibit at Monterey Bay Aquarium). So similar to the brachiopods in their ridged, hinged shells. Like picture A, these guys specialize in living on hard, rocky nearshore bottoms. Some cultures do apparently eat brachiopods (I have not), but I have little doubt that rock scallops are tastier.

C. These are also bivalves: windowpane oysters. Also known as capiz shell, they are commonly used for decoration and art due to their beautiful, thin semi-transparent shells. A large industry harvests them off the shores of the Philippines, where they unfortunately are growing scarce due to overexploitation.

D. These are not bivalves! They are crustaceans called clam shrimp. They have little legs poking out of a hard hinged shell, and have been found in some of the harshest environments on earth, where they wait in extended hibernation, sometimes years, between bouts of rainfall.

E. Not a bivalve. These are another kind of crustacean called ostracods. Like clam shrimp, ostracods live in a hinged shell and swim around with the help of tiny legs, filter-feeding in the water column. Ostracods are everywhere in the oceans and in freshwater, but have undergone an extreme process of miniaturization from their ancestral form, and are now represent some of the smallest complex multicellular life known.

F. These are fossil ostracods. You can see why they are sometimes mistaken for bivalves! The givaway is that one valve is overhanging the other. Most bivalves have symmetry between the two halves of their shell, but ostracods and brachiopods do not.

G. This is a snail, so it’s a close molluskan cousin of bivalves. Some snails feature a hinged lid at their shell opening called an operculum. This operculum can be closed to protect from predators and also seal in water to help land snails from drying out between rains.

H. This is a bizarre bivalve called a rudist. They were common during the time of the dinosaurs but went extinct during the same extinction, 66 million years ago. While they come in many bizarre shapes, this elevator form (or as I prefer to call them, trash-can form) would have been stuck in the sediment with its small lid poking out at the surface. They could open and close the lid to filter-feed.

I. This is a giant clam, Tridacna crocea! Its shell is hidden, embedded in the coral that has grown to surround it on all sides. Only the mantle (soft “lips”) are exposed, and are brilliantly colored by the symbiotic algae in its tissue. It harvests the sugars made by the algae for food. Despite being embedded in the coral, the clam does have enough room to close and pull back its mantle if a predator approaches.

J. This is a one of the weirdest modern bivalves, called a hammer oyster. These guys are found in the tropics, and the hammerhead part of their shell is actually their hinge, extended at both sides. The hinge provides the surface area needed to “snow-shoe” on top of the soft sandy bottom where they live. Other bivalves sometimes take advantage and live on the oyster like a raft!

K. This is a different brachiopod. Notice the lack of symmetry between the valves which gives it away.

L. This is by far the weirdest modern bivalve, a shipworm. These guys live buried deep within wood and are the number-one killer of wooden ships. They secrete a long tube of carbonate and have largely given up the hinged lifestyle, looking more like worms than mollusks.

You are isotopes (Part II)

This is the second part in a series how isotopes work and how they are scientifically fascinating. Part I here

It turns out a horse is not just a horse, of course. The horse is a collection of atoms, and each of those atoms has a particular isotopic “flavor”, and the collection of isotope types in the horse tells a story.  At the end of the day, scientists are simply interested in reading and telling stories about our world. The tail….er, tale of the horse is written by myriad interacting processes in the universe which influence the horse’s stable isotope ratios.

As I mentioned last time, carbon-12 is much, much more common than carbon-13 is on our planet, due to nuclear fusion of helium-4 in the sun. there are nearly 99 carbon-12’s on earth for every carbon-13. But that’s the base ratio if you took our whole planet, put it in a blender and mixed it all up. If you measured a particular object, such as a horse, it likely does not follow that measure exactly. It has become differentiated from the global average by numerous factors which have altered the isotope ratio.

In isotopic chemistry, fractionation is our name for any process which creates a preference for a certain isotope. If chemical reactions had no bias toward any particular isotope, that 99 to 1 ratio of carbon-12 to carbon-13 would be present in literally everything including you and me. But it turns out that the biochemical dice are loaded- to make the ratio even more biased!

The enormous Rubisco enzyme. No one said photosynthesis was simple. Source: Wikipedia

Photosynthesis is the process by which plants take carbon dioxide gas in the atmosphere and “fix” it to make sugars, which they then use for food. The core enzyme responsible for this carbon fixation is called Rubisco (short for Ribulose-1,5-bisphosphate carboxylase/oxygenase). This enormous molecule is likely the most abundant enzyme on earth. And it turns out that it has a favorite flavor when it comes to the carbon it fixes into sugar.

In fact, the entire plant is discriminating against carbon-13 in several of the processes of photosynthesis. Carbon dioxide molecules diffuse more quickly into the plant’s leaves if they include the lighter carbon-12 rather than carbon-13. “Light” CO2 also dissolves more easily in the plant’s fluids. But the biggest fractionation happens when the Rubisco molecule gets hold of CO2 and breaks it. At each of these steps, the light carbon-12 is more likely to be used by the plant than its heavier siblings. There are various thermodynamic reasons for why this is the case, but the plant is essentially a sieve removing more of those heavy carbons at every step. At the end of the process, the plant is left isotopically “lighter” than the CO2 gas surrounding it that it breathes in.

Because you are what you eat, this means that you are suspiciously carbon-light, and there’s nothing you can do about it. Should have thought of that before you decided to be dependent on plants as the factory for your carbon-based molecules. Next time, we’ll talk about how we measure this, and the kinds of science that can happen once you have a nice consistent measurement to use to compare isotopic ratios between samples.

You are isotopes (Part I)

As you may well know, every element is defined by its number of protons contained the nuclei of its atoms. Hydrogen has one. Carbon has six. This is non-negotiable. But every element can be found in multiple “flavors” known as isotopes. This flavor depends on the isotope’s atomic mass, which is determined by the number of neutrons present in the nucleus of that atom. Neutrons are kind of like atomic ballast. Unlike protons, which have a positive charge, they are neutral, but they do have a mass. Different isotopes have different numbers of neutrons, determining their atomic mass but preserving its particular elemental identity (which would only change if you changed the number of protons present).

Let’s focus on carbon, an element which I think about daily, though every element has isotopes and I could pick many other examples. Hope you’re OK with that, but if not it’s my blog so deal with it. So carbon has been found or created in up to 15 flavors. A whopping 98.9% of all the carbon on Earth occurs as carbon-12 (written as 12C), which has six protons and six neutrons, adding up to an atomic mass of about 12 atomic mass units (amu). It’s the most common because it’s the product of three helium-4 isotopes fusing together, each weighing 4 amu + 4 amu + 4 amu adding to make a single carbon-12. This is a very common reaction in stars, and because you are stardust, it is also the most common flavor of carbon in you.

But we make other flavors by adding neutrons. You can make carbon-13 with six protons and seven neutrons. This is a rare flavor, accounting for almost all of the remaining 1.1% of carbon found on earth. It is also the only other stable form of carbon. I note that it’s stable because all the other 13 known flavors of carbon are unstable, and many are only known from the laboratory because they are too short-lived to be found in the environment.

It turns out that if an element’s atomic nucleus is too light, or too heavy, that element will become radioactive and decay with time, continuously firing off pieces of itself out of frustration. Carbon-14 is the most famous and common of these radioactive isotopes of carbon, and it still only makes up 1 in every million million atoms of carbon on earth. Carbon-14 fires off particles and decays into nitrogen-14 because it is more stable orientation for the protons and neutrons to be in, for physics reasons I won’t get into here.

Carbon-14 does this in a very predictable, methodical pattern. It’s difficult to predict when an individual carbon-14 atom will do this, but if you take any object you have just created, like a piece of pottery, for example, you can be pretty much certain that in 5,730 years, only 1/2 of the carbon-14’s will still be present. The rest decided they’d rather be nitrogen-14. This is non-negotiable and you’d best learn to accept it. But it means that we can sniff out the age of a lot of interesting mysterious objects if we know the amount of carbon-14 present in the environment (which we often do) and measure the amount present in the object today. You have some restrictions. For example, for objects that are too old, too little of the carbon-14 would be left for you to measure accurately.

Carbon-14 dating, often just called radiocarbon dating, is very useful in figuring out the ages of stuff, but I’m mostly interested in the stable isotopes of carbon. Next week I’ll talk about why that is, and what kind of questions I can answer by looking at amounts of different stable carbon isotopes in a sample. See you then!

In grief for the America that was

I used to have pride in being American. I’m grateful for all the opportunities and privileges I’ve had being a citizen of this storied democracy. I held onto hope when my countrymen doubted the citizenship of my president. I held on when we elected a fraudulent, undignified xenophobe to succeed him. I held on when we left a climate agreement out of spite and began rolling back environmental protections left and right. But today, I don’t know if I can do it. I don’t really feel like part of this place anymore.

I’m still trying to figure out my career. If I stay here after grad school, I’ll be a more inward looking person; thinking about my own life, friends and family. But I’m looking into leaving. I don’t really feel like I can be part of this shared enterprise anymore. It’s really out of exhaustion more than anger. I’m tired of this feeling of grief. It’s analogous to the feeling I’d have after losing a loved one, when I just want to disconnect. The country I grew up in is no more, and it may be time to move on.

Fossil-Fueled Life

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Thick aggregates of Bathymodiolus mussels on a cold seep site off of Nantucket. Source: NOAA

Humans aren’t the only users of fossil fuels. In many parts of the ocean, natural gas (methane) is constantly bubbling out of the sediment. These areas are known as cold seeps and are often a marker of productive fossil fuel reservoirs in the crust underneath. The name cold seep is somewhat of a misnomer (they are often slightly warmer than surrounding waters), but they are indeed much cooler than the more famous hydrothermal vents, which form due to geothermal activity. They are often found in shallower waters than hydrothermal vents, which generally occur in the deepest regions of the ocean where the earth’s crust is rifting. As with hydrothermal vents, cold seeps provide a unique opportunity for ecosystems to arise which are based on chemical energy, rather than solar-powered photosynthesis like the rest of the biosphere. Unusual life forms harness the chemical energy of the methane and sulfide emitted at these seeps, and many can also be found at the more famous hydrothermal vents.

Crabs feeding on a bed of Bathymodiolus. Source: NOAA

Bathymodiolus mussels, vesicomyid clams, and other bivalves thrive at these seep environments, and have evolved to partner with bacteria in their gills and stomachs which can directly consume and produce energy from the reaction of methane and sulfate continuously being sourced from the seep underneath, creating bicarbonate and sulfide as products. This form of metabolism, chemosynthesis, is distinct from the familiar photosynthesis/respiration that most life-forms at the surface use to create energy. The partnership between a multicellular animal and chemosynthetic bacteria is called chemosymbiosis. These reactions are of course being utilized by all sorts of microbes not partnering with bivalves, but the bacteria that take on metazoan hosts have the advantage of a stable environment and a constant flow of fresh seep gas brought in by the bivalves’ gills. The bivalves feed on the products of the microbe’s hard work. As they are some of the only inhabitants that can tolerate the oxygen-free, toxic environment of seeps, they form dense thick shell beds wherever a seep appears.

A bed of tubeworms and a deep-living octopus in the Arctic. Source: MBARI via BBC

Other chemosymbiotic groups use the hydrogen sulfide byproducts from seeps, which they oxidize into elemental sulfur. The most prominent of these are the vestimentiferan tubeworms, which lack mouth or anus and are totally dependent on the activity of the bacteria that they house in a modified digestive tract. Some of these worms have been found in seeps in extreme environments, such as the truly cold cold seeps of the Arctic. They are less spectacular in appearance than their bright red counterparts from hydrothermal vents, but are believed to live for an extremely long time, depending on the consistency of the seep that they inhabit.


Hesiocaeca methanicola, one species of the poorly understood “ice worms.” Source: NOAA via Wikipedia

At the extreme pressures and low temperatures of the deep ocean, methane can freeze in combination with water molecules, forming structures called clathrates. Much of the deep ocean floor is dusted with deposits of clathrates. Microbes which feed on clathrates are believed to be a food source for grazing polychaete “ice worms.” These unusual organisms can survive up to 96 hours without a whiff of oxygen, an unbelievable feat for a moving, multicellular organism.

Imaginative artist representation of a probe visiting a vent under the ice of Europa. Source

Cold seep environments are perhaps merely one specific manifestation of a vast, poorly understood collection of biota which do not depend on the sun for their energy. We do not yet understand many of the deep ecosystems which may be present within the earth’s crust, in the deep ocean and trapped under polar ice. NASA studies cold seep and hydrothermal environments as the best analog for the conditions life could experience in the frozen oceans of Europa and Enceladus. It is eerie to think that such alien ecosystems  exist merely a few kilometers off of our familiar shores, and were using fossil fuel energy far before humans figured out how to combust it.

NOAA Ocean Explorer: Okeanos Explorer: Northeast U.S. Canyons 20
Methane bubbling out of the seafloor off of the Virginia coast. Source: NOAA


When a clam has a stowaway

My mussel contained a tiny half-eaten crab! - Imgur
Source: jeredjeya on Reddit

Bivalves put a lot of energy into their shells. These hardened, hinged sheaths of carbonate are an effective defense against many predators looking to get at the squishy clam’s body encased inside. Parasitic pea crabs have evolved to free-ride on the bivalves’ hard work.


(video courtesy Dana Shultz)

Pea crabs are small (pea-sized), very specialized parasites which live in the mantle cavity of many bivalve groups including oysters, mussels, clams and more. The mantle is the wall encasing the soft body of the bivalve, and the cavity is the space between this soft gooey tissue and the shell itself.

For a pea crab, there is no better place to be than this tiny, claustrophobic space. In fact, they can’t live anywhere else, though some species have been found in other unusual places such as inside the anuses and respiratory tracts of sea cucumbers (link SFW, fortunately, unless you’re a sea cucumber). In a bivalve host, the crab is protected from predation by the shell, and the bivalve provides a constant buffet of food as it sucks in suspended particles with its gills. The crab steals some of this food from itself before the bivalve can digest it.

As you might imagine, having a crab living in you taking your food and pinching at your gills is not an ideal arrangement for the bivalve. Pea crabs damage their hosts’ gills with their constant picking, and bivalves infected with crabs suffer slower growth than uninfected individuals, particularly for those unlucky enough to play host to the larger female pea crabs. At a certain point, the males will sneak out of their hosts and find a bivalve with a female crab inside. At this point, they mate inside the host’s shell, adding great insult to injury. The female releases her larvae, which swim out to infect new hapless bivalves and start the cycle over again.

Aww, she’s expecting! The papers refer to this as being “with berry” which I find amusing for some reason. (photo from Dana Shultz)


You might think that commercial oysters with crab parasites would be thrown out, but to the contrary, finding a pea crab or its close relative the oyster crab with your meal is a cause for celebration in some areas, such as the Cheasapeake Bay. The crabs are eaten whole and often raw, and are said to have a texture akin to shrimp, with notes of sweetness and umami. Personally I prefer surprises in my Kinder eggs rather than in my shellfish, but to each their own.

A pea crab serves as a nice side dish for this lunching sea otter. Source: Brocken Inaglory on Wikipedia