Upgrades in the Shipyard

R/V Sally Ride is currently in the shipyard for some upgrades. It was always part of the plan for the new research vessels to spend a few months there at the end of their first year in service. R/V Neil Armstrong, which was delivered to Woods Hole Oceanographic Institution, has been about six months ahead in the whole construction and verification process. As such, that ship is already done with its shipyard period and back to doing science. Sally Ride will soon be ready to get to work, with a full schedule already set for the rest of the year. Up first is a research cruise scheduled out of Newport, Oregon, and then the ship will return to San Diego just in time for the summer CalCOFI trip.

R/V Sally Ride in dry dock. The propellers have been buffed and the shafts and rudders are back in place. Note the blocks under the keel.
Picture by ROV technician Doug Penny.

The ship is currently in dry dock, which means it’s out of the water. Dry docking a ship is an involved process – the ship pulls into a submerged slip, which is then raised and the water drained. Divers steady blocks underneath the keel of the ship and secure it. This makes all areas, including those usually underwater, easy to access – and the work continuing over the coming weeks takes advantage of that.

A hole is cut in the side of the ship in order to add the
additional ballast. Photo by 3rd Mate Randy Christian.

One important item on the to-do list is to add more permanent ballast. The ship is lighter than expected, and thus floats higher in the water. This can throw off the instrumentation that is mounted to the bottom of the ship, including transducers that collect data about the seafloor, currents, and animals in the water column. Over 700,000 pounds of magnetite, a type of iron, have been added into chambers on the lower decks of the ship, which should lower the ship about a foot and a half. In order accommodate this work the propellers and shafts had to be removed, which required the rudders to come off as well. While they were off, the propeller blades were buffed and are all nice and shiny again (see above photo). 

Changes are being made to accommodate containers on the forward 01 deck, both for storage and lab space, which will lend more flexibility to Sally Ride‘s configuration. Currently, all containers are placed on the fantail, which is prime real estate for equipment staging and deck area for operations. This upgrade is no small task though, as the deck has to be reinforced in order to hold the weight of these containers and their contents, and sockets have to be added in order to secure them. The area in question is on top of the staterooms at the forward part of the focsle deck, including those for the Chief Scientist and Chief Mate. The entire deck will be sliced away and replaced with a new one that’s up to the task. Check out this post for pictures of that operation.

Shipyard workers wall off the opening between the wet lab and
what will become the new CTD hangar. Photo by Doug Penny.

Another big change is the addition of an enclosed CTD hangar on the starboard side. R/V Neil Armstrong got one just like it during its shipyard period and reviews are positive. Originally, the ships were designed with a rolling door between the wet lab and the deck, but reports of the wet lab getting too wet made it back from the Armstrong in time for the doorway to be patched on Sally Ride. Now that opening will be converted into solid wall, and paneling will be added to enclose the area forward of the CTD handling system (aka T-Rex arms). So CTD casts will still be deployed and recovered in the same way, but now the frame can easily be moved into a hangar, which makes sampling easier and more safe. 

There are also some changes being made for the comfort of crew and scientists aboard. One such example is that the opening between the galley and mess will be made larger. Lowering the bottom of the opening will allow shorter people to be able to reach salad fixings that are in the back row. And raising the top will make it so that taller people don’t whack their head every time (see Twitter pictures below). I was glad to hear of this plan – I am an average 5’7″ but have both hit my head and not been able to reach the snap peas.

Restech Keith runs cable on the 02 deck, also referred to
as the Hobbit deck, a low space just beneath the bridge.
Photo by Doug Penny.

Sally Ride will get a fresh coat of paint on those usually hard to reach areas – underwater and the freeboard (area from the waterline up to the main deck). There will also be upgrades to various pumps, drains, vents, tanks, and valves all over the ship. Once she emerges from the shipyard later this summer, R/V Sally Ride will be better equipped than ever to perform the numerous tasks that science parties require, including deployments and recoveries of myriad gear and top-notch sensor data collection. Scripps Institution of Oceanography is lucky to have such a workhorse in the fleet!

Check out these posts for more pictures from the shipyard

Back to the Shipyard

Shipyard Status Report


Crew Introductions: Electrician

“Sometimes it feels weird to be home. And when I get back to the ship, it just feels normal again. I really do enjoy going out to sea. I used to get homesick, but I’m glad I stuck it out. I actually found a job I enjoy.” 

Adam can usually be found in the electrician’s office just outside the lab.

Adam Goodbody has always had the skills and inclination to be an electrician, even helping his dad rewire the house as a kid. His uncle, a tanker captain and former SIO Chief Mate, suggested that he work at sea so that he could also see the world. So for the last three years, that’s exactly what Adam has done. Right out of high school, he began as an OS (ordinary seaman, see post about that job here) on the now-retired Melville. He then worked his way from wiper to oiler (see post about those duties here) in the engine room of R/V Roger Revelle. The Chief Engineer there knew he was interested in becoming an electrician, and made sure he learned those duties when he had time. Adam was then sent to R/V Sally Ride as day oiler while the ship was still in the shipyard in Anacortes, Washington. There, and on many of the science verification cruises, he trained under Manny, a long-time electrician on Scripps ships. And now the training wheels are off and Adam has been sailing as ship’s electrician for the last few months.

Coming aboard a brand new ship and learning about the electrical systems was a trial by fire experience (though thankfully not literally). As Adam says, “You start the engines from a screen, there’s no manual way to do it. The fact that everything is electronic on this ship means that my job is that much more important.” And he’s not overstating things, pretty much every component in every space falls under his purview. When things are running smoothly, he’s studying diagrams in anticipation of the day that something important breaks. “That’s my biggest fear. I want to have a basic understanding of everything on the ship before I have to fix some major problem. So I study constantly…and I hate studying.”

Adam at work, taking things apart and putting them back together.
This is his patient face, just after I made a joke about cutting the red wire. 

There are hundreds of these diagrams, and he showed me a few. To me, it just looks like a confusing jumble, which Adam assured me is normal. “It all looks like a bunch of jumbled up lines when you just look at it, but all you have to do is find a line and focus on it and you can tell where and what it is. There’s switches, junction boxes, but it’s not as complicated as it looks.”

Adam works a day shift. His morning rounds begin on the bridge and take him six decks down to the engine room. He checks on the lights and alarms all over the ship, as well as any equipment that’s plugged in outside on the decks. He also monitors the load on the ship’s UPS (uninterruptible power supply), which protects lab equipment from power surges and supplies a charge even if the main power is lost.   

The electrician is also treated like the ship’s resident MacGyver. If a scientist lingers sheepishly in the hallway outside the electrician’s office, you can bet that something has broken and they need help. I have definitely brought nonfunctioning instruments to them, putting on my nicest voice, and opening with “Hey…so, I have this problem…”

Adam trained AB Natasha and day oiler Dave on the operation of the winches, which run
the spools of cable or wire that scientists attach their instruments to before lowering them
into the ocean. I tried to sneak up on them to get a natural photo, but was noticed.

From waterproofing crates to soldering a circuitboard, from removing water from a winch on the back deck to fabricating Teflon pieces, or if the carburetor on your remote controlled kayak has stalled – Adam has seen it all and can probably help. Or give him a few minutes and he’ll catch up. Science parties try to bring everything they might possibly need (or at least they ought to), but if you forget tape, the drawers in the electrician’s office have like 12 kinds of tape, along with zip-ties (all sizes!), rope, screws, you name it. When asked what his favorite tool onboard is, Adam says, without hesitation, “…the sledgehammer. I’ve found there’s a lot of situations where it does the job. A few good smacks.” 

During his downtime on the ship, Adam shows up to game nights (see Twitter picture below), watches movies, and gets as much sleep as he can. Like many crew members, he extolls the virtue of having his own room. On Revelle, he had to change rooms often, moving in and out of other people’s rooms based on their schedules. Despite this, he says he’d be happy enough to go back to that ship, and says “It’ll be cool to see Revelle come into San Diego. I kind of miss that crew.” The ship just arrived into its home port for the first time since 2012, and will be working along the West Coast for the rest of the year.

Adam in the ship’s engine room.

Adam’s preferred schedule is to work about eight months a year, though this year he’ll only get two months off. When asked what he’ll do with that down time, he says, “I don’t have the full year with my friends and family, so I spend time with them. I enjoy whatever holidays I get at home. It’s not the same at sea – you still work your full day, though there’s usually some sort of treat from the galley.”

Down the line, Adam is interested in becoming an electro-technical officer, adding programming and networking knowledge to his skill set. There’s always work on drilling rigs in the Gulf of Mexico, where the money is astronomical. But he plans to remain aboard R/V Sally Ride, keeping the ship running smoothly so she can travel the world doing science. There’s still a lot he can learn onboard Scripps research vessels, and he’s eager to do just that. “I largely attribute why I enjoy working with Scripps to the crew. Any time I want to learn something, it’s not difficult to find a teacher in the crew.” Research cruises have taken him to nine foreign countries already in his short career, and Adam says that is a huge draw, “The adventure keeps me coming out.” 

Commemorative Coin

As you know, Sally Ride was America’s first woman in space. And now R/V Sally Ride is the only member of the academic research fleet named after a woman. Carrying her name is an important legacy, and one that we here at Scripps Institution of Oceanography are excited to be a part of. 

The coin on the highest deck of R/V Sally Ride, just before the mast
was placed. Photo by Paul Bueren. 

When the ship was being built in Anacortes, a bronze coin commemorating Sally Ride’s first mission into space was placed under the mast for luck. The coin, purchased on eBay by Chief Engineer Paul Bueren, shows the official NASA mission emblem, with the space shuttle flying over Earth. Seven stars and the shuttle’s robotic arm shown in the shape of the number seven denote the 7th shuttle mission. Sally Ride operated the arm in order to deploy and recover satellites during the mission. Also of note is the plus (female symbol) as part of the 5-pointed insignia, with the other four parts being arrows (male symbol) for the other members of the crew. 

From June 18-24, 1983 the space shuttle Challenger traveled 2.5 million miles with Sally Ride and the rest of the crew aboard. Though it’s impossible to compare, Scripps research vessels have traveled an estimated 7 million miles in our 100+ year history.

The mast is craned aboard. Note R/V Neil Armstrong already afloat in the background. Photo by Paul Bueren.
The coin (bottom center) was placed on the deck and the mast was lowered and guided into place on top of it. Photo by Paul Bueren.

Technicians At Sea: Computing Resources

“Yeah, it’s one big adventure, to travel the world, that’s cool and all – but the rewarding aspect I didn’t know until later was seeing the research I assisted with on the news. I felt proud to be part of something greater.”

Computer tech Daniel can often be found near the main lab’s wall of monitors,
keeping an eye on the countless systems he’s in charge of maintaining.
Photo by ROV tech Doug Penny.

Daniel Yang first started working for Shipboard Technical Support at SIO as an undergraduate student, programming applications for the Oceanographic Data Facility. Later he became one of the department’s Computing Resources (CR) technicians and in the last ten years has traveled around the world on Scripps research vessels, spending anywhere from a few days to a few months away from home. The techs are in charge of making sure everything digital onboard is working, including data collection and processing from all the sensors onboard. There are also ship networks to maintain, servers that the scientists use to share information. You’ve seen pictures of R/V Sally Ride’s “wall of monitors” in other posts – fifteen screens all showing readouts from different instruments  – and the CR techs are in charge of keeping them all up and running. 

Along with the resident technicians (restechs, see intro in a previous blog post here), the CR techs act as a liaison between the scientists and crew. No matter what the science objectives, every research cruise on R/V Sally Ride requires setup, tracking, and assistance from the computer techs. The coring group needed singlebeam echo sounder data to reliably collect sediment samples, the ROV group used an acoustic positioning system to track the submersible’s location, and many trips require CTD sensor data and bottle samples. In addition, there are many systems that run by default unless they interfere with primary science operations, like the seafloor mapping system and current profiler. Daniel works with the scientists in advance to make sure their needs will be met. “What the scientists want versus reality can be challenge, but we always try to accommodate the science,” he says, adding with a smile “We can’t break the laws of physics, but sometimes we’re asked to.” And if nothing else, no one can function without internet access these days, and Daniel is in charge of keeping that running as well.

Daniel gears up to climb the mast of R/V Roger Revelle to make repairs.

But he’s much more than just an at-sea IT guy. Daniel has had standard desk jobs in the past, and says “I probably wouldn’t want to go back to that. No, I don’t think I could sit in one place.” Trouble-shooting equipment on a research vessel can be “like a stair master when things go wrong,” he tells me, as there’s gear on every deck of the ship, not to mention up the three-story masts. The computer techs are also in charge of launching XBTs (eXpendable BathyThermographs), temperature probes used to determine the speed of sound in seawater, which can vary due to many factors and are needed to calibrate measurements made by onboard and deployed instrumentation. For this, Daniel dons the work vest necessary for any operation involving something placed over the side of the ship and makes his way to the fantail. For some reason, it seems to be tradition to prank a new scientist into helping with an XBT deployment and telling them how dangerous it is, loading them up with unnecessary protective equipment (see Twitter picture below). 

There is often only one computer tech on a research cruise, which means they may be called for assistance at any hour of the day. Without the routine of a work shift, Daniel adapts his hours to when he is likely to be needed. But that doesn’t mean he won’t get a call right after he’s hit an REM cycle or just gotten to the best part of a movie or book.

Daniel launches an XBT off the fantail of R/V Sally Ride.

Though it’s more likely to be interrupted, Daniel lists the same downtime activities that the other techs and crew members have mentioned in their interviews. “I read a lot of books, watch movies, rinse, repeat, eat, workout, that’s about it.” He also gets asked to help people with their personal computers, and is ready to help. It’s always good to be known as a helpful person and to make friends with the crew. “We’re stuck with each other for a month or more at a time, so it’s good to help each other out.” 

When asked what he would recommend for people who are interested in a job like his, he says “Practice being handy, even if you’re a programmer, knowing some basic things like soldering, hands-on stuff away from the keyboard, maybe build an RC car. Those skills really do come into play out at sea.” On one trip aboard SIO’s R/V Roger Revelle, the MET sensor stopped working. Short for Molecular Electronic Transducers, the gyroscopes, tilt sensors, and accelerometers are vital to both crew and science missions. Their location on the ship’s mast makes troubleshooting quite an undertaking. Daniel geared up with safety equipment, including a harness and hard hat, and made the climb. It turned out to be a short in the wire, which he cleaned up with a pencil eraser and then repaired – all while about nine stories above the ocean surface, in the middle of nowhere.

Having a brand new ship to set up and work with has been exciting for everyone at Scripps, but especially the technicians who are expected to know everything about keeping a research vessel running. R/V Sally Ride is now a passion project for those of us lucky enough to have been involved from the beginning, and one that Daniel is excited to be a part of for a long time coming.

“The ship is the most advanced in the world, and I really want to keep it that way.”

See more from Daniel 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.

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 http://siogames.ucsd.edu/Ship_Tracks/

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.