March for Science!

“Science is essential for our community, for our world, for our economy. There is a distrust in the objectivity of scientific advice, there’s also a lack of understanding of why it’s useful. This rocks us to our core, those of us who understand and appreciate science. We can’t deny that something fundamental has just changed, and we can’t sit down in our corners and say nothing about it. This is not a partisan activity.”    – Dr. Lynne Talley at the San Diego March for Science

Students make posters as the ship leaves San Diego Bay.
Photo by Natalya Gallo.

At any time, there are Scripps scientists on research assignments all around the world. Saturday, April 22nd was Earth Day, and around the world millions of people participated in the March for Science. Fifth year graduate student, Natalya Gallo, wanted to make sure she marched in solidarity despite being out at sea. Just off the coast of San Diego, R/V Sproul was out for a day trip for a class where undergrads get to see what research aboard a Scripps ship entails. While transiting out to sea for a day of CTD casts, net tows, and sample collection, Natalya broke out supplies to make posters and the whole group gathered on the back deck for a photo op. As she explains, “Participating in the March (in some way) was really important to me, both as a scientist and a public citizen. Making posters with the undergraduate students provided an opportunity to talk about the role of scientists in society, how scientists interact with the public and policy-makers, and share my thoughts about the value of scientific engagement across all sectors of our society. With the many critical problems our society currently faces (climate change, fisheries sustainability, pollution, antibiotic resistance, just to name a few) it is essential that the scientific method is understood, respected, and valued, and that scientists play a central role in these conversations.”

Supporters of science gather in downtown San Diego before the March for Science.
Photo thanks to Scripps Oceanography Communications office.

Like Natalya, it’s important to me that everyone knows that they use and benefit from science every day. Do you check the weather forecast on you phone? That info comes from satellites and weather stations. The phone itself is a feat of engineering. The data connection and WiFi wouldn’t be possible without a scientific understanding of radio waves. This is just one example, there are countless others that maybe we don’t think of as being “science” – the eradication of diseases, electricity, brewing, baking – these are all the scientific method at work. 

At the San Diego event, Scripps Institution of Oceanography professors Ralph Keeling and Lynne Talley spoke to the crowd. Dr. Keeling studies carbon dioxide levels in Earth’s atmosphere and is the “keeper” of the Keeling Curve, which has tracked increasing CO2 levels since 1958. Begun by his father, Dr. Charles Keeling, continuous measurements are taken at Mauna Loa observatory in Hawaii and show a drastically accelerating increase beginning when humans began to burn fossil fuels. 

In Lynne’s speech, she mentioned her faith, and growing up in a family
of engineers, teachers, and librarians. Photo by postdoc Isa Rosso.

Dr. Lynne Talley is an elected official of the AGU (American Geophysical Union) Ocean Sciences division and the AAAS (American Association for the Advancement of Science), both well-respected non-profits that promote cooperative research. In her speech, she got the crowd going with the chant: What do we want? Science! When do we want it? After peer review! Which made my nerdy heart happy.

I have been to sea with Lynne as the Chief Scientist, traveling for six weeks studying seawater properties from the Antarctic ice edge up to the tropics. She is also a Lead Investigator of the SOCCOM (Southern Ocean Carbon and Climate Observations and Monitoring) project, which deploys floats carrying sensors to study various ocean properties. The robotic float sends itself on casts down through the water column collecting data, and then it beams it back to land when it surfaces. Click here for a blog post I wrote when sailing on a SOCCOM cruise. Lynne says that she knows speeches from scientists “…are often too dry, give way too many facts, and don’t let emotion or their religious faith and principles creep in.” So instead, she made sure to cover “…what we are as scientists and what I believe, what do we know about the climate, what do we demand, and what can we do.” In addition to her participation in the march, Lynne spoke with KPBS about the importance of science – you can listen to that here.  

The March for Science aboard R/V Sproul.
Photo by Chris Welton. Header photo by Brice Semmens.

Scientists themselves don’t have all the answers, it’s a constant process of having ideas, testing them, and learning. The purpose of every science project is to better understand the world around us, and that is a worthy goal. And as Lynne said in her speech, “When I turn on that light switch, when I pick up my phone – that is not a political act.”

I enjoy bringing the science from R/V Sally Ride to you so that everyone can see the dedicated people behind the expeditions. Scripps Institution of Oceanography is full of people who love to explore and learn and share what they find. 

Thanks for your support!

A Swim for Science also took place, learn more here!

Check out this article about why UCSD staff, faculty, and students participated in the March for Science.


Back to the Shipyard

R/V Sally Ride has entered a shipyard period as it ends its first year in service. Upgrades and refits will be made over the next few months. After that, it will be back to science cruises! Follow along here for photos from the shipyard, including dry dock, where the ship is set up on blocks out of the water so that the outer hull, propellers, and other areas that are usually below the waterline can be accessed. Click for larger versions. For more details about the changes being made in the shipyard, check out this post. And this one for more pictures


Net Samples Join SIO's Invertebrate Collection

Scripps Institution of Oceanography is home to some of the preeminent biological and geological collections in the world, which are important repositories for samples from around the planet. On a recent R/V Sally Ride research cruise, biological samples (animals, in this case zooplankton) were collected using two different types of net systems and then sorted for various experiments by scientists onboard.

Linsey (orange pants) works with the Ohman group to collect and process
samples from the MOCNESS (frame on the left, cod ends on the right).

The manager of the Pelagic Invertebrate Collection, Linsey Sala, was onboard to help with the work. The trip was only a few days long, which kept the team constantly busy. She assisted with the bongo net tows to collect and sort live specimens, which were used by the Barbeau lab for their trace metals experiments. She also worked with the Ohman lab to collect samples from all ten of the nets that make up the MOCNESS. It’s a long process to rinse down each net into its basket, called a cod end, making sure to carefully retain all the plankton. The sample is then transferred to a bucket and hauled into the wet lab to be processed and preserved, but that’s just the beginning of the work. Training students to properly collect, preserve, and store the samples is part of Linsey’s job when she’s at sea, as well as identifying pelagic organisms. However, she was never too busy to answer questions or show off a particularly cool specimen magnified under a microscope (see pictures below). She has a seemingly encyclopedic knowledge of marine invertebrates and speaks in taxonomic terms, some of which I remember from my undergrad biology classes, but most of which I’ve since looked up. Instead of krill, worms, and jellies it’s euphausiids, chaetognaths, and scyphozoans.

Scientists sort live samples from the bongo nets.

In order to learn what happens to the samples once the ship returns to land, I recently visited the Pelagic Invertebrate Collection. Pelagic invertebrates are animals without a backbone that live in the water column, as opposed to bottom-dwelling, or benthic, invertebrates – which have their own separate collection at SIO. In the pelagic collection alone, there are over 137,000 sample jars, comprising more than a billion individual specimens. Tens of thousands of boxes filled with sample jars are vigilantly labelled (Linsey is clear that this is one of the most important parts of her job) and stored in earthquake-safe compact shelving. Included in the collection are thousands of reference specimens, kept on behalf of scientists who are considered experts in certain identified groups of marine invertebrates. Thanks to a generous donation, the collection is also home to a huge variety of nets, as different lengths, openings, and mesh sizes are optimized for sampling different types of organisms.

In the collection, Linsey ensures every sample jar, lid, and case
are properly labeled so specimens can be easily found.

As Museum Scientist and Collection Manager, Linsey is the main person working in this massive facility. With help from the curator, Dr. Mark Ohman, and an undergraduate assistant, she keeps up with cataloging the ever-expanding collection, responding to loan and species identification requests, providing specimens for SIO classes, and giving tours. A set of particularly interesting samples make up a small museum ready to be shown to visitors, housing everything from a 5-foot long Humboldt squid to Antarctic krill to larval lobsters. 

Linsey fields many requests from scientists all over the world to use samples from the collection. Many papers are published every year by researchers looking at the samples for their own purposes. When SIO graduate students, led by Miriam Goldstein, began to study the so-called garbage patch in the North Pacific Subtropical Gyre, they were able to analyze samples collected on CalCOFI cruises dating back to the early 1970s. Evidence of microplastics in these samples, as well as those collected on a research cruise conducted by the students in 2009 on R/V New Horizon, was the first definitive study of its kind that led to a deeper awareness of the dangers of plastic pollution in the ocean. Learn more here. As Linsey says, “While each expedition’s samples are collected with a specific focus, it’s always very exciting when we use archived materials to address a new hypothesis and continue to learn more about our oceans from these resources. Each sample is a unique snapshot in time of that window of the ocean that can answer a multitude of questions – some of which we haven’t even thought of yet.” 

(Left) Pregnant female copepod Euchirella pseudopulchra, eggs are blue, (middle) amphipod, an order of small crustaceans, and (right) a female
copepod of the family Pontellidae. Each animal is only a few millimeters in length and was photographed on the cruise using a microscope.
Photos thanks to Linsey Sala of the SIO Pelagic Invertebrate Collection.

Most samples are preserved in formaldehyde, which maintains the characteristics for visual species identification. Others are stored in ethanol, which keeps the DNA intact and can be used for genetic analysis. You may remember that on CalCOFI cruises, the sample from one side of the bongo net is preserved in each solution so that both methods can be used. The NOAA fisheries group that participates on those cruises takes the samples back to their lab first and sorts them. They keep the fisheries-related species – fish eggs and larvae, young cephalopods (squid, octopus), and lobster phyllosoma larvae (a specific stage in their life cycle). The rest of the sample is brought to the SIO Pelagic Invertebrate Collection.

Just one of dozens of shelves full of pelagic invertebrate samples.

On the day I visited, Linsey cheerfully rolled shelving units open to show me everything from the samples we collected on the recent Sally Ride cruise all the way back to the first CalCOFI trip in 1949. This time series data is an invaluable record of the ocean as it changes over seasons, years, and decades. When talking to her, it’s obvious that Linsey is inspired by the breadth of the collection, even though it means never-ending work for her. “These types of scientific natural history collections provide the opportunity for scientists and our community to study environmental health, our natural resources as it relates to fisheries science, climate effects on ocean ecosystems, and can provide materials for emerging technologies. Archiving and maintaining these well-preserved specimens allows us the possibility to access information from our past and present to better predict and direct our future.” 

As mentioned in a previous post, the scientists on the cruise collected samples concurrently with zooglider operations nearby. This autonomous underwater glider was developed at Scripps by the Instrument Development Group, in collaboration with Dr. Mark Ohman’s lab. It dives to a depth of 400 meters, using a zooplankton camera to capture photos that are used to infer the abundance of different species and a custom sonar to record zooplankton acoustic backscattering. Nets towed from R/V Sally Ride collected samples that are now part of the Pelagic Invertebrate Collection at SIO. As Dr. Ohman explains, “We took physical samples of zooplankton with an electronic opening-closing net (MOCNESS), to compare with the types of zooplankton imaged by the Zooglider camera. The MOCNESS samples have been accessioned into the Pelagic Invertebrate Collection and we are beginning to analyze them using a digital zooplankton scanner called a Zooscan.”  This scanner takes high resolution photos of the animals collected on the cruise, and a software program then classifies each into taxonomic groups for quantification.

Technician Emma lines the specimens up on the scanner (left), and then ensures image quality (right).

A technician named Emma Tovar oversees the process from start to finish. First up, the sample jar brought over from the collection is sorted into size fractions. Using small nets, specimens are separated into different jars – larger than 5 millimeters (1 mm = 1 thousandth of a meter) are classified as extra large, 1-5 mm are large, and less than 1 mm are small (see photos below). Emma then takes subsamples and arranges the specimens on the scanner. It looks similar to a normal flatbed scanner, but has a shallow pool of water on the glass. Emma is an orderly person so lines up all the animals in neat rows. This also helps the software separate and properly identify each. They are posed in a somewhat natural state, so that they will most closely resemble the photos taken of live animals by the Zooglider camera. After the scan is taken, Emma checks the images for quality, and then double-checks how the software has sorted them. It’s been developed over many years and is populated with images, from a few hundred to 20,000 examples of each type of animal. Emma has learned to identify all the usual suspects down to their taxonomic group. “I validate the images manually, sometimes it will be wildly off.” she says. The different-sized samples are then combined back together and returned to the collection.

Zooscan images of specimens collected in the MOCNESS. The extra large (left) category contains arrow worms, krill, jellies, ctenophores, and pyrosomes; the large (middle) contains mainly arrow worms, krill, jellies, and copepods; and the small (right) contains mostly copepods, krill larvae, and shelled pteropods – a type of free-swimming mollusc. Images provided by the Ohman lab. 

This is a look into the what happens with samples from one group onboard one research cruise aboard R/V Sally Ride. Just imagine how many people are at work in labs all around the globe based on expeditions on the Scripps research fleet!

Crew Introductions: Oiler

“I like the people at Scripps. It’s a tight knit family, which makes everything much more enjoyable, especially when you’re living here for two-thirds of your life, maybe more.” 

Willie Brown has been working in the engineering department of Scripps research vessels for 13 years. His dad worked with Captain Tom, master of R/V Sally Ride, and it was through that connection that Willie found out about an open job as wiper on the New Horizon. All three of his brothers followed in his footsteps, and two still work rotations at sea. A wiper works two 4-hour shifts per day in the engine room, assisting the engineer and oiler.

Willie (right) assists fellow oiler Dave in fixing a hydraulic fluid leak
on the ship’s A-frame. Though by this point he’d noticed the camera.

Willie has since moved up to be an oiler, working with third engineer Sarah during the 12-4’s shift (midnight to 4am and noon to 4pm) on Sally Ride. There are no wipers aboard the new ship, the trend towards automated equipment has led to less people being required to operate and maintain the engine room. Willie’s been learning everything he can on the job and watching online lectures in order to ensure he stays competitive in the narrowing job market, “before this AI takes over everything.” He says this is his usual deadpan seriousness, which can make it nearly impossible to determine if he’s joking or trolling you, both of which he does quite often. I’ve watched him humor people that are impossible to talk to, the kind of people I try to avoid sitting anywhere near at the dinner table. He’s also a master at finding people’s conversational triggers, and pokes them just to get a rant started. I’ve discovered over the years that he’s a nice guy, and it’s an excellent distraction in what can become monotonous interpersonal interactions at sea.

New Horizon’s ship track in a typical year.
Learn more at

Willie worked on New Horizon for most of his Scripps career, ending with that ship’s retirement in 2014. It was an intermediate class research vessel that operated in the northeastern Pacific, often out of its home port of San Diego. Willie was born and raised in Southern California, and enjoys the “normal life” afforded by working out of San Diego. Many of the crew don’t have this luxury, choosing to live elsewhere and fly to meet the ship and live aboard it in port. Under these circumstances, working about 4 months straight and then taking 2 months off is the usual routine. Willie tries to work as long as the ship is in its home port, saying he’s “24/7/365. It’s very expensive to live in San Diego, other people come here on vacation, so I’m not taking vacations.”

In its first year since leaving the shipyard, all of Sally Ride’s research cruises have been in and out of San Diego. Willie has been onboard most of that time, meaning he’s often training the other oilers when they switch out for vacation or rotations on other ships. The oilers are assigned to run the winches when science operations require them for deployment and recovery of gear, so Willie often spends a few hours of his shift doing that and a few hours of overtime training newer crew members.

Willie (back) oversees O/S Daris’ training on the scientific winch controls.

He’s also been known to stop by the lab to check out what the scientists are doing, “especially if they’re pulling up something besides water and mud.” If you’ve been following along on the blog, you know that much of oceanography is collecting water and mud, and Willie isn’t the only one who only stops by the lab when something else is going on. Many people crowd in to check out biological samples, gathered with nets towed over the starboard side or stern. In typical engineer style, when Willie is seen above deck, he’s often in coveralls, though his colorful board shorts are becoming legendary. 

Willie has done a few cruises aboard the other SIO research vessels, Revelle and Melville, which is where I first met him in 2010. He’s a workout champion, and being in the gym at the same time as him is intimidating. I’ve been on research cruises where other crew members join his workouts and follow his meal plan, bucking the trend by coming away more fit after a research cruise. Having access to three hot meals a day and never-ending snacks, on top of not being able to walk more than 200 feet in any direction at a time, often leads to gaining a few pounds – but not if you’re around Willie. Though he says the 12-4 watch is cramping his usual habits, “I cannot get used to it, no matter what. It’s the Reese’s peanut butter watch, I get the munchies, it’s the worst time to be up.” Rumors of an intensified workout were spreading last time I was onboard, so perhaps he’s stepped up his game to compensate.

I’ve managed to get only a few candid pictures of him, as he’s a complete ham and usually notices me after a few seconds and begins to mug and flex. He even suggested a topless welding photo, and we joked about a “men of Sally Ride” calendar, but instead we kept it to a staged session in the machine shop. And while fellow oiler Buck got a case of the giggles, Willie managed to keep a straight face in every single shot, even when wearing a welding helmet and holding an enormous chain wrench for no apparent reason.

SIO crew members together at The Loma Club.

Like others I’ve interviewed, Willie enjoys being on the Sally Ride. A key selling point for the crew is that they each have their own room. “Privacy is huge, I love it, I value it,” he says, continuing in his deadpan, “I can listen to podcasts out loud. I can walk around in my underwear doing karate moves. That’s very important to me.” It’s the simple pleasures that really add up. The ship has been keeping a busy schedule, out to sea more often than not. In what little time off in port they have, many of the crew members golf together. Enjoying each other’s company outside of work, especially since this isn’t your normal 9-5 job, really speaks to the cohesion and general happiness of the Sally Ride‘s crew. And, as the saying goes – happy crew, happy ship!

Photos from the Collaboration with Sproul and FLIP

The collaboration between research vessels Sally Ride and Sproul and research platform FLIP, all members of the Scripps fleet, wraps up in the next week. The three vehicles will return to port having run ~ 25 Remus missions, deployed and recovered wave buoys ~10 times, and completed many more operations with unmanned underwater vehicles (UUVs). Wave gliders and the moored wave buoy have been in the water throughout the trip. Sally Ride‘s small boat has been used for Remus operations, to conduct personnel transfers to FLIP, also bringing food and offloading trash, and to service the moored wave buoy.  

The Terrill group, led by Chief Scientist Sophia Merrifield, is maintaining three weather radar systems between FLIP and Sally Ride. Real-time radar data guides each day’s plans, with the UUVs programmed to sample relative to the wind and wave direction. The UUVs can move at speeds up to 4 knots and run coordinated missions sampling the water column to 100m. Data from the various instruments help scientists understand how the upper ocean evolves as conditions at the air-sea interface change. For more details, check out the previous post about this research cruise. For more on the Sproul‘s contribution, check out this post.


Working with R/V Sproul

R/V Sally Ride is out at sea studying surface waves and currents as part of a collaboration between scientists at Scripps Institution of Oceanography and the University of Washington (UW).

R/V Sproul as photographed from R/P FLIP during their collaborative operations
with R/V Sally Ride (not pictured). Photo by Randy Christian.

Other members of the Scripps fleet are in on the action as well, with R/V Sproul and R/P FLIP operating in the same area. Dr. Jim Thomson of UW, one of the investigators on this project, sums up the coordinated effort, “We want to know how winds and waves create turbulence in the ocean. We are looking for patterns in the turbulence, and that requires lots of instruments distributed spatially.”

R/V Robert Gordon Sproul is the smallest vessel in the fleet, at 125 feet long with a crew of five (compared to Sally Ride’s 238 feet and crew of 20), and generally keeps to the waters off Southern California. The ship’s first task was to assist with mooring the research platform FLIP in place (more on this in another post). Then science operations got underway, with autonomous floats built or modified by engineers at the Applied Physics Laboratory at UW being deployed from the ship.

Dr. Eric D’Asaro is chief scientist onboard, and the focus of study is on turbulence, the movement of the water itself. At the air-sea interface in the the upper 50 meters of the ocean, factors include the affects of temperature, wind, waves, currents, and mixing. While the FLIP and the instruments deployed from it remain in one place, the Sproul is deploying drifters, instruments without propulsion, that move with the water.

Scientists use a pole with a hook to snag
the float when it’s ready to be recovered.
Photo by Jeremiah Brower.

Dr. Tom Sanford describes the difference this way – “Consider a person measuring wind and temperature from a hot-air balloon. This is very different from what an observer sees on a fixed tower. For example, the former (hot air balloon) is more likely to observe turbulence without the confounding forces of the wind.”  

All of the floats on Sproul have a metal housing that holds batteries and electronics, with the usual temperature and salinity sensors mounted to it. Some of the floats sink into the water column to study processes over varying depths, and then resurface. Of these, one group has an instrument that measures the electric field due to the water’s motion through the Earth’s magnetic field and from this measures the water velocity. Another is able to be controlled on a fine scale, so its position in the water column can be dictated in order to profile currents using a mounted sonar. Other floats do not sink, and focus on measurements of wind and surface waves, along with the temperature of both the air and the sea.

Jeremiah, the restech in charge of all deck operations onboard Sproul, notes that the ship “is an ideal platform to launch drifters from because its back deck is lower to the water, allowing scientists and techs to simply hand

The floats (in high visibility yellow) are stored on the back deck of the Sproul.
Photo by restech Jeremiah Brower.

deploy many of the instruments.” Being a smaller ship, the higher seas associated with being outside the Channel Islands more often affects work onboard Sproul than it does for Sally Ride. A few times since they’ve been out, the outside decks have had to be secured, meaning everyone has to stay inside and no science operations can take place. The ship has even moved away from the working area in order to shelter behind Catalina Island, returning as soon as conditions allow. Each of the members of the Scripps fleet has its own capabilities, and this collaboration highlights how they are different but can all work in partnership to contribute to scientific goals. 

Crew Introductions: Senior Cook

“I have traveled all over the world. I get to work with a lot of interesting people. It’s what I do, it’s not only work for me, it’s part of my life.”

TGIS. A typical Sunday dinner menu,
plus a cheese plate and ginger beer.

Mark Smith has been a cook at UC San Diego for 22 years, first in a dining hall on the main campus and then onboard SIO’s research vessels. He’s cooked on Sproul, New HorizonMelville, Revelle, and is now senior cook on Sally Ride. Of working on the new ship, Mark says, “The pride factor is really high here, we want to keep this vessel looking good.”  I interviewed him during meal prep for Sunday dinner, which is the best night of the week thanks to him. It always includes surf and turf, plus special extras like a fancy dessert, cheese platter, and ginger beer. If there’s not scientists working on the fantail, the cooks or chief engineer often pull out the barbecue to grill steaks, filling the whole working deck and lab with the delicious smell. On this occasion, there were operations going on, and we got prime rib made in the galley instead (a worthy second choice). 

As senior cook, Mark is in charge of three meals a day, as well as placing the food orders. Generally every 2-3 weeks a truckload of fresh supplies pulls up to the ship in port. It’s an all hands on deck moment, with crew and science alike setting up a chain to get everything onboard (see the time-lapse video below from during the shipyard period last summer). On longer trips, the cooks have to make sure fresh food lasts as long as possible. I’ve had crisp lettuce a month in – meanwhile at home mine turns into brown sludge in the drawer after two weeks. “We have plenty of tricks for keeping food good that long,” says Mark. He also makes sure the mess is supplied with plenty of snacks for people working all hours of the day. At any time you can make a PB&J, heat up some leftovers, pour a bowl of cereal, grab a granola bar or handful of nuts, satisfy your sweet tooth with candy, or make popcorn. Stashes of tea, coffee, soda, water, and milk are also available.

Mark gets everything set just minutes before 5pm thanks to the galley clock
being set 8 minutes fast.

A second cook works with Mark, they trade off days being the primary cook: planning the menu and preparing the hot food like entrees and bread. The other person takes care of the salad bar, dessert, and cleaning the galley. To keep things fair, the primary person also gets to choose the music; you can tell it’s Mark’s day when you hear Prince getting funky as you walk down the hallway on the main deck. 

Mark has worked with a few other cooks on Sally Ride in its first year in service as the crew rotates their time off, or moves to other SIO ships. He gets along well with Nick, who was onboard the ship in November and again in March. “Sometimes you don’t know what to make. I like cooking with somebody like him, that’s different from me, who has their own thing.”  The cooks make sure to accommodate members of the crew and science party with specific diets – vegetarians, gluten free and other allergies, and I seem to detect slight changes under different captains as well.

Mark prepares 3 meals a day, keeping the crew and science party happy.

These are the hardest working guys on the ship from what I can tell, working 6am-6pm every day, no matter what the weather or other circumstances. Scientists often work a 12-hour shift, but get down time if seas are too high to deploy equipment. There is no autopilot function in the galley, and good food is as essential to a research cruise as any other factor. “I know that the food is a big part of morale on any trip. For most people, it’s work and eat and rest, that’s it, so if you have a bad meal, that’s not good for anybody.”

I’ve sailed with Mark numerous times since beginning my oceanographic career, and I’m always excited when I see him in the galley when I come aboard for a cruise. He’s friendly, and remembers people even if it’s been years since sailing with them. Recently I’ve developed an allergy to walnuts, and he’s always good about making sure I can easily avoid them. During my stretch onboard these last few months, pecans have been the go-to nut in cinnamon rolls, brownies, and other tasty treats, and I know he’s looking out for me. He’s a good guy to befriend, and makes sailing on R/V Sally Ride a great experience.

Check out this 360 degree view of the galley (kitchen) and mess (dining room).

See more from Mark at the R/V Sally Ride gallery at Birch Aquarium’s Explorations at Sea exhibit! Thanks to aquarium staff for the interview, taken for the “Meet the Crew” feature.

AUVs Studying Waves and Currents

Sunset recovery of a wave glider. The float portion is up near
the top of the crane arm, while the sub portion is at the rail.
Photo by Dr. Sophia Merrifield.

As you may recall, Dr. Eric Terrill’s group was onboard in December to test drones and a remote-controlled kayak for scientific purposes. They’re back aboard R/V Sally Ride, this time with a different set of autonomous vehicles. They have multiple instruments for measuring the air-sea interaction that occurs at the surface of the ocean and upper water column from the surface to 100 meters depth. 

Wave gliders have been deployed from the ship’s A-frame. For recoveries, the small crane, usually on the forward 01 deck of the ship to load food and other stores, has been moved to the back deck’s starboard rail. There’s two parts to these vehicles, one that floats at the surface and another submerged, connected by either a 4 or 8 meter tether. The sub has fins to harness wave motion into forward motion, moving the vehicle along at 1-3 knots depending on conditions – see the video below.  Sensors record data on the surface and subsurface portions of the platform. The floating platform includes wind, weather, and wave sensors, an ADCP for studying currents, and communications equipment to report its location back to the ship. Solar panels connected to battery packs means the wave glider can operate autonomously for weeks to months at a time. The two wave gliders are deployed from the Sally Ride and brought back onboard every 5-7 days to change sensors and download data.

Postdoc Megan unpacks a REMUS AUV onboard R/V Sally Ride.

The Terrill group also deployed three REMUS AUVs (Remote Environmental Monitoring UnitS Autonomous Underwater Vehicle), for studying subsurface features in the upper ocean. The REMUS is a propelled vehicle, allowing it to operate at speeds up to 5 knots, and down to 100 m depth.  Sensors integrated into the vehicles measure temperature, salinity, depth, chlorophyll, turbulence, currents, and acoustic backscatter.

A moored wave buoy was deployed within the study area to measure waves in one location. In addition, five drifting wave buoys have also been deployed that send real-time information about wave height via satellite.

Scientists and engineers from the Terrill lab track the AUVs and monitor
the WaMos radar from the main lab control center.

The Terrill group maintains a radar system mounted on the ship’s mast, called WaMoS (WAve Monitoring System), that collects information on wave height and surface currents. The data from this will be combined with that from the autonomous instruments. R/V Sally Ride is operating in the same area as the research vessel Sproul and research platform FLIP. Scientists onboard all three are collaborating to understand surface waves and currents using different approaches and technologies, which requires making measurements in rough seas. This marks the first time Sally Ride has teamed up with other members of the Scripps research fleet, and it definitely won’t be the last.

Trace Metals

Scientists set up to bring metal-free water onboard.

R/V Sally Ride has its first bubble! It consists of a fort of plastic sheeting with filtered air fed in through a flow hood to create positive pressure (see header photo). Dr. Kathy Barbeau and her graduate students set it up in the wet lab in order to keep their work area clean of contamination. Their experiments focus on such low levels of metals, in this case iron, that ambient levels and particles around the ship could interfere. In order to collect the seawater they needed, they rigged up an all-plastic system that was lowered into the ocean on the starboard side of the ship. Held a few meters away from the hull and a few meters below the surface, they pumped water into a carboy. The seawater that comes into the lab flows through metals pipes, which again would add contamination.

Inside the bubble, grad student Kiefer filters seawater to collect the
pellets to be studied.

They are studying the iron levels in fecal pellets of copepods and euphausiids (krill) in order to understand the cycle of trace metals in the ocean. This is part of a collaboration with Dr. Mark Ohman’s lab at Scripps. Both lab teams are onboard R/V Sally Ride collecting and processing samples. Bongo nets are towed over the starboard side of the ship, and the catch is rinsed down into cod ends, baskets at the end which can be brought right into the lab. In this case, copepods and euphausiids are separated out from other critters and kept in seawater rich in phytoplankton (their food source) in a walk-in cold room in the lab. 

On a longer cruise, trace metal work would likely be done in a lab van stored on the ship’s back deck. A container van can be converted into a clean lab, allowing for a contamination-free environment for scientists to work. R/V Sally Ride is designed to accommodate countless setups in order to meet the scientists needs. 



Zooglider Science

The zooglider is deployed and recovered using a small boat launched
from the Scripps pier. It’s 6 feet long with a 4 foot wing span.
Zooglider photos thanks to grad student Ben Whitmore.

Leg 3 of this R/V Sally Ride cruise is underway after switching out the science party in Oceanside. Samples are being collected by a few different groups, including Scripps professor Mark Ohman and undergraduate and graduate students from his lab. We are operating in the vicinity of a zooglider that was launched recently from a small boat. The glider is an unmanned vehicle that carries oceanographic sensors onboard and can sink to a depth of 400 meters on command. When it surfaces, it sends location information to the lab via satellite. It can stay out to sea for a number of weeks and is then recovered and the data downloaded from its sensors.

Scientists are collecting biological samples using the MOCNESS (multiple opening/closing net environmental sampling system), which is deployed from the back deck of R/V Sally Ride. They have done tows to 400m around noon and midnight each day, to account for the fact that critters move shallower in the water column after dark. The samples will be compared to pictures taken from a camera system on the zooglider, in order to determine whether krill and other animals may be avoiding the glider. The camera takes a picture every 0.5 seconds, capturing images such as those below. The abundance of various species can then be inferred based on how many were spotted by the camera. But it may be that those calculations aren’t indicative of the actual population, if the animals move away from the zooglider as it approaches. The net tows, however, are harder for them to avoid. 

Images from the camera on a zooglider. On the left is a jelly, and on the right is a copepod, the main subject of study in Dr. Mark Ohman’s lab. 

The MOCNESS tows take a few hours each. You can read more about how the net system works in a previous post. Sensors are mounted to the net frame, including a CTD (conductivity, temperature, depth), oxygen, fluorometer, and transmissometer. Live readings from these sensors are monitored by scientists in the lab during the cast, who give directions via radio to a crew member running the winch. When the package is brought back onboard, the ten nets are washed down with seawater. This rinses all of the critters caught along the length of the net into the cod end, which is then removed and brought into the lab. More rinsing and filtering is done, and then each sample is preserved for further study. Check out this 360 degree view of a MOCNESS recovery on the ship’s fantail.

The nets provide data about animals found in each depth range; each collects a sample covering 20-100 vertical meters at a time. With the camera, that resolution will be narrowed down to 5 centimeters, giving much more useful information about whether specimens are interacting with each other. This is the first study to take place when the zooglider and net tows are operating at the same time and in the same area as each other. Testing that the camera system can be reliably used to make inferences about zooplankton populations is part of making it a valuable tool. 

On deck, each of the ten nets are rinsed (left), flushing the sample into the cod end.
In the wet lab, students filter and preserve the samples for study back on land (right).