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.
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.
Certain fish that we collect have samples of their fins collected for DNA testing. For example, if a Spotfin Butterflyfish (Chaetodon ocellatus) is brought up in a trap, a small pair of scissors are used to clip a portion of its anal fin in order to obtain a sample that is then place in a micro-test tube containing a buffer. Back in the on-shore lab, technicians will obtain the DNA, which is then used to determine the genetic make-up of the population in a particular area.
Fin clip sample from Spotfin Butterfly fish. (photo by David Knight)
One may assume that the genetic make-up of a population is uniform across the east coast, after all, fish can swim, right? However, that is not necessarily the case. Changes in the frequency of particular alleles create spatial differences in some stocks of fish over a broad area. In other words, there may be slight genetic differences in a population of Gray Triggerfish off of the coast of North Carolina compared to those found in the waters of Florida.
Why does this matter? Currently, the management of most fish occurs over a broad area, often including many states. By understanding the slight differences that may be present in a smaller subset of a population, scientists can create better, more accurate management plans instead of a “one size fits all” model.
Gonads.
As written in an earlier blog, many fish in this region are sequential hermaphrodites and change sex during their life-time, starting off as females, then changing to males. By taking the gonads of certain species, scientist can determine if the fish is male or female, and taken together with size and age, it is possible to estimate when these fish are transitioning from one sex to another.
Ovaries from a Vermilion Snapper – I made a small incision so you can the eggs. (photo by David Knight)
By sampling the ovaries of fish, it is possible to estimate the fecundity of the species. Fecundity is the reproductive potential an organism possesses. The number of eggs in an ovary can be estimated and then, taking the age and size data of the specimen, it is possible to predict the potential a population has for growth. Many factors, such as the number of males in a population and the season, can influence the reproductive behaviors of fish, so sampling the gonads provides an additional pieces of data.
Finally, sampling the gonads of fish can help determine the sex ratio in the population. In fish that display sequential hermaphroditism, such as the Black Sea Bass, the number of males in the populations increase with age.
Question: Fisherman will be able to get more money for larger fish, so naturally they will want to “select for” larger fish, potentially decreasing the number of reproductive males in the population. If the number of large, reproductive males in a population decreases, then more females will transition to become male.
What may happen to the average age of sex transition in sequential hermaphrodites?
Diet.
A select few species have their stomach contents sampled. If we know what a particular species is eating, then we are able to understand the trophic interactions within the ecosystem much better. An ecosystem-based management plan will look at the interactions taking place between the many prey and predator species, whom are often competing for the same resources. Because the diverse species in an ecosystem are inextricably linked, an increase in one species is likely to affect the other. If one species is over-fished or not reproducing at its potential, this may create a ripple effect throughout the ecosystem.
Red Snapper (Lutjanus campechanus). I performed a gastric dissection to sample stomach contents (photo by David Knight)
Close up of stomach contents. Remember those Tomtate Tornados? There are now two fewer Tomtate to measure! (photo by David Knight)
Personal Log
The food on board the NOAA Ship Pisces has been great. The Stewards, Rey and Dana, have kept us well fed with a variety of great meals. We’ve had everything from hot dogs and hamburgers to bacon wrapped filet mignon and shrimp, and a crew favorite, Taco Tuesday! Meal time is very important because not only is the crew refueling for work, but it affords them a chance to sit down, talk, and to catch up on Chip and Joanna Gaines’ newest “Fixer Upper” on the TV that runs continuously. The first day on board, Operations Officer, Lieutenant Jamie Park, told me that any NOAA ship runs on two very important things: 1) diesel fuel, and 2) COFFEE. The galley is open 24-7 with snacks and drinks always available since crew members are working in shifts, with some getting off at midnight or 4 a.m.. And…., I recently found the freezer that contains Klondike Bars, popsicles, ice cream, and Hot Pockets.
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Did You Know?
The Red Snapper (Lutjanus campechanus) gets its name from its enlarged canine teeth. According to the 2016 stock assessment of South Atlantic red snapper, the stock is overfished and subject to overfishing, but is rebuilding. Management plans in the South Atlantic and Gulf of Mexico place annual catch limits on both commercial and recreational fisherman to decrease the pressure on the fish, as well as minimum size restrictions to protect young and juvenile snapper. Red Snapper can live over 50 years and are of reproductive age as early as two.
Range of Red Snapper-South Atlantic (NOAA)
Sites where traps were set. 32 nautical miles southeast of Cape Fear, North Carolina. Blue indicates deep water, Red indicates more shallow water. (image by Nate Bacheler)
