Just another site

Clogging the filters

One great advantage of field work in geochemistry is the ability to gain meaningful information from the environment by the simple act of being there. No analytical chemistry necessary. I remember how my advisor Phoebe showed me patches of silvery blue water along the darker back drop of the Southern Ocean surface water during our 2012 cruise on the R/V Revelle. These discolorations indicated dense populations of coccolithophores on ocean surface. Using the naked eye, we were able to hypothesize the chemical features of the water before us.

Several visual observations were similarly immediate and insightful on the Amazon main stem, as well. Upon arriving at the Óbidos site on our first full day, before even taking my first sample – long before actually analyzing it in lab back at home— it was clear that this water was packed with sediment, and by proportion, organic carbon. It was quickly apparent that the amount of carbon I collected per 100 liters at each Fazenda Tanguro stream I visited last November would not measure up to the quantity we could retrieve from filtering the same volume of sediment from the Amazon River waters.


Amazon River sediment clogged on a filter. Though it looks like milk-chocolate, I can assure you it certainly does not taste of it.

As a consequence, the orange murkiness of Amazon River discharge also gave away the unique logistical hurdles of sampling water here in April. On this first day at Obidos, we collected 100 liters of surface discharge near a center point of the river. Using pressure by manual bike pumps, we forced murky orange water through filters designed to collect all particles above 0.22 microns (1 thousandth of a millimeter!) in diameter. The filters clogged after just 1.5 liters. Because a large proportion of the work involved in sample processing during field work is manually exchanging clogged filters for new ones, the greatest challenge ahead was filtering the equivalent of 50 2-liter soda bottles before our trip’s end.

Fortunately, we have an efficient group of scientists on this river boat. João Felipe II is equipped with a diligent team of researchers from the Wood Hole Research Center and Universidade Federal do Oeste do Pará, quick learners of the act of water filtration. With just two bike pumps and three to five scientists, we are able to master a network of 4 filtration cylinders, passing a total of ~9 liters of water through filters at a time.


The filtration team. Even Kaka from Brazil’s 2010 National World Cup team lent a helping hand!

The great sediment concentrations in the river mean that we will go home with more than enough organic material to investigate its origin and transformation in the Amazon River system. We will be able to find specific biological molecules that have been produced by plants, riverine algae, and aquatic bacteria.

More importantly, we will have enough material from these samples to measure the relative proportions of two carbon isotopes in these specific molecules: carbon-12 and carbon-13. Isotopes are atoms of the same element that differ by the number of neutrons in their nucleus. Carbon-12 is the most common carbon isotope in nature; it has six protons and six neutrons inside its atomic nucleus (hence, 12 indicates the sum of protons and neutrons). By contrast, far less common is carbon-13, which is slightly heavier, as it has seven neutrons in its nucleus.

Living things incorporate different proportions of molecules with carbon-12 and carbon-13 when constructing or transforming organic matter. For example, during photosynthesis, plants use less energy in absorbing carbon dioxide with carbon-12 than carbon dioxide with carbon-13. Organic molecules produced by different plant types will demonstrate unique ratios of carbon-12 to carbon-13 based on these preferences.

Resolving the isotope ratios of specific biological molecules in our samples will help us track the history of organic carbon in the river, from its point of production to its journey into the river system and thereafter.

29 March 2014: Starting the rainy season

With the last trip to Brazil five months behind us, we arrive again for the next phase of sampling from the Amazon River Basin. For one week, I will visit one to two major sites on the main stem of the Amazon River with a team of scientists from Massachusetts-based Woods Hole Research Center and Brazil-based Universidade Federal do Oeste do Pará (UFOPA). These sites, Óbidos and Alter do Chão (a.k.a. the Caribbean of Brazil), sit a few degrees south of the equator, and wind through the northern states of Amazonas and Par, the quintessential Amazon rain forest, inside the “lungs” of our planet. Our visit coincides strategically with the start of the rainy season (and the end of Carnaval season), as daily rainstorms and river discharge are on the rise.



Typical river boats docked along the Rio Tapajós in Santarem, Pará, near its meeting with Rio Amazonas



At its core, the current mission is the same as my first trip in November. We return in search of sediments of organic carbon suspended in river discharge. Alongside the other scientists traveling from Woods Hole, we bring about two hundred pounds of equipment in our luggage. Once again, a disproportionately large fraction of this weight is comprised of bicycle-pump-powered devices for catching and filtering river water.

But, this time, we are sampling the main stem of the Amazon River, and by this fact alone, I expect this trip to differ dramatically. The suspended sediments I collected from Fazenda Tanguro in November flowed through small streams with limited catchment areas, through which underground water and rainfall drained into the river. This meant that the particles of organic carbon in my sediments have a unique terrestrial origin. If I collected sediments from a stream that flowed solely through soy cropland, for example, I could quickly surmise that most of the organic material in my samples came from soy agriculture.

Sediments suspended in the main stem of the Amazon River tell a broader story. There is a reason that station Óbidos has been visited by scientists of Amazonia for several decades. The flow rate of the river through this site varies by a factor of three, from ~100,000 m3/sec during the dry season (November – January) to ~300,000 m3/sec during the wet season (April – July) (Moreira-Turcq et al. 2013), the volume of 50 to 150 million soda bottles flowing through the river each second. Because water at station Óbidos has traveled extensively across the Amazon landscape, from the high Andes in Peru to the wide floodplains below, scientists have used measurements from Óbidos alone to learn about large-scale interactions between entire river network and the global carbon cycle.

Alter do Chão, which sits near the confluence of the Tapajos River tributary and the Amazon River, similarly draws water from an extensive catchment area. As a consequence, the organic carbon in suspended sediments from the Tapajós and Amazon River waters pools together a variety of sources from different landscapes. As we are interested in the role of different landscape types on the movement of carbon through the river system, isolating the origin of this organic matter is not trivial.

For this reason, the measurements that stem from this trip are ever the more valuable alongside the samples we collect from more isolated sites like Fazenda Tanguro. What comparisons can we draw between the large scale and the small scale within the Amazon River network? What is the pooled of effect of land use change spanning across all of Amazônia, one of the greatest terrestrial carbon sinks on Earth, on the movement of organic carbon from land to river to sea?

How-to Guide for Building a Lab


Early on, setting up for a week’s worth of work.

In the past week, I learned how to transform a chicken coop into a laboratory. The transformation had already started long before I arrived last week, but my short, quick stay at Fazenda Tanguro has still provided some important insights into the process.

 Most fundamentally, improvisation is key to drawing the blueprints. There is clearly a strong correlation between surprise and creativity here. The more unexpected turns I encountered, the more scientific innovation came out of improvisation.

I learned this with an early obstacle: blowing not only the fuse but moreover the capacitor of the power box for the peristaltic pump in incompatible Brazilian outlets. I planned to use this pump to suck water from a collection container and push it through filters on the other end, but now I had no more power to drive it, or collect half of my samples. For half of this half, I needed to pump water through a filter that removes particles from river water, allowing me to collect the throughput for other scientists at WHOI to measure nutrients and ions. For the other fourth, I needed to force water through cartridges that trapped lignin molecules dissolved in water, which are produced by vegetation and therefore help track the presence and influence of land plants in rivers.

But, maybe, the effect of arriving on a ranch over an hour removed from the nearest town and perhaps a half-day’s travel away from the nearest big city, makes you think in different ways. Certainly outside the box, as they say. As it turned out, replacing my pump was easy because the chicken coop lab had another. Most of the work entailed finding a car battery to power it, and fitting tubes of different sizes together pass water.

Other challenges, however, became clear with time. Most notable was the lack of a fume hood. Ventilation was ample in the lab, but no matter how much of a breeze passes through the open windows, hydrochloric acid is still hydrochloric acid, and extremely –literally – painful to smell. In the hottest of climates, I needed a small quantity of this caustic acid, which when added to my river water samples, helps extract the lignin molecules from the rest of the water feeding through the peristaltic pump.

So even in the tropics, it is useful to have some long sleeves and closed toe shoes, and gloves and goggles if you can manage it. Aside from these essentials, Paul – maybe the master lab architect here – also helped me fashion a trusty apron with a garbage bag, a fan to ventilate, a plastic sheet to serve as a hood-esque shield, and, finally, a bucket of water on standby as an emergency shower. This is how you build a fume hood in a chicken coop.


Later, wearing my lab gear after using the Hydrochloric Acid.

As I reflect, the odds seemed against collecting lignins for the Woods Hole Research Center. But, despite all the troubleshooting, I think I can return home with some vegetation to track from the streams at Fazenda Tanguro. 

Though I may not go back to the ranch for my thesis at WHOI, I am curious how the lab will continue to change into the future. What new innovations will occur? Will future generations of scientists soon forget that it once housed chickens? I will be particularly curious to learn whether anyone secured a system to keep insects, our great contaminants, away from field samples.


It probably took me five repetitions to engrain the word “multi-tirao” into my new vocabulary. And I’m not sure if you can even find it in a proper Brazilian Portuguese dictionary. Nonetheless, I will try my best to define it here because, in just three syllables, it adequately conveys the way field work gets done on Fazenda Tanguro, my field site over the past few days (fazenda means ranch). 

Oftentimes, dictionaries break down words into their different roots, so I will start with this same approach. First off, just like it would in English , “multi” means many. And indeed, at this fazenda, things exist and proceed in multitudes. I see multitude in the ten or so ripe mango trees that line our row of dormitories, kitchens and labs. I see multitude in the ostrich-like rheafamilies that roam the wide, flat fields of soy and corn. I certainly see multitude in the beetles swarming to my makeshift  laboratory when it is the only bright light on the grounds at night.


These are the rheas who run often through the crop fields in family-sized packs. I can’t remember their name in English. 

Following this track, there is multitude in how research gets done here, as well. While I seek to describe the chemistry of rivers draining through different land types (i.e., farm vs. pristine rain forest), the other scientists stationed here have several other questions to answer. Daniel and Paulo from Sao Paulo, observe how fish grow in similar parts of watershed. Rafael and Junha, also from Sao Paulo, are after the butterflies that live on the ranch, how they respond to forest fires. Paul and Marcia from the Woods Hole Research Center are investigating regional hydrology and soil water chemistry across different land types. Only a multitude of scientists can sufficiently tell the environmental story of Fazenda Tanguro, and perhaps contextualize this one ranch in the greater mosaic of landscape conversion in the Amazon River Basin.


 Taking a soil sample from a soy field.

The next part of my new word is more difficult to decipher: “tirao”. From my limited history speaking Portuguese, I have heard the verb “tirar” used in the context of taking photos or grabbing something. Assuming that the noun “tirao” is derived from the latter meaning, we do a lot of it on the fazenda, as well. All my field work is grabbing. I grab at least one hundred liters of stream water from each field site. I scoop soils from the land types surrounding each stream. The laboratory processing of these samples comes later, and certainly takes up the majority of my hours here. But, it all begins with the act of “tirao”.

Of course, compound words take on new meanings that surpass the sum of their parts. “Multi-tirao” as a whole also expresses a sentiment of teamwork and force. When the full-time Fazenda Tanguro crew helped me take 100 liters of water from a stream flowing through my one pristine rain forest site within a half hour, this was a multi-tirao. (In fact, this is when they taught me the word!) Not unlike my Indian Ocean expedition, field sampling is done best with many helping hands. A hundred liters is not an easy volume to carry, so the multi-tirao saved me a few more hours of energy that I could devote to post-collection processing in lab.

Just under 70 pounds

Image (Above: Before landing in Goiania, capital of the state of Goias in central Brazil).


Packing light is not the central philosophy of preparing for field work, and the baggage I am tied to for the next 10 days in central Brazil affirms this. One 68 pound suitcase, and a duffel bag that can fit an average-sized adult. Fortunately, the approximate weight limit of what I can carry on my own equally matches the weight limits for check-in.

In the past 24 hours, I have grown ever the more aware of the trust we put into the check-in agents at airport gates. Perhaps I should not take for granted that all the equipment essential to make a worthwhile field expedition in the Amazon River Basin can actually survive three flights from Boston to Brasilia to Goiania, a sprawling city that sits just beyond the intersection between dry cerrado forest and humid rain forest, at the center of the Brazilian Amazon.

My goal for the next few days is to collect hundred liters of river water from streams flowing through a giant ranch 12 hours away from Goiania by bus (stay tuned to see if my luggage survives that too!). And so it follows that most of my baggage contents are empty plastic containers, from bottles of various size to huge collapsible cubitainers, which can expand to hold almost 20 L of river water (or 5 gallons) at a time.

Although I might have over-packed my water sampling supplies, I do not actually plan to carry hundreds of liters of water back to the United States. If all goes well, I will leave with just the suspended particles of organic carbon and minerals, the soils and plant remains that have washed into the water from adjacent lands. When I analyze these solid materials back in lab, its chemistry will (hopefully) tell us something about which plant types produced this river-borne material in the first place, as well as the history of this organic material since being introduced to the soil and riverine environments. Because this organic material originally came from carbon dioxide in the atmosphere, many scientists are interested in keeping track of its movement from plant to river.

And hence the 68 pound suitcase is full of filtration units to separate the solids from this water. These units have been developed and refined through years of field work by scientists from my rivers research group from Woods Hole Oceanographic Institution and Research Center. A vertical cylinder, the filtration units accept water from the top and pushes it through a filter at the bottom that, very much like a coffee filter, collects only solid materials (or the coffee grinds) too large to pass through its small pores.

Image (above: A filtration unit when connected to a bike pump, during a practice run in Woods Hole with the more experienced river scientist Britta Voss)

With gravity alone, it would take much longer than my daylight hours to get all the water through the filter. So us river scientists are also typically equipped bike pumps, which I will use to pressurize the air inside the cylindrical filtration units, pushing the water downward past the filters faster than gravity would manage alone. Imagine being able to have your drip coffee ready in a few seconds rather than a few minutes. I hope that this bike pump accelerates my work over the next week by a comparable order of magnitude, as well.

Re-lighting a sunset on Woods Hole Road

Here I display several combinations of two photos that I captured at sunset in Woods Hole, Massachusetts. I shot both pictures at consecutive points in time, less than one minute apart. The first photo was taken with a car’s tail lights facing the camera, moving away on the right. The second photo, taken shortly after, depicts the same frame with a car’s headlights approaching the camera on the left. I thought that the cars in the two photos provided two subtly different lighting variables for the same environment. Here are the photos:



On IrfanView, I proceeded to experiment with these two pictures and “lightings” by applying different filters to them. Here is what one photo looks like with a sepia coloration:


Here is what one looks like when I increased the red and blue coloring while decreasing the green coloring:


Finally, I tried to overlay both photos, each with a different coloring filter/scheme. Some examples include overlaying:

(1) one photo negative with one originally colored image. Now the cars appear to be on the same road at the same time.


(2) One sepia-colored image with one image that had heightened red&blue coloring.


(3) One image that had heightened green coloring with one image that had heightened red&blue coloring. Now the cars not only appear to be next to each other in real-time, but also drastically contrasted by color.


I used a Canon 12.1 Megapixel camera with 5.0-20.0mm lens. I adjusted the ISO settings manually to accommodate the lighting at dusk.

Salting Out

At 07:00 a.m. on March 23, we arrived in Henderson, Australia, our first sign of civilization in 5 weeks and the finale of our research expedition across the Indian Ocean. At the beginning of the trip, it was too early to mention the idea of land. But in the days leading to the finish line, being on land again became frequent conversation.


The first views of arriving in Western Australia at dawn.

Jay told me that smell is one of his first sensations upon returning to land. Indeed, when the sun rose over the first sightings of Australia, the scent of maple syrup filled the air as it passed over the bow. Two other immediate impressions were calmness and strangers. We remembered what it was like to walk on level ground and interact with people beyond our small community. As soon as we were moored to the pier, Revelle invited Australian dock agents and its new crew on board. We were no longer alone on the Southern Ocean.

Secured from great ocean swells, we prepared for the commotion of the Henderson shipyard. By day, this meant packing everything out of our laboratories, craning them onto the pier and getting all our boxes into giant storage containers to be slowly delivered on cargo ships back to Woods Hole, Scripps in California and Bigelow in Maine. I discovered that being a good Tetris player is perhaps more essential than brute strength in getting this job done.

Afternoon off

A bunch of the science party got to take the afternoon off from the second packing day. Here we are venturing back into the world on a public bus. Note that there is no water in the background.

By night, this meant showering, wearing different (summer!) clothes, and venturing into the real world where cash is currency, where your legs bring can bring you farther than 200 feet, where more life choices are possible, where music is loud, and where celebration is well-deserved.

So the ultimate conclusion here is that cruise number one in my life was a success. In sailor vocabulary, there is an adjective that describes one who has learned the way of life at sea: salty. Here are the ways that I have become saltier.

I learned that people really make the experience, and they will be my greatest misses as I return home. I learned that if you tie knots five times in a row, they are easier to remember and do again. I learned that perspective needs to be large and flexible on the open ocean, so that even the largest waves can gradually look smaller and smaller through the course of time.

Another key perspective: the countless hours of science and labor that make one graph on a research paper, some of which hours include the roughest events on ocean terrain. Very much at the core of these graphs is the ability to make scientific decisions at sea and in lab. I learned that the unpredictability of the seas, combined with an unrelenting attitude of carpe diem, provide some of the best lessons in decision-making, in learning the how and why of every step in marine chemistry.

Catching the Blooms

Yesterday, March 20, was the first day of Austral Fall (and Springtime in the U.S.!), as well as was the last pump deployment for Phoebe, Dan and me in our cruise across the southern Indian Ocean. Just after surviving a rather rough day on the ocean, we reached this last mega-station in the morning with clear skies, warmth air, and gentle rolls. Fortunately, this was an easier ending than I could have asked for.

Standing nearly at the finish line of our expedition, I think it gives perspective to remind myself why we spent 5 weeks crossing one of the harshest oceans in the world.

If I really were to get at the root of things, we are all here for the coccolithophore. There is just about as much to coccolithophores as there are syllables in their name (to be accurate, however, there is more to them than the name itself). They are microscopic organisms living at the ocean surface that produce skeletons of calcium carbonate, or calcite. The calcite on their bodies is the same mineral shallow-water corals use to build their famous reefs across the world.

While coral have global recognition, coccolithophores received their fair share of limelight on the Revelle as well. Every Austral summer, the coccolithophore populations at the surface of the Southern Ocean surface explode. These coccolithophore blooms can be seen from satellites. They are strong but fast, magnificent but transient. As a result, while there are many good questions to ask about these blooms, the in-field oceanographer must get the timing right in order find the right answers. Catching the bloom is particularly challenging on a research cruise; it is one limited and expensive shot at a remote and quick phenomenon.

A bigger scientific question, larger than our cruise, is what causes coccolithophore blooms. For Jason Hopkins, Helen’s seafaring scientific companion, that question is at the heart of his research in his first year at University of Southampton. Unsurprisingly, there are many ways the oceanographer can answer this. For instance, from a chemistry perspective (my perspective in training), field scientists might measure the abundance of nutrients in coccolithopohores and their surrounding seawater. Assuming coccolithophores are what they eat, us chemists presume that blooms analogously arise from the presence of certain dissolved elements in the ocean.

In oceanography, things often follow a chain. Knowing the cause for coccolithophore blooms might help explain their greater effects on the oceans. Given the size of these blooms, these ocean-based effects could have consequences for other parts of our planet, like our atmosphere or climate. Coccolithophore communities, especially in bloom period, are huge storage houses for carbon in several forms. There is carbon in their calcite shells. There is carbon in their organic  tissue. Where it ends up—in the ocean or as an atmospheric greenhouse gas—is a motivation for many, including myself, to study the coccolithophore’s role and, also importantly, to learn how to pronounce their name.

In Between Work and Science

Now that we have completed nearly the 5 full weeks of this cruise, I can begin to reflect on how much I have learned about the proper usage of free time at sea. It is both a treasured and telling type of time. When work happens every day, possible at any hour, and when Saturdays and Sundays are just another work day, free time is not to be taken for granted (although it is still to be taken lightly).  At the same time, when the resources of fast internet, Youtube, and real-world space are virtually non-existent, creativity becomes a very important surrogate.

Ping-pong brackets

The massive family tree and scoreboard of contestants in this year's ship-wide ping-pong tournament on Revelle.

One of the greatest creations has been the Revelle ping-pong tournament. It has now mustered together most of the science and ship’s crew, forging allegiances and adversaries that would have been unfathomed otherwise. The ping-pong table is situated at the center of the Main Lab on the ship, and at all times of day a passer-by just might hear the sounds of bouncing balls, cheers and groans amidst the drones of filtering pumps and seawater chemistry analyzers.

In the tournament, there are two brackets: one for advancing winners and one for advancing losers. For the first place of the winners tier, Mike, a graduate student at Dalhousie University in Nova Scotia, is slated to take on Eddie the oiler (an engineer’s companion). As both are highly adept and reputable players within the Revelle league, it is difficult to predict who will take the final victory for first place. These tournament games are not short of their own twists and turns. The losers’ bracket has its share of talented players, as well, who just had one bad day or just could not cut it against their first opponent. Among them are Phoebe and Patrick. As the eldest female and male ping-pong players on board, Phoebe and Patrick have banded together in challenging the entire ship in team tennis outside the Tournament.

While ping-pong goes on, several other things happen as we alternate through different breaks. Every other night is poker night, where I have learned the complexities of reading people, memorizing the rules of cards, and adopting new traditions. I would say that there is slightly more stress and more at stake (5 dollars, to be precise) at the poker table, but then again, there are some who really, really want to win ping-pong, too.

Finally, there is no shortage of board games here. Sometimes rolling waves make it impossible to survive a game of chess or Scrabble. But cards are popular, and far more manageable. I notice that people’s different passions come out with cards, for there are so many different games and so many strange games, for that matter. For some, the best kick comes out of the Bean Game, which is reminiscent of Go Fish, but at its heart a game of farming and trade, capitalism and communism. For others, the classic 52-card deck makes for a good afternoon or evening. Most importantly, there is always someone else around, so solitaire is almost never the likely choice.

The Meaning of “Mega”

At sea, it helps when life has some semblance of a pattern. There are many types of routines on board: work shifts, snacks, and even poker matches. For many scientists here, routines are dictated by the pattern of sampling stations. The most distinct pattern for me is the mega-station day, which occurs every other day. It is an event named as such for being a conglomerate of all the non-CTD deployments. Because so many different groups participate in these events, they have become regularly synchronized collection frenzies for the much of the science crew.

Matt, the resident technician

This picture belies the general fast-paced, fatigue-inspiring work of the mega-station. Ironically, it is the Resident Technician who is rarely so stationary.

There are 5 main ocean deployments in one mega-station. Usually, the first on queue is Helen’s snowcatcher, which takes a quick dip to a specific depth before returning. Following Helen are Ben, Sara and Angel, who collect bottles of seawater to measure trace metals. Next are the lengthy pump casts, which Phoebe, Dan and I send down to about 800 meters. Our thorium deployment follows quickly after; it uses the 12 Niskin bottles from the CTD rosette to retrieve seawater for thorium analysis.

If it is sunny enough, an additional optics cast happens too. Barney Balch, the chief scientist here on Revelle, leads this operation. During the cast, he submerges an Ocean Color Profiler to measure light hitting the instrument from below (deeper) and from above (shallower). Because the Calcite Belt, our expedition’s theme, has a unique appearance in water, these optics casts help us understand whether calcite-producing organisms might be living in the water.

For many of us, mega-stations make for the most tiring and eventful days. But, there are important reasons to combine these sampling efforts. First and foremost, as we are a proper research cruise, each science group is interested in a central theme, the Calcite Belt, from a different but complementary angle (e.g., thorium or trace metals). By analyzing the same seawater through mega-stations, we might be able to tell a bigger, more collective story of the Southern Ocean, as well.

Phoebe on deck

More commonly, a mega-station looks like this. This is Phoebe being very attentive from the main deck during a pump cast. She is looking up toward the winch deck from which the deployment wire descends.

I suspect that a secondary reason is the camaraderie. When you have to wake up at 3:00 a.m. because the ship arrived ahead of schedule, at least everyone else is pretty exhausted, too. Moreover, each deployment is a team effort. My role in the pump cast is to lower them into the water using a winch, while on the main deck, Phoebe, Dan and our gracious helpers (usually Jason and Patrick) attach them to the wire.

The team is larger than the scientists alone. Because I cannot actually see the pumps from my winch, it is up to another to “be my eyes” (in Phoebe’s words). On this cruise, my eyes are Matt, the Resident Technician, who communicates to me how I should be wiring out the winch based on his view of what is happening on deck. Other possible titles Matt might receive are the Winch Companion, Knot Instructor, Safety Dictator and, most importantly, the Board-Game Adversary. He is present for every cast on the mega-station, and connects our science to their technical operations on deck. It is through this crucial team member that we are aware of the greater team that we belong to in doing science on the Revelle.