Notes from the Field

The current project on R/V Sally Ride has made SIO’s photo of the week! I’m currently assigned to a different research vessel in the Southern Atlantic Ocean working and writing for the SOCCOM project, so it’s hard to keep in touch with the goings on of the ship. Apologies for the lack of regular posts. There are ongoing posts and pictures from the ships and planes involved here.

Based on a report from UNOLS master technician Drew Cole, who is working as a restech, 42 moorings were deployed from Sally Ride in a matter of days. Now underway are surveys using the ship’s sonars and a few additional ones that the science party has mounted in various ways. This includes an ADCP on a pole and a profiling instrument on a heavy-duty fishing reel that measures turbulence, among other properties. 

Scientists ready for a night-time deployment from the ship’s stern.

A report from Chief Scientist John Colosi: 

“The R/V Sally Ride is well into week 2 of our observations of the dynamics of the inner continental shelf just south of Pismo Beach. We have been dividing our time between two distinct inner shelf environments. One location, Oceano Beach, is a straight sandy-bottom coastline, and the other location, Point Sal, is a complex rocky headland with outcrops, promontories, and a large pocket beach. These location choices help our groups to dis-entangle the important dynamical processes associated with beach inner shelf interactions such as rip currents and surface waves, internal waves which are like surface waves except they exist within the ocean water column, wind driven circulation such as upwelling and down welling, ocean eddies which represent the “weather’’ of the ocean, and topographic effects.

 “The experimental effort would not be possible without an extremely capable and collegial group of scientists from SIO, NPS, OSU, and UW. With over 170 moorings measuring temperature, ocean currents and mixing, 3 large vessels (R/V Sally Ride, Oceanus, and Sproul), 4 small boats R/V Kalipi, Sally Anne, Sounder and Sand Crab), 2 airplanes from SIO and UW, and coastal radar supplied by SIO and OSU, there is a dizzying amount of equipment involved in this work.

 “Some highlights of the work so far include wonderful observations of energetic bore-like and short pulse internal waves with beautiful turbulent wakes and associated biological activity, headland wakes and eddies and their associated complex re-circulation patters, strong upwelling and eddy activity due to a major wind event, and observations of vorticity (circular water motions) from 5 vessel synchronized surveys along the 10-50m isobaths.

“Our delightful experience of the inner shelf is that every day is different and the various dynamical processes at work, tides, wind, waves, turbulence, and topographic effects, evolve as a complex, but understandable pattern that has been a joy to observe.’’

Blog posts and pictures from the scientists onboard are also here.


Sally Ride, Team Player

R/V Sally Ride is finishing up mooring operations for Chief Scientist Dr. Bill Hodgkiss and will soon be headed back to port. It’s another quick turnaround, the ship heads out next week to an area just off the coast of Southern California between Point Conception and Avila Beach. An ONR (Office of Naval Research) funded project, scientists will be aboard from Scripps, Oregon State University (OSU), University of Washington (UW), and the Naval Postgraduate School (NPS) in Monterey. And it won’t just be Sally Ride at work. OSU’s research vessels Oceanus and Kapili will also be in the area, as well as SIO’s Sproul. Small vessels and even aircraft will be part of the joint effort as well.

This intensive observing effort is part of a multi-year effort to to better understand the “inner shelf”, the part of the coastal ocean offshore of the surf zone but onshore of the shelf break (where the ocean depth plummets to hundreds and thousands of feet).  This area is governed by unique but complex physical processes, including wind-driven circulation, upwelling, breaking waves, wakes and instabilities, and internal waves (that ride on density interfaces below the surface). The map on the left shows the study area, with various symbols representing sites for wave observations, sonar surveys, drifter and mooring deployments, wave gliders, quadpods, bottom landers, ship’s radar, and even drone flights with an infrared camera. More on how all these technologies work together to tell a story coming in future posts.

The scientists will collect every feasible bit of data they can. Combination of all of these observations will help them both understand the basic processes, and use that understanding to improve forecast models of the coastal ocean.

A variety of aerial images of the work site add data on properties of wind, waves,
and currents. Photo credit to Gordon Farquharson (UW).

For her part, Sally Ride will deploy twenty-two moorings during the course of the cruise. These are done during daylight hours to make the operations safer and easier. Overnight and then for an intensive period after the mooring deployments, the ship will conduct ADCP (Acoustic Doppler Current Profiling), density, and turbulence surveys to study these complex phenomena. You may remember another internal wave project performed aboard R/V Sally Ride, check out this post to learn more.  

Stay tuned! Co-Chief Scientists Dr. John Colosi (NPS) and Dr. Jennifer MacKinnon (SIO) will be blogging on this page, as well as Sproul’s Chief Scientist André Palóczy (SIO). There are also blog posts here. And for all the details you could possibly want, check out the publicly available experiment plan.


The Study of Sound

Technicians Gabriela and Jeremy deploy a surface buoy. Below the surface is a
thermistor string, along with floats and weights to keep it vertical in the water column.

Dr. Bill Hodgkiss is back aboard R/V Sally Ride, along with engineers and technicians from his group at SIO’s Marine Physical Laboratory (MPL). As with their cruise last year, which was the ship’s first official science verification cruise, they have brought along multiple instruments used to study acoustics off the coast of Southern California. On that cruise, the moorings were anchored to the seafloor using old train wheels. This expedition, however, focuses on drifting moorings that are not anchored. Instead they are connected to surface buoys with GPS for keeping track of its position, as well as lights and a beacon to aid in recovery.

The sound source is deployed and towed behind the ship for a few hours
each day.

In order to calibrate the acoustic instruments deployed, a sound source is towed behind the ship. The known noise level and distance from the recording devices puts every other noise recorded into perspective. CTD casts are also performed on a regular basis in order to provide a sound speed profile (more on the importance of that in this post). An echosounder survey was also conducted in order to determine the properties of the seafloor (see more about the Chirp system here). 

This science party has been aboard a few times, and always puts Sally Ride through her paces, using ship’s equipment such as the crane and A-frame, as well as the CTD and many other shipboard science systems. Not to mention the bridge crew who navigate the ship with the necessary precision and help look out for floats upon recovery. Thankfully, the Hodgkiss group also come prepared and have a lot of experienced hands, so it’s time well spent.

 

 


Shipyard Upgrades In Action

R/V Sally Ride has successfully completed two science cruises since leaving the shipyard last month. The first involved visiting a research site in the Gulf of Alaska in order to switch out long-term moorings. That cruise off-loaded in Newport, Oregon and the ship then headed to San Diego. Multiple Scripps technicians were onboard for the transit south in order to tie up loose ends (in some cases literally) and get the ship ready for the demands of a CalCOFI cruise. The seasonal trip fills the ship’s staterooms and labs with scientists and uses pretty much every capability – from underway sampling to deployments to sonars. And on this cruise, Dr. Uwe Send’s group also loaded up a buoy and other instruments as part of an opportunistic mooring deployment. So it was a very full ship!

The new main lab setup. For pictures of the lab before the shipyard changes,
check out this post http://go.ucsd.edu/2xd27W2

You may remember that the CalCOFI group was also aboard Sally Ride for their fall trip last November. So they were able to compare the ship as it was then, after just a few science verification cruises, and now, after the shipyard period. What made the most difference to them was the reconfigurable lab spaces. Gone are the rows of narrow tabletops with cabinets above and below, replaced with custom-made easy to move nesting tables of varying sizes and heights. They come with the extra perk of storage space underneath and it’s a necessity at sea that everything be easily secured. The tables bolt into the floor, the lab has holes every two feet in a grid pattern, and gear can be screwed into the tabletop or strapped to the frame. “The new tables are great!” says CalCOFI Chief Scientist Jen Wolgast, adding that it made it much easier for the various groups aboard to have the work areas that they needed while sharing limited space. “It’s nice to be able to get to all sides of the tables, it lets people move around easier,” said LTER scientist Shonna. I’m glad to hear that the new lab setup is working well, and can’t wait to see how each science party customizes it.

The forward area of the wet lab, now with a watertight door leading
out onto the deck near the CTD sampling area. Note CalCOFI’s famous
espresso setup – they know how to live.

The wet lab also got an update. As outlined in a previous post, the name was a bit too literal at first. Sister ship R/V Neil Armstrong was first out of the yard, and reported water making its way into the wet lab through the rolling door connecting it to the starboard working deck. Now, that door has been converted to a solid wall and instead there’s a watertight door that leads from the forward part of the wet lab out onto deck. Chief Scientist Jen Wolgast reports, “We used the door from the wet lab to help with landing the CTD, it’s in the perfect spot to assist with getting the rosette right where we need it in order to sample all the way around.”  

The forward 01 deck also got reinforced so that containers can be housed there, both for storage and additional lab space. This was quite an undertaking in the shipyard, and there are dramatic photos of the transformation in a previous post. A second ladder (stairway, see header photo) was added from the forward focsle deck, so that there’s still easy access no matter where the containers are placed. No science group has needed that extra functionality yet, but you can be sure that once they do, you’ll see pictures of it here. 

 


A Quick Turnaround

Last week R/V Sally Ride returned to San Diego after months away. But that doesn’t mean that the ship or her crew got much of a break. Within 72 hours, they were underway again. The summer CalCOFI research cruise will spend 17 days at sea, occupying 75 science stations to collect data as part of its historic data set. 

The marine mammal acoustic team readies their array, while restechs
and technicians from Uwe Send’s lab bring a mooring buoy aboard.

First up, there was lots of gear to unload from the shipyard period. The ship’s crane alternated moving this off onto the dock, and bringing on gear from the many groups that participate in a CalCOFI cruise. It is a full ship, with the labs and staterooms full of scientists. The back deck is more crowded than usual, home to mooring instruments from Uwe Send’s group that will be deployed once all the usual station work is complete. This is a project of opportunity that is part of a NOAA-funded array making observations in the CalCOFI region

The crew also had a few projects to complete, so everybody pitched in to get the ship ready. 

You may remember that Sally Ride hosted the fall CalCOFI cruise last November. To learn more about the science taking place onboard in the next few weeks, check out these posts from that time.

Science Focus: Hydrography

Science Focus: Fisheries

Science Focus: Marine Mammal Observations

Science Focus: Long Term Ecological Research

Science Focus: Plankton sensor

Project of Opportunity: Quantifying Carbon Export

 


Mooring Work in the Gulf of Alaska

R/V Sally Ride is back out at sea after months of upgrades in the shipyard. This first research cruise has scientists from Woods Hole Oceanographic Institute and Oregon State University working on site at an array of moorings in the Gulf of Alaska to recover and deploy anchored strings of oceanographic instrumentation.

Illustration of all the equipment monitoring station Papa.
From OOI’s website.

Station Papa has been a community study site for nearly 70 years and currently supports multiple mooring strings, including a NOAA surface buoy. The OOI (Ocean Observatories Initiative) has been deploying three moorings there since 2013. Once a year, a research vessel full of OOI scientists and technicians makes the trip in order to change out equipment. This year’s trip aboard R/V Sally Ride will recover and deploy replacements of all three OOI mooring strings. All three deployments have taken place and recoveries have just been completed successfully. Each deployment takes up a whole day of work, as they are over 4,000 meters (two and a half miles!) long. They sit on the bottom of the ocean, weighed down by a 6,000 pound anchor, and reach to either 30 or 150 meters below the surface. Check out an earlier post about moorings, back when the ship was in science verification mode, for more details about how scientists use the ship’s equipment to deploy and recover instruments. 

Technicians prepare to deploy a WFP, which travels part of the mooring wire
to sample at different depths. Photo by UNOLS technician Tina Thomas.

There are multiple sensors on each string, including for temperature, salinity, oxygen, fluorescence, turbidity, and density. CTD casts are taken with each deployment in order to calibrate the new sensors using those connected to the rosette frame. Water from the bottles is analyzed in the lab onboard as well. One of the moorings has two WFPs (Wire-Following Profilers, the yellow instrument in the photo on the right), each of which travels up and down a certain part of the wire, sampling throughout its assigned portion of the water column. Each mooring also has sonars to measure backscatter. The large orange spheres in the photo below contain acoustic sensors. A sound wave is produced, and the reflection recorded, from which plankton and other biological populations can be determined. These are similar to the fish finder sensor that Sally Ride has mounted to her hull. 

R/V Sally Ride‘s fantail is part storage (anchors at far left) and part working deck (the anchor to be used for this deployment is in place at the edge under the A-frame) during mooring deployments. The orange spheres house sonar equipment, and the yellow ones are floats that keep the mooring string straight in the water column and bring the instruments to the surface when it’s time for recovery. Photo by UNOLS technician Tina Thomas.

With scientific work completed, R/V Sally Ride has started transiting to Newport, Oregon for offloading. It will then head south to its home port of San Diego. A busy schedule of cruises kicks off with the summer CalCOFI trip. More on that soon!


Back to Work!

The final steps of the new paint job were done with the
entire ship under cover. Photo by 2nd Mate Randy Christian.

R/V Sally Ride is back in the water after two and half months in a shipyard dry dock in Alameda, California. As you may remember from previous posts (here and here), there was a lot of work done to the ship during that time. Everything on the to-do list has been completed, including the addition of a CTD hangar, a reinforced forward 01 deck, and a new paint job. The crew is excited to have the ship back, and took her out in San Francisco Bay for a series of sea trials to make sure all the systems are working properly.

Scientists are now onboard and loading their gear for a research cruise. It will be a mooring trip out to Ocean Observatories Initiative (OOI) array at Station Papa, which is in the Gulf of Alaska, about halfway between Seattle and the Aleutian Islands. As with other mooring trips aboard R/V Sally Ride, this one will include the deployment and recovery of instrumentation designed to spends months to years in the water column.  

The transition time between shipyard work and this research cruise is brief, so everyone has been working flat out to make it happen. It’s gone from the seeming chaos of just a week or two ago during the final stages of work in the shipyard to the orderly setup of the working deck, where every piece of equipment is secured in place and ready to head out to sea.

What a difference a week makes! The back working deck of R/V Sally Ride towards the end of shipyard work (left, photo by restech Keith Shadle). The walkway is actually the top of the ship’s A-frame, which is in maintenance mode, lowered all the way onto the deck. On the right, taken this week, all that clutter is gone, the A-frame is in its usual configuration, and mooring gear such as anchors and floats full of instrumentation have been loaded and secured in place. (Photo by 2nd Mate Randy Christian, note the lovely San Francisco skyline in the background.)

At the end of this cruise, R/V Sally Ride will return to her home port of San Diego, where there’s a busy schedule of research cruises for the rest of 2017. We hope you’ll follow along!

R/V Sally Ride is back in the water after two and a half months in a shipyard dry dock. As 2nd Mate Randy put it "…as…

Posted by UC San Diego R/V Sally Ride on Saturday, July 1, 2017

 

 

 

 

 

 


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.” 


Net Samples Join SIO's Invertebrate Collection

Scripps Institution of Oceanography is home to some of the most 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 cod end, making sure to carefully retain all the plankton. The sample is then transfered 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’s Ohman 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 (1mm = 1 thousandth of a meter) are classified as extra large, 1-5 mm are large, and less than 1mm 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 also 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. 

 


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!