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Notes from the Field

Science Challenges at Sea: A Plumbing Story

January 31st, 2017 by Seaver Wang, PhD student, Duke University

This is my instrument, which is designed to measure dissolved gases in seawater to detect the oxygen produced by algae. Sea Sparkle, my trusty green stuffed plankton assistant, is keeping a careful eye on the data we’re collecting!

When people think of science, the first examples that come to mind are often dramatic triumphs—the moon landing, the invention of DNA sequencing, or the discovery of the polio vaccine. Almost every exciting experimental result, however, is the result of an enormous amount of unseen effort. Thorough preparation, resourceful improvisation, success and failure, and improvement through trial and error are all deeply familiar to any researcher!

At sea on the Falkor, the challenges that we face as a part of ocean science are unique. After all, any unanticipated problems must be solved using only the resources on board our two-hundred-foot vessel.

Our first two days at sea have presented their fair share of challenges. Our cruise plans have changed almost daily in order to adapt to weather patterns and the ship’s limits in terms of speed and range. In the “wet” lab, anywhere from six to eight science team members must work elbow-to-elbow with all of their equipment packed into a space little larger than an examination room at the doctor’s office.

For my research, which involves measuring dissolved gases from seawater to detect plankton activity, plumbing has been my biggest enemy so far.

The seawater I am measuring is piped continuously aboard ship via a pump, and this water is available from only two outlets in the already-crowded lab. My original plan to use seawater from one of the two faucets was scuppered when a crucial valve broke, spraying the lab with ocean water like a fire hose! After shutting the faucet and confirming that none of our sensitive electronic instruments had been damaged, we realized that I would now have to take my water from the second outlet—located on the opposite side of the room from where I had set up my seawater supply tubing…! In addition to reorganizing all of my plumbing, I would also have to find materials to connect to the second faucet, which uses a different connection from the first.

Luckily, scientists can be pretty inventive! My seawater supply pipe was moved to hang from the ceiling in order to cross the room, and I borrowed parts from other members of the science team in order to fit my tubing to the new faucet. Sharing the lab space is also an important part of ocean science, and so Ryan, another scientist on board, graciously moved some of his equipment to give me access to the faucet.

When doing science at sea, it’s also important to learn from mistakes and bad luck quickly. This time, we fitted double metal clamps to the faucet connection to reduce the risk of unleashing a second fire hose event. With that final step, my plumbing was finally usable, allowing me to switch on my instrument and start collecting my valuable data!

In the end, we spent several hours fixing this incredibly boring problem—one which has very little to do with actual science. Paradoxically, however, all of our tinkering with tubes and faucets was essential in order to perform my research. This is just one of the many small challenges that we have dealt with as we prepare for one of the busiest parts of our expedition. Even though many of our problem-solving stories will never be mentioned when we publish our research results, they are just as much of a part of our science as designing experiments or picking locations for the Falkor to explore.

It’s little challenges like this that help me remember that every scientific discovery, great or small, is built on a huge foundation of invisible work!

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Research Vessel Falkor. Credit: Schmidt Ocean Institute

In just two short weeks I’ll be trading the cold, snowy beaches of Rhode Island for the warm, tropical beaches of Hawaii. Such is the life of an oceanography graduate student!

Although I do enjoy traveling and discovering new places, what’s most exciting is that I’ll have an entire month to conduct my research in the Pacific Ocean alongside some of the top scientists in optical oceanography. Together we’ll be looking at particles in the upper layers of the ocean during the Schmidt Ocean Initiative’s Sea to Space Particle Investigation aboard the R/V Falkor.

So what exactly will I be doing while I’m in the middle of the Pacific Ocean? Here are my top three activities at sea:

  1. Assist in the completion of the primary science mission: ground truth satellite estimates of particle size distribution. Although this is highly dependent on the needs of the chief scientist, on previous research cruises this has involved standing watch on instrument readouts to make sure everything’s running smoothly, deploying a water column sampling device called a “CTD”, or simply lending a hand to move equipment around while we’re underway. Science operations run 24 hours a day so it’s important to be a good team player and distribute the continuous workload.

  2. Gather measurements of the carbon cycle that will be used in my graduate work at the University of Rhode Island. Carbon in the atmosphere has historically been a good thing for the habitability of our planet (it makes it warm!), but too much carbon has led to global warming (a bad thing for the habitability of our planet). It’s estimated that one quarter of the carbon emitted from human activities is absorbed by the ocean via microscopic ocean plants called phytoplankton. Although many of these plants are eaten by larger organisms, a small fraction gets down deep where its carbon is out of contact with the atmosphere.The sinking (or export) of these carbon particles to the deep ocean is what I study. In our lab, we use an underwater holographic microscope to take 3-D pictures (the size of the tip of a needle) from the surface ocean all the way down to around 600 feet deep. Using these pictures we try to estimate how much carbon is being exported. It’s super fun! I’ll also be working with a computer scientist to analyze these images after we collect them on the ship’s high performance computing cluster.

  3. Deploy homemade underwater time-lapse cameras. In addition to the holographic microscope, we also measure carbon export directly by catching and then counting these sinking carbon particles in gel-filled cups. Beneath each of these cups (called sediment traps) we plan to enlist the high-caliber photographic abilities of a discarded smart phone to record these particles as they collect. We’ve designed and developed a special pressure housing and lighting system to keep the camera working and well lit under all that pressure and darkness. Who knew the iPhone 5 could be used for science 400 feet below the ocean’s surface?

Going to sea is a lot like being at a high-end summer camp—someone cooks your meals and does your laundry while you spend almost all day engaging in an exciting stream of team activities. It’s a very social experience with many late night hours talking science and scheming the next experiment all while working on the most urgent area of science: climate change.  I couldn’t be more excited.

 

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Video “Games” for Science

August 19th, 2014 by Carlos Carrizo, The City College of New York


Update:
The R/V Endeavor returned from sea on Aug. 6, concluding the fieldwork component of the 2014 SABOR experiment.

As mentioned in the previous blog (“A Vast Ocean Teeming with Life”) ending this cruise is not an easy thing to do. Especially if you experienced the majesty of the crystalline blue water in the open ocean as well as the magnificence of the wildlife surrounding it for the very first time. I am currently coursing my third year as a PhD student in the Electrical Engineering Department of The City College of New York (CCNY). I work as a research assistant for a small department in the Optical Remote Sensing Lab called Coastal and Oceanic waters group. We may look like a group of cool guys going out for fishing (as it seems on the left side of the picture), however, we are a team who works hand to hand together (depicted on the right side of the picture … why does the right side always seem right?)

"Cool guys” aka Coastal and Oceanic waters group, members of the ORS Lab at The City College of New York (CCNY). Courtesy of Lynne Butler

“Cool guys” aka Coastal and Oceanic waters group, members of the ORS Lab at The City College of New York (CCNY). Courtesy of Lynne Butler

My research consists of using polarization properties developed as the light field propagates through the water body and use this information to characterize and retrieve water constituents and inherent optical properties (also called IOP’s) from polarimetric measurements. The basic idea is that as light propagates through the water it experiences significant attenuation due to absorption by water and suspended/dissolved matter as well as scattering by water and suspended particulates. These effects, both absorption and scattering, result in signal degradation of the radiance captured by sensors in our instruments. The additional information obtained when using polarization properties of underwater light propagation can provide a better understanding of this propagation and methods for improving image quality and increase underwater visibility … wait! (at this point you may be asking yourself).

So how can this have a real contribution to the goals and objectives pursuit by the SABOR (Ship-Aircraft Bio-Optical Research Campaign) cruise? Well, the answer could be very simple. The ocean is too big and in-situ measurements are too expensive to cover the entire water mass on Earth. Having this in mind, it is very clear that we need to adopt another cost-effective approach and that is the reason why we use satellite observations to account for many changes that take place in the ocean and coastal waters. Satellites provide very useful information when properly calibrated. As you may already know, sensors deteriorate over time and satellites go out of commission. However, polarization features are preserved even when the sensors may have experienced normal degradation and knowledge of this features can contribute in the development of future technologies to be used in satellites when more accurate and reliable information is to be acquired. Some living and manmade objects in water have partially polarized surfaces, whose properties can be advantageous in the context of target camouflage or, conversely, for easier detection. Such is the case for underwater polarimetric images taken to detect harmful algal blooms (red tides) or to assess the health of marine life and coral reefs which are of significant scientific and technical interest.

The main challenge faced by these images is that of improving (increasing) the visibility for ecosystems near and beyond the mesophotic depth zone. Data collected in the form of images, videos and radiance was acquired using a green-band full-Stokes polarimetric video camera and measurements of each Stokes vector components were collected as a function of the Sun’s azimuth angles. These measurements are then compared with satellite observations and model using a radiative transfer code for the atmosphere-ocean system combined with the simple imaging algorithm. The main purpose of this task is to validate satellite observations and develop algorithms that improve and correct these observations when needed.

But seriously… Are you playing video games? Courtesy of Lynne Butler and Ivona Cetinic

But seriously… Are you playing video games? Courtesy of Lynne Butler and Ivona Cetinic

It always looks like I am playing video games but in order to have very accurate information it is advisable to position the instrument at a certain orientation with respect to the Sun’s azimuth angle. The instrument depicted here is called Polarimeter and as Robert Foster suggested in his blog it has a very boring name, so we are still in search of a cool code name after someone suggested (unsuccessfully, and I am glad for this) to call this instrument Carlos. A real issue came across when they were thinking to put Carlos in the water … an idea that I didn’t share. The polarimeter, let’s forget about Carlos for a moment, is a set of Hyperspectral Radiance sensors with polarizers oriented in the vertical, horizontal and 45° from a reference axis. This sensors can capture light coming from any point in the water body thanks to a combination of a step motor which can be programed to stop in any sequence of angles in the range of 0 – 360° (from vertically up to vertically down) and a pair of thrusters (or propellers) which can rotate in the azimuthal direction (both clockwise and counter-clockwise). This scenario allows for vitually a 3-D range of hyperspectral measurements. Pretty cool, huh? The set of bouys at each corner allows us to have a very stable system and prevent the instrument from going very deep down in the case that cables and safety line get cut.

When things go like they do in the left image, we always have to do  the right thing. Courtesy of crew members and Ivona Cetinic

When things go like they do in the left image, we always have to do the right thing. Courtesy of crew members and Ivona Cetinic

Very far from what most of us have probably experienced in a cruise or fishing trip, the ocean is not always calm. In our twenty plus days in the ship, we came across a system which was playing very rough against the R/V Endeavor. Fortunately for us, this cruise was under the supervision of very talented and experienced people. I am not talking only about the captain, but also his outstanding crew members, chief scientist and marine technician. Although we have some minor difficulties (… you should know by now that sea water and electronics will never be good friends) we fixed them as soon as the storm was gone. It is not that Robert and I are playing as firefighters rescuing a dispaired kitten from a tall tree.

I want to end my vision of this field campaign with a summary of the awesome marine wildlife that somehow approach to us to say hello, some species more shy than others, to this group of scientists which were part of NASA-SABOR. As depicted in the picture (left-to-right and top-to-bottom), one of the first appearences was that of a seagull. It doesn’t look that shy since it preferred posing for us on top of the Polarimetric Lidar (owned and operated by scientist from NRL). Very intelligent creature this particular one, the others were just swimming in the waters and preparing to be a snack for a hungry shark as depicted in the image in the top center. Another interesting character which showed up near the surface was previously mentioned by Matthew Brown from Oregon State University in the previous blog post and it was a species of blueish salp with very long tentacles. The next creature is a very friendly dolphin which pretended racing us so we could take very amazing pictures. Dolphins always so adorable, appearing in pods and jumping out of the water around the research vessel or just posing underwater in front of the polarimeter! The last living character was a very shy sperm whale. Always keeping the distance but letting us know it was present leaping out of the water at most 300 feet from the ship!

Wildlife in action. Courtesy of crew members, Courtney Kearney and Ivona Cetinic

Wildlife in action. Courtesy of crew members, Courtney Kearney and Ivona Cetinic

These past three weeks in the R/V Endeavor had been very amazing although intense. Waking up and knowing that you are far from home, your friends and family may sound questionable but understanding that you are in front of one the most wonderful and powerful sources of life is a priceless experience not all of us can witness. That is why I am writting this blog and I hope you have enjoyed reading all our blogs and could have a taste of what is like being in the sea for three weeks!

A Vast Ocean Teeming with Life

August 14th, 2014 by Matthew Brown, Oregon State University

August 5, 2014

Three weeks at sea is a long time for someone who has never been out of sight of shore. My greatest impression during my time out here is the one I first had when we first set out: the ocean is really, really big! I realize that probably sounds too obvious to be worth mentioning, but the sheer vastness of the ocean is hard to overstate. Standing on the deck, turning 360 degrees and seeing nothing but smooth, blue water as far as the horizon, it’s hard not to be struck by how empty it all appears.

The SABOR science party on the deck of the R/V Endeavor. Front row: Wayne Slade (Sequoia Scientific), Deric Gray (Naval Research Laboratory); second row: Kimberly Halsey (Oregon State University), Alex Gilerson (City College of New York), Nicole Poulton (Bigelow Laboratory for Ocean Sciences), Matthew Brown (Oregon State University), Lynne Butler (University of Rhode Island), Nerissa Fisher (Oregon State University), Ali Chase (University of Maine), Nicole Stockley (WET Labs), Robert Foster (The City College of New York), Coutrney Kearney (Naval Research Laboratory); back row: Carlos Carrizo (City College of New York), Allen Milligan (Oregon State University), Jason Graff (Oregon State University), Ivona Cetinić (University of Maine). Credit: NASA SABOR/Wayne Slade, Sequoia Scientific

The SABOR science party on the deck of the R/V Endeavor. Front row: Wayne Slade (Sequoia Scientific), Deric Gray (Naval Research Laboratory); second row: Kimberly Halsey (Oregon State University), Alex Gilerson (City College of New York), Nicole Poulton (Bigelow Laboratory for Ocean Sciences), Matthew Brown (Oregon State University), Lynne Butler (University of Rhode Island), Nerissa Fisher (Oregon State University), Ali Chase (University of Maine), Nicole Stockley (WET Labs), Robert Foster (The City College of New York), Coutrney Kearney (Naval Research Laboratory); back row: Carlos Carrizo (City College of New York), Allen Milligan (Oregon State University), Jason Graff (Oregon State University), Ivona Cetinić (University of Maine). Credit: NASA SABOR/Wayne Slade, Sequoia Scientific

Of course, that’s not true at all. The ocean, far from being empty, is teeming with life. Most of it is too small for us to see with the naked eye, but it’s there all the same and it affects each and every one of us even if we’ve never been to the sea in our lives. Phytoplankton, the microscopic algae that live in the sunlit regions of the ocean, not only provide much of the oxygen we breath, they also play an important role in managing the earth’s climate through their roles in uptaking CO2 from the atmosphere and cycling nutrients like nitrogen and sulfur through the ecosystem.

A big part of what our group does is trying to understand how different aspects of the ocean environment (light, nutrients, grazing pressure) affect the ability of the phytoplankton to photosynthesize and grow. One way we do this is through a piece of equipment called a fluorometer, which can give us an indication of how efficiently algae are absorbing photons from the sun and turning their energy into carbon. It works by hitting them with a large amount of light, then measuring what percentage gets released back after getting absorbed. A simple enough technique in principle but one that can tell us all sorts of things, from the size of the molecular antennas the algae use to harvest light to the degree that electrons can be shared between different reaction centers in the chloroplast.

Another technique we use which is pretty cool (or rather, hot) is the use of radioactive isotope as tracers to measure carbon uptake. On the Endeavor that activity takes place in the Rad Van, which is named for radiation and not, unfortunately, for how radical it is. By allowing algae to photosynthesize in the presence of CO2 formed with the carbon isotope 14C, we are able to track how much the carbon is taken up under a variety of different conditions.

Well, three weeks have come and gone and we put into port tomorrow. It will be nice to be back on land, but I will miss the excitement of the ocean. Today, we got a going away surprise in the form of a pod of dolphins that came near our boat and splashed around for awhile. In addition, the water around the ship was filled with a species of salp, gelatinous creatures which kind of look like sea jellies, that was bioluminescent and gave off a brilliant blue light. It was almost like the ocean knew we were leaving and decided to give us a show to send us off.

Deep Blue Water and a Roller Coaster Ride

July 29th, 2014 by Ali Chase

After just over a full week at sea, we have found the rhythm of our life and work routines. We collect water with the CTD rosette, deploy instruments over the side of the ship, work in the lab, eat, and sleep. That might sound like a lot of work and no play, but we do manage to have fun while we work (think lab dance party while filtering water samples). We’ve also taken time to observe the vast blue around us from the upper deck of the ship, where we recently watched a gorgeous sunset. No green flash sightings yet but I continue to hold out, hoping to see this optical phenomenon – a green flash of light that can sometimes be seen just before the sun disappears below the horizon.

Left: View of the sunset from the top deck. Right: Deck operations just after sunset, which includes deploying two instrument packages that measure a variety of optical parameters, and the CTD rosette, which collects water samples from different depths. Credit: Ali Chase

Left: View of the sunset from the top deck. Right: Deck operations just after sunset, which includes deploying two instrument packages that measure a variety of optical parameters, and the CTD rosette, which collects water samples from different depths. Credit: Ali Chase

Several days ago we crossed into the Sargasso Sea, which is an area of very clear blue water due to low amounts of phytoplankton and dissolved matter which absorb light and make the water in some areas, such as coastal regions, a greener color. But here the water is an amazing deep blue color, which is the color of ocean water when there is not much there besides the water itself. One life form that is prevalent is a seaweed called Sargassum, which we frequently see floating by.

The very blue water of the Sargasso Sea, with a few floating pieces of Sargassum. Each piece is roughly the size of dinner plate, for scale. Credit: Ali Chase

The very blue water of the Sargasso Sea, with a few floating pieces of Sargassum. Each piece is roughly the size of dinner plate, for scale. Credit: Ali Chase

Speaking of things that absorb light in the ocean, much of the work we do in the “wet lab” is related to the absorption and scattering of light by different particles in the ocean. This optical oceanography work allows us to measure the way light interacts with particles, in particular phytoplankton, which absorb and scatter light differently depending on the types and amounts of phytoplankton present. Throughout this cruise we are collecting water continuously using a system involving a boom that extends over the side of the ship with a hose hanging from it into the water. A pump on deck constantly brings water from approximately three meters depth through the hose and into the wet lab, where it then flows through several instruments and provides us with constant information about the optical properties of whatever is in the water.

But, the ocean is a massive place, something that we are very much reminded of while working at sea with no land to be seen in any direction. Even sampling the water continuously during this three-week trip will just give us a small snap shot of ocean conditions. This is where satellites come into play, as they can provide a much broader spatial view of the world’s oceans. However, work in the field is necessary to “ground-truth” what the satellites tell us, to be sure that such expansive information can be accurately related to what is present in the ocean. During this research cruise we will pass through several types of water, such as the warm/salty/fewer phytoplankton water like we see here in the Sargasso Sea, versus cooler/nutrient rich/lots of phytoplankton water in coastal areas such as the Gulf of Maine. Understanding the differences between these regions can be useful for interpreting satellite information about phytoplankton and their role in the earth’s carbon cycle.

Left: The flow-through intake system; the hose hanging from the end of the black boom sucks up water continuously using the pump located in the black box on deck. Right: The wet lab in all its glory – the tubing with the water pumped from outside can be seen running up near the ceiling; it then flows through several instruments positioned both in the sink and on the bench top. Credit: Ali Chase

Left: The flow-through intake system; the hose hanging from the end of the black boom sucks up water continuously using the pump located in the black box on deck. Right: The wet lab in all its glory – the tubing with the water pumped from outside can be seen running up near the ceiling; it then flows through several instruments positioned both in the sink and on the bench top. Credit: Ali Chase

A couple of days ago a storm system passed over us, and the winds came up to about 30 knots. With winds that high, waves crash onto the deck and it is unsafe to deploy instruments over the side of the ship, so our work was put on hold for a day. I spent some time on the bridge (where the ship’s captain and crew navigate from) and watched the bow of Endeavor ride the waves like a roller coaster. Every now and then the bow came down against a big wave and an impressive spray of ocean water was sent flying, with water reaching as far as the windshield of the bridge where we were watching!

The ship crashes into a large wave during high seas. Credit: Ali Chase

The ship crashes into a large wave during high seas. Credit: Ali Chase

To document our work and life on board we have been putting GoPro cameras on everything, including hard hats and instruments that are deployed over the side of the ship. Recently a GoPro went for a ride on the “Polarimeter”, an instrument that measures the polarization state of light, which Robert mentioned in the previous blog post. While the GoPro was underwater, a big group of dolphins came to say hi, and the GoPro caught it on camera – very cool! We also lowered Styrofoam cups down with the CTD to a depth of 1,000 meters, where the pressure compresses them, along with any writing or pictures that have been drawn on. We sent down a bunch of cups from a school group that had visited the University of Maine’s Darling Marine Center, and we added a few that we decorated ourselves for souvenirs to bring home.

Left: A selfie I took while wearing the GoPro on my hardhat. Credit: Ali Chase; Right: Dolphins near the Polarimeter deployed with a GoPro attached. Credit: Wayne Slade

Left: A selfie I took while wearing the GoPro on my hardhat. Credit: Ali Chase; Right: Dolphins near the Polarimeter deployed with a GoPro attached. Credit: Wayne Slade

 

Styrofoam cups that were attached to the CTD and lowered to 1,000 meters, where the pressure compresses them (top = before, bottom = after; box of tea shown for scale). Credit: Ali Chase

Styrofoam cups that were attached to the CTD and lowered to 1,000 meters, where the pressure compresses them (top = before, bottom = after; box of tea shown for scale). Credit: Ali Chase

I feel very fortunate to be included in this adventure at sea with such a great group of scientists and crew. I am constantly learning about the ocean and how we understand it as oceanographers, as well as all of the techniques and logistics that go into the collection of quality data. It is certainly humbling to be out on the ocean with nothing but blue all around, and I am reminded of why I am drawn to this field of study and how much of our planet is covered in this blue expanse. Thank you for taking the time to read our blog and I hope you’ve enjoyed this glimpse into our life and work at sea!

Ali Chase is a graduate student in oceanography at the University of Maine’s School of Marine Sciences.