Mission: Integrated West Coast Pelagics Survey (Leg 2)
Geographic Area of Cruise: Pacific Ocean, California Coast
Date: July 10, 2025
TAS Jojo Chang
Weather Data from the Bridge
It’s noon, and the weather is cloudy and foggy. We are passing the coastal city of Carmel, California, but only a tiny sliver of land is visible from the ship. We are sounding the fog horn and traveling slowly. Currently, the air temperature is 54.5 degrees Fahrenheit, and the wind speed is 14 knots.
Culinary: Art and Science
Let’s talk about Chef Phil, the Chief Steward on board. First things first: we are eating very well out here. And by “well,” I mean gourmet-level delicious. Chef Phil is a culinary artist, crafting remarkable meals that blend creativity and technique, even as the ship rocks and rolls like a theme park ride.
Chef Phil Jones
His knife skills? Let’s just say they’re literally “rolling with it.” That’s how he describes chopping food at sea—adjusting in real-time to the ship’s motion.
Chef Phil has a rich background in the culinary world. He once spent six months perfecting the art of sushi rice with Morimoto, the world-renowned Japanese culinarian (made famous for his role on the TV series Iron Chef). Phil has also cooked for Disney at the Hilton Orlando and aboard multiple cruise lines.
Sample daily menu . YES! We did have real gator nuggets.
“I’m not looking for a Michelin Star,” he says. “I just love what I do.”
Louisiana dinner menu
And that love shows—every single day. His food doesn’t just nourish, it brings joy. Thank you, Chef Phil, for making this ship’s mess hall taste like world class cuisine. It’s not a Michelin Star, but I’d give you five Shimada Stars. Chef Phil is assisted by Ted in the mess hall, preparing three amazing meals every day.
Ted Partosan: Kitchen assistant
Market Squid
In the wet lab, we encounter the ocean food web on a very real level every day with each trawl that comes up from the depths of the sea. It’s one thing to read about the food web; it’s an entirely different thing to see the organisms arrive in a basket for dissection and inspection. You should know that before I came on this boat, I had only dissected (reluctantly) one small frog in high school biology class. In college and graduate work, I studied education and American literature. There was nothing in my Captain Ahab/Moby Dick thesis paper that prepared me for this experience except background research into the Nantucket whaling industry of the 1800s.
Now, my scalpel skills have become quite remarkable. I have seen the insides of hundreds of hake fish and preserved many an ear bone for science. Inside, I’m telling myself, “I can do hard (and often gross) things.” When I say this is a life-changing experience, I’m not kidding. It is life-changing because of the wonder and amazingness of the life force of the underwater world, which is both fascinating and mysterious. I loved the ocean before I came out here, but now I’m just blown away by the life and living creatures that are under the sea.
One creature that comes into the wet lab regularly is the market squid. At first, they seem rather ordinary, but on further inspection, these creatures have the most beautiful pink, yellow, and brown random polka-dotted pattern. It turns out that this crazy cool feature is called chromatophores (cells that produce color) , and cephalopods use them to communicate, camouflage, and attract a mate.
Most days, we haul in 100s of these remarkable sea squids. The magic can be seen by tapping them lightly, and watching as the polka dots appear. The transformation is fleeting, but amazing. Unfortunately, it is an important feature for live squid, and as they die, they lose the chromatophores.
Chromatophores on market squid.
Video showing how the polka dots magically appear and disappear.
Fish Vocabulary
So, I have all these new science friends, and at first, they seem like totally normal ocean-loving people—you know, the kind who go on coastal vacations, talk about scuba diving, and swap fishing stories. But get them into the wet lab? Suddenly, it’s like flipping a switch. These folks light up over fish ovaries, otoliths, and fin clips like they just unwrapped an Apple Watch on Christmas morning—or scored Tiffany diamonds from a secret admirer. I’ve never seen someone so genuinely thrilled to dissect a hake fish. It’s both impressive and slightly shocking. However, what I see with everyone on board, from the deck crew to the engineers, is joy in their occupation. There’s a passion and a purpose to what they are doing that is both impressive and heartwarming.
Sabrina Beyer inspecting fish ovaries through a microscope.Sabrina Beyer and Amanda Vitale searching for a fish species.
Before arriving on this boat, I had never heard of an otolith, aka oties. This is a fish ear stone or ear bone, and is the most commonly used item for understanding the age of a fish. Scientists count the rings on a pair of otoliths to age a fish much like they count the rings on tree. Ear stones and tree rings are like nature’s timekeepers and just as trees lay down a new ring each year as they grow, many fish form growth rings on their otoliths. These rings can be counted to estimate the fish’s age, offering a biological calendar etched in bone.
A large pair of hake otholiths. They look like feathers.A photo from a Redwood tree in Muir Woods showing tree rings.
Both items that appear in Mother Nature’s patterns reflect changes in growth rate, which are influenced by environmental conditions. For trees, wider rings typically suggest years of good rainfall and favorable climate, while narrow rings indicate harsher times. Similarly, in fish, the spacing between otolith rings can vary depending on water temperature, food availability, and seasonal changes. Scientists aboard NOAA ships collect fish oties because they tell a hidden story about the life history and environment of the organism.
These ear bones are important to living fish for other reasons. According to NOAA Fisheries, “Otoliths are part of the fish’s inner ear, allowing fish to hear and sense vibrations in the water and providing a sense of balance so they may better navigate their surroundings.” Once, when my children were small, we had a pet fish named “Bubbles”. Bubbles swam upside down. I guess he must have had an otie issue.
Animals recently spotted from the ship or in the wet lab
Common dolphin, Risso’s dolphin, rockfish, dogfish shark, strawberry squid, baby octopus, hake, butterfish, anchovy, market squid, king of the salmon
Live dogfish shark on board.
Bringing in a ribbon fish known as king of the salmon. This is fish is not a salmon but is named such because of the legend that it leads salmon to its spawning area.
Geographic Area of Cruise: Pacific Coast, near Northern California
Date: September 2, 2024
Weather Data from the Bridge (Humboldt Canyon)
Latitude: 41.6º N
Longitude: 124.8º W
Wind Speed: S at 4.59 knots
Air Temperature: 15.1º C (59.18º F)
Conditions: Mostly Sunny
Science and Technology Log
One of the other interesting components of the EXPRESS Project is the use of MultiNets to study plankton in the mid layers of the water column. MultiNets are exactly what they sound like – a collection of nets that are lowered into the water to grab a sampling of plankton from the area. There are different ways of using MultiNets. Sometimes they are used horizontally, where they are dragged through the water to grab samples. For our mission, however, they are being deployed vertically.
MultiNet being lowered into the water with the ship’s winch
There are 5 nets that are each attached to a red canister. The net bags are all closed prior to deployment in the water, so that water flows freely through the frame. Upon the net frame being lowered to the deepest desired depth of study, the first net is opened to collect the water at that depth. As that canister is closed, the next one is opened at the new depth. This goes on as the MultiNet is pulled upwards until all 5 canisters have collected samples at the varying depths being studied. The MultiNet that is being used for this project also has a side net. The side net is used for capturing everything in the water column all the way up from 1000 meters upwards.
One of my favorite parts of the day is what I call “Show and Tell with Jenn,” where Jennifer Questel, the scientist deploying the MultiNet, goes through everything found in the collection from the side net. She pours small portions of the samples from the side net at a time into a glass dish to sift through and pull out the organisms of interest for separate preservation to study in a lab later.
Jennifer, sifting through the samples from the day’s collection
The jar of collected samples from the side net
The very first time she did this, I was so excited to see a few jellyfish and a lantern fish. I thought that was all that was caught. When Jenn went through the samples, however, she pulled out these incredible clear living organisms that I hadn’t even noticed floating in the sample water.
Examples of what Jenn found in her samples
I even got to hold a salp, which looks really squishy and slimy, but does not feel that way – it definitely has its own structure!
Holding a salp!
Personal Log
Captain Laura Gibson arranged for me to get a tour of the engine room. Although there is plenty of science in the ship’s day-to-day operations, too, I’m going to use the “Personal Log” section of my blog to discuss ship specifics, particularly since I’ve gotten so many questions about life on NOAA Ship Bell M. Shimada.
There are many systems that keep the ship operating. Obviously there is the engine that keeps the ship running, but there is so much that many people wouldn’t think of. For example, did you know that the water is put through a reverse osmosis system so that it is drinkable? I know we have a system like this in my basement for my house, but it is nothing compared to this system!
Reverse Osmosis System for the ship
There is a very important system on the ship that handles all of the waste from the toilets. It is a very sensitive system and it was reiterated many times that you CANNOT flush anything other than toilet paper down the pipes, or you will be very unpopular amongst the ship engineers! In fact, we learned that most ‘flushable wipes’ that you find are not flushable in any marine system. I imagine this is a system many of you would not have thought about, but it is a system that you definitely want to be working smoothly!
Engine room control board
The Chief Marine Engineer Rob Dillon has a digital system in which he can watch all aspects of NOAA Ship Bell M. Shimada in action at any given moment. He is retiring in a month, and it was fun to hear his stories of working on steam ships first, then diesel, and also watching the transition to the digital displays. He has been all over the world, including making deliveries to the USSR before the end of the Cold War. I could have listened to his stories all day long!
Rudder Post – I could see the subtle turning as we were standing there!
The real fun was seeing the rudder control and the ship propeller. It was such a fascinating feeling to imagine what was happening in the water just on the other side of what I was seeing inside the ship!
Getting to the ship’s propeller shaft!
The ship’s propeller shaft – the cloth is there because they clean the shaft often to keep it running smoothly
Music Connection
Today’s music connection comes courtesy of Ensign Megan Sixt. I was visiting the bridge, and asking questions about the structure of the NOAA Corps (the uniformed service men and women who run the ship operations) and the science teams. Megan beautifully explained that the ship runs like a symphony orchestra – every person has their role, and each role is important. She talked about how there are certain roles on the ship that would be very difficult for her to do, and she is grateful for the people who do them so well on NOAA Ship Bell M. Shimada.
It is a very inspiring experience to watch the NOAA Corps and the science team collaborate. Both parties highly respect what the other is doing, and you can see that in every interaction. Everyone on the ship wants the mission to be successful and they all understand their individual role in making it happen. Just like in an orchestra where a trombonist would not be covering an oboist’s part, the people on NOAA Ship Bell M. Shimada know their role and do not try to tell other people what to do in their roles. It is so refreshing to be in a place where everyone appreciates and supports each other fully. The trust in each other and respect for each person is very high here, and it is a great lesson for the students I teach to hear about. There is rarely a collaboration that does not end in thanking the other person for their help, insight, or critique. The bigger picture – whether it is a scientific mission, or a symphony orchestra performance, is the ultimate goal that everyone focuses on.
Also, I want to share another audio clip with you all – this is what a group of albatross sound like. You can hear Popoki, as well, as we are recovering her from her dive.
This audio clip contains the sounds of the albatross
Student Questions
Part of the homework I had to do for the students I work with was to find out about squid in the area I am working. They will be excited to know that I saw one off the side of the ship tonight! I couldn’t get a picture of it, as the lighting was not great for an iphone photo. However, there also happens to be a squid in the lab for the freezer.
Pretty sure this guy wants to say hi to St. Bruno Wildcats!
The samples from the MultiNet have also included some tiny squid.
Jenn says this is paralarvae, probably from a squid, found in the side net collection
Mission: Pacific hake (Merluccius productus) Survey (Leg 3 of 5) Geographic Area of Cruise: Pacific Ocean off the Northern California Coast working north back toward coastal waters off Oregon. Date: Tuesday, August 1, 2023
Weather Data from the Bridge Sunrise 0613 | Sunset 2034 Current Time: 0900 (9:00 am Pacific Daylight Time) Lat 42 32.8 N, Lon 125 00.9 W Visibility: <1 nm (nautical miles) Sky condition: Overcast Present weather: Fog Wind Speed: 15 knots Wind Direction: 350° Barometer: 1017.9 mb Sea Wave height: 2 ft | Swell: 340°, 3 ft Sea temp: 16.6°C | Air Temp: 16°C Course Over Ground (COG): 090.2° Speed Over Ground (SOG): 9.9 knots
Science and Technology Log
Second Engineer Justin Halle provided a tour yesterday of the engine room and associated machinery kept running smoothly by the Engineering Department. Four Caterpillar brand diesel engines use about 1,800 gallons of fuel per day, although that number fluctuates depending on operations and weather. There are multiple fuel tanks in reserve that hold 5 – 15,000 gallons. A fuel manifold regulates fluid intake and a camera is fixed on fuel levels so the engineers can monitor them. Two valves per tank allow for filling or suction. Water evaporators separate sludge and water to keep fuel clean and bacteria free. We also looked up the exhaust shaft which vents out the top of the ship above the level of the flying bridge.
We viewed the propellor shaft that drives the main propulsion of the ship. A secondary means of propulsion is the bow thruster, but it is primarily used in close quarters situations such as docking and undocking. We did not view the bow thruster on our tour.
Two of the four diesel engines. OWS – oil & water separatorThe fuel manifold.The vacuum system that sucks our fluids down the drain. Second Engineer Justin Halle at the control panel.A tidy workbench.
There’s a whole water treatment system. The sewage part has a macerator that blends up, er, things just like the Ninja blender in your kitchen. Treated wastewater is vented to the ocean every few days, but cannot be pumped within three miles offshore or within marine sanctuaries. We consume approximately 1,400 gallons of water per day, and the ship can make potable water from seawater through reverse osmosis, evaporators, and water brought aboard from port. Water is treated with bromine, which is often used as an alternative to chlorine in swimming pools.
Workbenches and tools are kept tidy, with some tools and parts kept in a veritable library of large metal cabinets. An impressive control panel allows the engineers to look at the status of various systems at a glance. Performance logic controllers enable engineers to turn things on or off in the engine room from the control panel. Additional screens show a camera feed of potable water levels, the propulsion system, and the fire pump (only accessible down a hatch in the bow thruster space), which are all prone to flooding. Additional specifications for NOAA Ship Bell M. Shimada can be viewed here.
Career feature
Matt fillets rockfish caught in the bycatch for a special lunchtime treat.
Matt McFarland, Chief Bosun
Give us a brief job description of what you do on NOAA Ship Bell M. Shimada.
We do a lot of fishing operations and I run all the gear. I run the nets and the winches. I put the nets out wherever the scientists are seeing the fish and we’ll go down to that depth. I’m responsible for the efficiency of the operation and safety of the six deck hands I have underneath me.
Note: Matt is also a “plank owner” meaning he was a member of the ship’s crew prior to the vessel being placed in commission. So, he has been with the Shimada before it was owned by NOAA and still belonged to the shipyard. The ship was built in Moss Point, Mississippi and Matt was a part of the crew when it was taken through the Panama Canal to serve in research operations on the West Coast.
What’s your educational background?
I grew up commercial fishing. After high school I went to a technical college for marine technology. So I can work at marinas, on boats and motors and this and that. After school I went back to commercial fishing for a while along with carpentry to supplement. Then about 2008 I decided I wanted to be a professional mariner and get my U.S. Coast Guard license. From there I found out about NOAA, joined in 2009 and have been here ever since. The Coast Guard license is about a three-week course; they teach you basic seamanship. In order to be in my position out on the ocean you need an AB, meaning able bodied seaman. The Ordinary Seaman (OS) is entry-level and I worked my way up over the years. So on the fishing boats we have different levels: general vessel assistant (OS), fisherman (the equivalent of an AB), the next step is skilled fisherman, then lead fisherman, then Chief Bosun is the leader of the Deck Department.
What do you enjoy most about your work?
I enjoy the ocean. I love being out here. Growing up in commercial fishing, you work really hard and there’s no guarantee you’re going to get paid: if you don’t catch fish you don’t get a paycheck. So being here with NOAA means I get to continue to do what I love and if we don’t catch fish I still get paid. It’s a secure job. I have a passion for getting the science right and making sure things are getting done the way they should be done. We’re making regulations for the commercial industry and if our science is faulty, if we aren’t being efficient, then that’s not fair to them. I have family in commercial fishing, so it’s important to me. A lot of these guys are new to sailing and have never fished, so I’m passing on that knowledge. This isn’t as grueling as commercial fishing. It’s important to me to keep the industry going and get the science right.
What advice do you have for a young person interested in ocean-related careers?
Start with small trips. Make sure you like it. It’s not always beautiful out here. Some days there are rough seas, some people get sick, and for some people it’s just not for them. I would encourage youth to pursue it though. It’s a good way to get away from the news–you’re in your own little world out here. It’s a nice alternative lifestyle.
Do you have a favorite book?
I’d say Captains Courageous, by Rudyard Kipling. The 1937 film version was actually done in my hometown of Gloucester, Massachusetts. Gloucester is the oldest commercial fishing seaport in the United States. (The link will take you to some oral histories of Gloucester residents.)
XO Gibson considers a route using the nautical charts.
Laura Gibson, XO
Give us a brief job description of what you do on NOAA Ship Bell M. Shimada.
My job is the administrative side of the ship which includes staffing, budget, and spending a lot of time at my desk.
What’s your educational background?
I went to college in Myrtle Beach, South Carolina. I have a Bachelor’s in Science with a Geology focus.
What do you enjoy most about your work?
I enjoy the camaraderie of the crew. Sometimes we’ll play games. I have a good time and feel like I’m doing a fine job when they are having a good time.
What advice do you have for a young person interested in ocean-related careers?
If you’re not opposed to sailing, check it out; there’s a high demand. It’s not the easiest lifestyle for everyone. You could be very successful at a young age in a maritime career. There’s a clear path forward. I was a merchant mariner before sailing with NOAA. They call it coming up the hawse pipe when you learn on deck how a ship works. I didn’t go to an academy but learned on the job. I accepted a commission with NOAA as a junior officer and started on NOAA Ship Pisces in Mississippi 14 years ago. While on the Pisces I helped with the cleanup of the Deepwater Horizon oil rig disaster. I was proud to be a part of the fleet of vessels that supported the aftermath of that event.
Do you have a favorite book?
The Gunslinger or Misery, by Steven King. I’m a King fan.
Taxonomy of Sights
Apparently there are more marine mammal sightings in Southern California and fewer as you head north. However, there have been whale spouts sighted every day. Our Chief Scientist says the humpback sightings pick up near Vancouver Island and waters north–although Leg 3 doesn’t extend that far..
Day 8. Bycatch highlights: splitnose rockfish, a 43-lb squid, the egg case of a skate, and a single lamprey. In the evening: whale spouts from the flying deck, and an aerial show from a brown booby (a seabird not normally seen this far north; it may have been a sub-species called Brewster’s brown booby) attempting to land on the jack staff and then on the bow–with limited success in a 24 knot wind Day 9. Saw Humpback flukes as they dove. Day 10. Beautiful shades of ocean blue…
Brewster’s brown booby photo taken by Nick, OSU Marine Mammal & Bird Observer
You Might Be Wondering…
How’s the food?
I am told our Chief Steward, Ronnie Pimentel, is one of the best in the NOAA fleet. Ronnie and Rich Lynch (Second Cook) tirelessly serve up breakfast, lunch and dinner every day. Creamy breakfast grits, blueberry pancakes, pulled pork sandwiches, soups, peanut butter cookies, lamb chops, taco Tuesdays, pizza night, yuuuum. Ronnie has been with NOAA for a year, and prior to that served the Navy 21 years as a Steward. Ronnie spends about $15,000 a month on food, which varies depending on the length of the voyage. Food is stored in two freezers (one large, one small) and two chill boxes (one large, one small). He typically uses about 300lbs of frozen vegetables, and has about one case of each type of food, like one of apples, one of bananas, etc. Depending on the size and tastes of the crew he’ll pack 60lbs of bacon, and various cakes for tempting treats.
tasty dinner
tasty breakfast
Floating Facts
NOAA Corps is the eighth uniformed service in the United States, although it is not an armed force—Army, Navy, Air Force, Marines, Coast Guard, Space Force—and falls under the Department of Commerce, not the Department of Defense (DOD). Interestingly, the U.S. Coast Guard is not under the DOD either, but acts as a military branch and federal law enforcement agency within the Department of Homeland Security. The Public Health Service is the other unarmed, but uniformed service.
NOAA Corps has the same benefits and rank system as the military. Currently NOAA Corps has three admirals. Read more about one of the admirals here. Officers are “active duty” meaning they have full-time employment and may be directed to go where they are needed. The term “billet” refers to the current job in which an officer is placed. Members of the Corps do a rotation of two years at sea and three years on land.
Personal Log
I have clean clothes! While using the washer and dryer machines on Sunday I saw why cleaning the lint traps is taken so seriously.
Clean the lint trap, save lives
Washing machines and dryers
Humor is the best medicine, and a great way to reckon with being cooped up on a ship for two weeks with 33 people. While reading through some posted protocols in the acoustics lab I came across this gem in the last row of “Shimada Sonar Frequencies.”
Shimada Sonar Frequencies
Another bit of humor comes from the bridge, where there used to be eight camera buttons. For the record, there are NO torpedo tubes aboard NOAA Ship Bell M. Shimada.
Repurposed camera buttons
I am attempting to collect permissible items from the catch, such as hake young-of-the-year, to take back to my classroom and incorporate in lessons for students. In doing so, I’m getting a crash course in properly preparing wet specimens. My first lesson was that freezing is the best route until items can be processed. This site was helpful to me in figuring out what additional tools I needed to do it properly. While I brought several glass vials for collecting, I did not bring formalin, isopropyl alcohol, or needles. So, for the duration of the research cruise my specimens are in the freezer. I live close to my port of return and so have a personal vehicle to transport items home. For future Teachers at Sea: If you are flying, there are limits in checked baggage. There are also strict rules for shipping. Start your research about shipping hazardous fluids here with FedEx, or here in a publication from Oregon State University.
Librarian at Sea
Librarians specialize in acquiring, organizing, and disseminating information for their target populations. The NOAA Central Library provides access to seminars, journals, NOAA publications, and daily weather maps to name a few. Then there’s NOAA’s Photo Library, which has over 80,000 searchable images in its online database. If you type in “hake” there are 114 results. I anticipate incorporating both databases into future lessons for my students.
A squid and I contemplate life in the Wet Lab.
LampreyPorbeagle shark photo taken by Nick, OSU Marine Mammal & Bird Observer
Hook, Line and Thinker
The title of today’s post comes from Siletz Nee-Di, an endangered language spoken by some of Oregon’s First People. In 1977, The Confederated Tribes of Siletz were second in the nation and first in Oregon to regain federal recognition. What is now Newport, Oregon was originally home to villages and family groups of the confederation—whose descendants still live in the area.
NOAA Fisheries includes tribal, indigenous, and underserved communities in their strategic priorities for 2023. (See strategy 1.5 in the document available here.) Oregon’s Senate Bill 13 (Tribal History/Shared History) directs educators to include curriculum about contemporary indigenous communities. I am interested in knowing more how NOAA Fisheries partners with local stakeholders in Oregon.
If access to your family’s traditional fishing grounds—a primary source of food and revenue—were suddenly cut off, what would you do to regain entry to those waters?
Read about a Washington state tribal leader who fought for fishing rights and will soon have a U.S. Navy ship named after him.
“What’s good for the fish is what’s good for the people.”
Map of Ancestral Tribal Homelands along the Oregon Coast
Flag of the Confederated Tribes of Siletz Indians
A Bobbing Bibliography Favorite books among the science crew:
Nick – The Earthsea Saga, by Ursula K. LeGuin Ethan – The Snowball: Warren Buffett and the Business of Life, by Alice Schroeder Liz – A Sand County Almanac, by Aldo Leopold Jake – In the Name of the Wind, by Patrick Rothfuss Sam – Where the Crawdads Sing, by Delia Owens
Mission: Fisheries: Pacific Hake Survey (More info here)
Geographic Region: Pacific Ocean, off the coast of California
Date: July 10, 2023
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Weather Data from the bridge:
July 7 (1200 PT, 1500 EST) Location: 36° 00.4’ N, 122° 05.9’ W 16nm (21mi) West of Big Sur, CA
Visibility: 10 nautical miles Sky condition: Overcast Wind: 20 knots from NW 330° Barometer: 1013.1 mbar Sea wave height: 3-4 feet Swell: 6-7 ft from NW 320° Sea temperature: 14.0°C (57.2°F) Air temperature: 14.4°C (57.9°F) Course Over Ground: (COG): 323° Speed Over Ground (SOG): 10 knots
July 8 (1200 PT, 1500 EST) Location: 36° 34.5’ N, 122° 05.3’ W 17nm (20mi) Southwest of Monterey, CA
Visibility: 10 nautical miles Sky condition: Few clouds Wind: 19 knots from NW 330° Barometer: 1013.8 mbar Sea wave height: 5-6 feet Swell: 6-7 ft from NW 330° Sea temperature: 14.0°C (57.2°F) 13.7 Air temperature: 14.4°C (57.9°F) 14.3 Course Over Ground: (COG): 089° Speed Over Ground (SOG): 10 knots
July 9 (1200 PT, 1500 EST) Location: 37° 06.8’ N, 123° 00.5’ W 30nm (35mi) West of Pigeon Point Light Station, Pescadero, CA
Visibility: 10 nautical miles Sky condition: Overcast Wind: 13 knots from NW 332° Barometer: 1016.0 mbar Sea wave height: 2-3 feet Swell: 4-5 ft from NW 310° 4-5 Sea temperature: 14.3°C (57.7°F) Air temperature: 15.2°C (59.4°F) Course Over Ground: (COG): 093° Speed Over Ground (SOG): 10 knots
July 10 (1200 PT, 1500 EST) Location: 37° 26.7’ N, 123° 06.4’ W 32nm (37mi) West of Pescadero, CA
Visibility: 8 nautical miles Sky condition: Overcast, fog in vicinity Wind: 20 knots from NW 330° Barometer: 1015.9 mbar Sea wave height: 2-3 feet Swell: 3-4 ft from NW 320° Sea temperature: 14.5°C (58.1°F) Air temperature: 13.6°C (56.5°F) Course Over Ground: (COG): 314° Speed Over Ground (SOG): 3 knots
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Science and Technology Log
Me holding a Hake before sorting. After observation, we determined this was a developmentally mature female, measuring 50cm (20in) long!
In my July 6 blog post, I explained how NOAA Ship Bell M. Shimada is equipped to collect acoustic data in the form of echo grams. The acoustics team uses the data to determine if there are enough return signals to suggest fish are present and attempt a trawl. In this blog post, I will explain how we get the fish onboard, and what we do with the sample of marine life once it is collected from the net.
One question I had after learning about the acoustics and environmental DNA (eDNA) pieces of the survey mission was, “How does physically collecting and researching Hake samples fit into the puzzle of understanding their ecosystem and supporting sustainable fisheries?” (NOAA Fisheries quick facts and video here)
“While echosounders are useful, they do not provide certain quantitative data that researchers need to understand the ecology of these organisms and the midwater zone. To collect quantitative data, such as biomass, length and weight, and age class distributions, researchers must gather representational samples and take direct measurements of them. The best way to do this is by employing trawls.”
So, although acoustics and eDNA research is important to the overall survey, they are only pieces of the puzzle, and the puzzle is not complete without conducting trawls and physically researching samples. NOAA Ship Bell M. Shimada uses a midwater trawl net that is deployed from the stern over the transom, and towed behind the vessel. As the name suggests, midwater trawls occur in the middle section of the water column, versus surface and bottom trawls. The net is conical in shape and uses two metal Fishbuster Trawl Doors, and two sets of heavy chain links called Tom weights, in order to keep the trawl in the middle of the water column.
“The midwater region is especially important because the creatures that inhabit it constitute the majority of the world’s seafood. Understanding the ecology of midwater organisms and their vast environment can provide us with better information to manage these important natural resources and prevent their overexploitation.”
Deck department assisting in recovering the trawl net after a successful deployment.
Once the net is onboard, the net is emptied one of two ways depending on the size of the sample. For large samples, marine life is deposited into a hopper and subsequent conveyor belt. For smaller samples, the Hake will be put into a large basket then divided into smaller baskets of approximately 100 Hake each. Any other marine life like Salps, Myctophids, Pyrosomes, Rockfish, King of the Salmon, and small bony fish, etc. are recorded in the database and returned to the ocean.
“The ship’s wet lab allows scientists to sort, weigh, measure and examine fish. The data is entered directly into the ship’s scientific computer network.”
NOAA Office of Marine and Aviation Operations (OMAO): “Bell M. Shimada”
Large basket containing a sample of Hake with a few (red) Splitnose Rockfish.
NOAA Ship Bell M. Shimada’s Wet Lab with multiple scales, Ichtystick electronic measuring boards, trawl camera, vials for otolith (ear) bones, disposal chute, and tools including scalpels, tweezers, and knives.Wet Lab team member Maddie Reifsteck holding a Hake sample.Hake coming down the hopper ramp and onto the conveyor belt. Also in photo: Pinkish-brown Sea Pickle (Pyrosome) and translucent Salp.Basket of freshly caught Hake waiting to be sexed, sorted and have their length measured.Chemistry Lab team member Abi Wells using a scalpel to remove an organ sample from a Hake for further research of RNA.
With our boots and bright orange rubber pants and gloves on, our first task is to distribute the sample of Hake into baskets of about 100 each. Based on how many baskets we fill, a random selection of baskets will be kept, and the others will be returned to the ocean. With the remaining groups of Hake, we determine their sex and length.
In order to do this, we use a scalpel to make an incision on the underside/belly of the Hake. Once open, we are able to examine their organs, including the gonads to determine if the fish is male or female, and if they are developmentally immature or mature. Young Hake are difficult to sex, and it takes practice to get over any initial fears of cutting into an animal; let alone being able to locate and identify the gonads. Hake usually spawn in early winter, so many of the smaller Hake we sample from during the summer are age one or younger.
Our largest Hake thus far was a developmentally mature female, measuring 50cm (20in). In order to accurately and consistently measure the length of the sample, we use a waterproof, magnetic plastic board with metric (centimeter and millimeter) markings called an Ichthystick (think: high-tech meter stick). The fish is placed on the board with its mouth touching the black board at 0cm, then a magnetic stylus is placed at the fork of the fish’s tail. Once the magnetic stylus is placed on the board, the length to the nearest millimeter is displayed on the LCD screen and automatically entered into the database program. The length data is grouped with the date, time, and identified sex for later observation and comparison.
Additional information, abstracts and outline about Ichthystick here
Ichthystick’s LCD display, motherboard, magnetic board, and magnetic stylus. Digital scale in background.
An even smaller subgroup is then selected and examined to record weights of individual Hake, collect ear bones called Otoliths for aging, stomach samples for diet, liver for RNA, and ovaries for maturity development. Otolith bones help determine the age of the Hake because they grow a new “layer” of bone each year, similar to coral structures and annual tree rings. Organs and bones removed from the Hake are sent to NOAA Fisheries centers for analysis and included in databases with the date, identified sex, length, weight, and location in which they were collected.
This data is used to build more of the puzzle, along with acoustical information, water samples, and eDNA data in order to further understand the ecosystem, biomass, diet, and
“support sustainable populations of Pacific hake on the West Coast.” (…) “It provides vital data to help manage the migratory coastal stock of Pacific hake. The hake survey, officially called the Joint U.S.-Canada Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey, occurs every odd-numbered year.”
Although this subtopic of explaining the Integrated Ecosystem and Pacific Hake Acoustic Trawl Survey is a bit easier to understand than my July 6 Acoustics Lab post, it certainly does not mean it’s an easy task!
When I had a tour on July 4, I remarked how clean and organized the Wet Lab is. I hadn’t see it in action yet, but noticed how everything had its place and use. On July 6 we conducted our first trawl and collected a sample of 11 baskets of Hake (approximately 1,100 Hake since we group about 100 Hake together in each basket.) From that sample, we kept four baskets and counted, sexed, and measured 541 Hake.
Five of us were working together in the Wet Lab for that haul. I’ll admit I probably didn’t sex 100+ Hake. It took a few minutes of watching the others carefully and swiftly cut into the underside of a fish, open the two sides, and know what to look for to determine the sex of very young Hake. Eventually I found the courage to slice in and take a look. By the fourth or fifth Hake, the uneasiness had subsided and I found the process very interesting and educational. Although young samples are hard to sex as they are often undeveloped, the others encouraged me and answered my questions and guesses with enthusiasm and support.
While working on measuring the lengths of our samples, one Science Team member paused and remarked how beautiful he found the fish. Although they do not have vibrant, bold colors, shimmering scales, or anything else particularly remarkable, he found the beauty in them. He digressed into a conversation of their role in the ecosystem, how they are living and breathing creatures, and how they probably all have their own personalities and slight physical differences. I noticed some of their eyes were shiny and sparkling, and how their faces and expressions were noticeably unique the more you looked. That “down to earth”, heartfelt discussion was very special and demonstrated how the crew respects the process of catching and sampling Hake, while keeping each other and marine mammals safe.
From the NOAA Corps Officers, to the deck department, to the engineers, electronics, science team, survey team, galley crew, volunteers, and everyone in between; the crew on NOAA Ship Bell M. Shimada is special. They take pride in their vessel and job, and always seem to have a smile and kind greeting. Being away from land and loved ones for weeks and months at a time will certainly take a toll on the body and mind, but this team is there for each other. To all of the crew, thank you for making me feel so welcomed and appreciated. We’re almost halfway through the mission, and as tired as I may get after (sometimes) 12+ hour days, I sleep well knowing the crew trusts their vessel and each other; and look forward to learning and becoming more and more acquainted each day with the people that make this mission possible. Thank you!
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Did You Know? (FAQs)
1. Are you finding schools of them?
We’ve had seven successful trawls out of nine attempts for Pacific Hake fish. They often come with pyrosomes (Sea Pickle) myctophids (Lanternfish), and salps in the net too. Some trawl attempts are successful without a hitch, but more often than not we have to restart our Marine Mammal watches a few times before deploying in order to keep our ocean life safe and not get tangled in the net. Two trawl attempts have been abandoned because of the amount of persistent marine mammal life and playfulness near the ship. (I think they know we’re watching and show off for our cameras.)
2. What’s your average depth?
The transects (Set and numbered longitudinal east-west lines NOAA Ship Bell M. Shimada navigates on while collecting acoustic data) usually range from 50m – 1,500m (164ft – 4,921ft) in depth.
However, right now one of the displays in the Acoustics Lab, the depth reading is 3,240m which is about 10,630ft or just over two miles deep!
This depth is only 1,870ft shallower than the wreck of the RMS Titanic!
(We were on a long transect, we do not often see depths this great.)
3. Have you gotten seasick? Seasickness should subside after about 3 days.
I’ve never gotten seasick thankfully! Knock on wood and all the other premonitions, please.
4. What is the Hake role in the ecosystem?
More info on this coming in later posts after explaining our Chemistry lab and technology aboard!
However, as predators, they can be cannibalistic towards their own kind.
As far as their role in human consumption: They are often used as a substitute for Cod and Haddock, and in fish sticks and imitation crab meat.
June 2, 2019 Game Plan and Trawling Line: 5 hauls in the Piedras Blancas Line near San Simeon, CA. Piedras Blancas is known for its Northern elephant seal colony, M. angustirostris. Hauls were conducted outside of the marine reserve and we did not encounter seals.
Catch Highlights: The night started off with excitement when Keith Sakuma brought in an Pacific electric ray, Torpedo californica, and we all got to see it up close before releasing.
Chief Scientist Keith Sakuma holding a Pacific electric ray, Torpedo californica
In Haul 3 we collected a pelagic octopus, Ocythoe tuberculata, shown below. Chromatophores in cephalapods, including squid, cuttlefish and octopus, are complex organs made up of both muscle and nerve and provide the ability for the animal to rapidly change its skin color in order to blend into the surrounding environment to avoid predation, communicate, or send a warning signal. It was impressive to watch the chromatophores at work as the pelagic octopus attempted to blend into the white background of his tank by turning white (see photos below) We released it back to the sea.
Pelagic octopus (Ocythoe tuberculata) attempting to camouflage with the background and flashing white
Pelagic octopus (Ocythoe tuberculata) with chromatophores expressing orange, purples and pinks. The beak is exposed here.
The differences in skin coloration of the five primary squid species we are catching including Boreal Squid, Blacktip Squid, Unknown Squid, Gonadus Squid, and Market Squid (see image below) are noteworthy. While living market squid exhibit brown, pink and purple skin color (see image below) the Chiroteuthis squid tentacle displays orange and red chromatophores (see image below).
Common squids in our catches. From top to bottom, Boreal Squid, Blacktip Squid, unknown species, Gonadus Squid, and Market Squid.
Living market squid exhibiting brown, pink and purple chromatophores.
Pink and purple chromatophores on the mantle of a market squid.
Orange and red chromatophores on a tentacle of the Chriroteuthis squid.
In Haul 4 we collected a Cranchia scabra, which Chief Scientist Keith Sakuma calls the “baseball squid” or glass squid whose body is covered with tubercles (brown spots on mantle in photo below). This animal attempted to hide from us by turning white, retracting its tentacles and inflating himself into a ball, somewhat resembling a baseball. After a few pictures, we released it back to the sea.
Cranchia scabra or “baseball squid”
Another exciting deep-sea creature, the Pacific hatchet fish, Argyropelecus affinis, was collected in a bongo net deployed prior to CTD, for Dr. Kelly Goodwin’s eDNA research. The fish we collected below still has intact blue scales due to being well preserved in the bongo. The hatchet fish lives in mesopelagic zone down to 2000 m depths where the CTD sensors recorded a temperature of four degrees Celsius! Hatchet fish have upward facing eyes and mouths and swim up to the the epi-pelagic zone at night to feed on salps and krill.
Pacific hatchet fish, Argyropelecus affinis
Kelly conducted a quick surface bucket dip prior to CTD deployment in which we found a small (~2 inch) siphonophore, which I was very excited about since this was my first one to ever see in person! Siphonophores are colonial Cnidarians composed of individual animals called zooids. Moss Landing Graduate Student Kristin Saksa and I were able to confirm the identification of this beautiful creature as a siphonophore using an invertebrate field guide that Keith Sakuma brought on board. Perhaps due to the temperature change from being in the sea to being observed in a cell culture dish under the microscope, the siphonophore broke apart into its individual zooids right in front of my eyes. See before and after photos below.
Intact Siphonophore colony from bucket dip, note tip or “hat” at the bottom on the animal.
Siphonophore individual zooids appear as semi circles consisting of small brown semi-circles.
Tonight I was also able to observe living salps that were pulled up in the bongo net and take a video. It was neat to see the salps pulsing.
Haul 5 was a massive haul full of pyrosomes, Pyrosoma atlanticum. Kristin Saksa volunteered to stir the bucket of pyrosomes (using her arms) so that we could obtain an accurate distribution of organisms for the initial volume count and analysis. As I video of this event (see stills from the video below), we were all laughing and realized that Kristin may be the only human on Earth who has ever stirred pyrosomes.
Kristin Saksa stirring a bucket full of Pyrosoma atlanticum
Kristin Saksa stirring a bucket full of Pyrosoma atlanticum
In haul 5 we were surprised to find a Giant 7-armed Atlantic octopus, or blob octopus. Keith Sakuma explained that the males have 7 arms as the fifth is a sex appendage whereas the female has 8 arms. After photographing this beautiful deep-sea octopus, we released him back to the sea.
Giant Seven-Armed Atlantic Octopus or “blob octopus”
June 3, 2019 Game Plan and Trawling Line: 5 hauls Outside Monterey Bay
Catch Highlights: Two of the hauls produced a lot of krill. The hauls had a high species density with a lot of myctophids, salps and blue lanternfish. Such hauls are time consuming to sort so as not to overlook something new and small. In one of the hauls we found a new-to-me myctophid called Nanobrachium. I dissected some of the fish and found that CA lanternfish and Northern anchovies were full of eggs, and their age/reproductive status was previously unknown.
A catch with a high krill count
We caught 2 young ocean sunfish, Mola mola. Both were immediately returned to the sea.
Scripps Graduate Student Kaila Pearson with a young ocean sunfish, Mola mola.
LTJG Keith Hanson with a young ocean sunfish, Mola mola.
We found several species of deep sea dragonfish which we arrayed below on a ruler. Most of these fish are less than 6 inches long, no bigger than a pencil, but they are equipped with sharp fangs and are apex predators in their realm! Dragonfish have large bioluminescent photophore organs underneath their eyes (and sometimes lining their bodies) which produce light and are used to attract or deter prey and attract mates.
All of the dragonfish caught on June 3, 2019 on the NOAA Ship Reuben Lasker.
Longfin dragonfish, Tactostoma macropus, on left and a Pacific black dragon, Idiacanthus antrostomus, on right. Also in the photo are a krill (on the left of the dragonfish) and a Gonatus Squid (top left corner of photo).
Longfin dragonfish, Tactostoma macropus, with large photo organ underneath the eye
We collected a stoplight loosejaw, Malacosteus niger, which can unhinge its jaw in order to consume large prey.
Stoplight loosejaw, Malacosteus niger.
Face of stoplight loosejaw, Malacosteus niger.
June 4th: Davenport Line
The highlight of today was at 5:45 P.M. when team red hats went to the flying bridge for our workout and to hang out with Ornithologist Brian Hoover. There was a lot of Humpback whale activity. I counted around 20 spouts. We observed one whale that flapped its tail against the sea surface around 45 times in a row, perhaps communicating to nearby whales by generating pulses in the water or creating a visual cue. We saw several full breaches. We finished up the Davenport Line at 6:00 AM as the sea became rough. Thanks goodness for handrails in the shower.
The sorting team, aka Team Red Hats. From left: Kristin Saksa, Flora Cordoleani, Karah Nazor, Ily Iglesias, and Kaila Pearson.
June 5th: Outside of Tomales Bay
I woke up at 4PM and headed to the galley for dinner at 5PM. The boat was rocking so much that I became dizzy and knew that I would become sick if I tried to eat dinner, so I headed straight back to bed. Around 9PM the sea seemed to have calmed a bit, but I soon learned that it only felt calmer because the ship was traveling in the same direction as the swell at the moment but that we were about to turn around. Due to the rough conditions, the first haul inshore at Tomales Bay was delayed until midnight so the fish sorting team decided to watch “Mary Poppins Returns” in the galley. The talented chefs of the Reuben Lasker made the most amazing almond cookies today and, thankfully, temped me to eat again.
Catch Highlights: Haul 1 at station 165 was one of the easiest and most exciting catches of the survey so far because we collected a lot of jellyfish – my favorite! We counted 66 West Coast sea nettles, Chrysora fuscescens, seven Northern anchovies (7) and 24 market squid. I actually have a tattoo of West Coast sea nettle on my ankle. We placed the jellyfish flat on the lab bench and quickly measured their bell diameter before returning them to the sea. They did not sting us as most of the nematocysts were likely triggered during haul in. I removed a rhopalia, a sensory structure that lines the margin of the bell of Syphozoans (the “true” jellyfish). West Coast sea nettles have eight rhopalium which house the the ocelli (light sensing organ) and statolith (gravity sensing organ). A photomicrograph I took of the rhopalia under the dissecting microscope is below.
Teacher at Sea Karah Nazor measuring a West Coast sea nettle Chrysora fuscescens.
Karah Nazor examining a West Coast sea nettle, Chrysora fuscescens.
Scripps graduate student Kaila Pearson examining a West Coast sea nettle, Chrysora fuscescens.
Moss Landing graduate student Kristin Saksa examining a West Coast sea nettle, Chrysora fuscescens.
Photomicrograph of the ocelli or light sensing organ in the rhopalia of a West Coast sea nettle, Chrysora fuscescens.
Haul 2 mostly consisted of Northern anchovies, 1 krill, a few moon jellyfish, Aurelia aurita, a few squid, which made for another very short and easy sort (see photo below). I study moon jellyfish in my lab back at McCallie High School, so I was curious to look inside of the stomach and reproductive organs of these wild jellyfish. Under the dissecting microscope, eggs were present and were purple in color (see photomicrograph below).
Photomicrograph of purple eggs and clear gastric filaments of the moon jellyfish, Aurelia aurita
Kaila Pearson (left) and Karah Nazor and Keith Hanson sorting Haul 2.
Haul 3 had a lot of krill, young of year (YOY) Pacific hake, Merluccius productus, one large hake, and a few market squid. This sort was also super easy except for separating the small YOY Pacific hake from the krill.
Sorting of haul 3 which had a lot of krill and young of year (YOY) Pacific hake, Merluccius productus.
June 6th: Outside Farallones. On our final night, we conducted three hauls with very small harvests consisting of few organisms and low species density. One new to me fish in the final catch was a top smelt fish (see image below). These were the three easiest sorts of the survey. It was suggested by Keith Sakuma that the catches were small due to the stormy conditions.
A small catch from the last night June 6, 2019, with one West Coast Sea Nettle, a Gonatus squid, and two topsmelt silversides, Atherinops affinis.
Moss Landing graduate student Kristin Saksa with a topsmelt silverside, Atherinops affinis, from the final haul of the survey.
June 7, 2019: Return to San Francisco
In front of the Golden Gate Bridge at the conclusion of the cruise. From left: Brian Hoover, Kelly Goodwin, Ily Iglesias, Karah Nazor, Flora Cordoleani, Kristin Saksa, Lauren Valentino, and Jarrod Santora.
In front of the Marin Headlands at the conclusion of the cruise. From left: Ily Iglesias, Kristin Saksa, Flora Cordoleani, Kaila Pearson, Lauren Valentino, and Karah Nazor.
