CTD – Page 3 – NOAA Teacher at Sea Blog

August 17, 2023August 18, 2023

Gail Tang: Contemplating the Enormity of the Minuscule, August 14, 2023

NOAA Teacher at Sea

Gail Tang

Aboard NOAA Ship Oscar Elton Sette

August 4, 2023 – September 1, 2023

Mission: Hawaiian Islands Cetacean and Ecosystem Assessment Survey (HICEAS)

Geographic Area of Cruise: Hawaiian archipelago

Date: Tuesday August 8, 2023

Weather Data from the Bridge

Temperature: 27.06° C

Latitude: 29°53’0” N

Longitude; 174°24’0”W

Science and Technology Log with Career Highlights

Previously, I wrote about the day-time operations focused on surveying whales, dolphins, and birds. Through the 25-powered binoculars (big eyes), the large mammals in the distance look microscopic. Now, the sun has set and I take us underwater to learn about the tiny world of ichthyoplankton, magnified to reveal intricate details of their exquisite structures.

Weather permitting, Nich Sucher (Survey Technician) works with the deck crew to deploy the CTD, which measures conductivity, temperature, and depth. This information is used to help scientists understand the physical, chemical, and biological changes of the ocean to help inform them of environmental changes. For example, Nich explained that data from CTDs are used to better understand why tuna were migrating away from Hawaii and towards California. The data can help answer whether the tuna are moving north for access to more oxygen in the water or for cooler temperatures. On our project, we deploy the CTD down to 1000m because that is where some of our deep diving cetacean species feed. Also, the temperature & pressure affects how sound travels through the water. This information can be used to calculate the speed of sound at different depths.

a view down the starboard rail of NOAA Ship Oscar Elton Sette. We see Logan, wearing a hard hat and life vest and facing away from us, lean his right arm over the rail. He looks down at the water as the CTD apparatus descends below the purple-blue surface of the water. In the distance, the sun has just set over the horizon, leaving orange, yellow, pink, purple skies dotted with a few scattered clouds. — Logan Gary (Able-bodied Seaman) deploys the CTD at sunset. Photo Credit: Gail Tang

Nich wanted to work for NOAA since he was in middle school! In high school he fell in love with fish. Initially he went to college in Iowa for soccer and then transferred to Carthage College, in Kenosha, Wisconsin to study environmental science, conservation and ecology. Nich did an independent study with his aquatic ecology professor on a coral reef project in Roatan, Hondurus. His senior thesis investigated the feasibility of releasing captive-bred axolotl (an adorable salamander that’s critically endangered and possibly extinct in nature) into the wild. After college, he had a job at an aquarium, and while he temped at US Fish and Wildlife studying chub and salmon, NOAA reached out about his job application. He started in January 2022 on the NOAA Ship Oscar Elton Sette!

Nich, wearing a hard hat, life vest, and an illuminated flashlight attached to his vest, looks straight at the camera as he holds up with both hands a styrofoam head decorated with marker designs and compressed (by water pressure) from its original size. — Nich Sucher (Survey Technician) with recently pressure-shrunken styrofoam head. Photo Credit: Fionna Matheson (Commanding Officer)

Since the CTD is deployed to 1000m, a common extracurricular activity is to attach styrofoam objects to the instrument because they shrink as a result of the pressure! On a previous leg, Commanding Officer Fionna Matheson shrunk a styrofoam head, which can be seen in the picture of Nich above. A few of us shrunk decorated styrofoam cups.

photo of a hand holding up a full-size styrofoam cup, upside down. it's decorated with many triangles drawn in black marker. the rim of the cup reads HICEAS 2023. we can see a view of a deck beyond. — Regular-sized styrofoam cup with Sierpiński’s Triangle Design

photo of a hand holding up a compressed styrofoam cup, upside down. it's decorated with many triangles drawn in black marker. the rim of the cup reads HICEAS 2023. we can see a view of a lab beyond. — Regular-sized styrofoam cup with Sierpiński’s Triangle Design

a hand holds up a stack of four upside-down compressed styrofoam cups, decorated, top to bottom, as purple design, smiley face, triangles, orca with hearts. — Artist of the cup from top to bottom: Jennifer McCullough (Lead Acoustician), Erik Norris (Acoustician), Gail Tang (Teacher at Sea), Alexa Gonzalez (Acoustician). Photo Credit: Gail Tang

The whole process of the CTD deployment and retrieval takes about an hour to an hour and a half. The Isaacs-Kidd Midwater Trawl (IKMT) net tow usually follows. Jessie Perelman and Dre Schmidt are the plankton researchers on board this leg of HICEAS. Most nights, we do 2-3 tows of the net. (They are affectionately called a “tow-yo” because the net gets towed in and out several times.) They use an inclinometer, a.k.a. angled angle, to measure the angle of the line (see picture below) and then confer with a chart to determine the length of the line needed to reach the desired depth. The chart is a good way to avoid on-the-spot trigonometric calculations. But it’s a good exercise to ask yourself anyway: if you know the desired depth and the angle, how would you calculate the length of the line needed?

Dre stands on deck at night, facing away from the camera, over the rail. She wears a jacket, a life vest, and a hard hat. Beyond her, we see a davit arm leaning over the water and a cable (attached to the net) extending at an angle off to the right. With her right arm, Dre holds out an angled angle - it's a metal semicircle, like a protractor, with a swinging arm attached at the center point of the straight edge. Dre holds it by a handle, lining the straight edge parallel to the extended cable. The swinging arm hangs straight down to the ship. Dre can read the resulting angle in the markings on the semicircle. — Dre Schmidt measuring with the angled angle. Photo Credit: Gail Tang

After the tows, we bring the larvae into the wet lab and the fun begins. The goal is to sort out the fish larvae from the other larvae. Truthfully, I am not very good at sorting the fish and I just like to look at the organisms under the microscope. The most awe-inspiring creatures I saw under the scope were the shelled pteropods (sea butterflies) and a juvenile sea star that, according to Dre, may have recently morphed from the larval stage. With the naked eye, they look like marks made with a sharp pencil, but under the scope, the enormity of their existence is profoundly moving. While I could not capture these beauties in a photograph, I was able to capture other creatures.

view through a microscope of a phronima animal living inside a (clear, jelly-like) salp. — Phromina living inside a salp. Photo Credit: Gail Tang

view through a microscope of a tiny squid and a polycheate worm. — Phromina living inside a salp. Photo Credit: Gail Tang

view through a microscope of a tiny squid surrounded by other, unidentified organisms. the squid's large purple eyes stand out. — Squid

Personal/Food Log with Career Highlights

As I fall into a daily routine, I periodically need small bits of irregularity for stimulation. This week, I was privileged enough to work with Chef Chris. Chef Chris is originally from north Philadelphia. In the absence of cable during childhood, he watched cooking shows like Yan Can Cook, Frugal Gourmet, and Julia Child on PBS. He started off cooking on NOAA Ship Rainier and now is the Chief Steward on NOAA Ship Oscar Elton Sette. We collaborated to make some pork dumplings and vegetable spring rolls for everyone. I cook at home often, but not for so many people, so Chris was essential in helping me scale up the dishes. We bonded over not measuring out ingredients so here is approximately the two recipes we used.

Chris, wearing a black chef's cap, stands at a large fryer in the galley. he's cooking three foods - eggs, pork, onions in large piles - and he reaches toward them with a spatula or perhaps a large knife. — Chief Steward Christopher Williams cooking the eggroll fillings. Photo Credit: Gail Tang

Pork Dumpling Filling

5 lbs of ground pork (when my mom makes these, we use a mix of lean ground pork and fatty ground pork)
Mirin (I use Shaioxing wine, but mirin is a good substitute!)
Soy sauce (we used Kikkoman; I like to use Pearl River Bridge Light Soy)
Green onions
Sugar

a plateful of prepared (but not yet friend) pork dumplings — The most gorgeous dumplings

a cafeteria-style pan of perfectly fried pork dumplings — The most gorgeous dumplings

Egg Roll Filling

Green cabbage
Red Cabbage
Carrots
Mushrooms
Soy sauce
Hoisin

a sheet pan of about 30 wrapped but uncooked egg rolls — Freshly wrapped vegetarian egg rolls

a cafeteria style pan of fried egg rolls — Freshly wrapped vegetarian egg rolls

Several of us worked together to help fold the dumplings and egg rolls. I delighted in the number of different hands that contributed to feeding our community. Chef Chris expertly cooked everything and it was all gobbled up!

Chris and Gail, sitting across from one another at a table, each hold up a freshly-rolled dumping to show off. we can see a large metal bowl of pork filling on the table between them. — Chef Chris Williams and Gail Tang

Four people around a table in the mess with a plate full of wrapped dumplings and dough circles and a bowl of pork filling. — Chef Chris Williams and Gail Tang

four people around a table wrapping egg rolls; there's a large bowl of filling, a tray of completed rolls, and two rolls in progress. — Gail Tang, Octavio De Mena, Jamie Delgado, Jessie Perelman rolling eggrolls

At night, I assist Jessie Perelman and Dre Schimdt with their plankton research. They were the first to come by to help fold dumplings. Jessie did her undergraduate work in biological science at University of Southern California (USC) with a plan to go to veterinary school. She worked in a marine science lab at USC, and then studied abroad in Australia to take more marine biology classes not available at USC. After she graduated, she got a job as research assistant at Wood’s Hole Oceanographic Institution, where she solidified her passion for research. She applied for graduate school and ended up at the University of Hawaii studying biological oceanography. Her dissertation focused on oceanographic influences on mesopelagic communities across eastern Pacific Ocean using insights from active acoustics, nets, and other sampling techniques. An interesting interdisciplinary part of her background includes learning about international policy on issues like deep sea mining. The international meetings with delegates were very informative for her. She’s also worked on science communication writing, such as science blogging. In Fall 2022, Jessie started as a Marine Ecosystem Research Analyst at NOAA!

Dre Schmidt received her bachelors in biology at Florida State University. She took Calculus, Mathematical Modeling for Biology, Analysis and Statistical Design, and Physics to supplement her biology degree. She volunteered at a research lab on campus and after college, took a couple of years off to work in marine science education for 5th grade to college level students. She went for her master’s degree in Kiel, Germany to study physiological effects of low-level warming on coral and their larvae. She has been at NOAA for 2 years, first as a research associate and now as an essential fish habitat coordinator. What she loves about her job is the variety of responsibilities. She keeps busy by sorting plankton, doing genetics lab work, analyzing data in R, writing up results, and going to sea! Engaging in these different tasks help to activate different parts of the brain, which I can totally relate to! Her advice to students is to know your worth and ask for what you deserve. Her favorite fish larva is the very ugly Centrobranchus andreae simply because her name is found within the name of the organism. I can’t blame her because my favorite flower is the Gaillardia for the same reason.

Andrea, wearing a mask, stands for a photo in front of a screen displaying a larval fish — Andrea with Andrea

Matt Benes (Able-bodied Seaman and Deck Boss) took a break in his duties to fold some dumplings with us. Though Matt declined to be interviewed, I can tell you we share a deep appreciation for food as a mechanism for cultural, historical, and political understanding.

Jamie Delgado (Medical Officer) joined in on the egg roll wrapping. Jamie received her bachelor’s in science and nursing at Rutgers University. She joined the Public Health Service (PHS), and worked at the Indian Health Service (IHS) in northern Arizona. Later, she worked at the National Institutes of Health (NIH) as a research nurse specialist. Jamie earned her Doctor of Nursing at University of Maryland before coming to NOAA as ship medical officer. Jamie has so much good financial advice about scholarships and loan repayments programs. Check out these links to learn more:

She also shared that you can retire in a total of 20 years with uniformed services, you get a pension, healthcare benefits, a housing allowance, a food allowance, 30 days paid leave, and unlimited sick leave. Jamie has been in service for 10 years, and with NOAA for 1 year and 5 months.

Jamie also helped me out during our in-port during Leg 1. Snorkeling had dislodged some ear wax and clogged my ear for a couple of days making daily life really uncomfortable. Jason Dlugos’s (3rd Assistant Engineer) “ear beer” helped, but I was still off balance. Jamie had to endure the task of flushing my ear out over the course of two days. Eventually, I did have to go to urgent care to get the rest out. Now I’m 100%!

Last but never least, Octavio De Mena, a.k.a OC, (General Vessel Assistant in the Deck Department) came by to roll some egg rolls. He is originally from the Republic of Panama and loves classic rock music. While we have no intersection in our movie tastes, we share some similarities in the food we ate growing up due to the large Chinese population in Panama. According to the Harvard Review of Latin America, the first Chinese immigrants arrived in Panama in 1854 to build the Trans-Isthmian Railroad. The inhumane treatment and disregard for the workers’ welfare is reminiscent of the situation a decade later with the Transcontinental Railway in the United States. This convergence of cultures led to haw flakes and dried plums in both our childhoods!

OC was an aircraft mechanic in the military reserves, and a security contractor in Latin America. He decided to come back to the U.S. to fulfill his dream job as a professional mariner. On his journey in pursuing his dream, he volunteered for the civil air patrol, and served as an auxiliary for search and rescue flying small Cessnas. He saw a NOAA ship at this job which prompted a search for a position within NOAA. He has been on the NOAA Ship Oscar Elton Sette since February 2023. On the ship, OC and I are regulars in the forward mess. Sometimes having opposite tastes works out in your f(l)avor, as I get to eat OC’s tomatoes and watermelon jolly ranchers.

Did you know?

You can track us! Visit this site to see where we currently are: https://www.windy.com/station/ship-wtee?26.549,-172.551,5

August 9, 2023August 10, 2023

Germaine Thomas: The Adventure Begins Aboard NOAA Ship Oscar Dyson, August 7, 2023

NOAA Teacher at Sea

Germaine Thomas (she/her)

Aboard NOAA Ship Oscar Dyson

August 7 – August 21, 2023

Mission: Acoustic Trawl Survey (Leg 3 of 3)
Geographic Area of Cruise: Pacific Ocean/ Gulf of Alaska
Date: Monday August 7, 2023

Weather Data
Lat 58.31 N, Lon 151.58 W
Sky condition: cloudy
Wind Speed: 12.43 knots
Wind Direction: 357.55°
Sea Wave height: 1 ft | Swell: 340°, 1-2 ft
Air Temp: 12.35 °C

Science log

The purpose of this trip is acoustic trawl sampling for pollock (Gadus chalchogrammus). There are other projects that people are working on during this leg that I will report on in other upcoming blogs.

Today, at about 5:30 pm we deployed a CTD (Conductivity, Temperature and Depth – Probe). This probe measures the salinity using conductivity, the temperature with a digital thermometer, and records the data all at different depths in the water column. This CTD also records fluorescence which is an easy way to determine the amount of plankton present. The plankton at the surface are producers and have chlorophyll, which reacts to fluorescence and can be recorded. This information will be important when we start taking trawl samples, so the ships crew will routinely send out the CTD while we cover our transects.

Watch the videos below of the crew members deploying and recovering the CTD.

Crew members deploying the CTD

Recapturing the CTD

The data from the CTD collection are shown on the picture of the computer screen below:

a photo of a computer monitor showing a screen with three graphs in a row. The first depicts fluorescence (indicating chlorophyll levels) and turbidity v. depth. Chlorophyll levels start out high toward the surface but asymptote toward zero as the probe travels deeper. The central graph is blank. The third depicts salinity and temperature v depth. Salinity stays largely constant, but it does gradually increase with depth. Temperature is higher toward the surface, declines quickly and then slowly with depth. — CTD Data: Fluorescence, or Chlorophyll (green) and Turbidity (orange) v. Depth on the first graph, and Salinity (yellow) and Temperature (blue) v. Depth on the third graph.

The data from the CTD are presented in graphical form. The first frame shows chlorophyll, which is the green line. The second frame is percent oxygen (which they were not measuring so it remains zero). The third frame shows salinity (yellow line) and water temperature (blue line).

Personal log

Currently we are cruising out to our transect destinations over the continental shelf. The seas are a little rough (6-8 foot waves) and I am enjoying some saltine crackers that help with mild sea sickness. It has been a while since I have been in a large boat in rolling seas.

Three days ago, I flew from Anchorage to Kodiak Island on an a sunny afternoon and met the science team for the cruise. The whole team was extremely welcoming, sharing stories of past cruises, colorful characters and the science behind acoustic trawl sampling. Later, they invited me to go surfing the next day at a beach on the far side of the island.

Through the camaraderie of playing in the waves I was introduced to these amazing people and their knowledge and love of the ocean. They are very professional and willing to share what they are studying. They also have a deep concern for the changes occurring in the ocean and honestly hope that their information can be shared and understood in order to mitigate the impact of change. Sitting on my surfboard I quickly learned I was the beginner, and they were the experts. With the experience of time, they would effortlessly snap up and slice through the waves. Smiles and whoops encouraged each other as the sea crashed into the beach.

Four surfers sit on surfboards, facing away from the camera, awaiting the next wave. Beyond the surfers we see a line of mountains. The image is a color palette of grays: gray cloudy sky, gray ocean, dark gray-blue mountains. — Surfing off of Kodiak Island. Photo credit: Mathew Phillips

A surfer rides a wave back toward shore. We can see a mountain, part of Kodiak Island, behind the surfer. Both the sky and the ocean are gray. — Surfing off of Kodiak Island. Photo credit: Mathew Phillips

Surf photos courtesy of Mathew Phillips

The next day was spent with the science crew getting ready to bring aboard equipment they will be using, accessing and streamlining the information they need for the data collection, and also a little bit more shore time with fishing and hiking. I hiked up a local mountain called Pyramid.

Overall this has been a great start for a wonderful trip. I love to get my students outside experiencing the real world. After a year of taking both Oceanography and Marine Biology my students get to touch, see and smell the ocean through a field trip. They get to see marine birds and mammals, touch and taste icebergs and smell the brine scent of the ocean. They also get a chance to apply the knowledge and skills that they have learned in my class. The NOAA as Teacher at Sea Program is my field trip. I get to see the science and technology in action and share it with my students, friends and family. Thanks so much for letting me play!

August 1, 2023August 2, 2023

Martin McClure: Starting the Survey, July 30, 2023

NOAA Teacher at Sea

Martin McClure

NOAA Ship Oregon II

July 25– August 9, 2023

Mission: Shark/Red Snapper Bottom Longline Survey

Geographic Area of Cruise: Gulf of Mexico/Atlantic Ocean

Date: July 30, 2023

Latitude: 31°21.967’N

Lonfitude: 80°12.135’W

Air Temperature: 27.5° C.

Wind Speed: 6.79 kph

Science and Technology Log: Longline Fishing

Teacher at Sea Stephen Kade created this graphic to help explain longline fishing.

We have started the longline survey and it is well organized and exciting. The first part of the process is called the set. We start the fishing process by baiting circle hooks. These hooks are attached to a 12 foot length of 3 mm line called a gangion (gan-jin). We use mackerel for bait. Each piece of fish is hooked through a circle hook.

Circle hooks ready for baiting

Next we drop over a buoy with a radar reflector on top called a hi flier. Attached to this is a 4 mm line called the main line. Then a weight is attached to the line and dropped. This anchors the beginning of the fishing line to the seafloor. Next, a numbered clip is attached to each gangion. The gangions are attached to the main line in order from 1- 50. A second weight is then attached to the main line and the process is repeated with gangions numbered 51- 100. A third weight is then attached to anchor this end of the line to the seafloor.

Tagging and attaching the gangions

Finally, a second hi flier buoy is attached and released to mark the end of the line. As each of these steps is done a member of the team records it on a computer. This gives a precise time that each baited hook went in the water as well as when and where the anchors and buoys were released.

Ready to drop the hi flyer

The next step is to take water measurements. This is done with a remarkable device called a CTD. CTD stands for conductivity, temperature and depth. Conductivity is related to how much salt is in the water (salinity) and is related to how well it will conduct electricity. It also measures the temperature and depth of the ocean at that spot. We attach a camera to it to see what the seafloor is made of at that spot. We want to know if it is a sandy bottom, sea grass, muddy, etc.

The CTD

Then we wait one hour.

The second part of the process is called the haul. The haul is simply the set done in reverse, except that we often catch fish. The fishermen use a grappling hook to retrieve the main line attached to the hi flier.

Grappling hook ready to thrown

When it is brought on board, the main line is attached to a winch. The winch is used to pull the main line up of the seafloor. As the main line is pulled in the gangions are detached and replaced in a barrel, the numbered clips are detached and kept on a line in number order. That way, everything is ready to be used for the next set. Whatever is on, or not on, the hook is recorded on the computer. If the bait is missing or damaged is noted.

Weighing a barracuda

Any fish caught is noted on the computer and the team jumps into action. For sharks there are several things that happen. They are identified by species. The hook is removed and the shark is weighed. It is then measured for three different lengths, precaudal (before the tail fin), fork (at the fork in the tail, and total (the end of the tail fin). The sex, male or female, and maturity is determined. Tissue samples are taken by cutting off a small piece of a fin. This tissue sample is placed in a small plastic vial and labeled. They are also often given a numbered tag. This information is all recorded and entered into the computer.

Me, tagging a sandbar shark.

Meet the Crew: Lieutenant James Freed

NOAA Corps Lieutenant James Freed is the operations officer for the Oregon II. He has many responsibilities as part of his job. Part of his job is to liaison, or maintain communication, between the science party and the ship’s commanding officer (CO). That means making sure that everything that the science team needs is on the ship. If the science team has needs then we would go through him and not directly to the CO. As Operations Officer he is also in charge of organizing materials when they come aboard the ship. He posts the Plan of the Day which lets everyone on board know what to expect that day. Lieutenant Freed coordinates port logistics for the ship. This means he coordinates the loading and unloading of materials. His duties also include acting as Officer of the Deck (OOD). During this 4 hour shift he is responsible for the ship’s navigation and safety. His emergency response assignments on the Oregon II include being the nozzleman on the fire team, launching life rafts for abandon ship and he goes out on the rescue boat for man overboard.
Lieutenant Freed grew up in Santa Rosa, California. He attended Santa Rosa Junior College and then transferred to University of California, Santa Cruz where he studied marine biology. During this time he worked as an intern on a fishing vessel and this is where he first heard about the NOAA Corps. He has now been in the NOAA Corps for 6 years. Before being assigned to the Oregon II he was first assigned to the NOAA Ship Bell M. Shimada in Newport, Oregon. He then moved to Seattle working with the Marine Mammal Laboratory at Alaska Fisheries Science Center. For this assignment his duties were quite varied. They included doing a lot of field work, flying drones, and doing whale biopsies.
Lieutenant Freed is clearly enthusiastic about his career in the NOAA Corps. He describes it as an “incredible career” that supports his growth with leadership and management training. The NOAA Corps is growing with new ships and aircraft and will need to recruit new members.. The ships participate in a wide variety of tasks including fisheries research, oceanographic and atmospheric data collection and hydrographic mapping.

Personal Log

Well these last few days have been quite a transition. After 2 1/2 days of transit from Pascagoula, MS to Miami. It was a bit shocking to see how the skyline has changed after 40+ years. It has grown, to say the least. We started fishing just north of Miami. The 10 person science team is split into two shifts. I am on the “day” shift. We work from noon to midnight. These long shifts are filled with alternating periods of activity and waiting. After the set we wait for an hour before the haul. Then, depending on where the next set is, there will be another wait of between two to three hours. The hauls seem to follow the same patterns. As the mile of line is reeled in, there are long periods with not much happening. Then, there might be three fish online within a few hooks. Last night it was two baby tiger sharks and a 1200 mm (3 ft. 11 in.) barracuda within about 5 minutes. When there is a shark too big to haul up by hand on the gangion, the crane is used. We all don hardhats, the crane is moved into place and everyone is busy taking measurements, preparing tags, and taking tissue samples. I was warned to bring a lot of reading material for the down time and I did that. However, with so many things to learn, interesting people to talk to, and beautiful scenery to watch, I have had little time for boredom to creep in.

Ready to release a baby tiger shark.

One of the most common questions that I had before I left concerned getting motion sick. Dare I utter the word… seasick. So far, I have been lucky… hmm, I can’t seem to find any wood around here to knock on. I started the voyage with what I consider to be a rational decision, take the Dramamine. We started with two days of beautiful weather. By the first sign of rough seas I had stopped taking the Dramamine so I went outside and watched the horizon for about an hour. I decided that watching the horizon on a beautiful day at sea had no drawbacks. I never did feel nauseaus. Some people recomended that I buy the accupressure bands which I did. When seas get rough and I am inside I will sometimes wear those. I have not been seasick, yet. I still take precautions like not doing computer work inside when in rough seas but so far I have been fine. In fact, as far as I know none of the volunteers or crew have been sick.

I cannot end this blog without acknowledging the stewards in the gally and the impressive menu available at each meal. I think that there are always three choices for a main dish and a variety of sides. Additonally, a salad bar is always available, snacks, and my favorite, ice cream.

Just one of three delicious options that night

Animals seen: sea turtle, dolphin, snake fish, spotted eel, barracuda, shark sucker. Sharks: sandbar shark, tiger shark, Atlantic sharpnose shark, scalloped hammerhead

shame faced crab

Did you know?

Most of the fish that we catch have parasites living in and on them?

July 18, 2023July 20, 2023

Elli Simonen: Data, Calibrating Data and Surveying, July 15, 2023

NOAA Teacher at Sea

Elli Simonen (she/her)

Aboard NOAA Ship Fairweather

July 10, 2023 – July 28, 2023

Mission: Hydrographic Survey of the Pribilof Islands

Geographic Area of Cruise: Pribilof Islands, Alaska

Date: July 16, 2023

Weather Data

Location: 55’21.02° N, 161’02.02° W

Outside temperature: 11°C

Water temperature: 10°C

True Winds: 337°, 6.5 kts

Skies: Overcast and Cloudy

Science and Technology Log

What is Surveying?

I was in port with the NOAA Ship Fairweather for a little under a week but right now we are en route to the Pribilof Islands. During the time at port, the survey team surveyed surrounding areas, calibrated equipment and practiced troubleshooting survey systems. The goal of surveying is to gather the bathymetry data of the seafloor, or the depths and shape of the seafloor.

Surveying equipment is located on NOAA Ship Fairweather as well as four smaller boats called survey launches, which each get deployed from the ship. Depending on the mission, sea conditions and the project plan, the ship or launches may both be used, or a combination of both.

Global Positioning System (GPS) records position. The Inertial Measurement Units (IMU) measures the motion of the ship. Multibeam Echosounder (MBES) is when sound is pinged from a vessel to the seafloor and the time lapse is used to determine the depth of the seafloor. MBES is a type of sonar that uses multiple beams to get a more complete picture of the seafloor with depths and characteristics. After the data is pinpointed to a specific location, variability associated with tides is also taken into account by transforming the data vertically to the mean lowest low tide. Bathymetry data taken on NOAA Ship Fairweather as well as its four survey launches appears as strips on a map, as the ship or boat moves.

Data is measured to the mean lowest low tide because that level of water is on average the lowest of any tide for a given area. Using the lowest depth in navigation is conservative, thus allowing vessels to navigate safely through mapped waters.

photo of two adjacent computer monitors with different views of the collected survey data imposed on charts or maps

Survey Data shown as green strips.

a small boat (a survey launch) mounted on the port side of NOAA Ship Fairweather, as seen from the deck in front of another mounted launch (only partially visible). Beyond the side of the ship, the still water of a bay extends toward the steep green hill that lines the far side. Another launch, already deployed, is visible on the water at a distance.

Survey launches being stored on NOAA Ship Fairweather as well as one deployed in the harbor

Elli stands on the deck of a small boat. She's wearing a life vest and her Teacher at Sea hat. We have a partial view of the launch's wheelhouse to her left and an electronic winch to the right. Behind Elli the waters are calm, and we can see mountains in the distance.

TAS Elli Simonen aboard one of the survey launches.

Calibrating the Data

During our time in port we took out some of the survey launches to perform a patch test; that is, calibration procedures to ensure the data we collect is as accurate as possible. A correctly calibrated system will show the same mapping of the seafloor in repeated tests, without the influence of confounding variables – speed, direction and ship motion. In a patch test, time delay, pitch, roll and heading are calculated multiple times over different depths, obstructions and slopes on the seafloor and compared to known data. The obstruction we surveyed was a shipwreck.

view of two computer monitors, two keyboards, and two computer mice on a desk

Planning the Patch Test

photo of a computer screen; it is difficult to see what is being displayed, but Elli has circled one area and added the label "shipwreck"

Map of the planned surveys for the Patch Test.

photo of a computer screen displaying bathymetric data. much of the area appears flat (colored teal blue) but there is a small, raised, orange portion in the shape of a ship lying on its side

Survey Data showing the Wreck

To correct for how the speed of sound changes in ocean water, during surveying every four hours Conductivity, Temperature and Depth (CTD) is measured. The CTD measures Salinity and Pressure of the Water Column, aspects that can change the speed of sound. The CTD is used to further calibrate data because different depths have different levels of salinity and temperature, and therefore distort how fast the sound travels. CTD data is used in post-processing to correct for any distortions.

a conductivity, temperature, an depth probe stored in front of a computer tower inside the survey launch's wheelhouse. the probe looks like a white cylinder strapped inside a metal frame that tapers at the top

CTD on the survey launches.

three crewmembers, wearing orange life vests and white hard hats, stand around a piece of equipment mounted at the corner of the aft deck of NOAA Ship Fairweather. a computer is mounted in a blue frame; above extends a blue boom and pulley. a coil of rope hangs on the side. Beyond the ship, the waters are gray with some caps, distant mountain ranges appear in shades of dark blue, and a cloudy, gray-white sky tops the picture.

Moving Vessel Profiler (MVP), a type of CTD that can be used while the ship is in motion, being deployed on NOAA Ship Fairweather by members of the surveying team.

Where does the data go?

Once the survey technicians gather bathymetry data, they still need to edit it before passing it along to National Centers for Environmental Information (NCEI), who package it for public view and is the data repository for environmental data in the U.S. and the U.S. Office of Coast Survey who create navigational charts. Editing the data involves rejecting spurious noise that MBES picked up that is out of range or incorrect. This data then is transformed into charts and more standardized bathymetry data.

two people look at a computer screen in the computer lab. The survey tech, seated at the computer station, points toward multicolored swaths against a black background on the right monitor. Elli stands be hind him to view over his shoulder. On the desk are messy folders and papers, a small potted plant, and an action figure.

Survey Technician showing TAS Elli Simonen the process of cleaning survey data

Personal Log

Members of the survey team are all smart, respectful and patient and take the time to explain to me the science at play no matter how many questions I have. I spend the majority of my day with the survey team but also explore other areas of the ship. I have now been onboard for over a week and things are beginning to feel routine. The sun does not set here until about 10:30pm and rises around 6am. Meals are served at regular times and more importantly, at least to me, coffee is available 24/7.

a view of Elli's stateroom. To the left is a metal warddrobe and a metal sink. To the right is a filing cabinet, a simple bed, and the edge of a metal chest of drawers. There's an open porthole along the back wall, and light shines through it onto the wall, forming a bright circle above the bed.

This is TAS Elli’s room aboard NOAA Ship Fairweather at 9:45pm

view through a sea-sprayed porthole of water and mountains. the sun is low in the sky.

View out my window in the Gulf of Alaska.

Did you know?

The USA offers their bathymetric data for free; Not all countries do this. (https://www.opencpn.org/OpenCPN/info/chartsource.html)
75% of the ocean floor has not been mapped

screenshot of a political map of the continents of the world, with North America at the center. Neon green lines color the North American coastline and extend in webs throughout the rest of the ocean. the map is titled "Data Centre for Digital Bathymetry Viewer."

This map shows, in green, the areas of the world that have bathymetry data, from NCEI, https://www.ncei.noaa.gov/maps/iho_dcdb/

Animals Seen

an otter floats on its back in the water.

Otter swimming near NOAA Ship Fairweather

July 13, 2023July 19, 2023

Lisa Carlson: Where Did You Come From, Where Did You Go? July 13, 2023

NOAA Teacher at Sea

Lisa Carlson

NOAA Ship Bell M. Shimada

July 5, 2023 – July 19, 2023

Mission: Fisheries: Pacific Hake Survey (More info here)

Geographic Region: Pacific Ocean, off the coast of California

Date: July 13, 2023

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Weather Data from the bridge:

July 11 (1200 PT, 1500 EST)
Location: 37° 46.7’ N, 123° 26.6’ W
43nm (50mi) West of San Francisco, CA

Visibility: 2 nautical miles
Sky condition: Overcast, fog
Wind: 20 knots from N 250°
Barometer: 1015.2 mbar
Sea wave height: 2-3 feet
Swell: 6-7 ft from NW 320°
Sea temperature: 12.2°C (57.2°F)
Air temperature: 12.7°C (57.9°F)
Course Over Ground: (COG): 270°
Speed Over Ground (SOG): 10 knots

July 12 (1200 PT, 1500 EST)
Location: 38° 06.8’ N, 123° 01.6’ W
7nm (8mi) North of Point Reyes Lighthouse, Inverness, CA

Visibility: 2 nautical miles
Sky condition: Overcast, fog
Wind: 12 knots from N 350°
Barometer: 1016.0 mbar
Sea wave height: 1-2 feet
Swell: 3-4 ft from W 280°
Sea temperature: 11.0°C (57.2°F)
Air temperature: 11.5°C (57.9°F)
Course Over Ground: (COG): 270°
Speed Over Ground (SOG): 10 knots

July 13 (1200 PT, 1500 EST)
Location: 38° 17.3’ N, 123° 06.1’ W
2.5nm (4mi) Southwest of Bodega Bay, CA

Visibility: 3 nautical miles
Sky condition: Few clouds, fog
Wind: 13 knots from NW 300°
Barometer: 1015.9 mbar
Sea wave height: 1-2 feet 1-2
Swell: 3-4 ft from NW 300°
Sea temperature: 10.7°C (51.3°F)
Air temperature: 13.7°C (56.6°F)
Course Over Ground: (COG): 340°
Speed Over Ground (SOG): 10 knots

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In my July 6 post, I explained how NOAA Ship Bell M. Shimada is equipped to collect acoustic data in the form of echo grams and therefore find fish to trawl for. In my July 10 post, I explained how we get the fish onboard, and what we do with the sample once it is collected from the net. These entries described what work is done in the Acoustics Lab and the Wet Lab, but there is one more Lab onboard to explore and explain: the Chemistry Lab.

view down the starboard side of NOAA Ship Bell M Shimada shows a wooden nameplate (reading Bell M Shimada) on a railing, the fast rescue boat mounted aftward, and the Golden Gate Bridge in the background. — NOAA Ship *Bell M. Shimada* leaving Pier 30/32 in San Francisco, CA on July 5, 2023. (Just a nice photo taken by me that I wanted to include)

Science and Technology Log

Each morning after breakfast, we usually gather in the Acoustics Lab, determine what transect we are on, if we are inshore or offshore, and in some ways: hurry up and wait. Once certain patterns and blips show up on the echo grams, the Acoustics team talks with the bridge and may request to turn around and attempt a trawl. After all marine mammal observations are completed, the net is retrieved, and the samples are brought to the Wet Lab, we sort and collect data on the samples. These operations usually take place between 0800 and 2000. (8am to 8pm)

So what happens at night? In the Chemistry Lab, scientists work with the Deck and Surveys Departments to deploy a collection of electronic instruments and 12 Niskin bottles (open bottles used to collect and hold water samples, about one meter long) secured to a cylindrical frame called a rosette. It is deployed from the side sampling station instead of the stern. Scientists onboard NOAA Ship Bell M. Shimada use the instruments and collection of water samples in two ways: measuring Conductivity, Temperature, and Depth (CTD) within a water column to study oceanography, and collecting environmental DNA (eDNA).

photo of a large piece of sampling equipment on deck. a large white metal cylindrical frame houses a ring of perhaps ten tall gray canisters - the Niskin bottles. The bottles circle the conductivity, temperature, and depth probe, which is barely visible. Behind the frame, past the ship's rail, we see vivid blue water with a few white caps and a coastal mountain range beyond.

CTD Niskin bottles arranged on a circular rosette frame.

“Nighttime operations primarily consists of deploying the Conductivity-Temperature [-Depth] (CTD) rosette which gathers oceanographic data such as conductivity, temperature, dissolved oxygen, and chlorophyll fluorescence. The CTD can also be triggered to collect water at specific depths.”
NOAA Fisheries: “eDNA Part 2: There’s a Lot of Water in the Sea – and the Chemistry Lab”

NOAA Ocean Exploration: “What does “CTD” stand for?”

Conductivity, Temperature and Depth: CTD

CTD stands for conductivity (ability to pass an electrical current), temperature, and depth. Scientists use the rosette frame, which is attached to the ship by cables, and has the CTD and 12 Niskin bottles attached, to collect electronic data and multiple water samples.

“A CTD device’s primary function is to detect how the conductivity and temperature of the water column changes relative to depth. Conductivity is a measure of how well a solution conducts electricity and it is directly related to salinity. By measuring the conductivity of seawater, the salinity can be derived from the temperature and pressure of the same water. The depth is then derived from the pressure measurement by calculating the density of water from the temperature and the salinity.”
NOAA Ocean Exploration: “What does “CTD” stand for?”

Senior Survey Technician Elysha Agne gives commands to the Deck Department running the winch and cable to the rosette, and ensures quality data is being collected at each sampling depth.

“For more detailed analyses back in the lab, each of the large gray bottles captures a water sample at a different depth. The data provide scientists important information about the local aquatic environment.”
NOAA: “Photo story: Virtually cruise aboard a NOAA ship for a fish trawl survey”

Depending on the depth at which the vessel is currently operating, the rosette will descend to one to five predetermined depths (50m-500m) for sampling. For example, if the vessel depth reads 400m, water samples will occur at 50m, 150m, 200m, and 300m (more information in Table 1 below). A water sample is also taken just below the ocean surface using a through hull fitting, which allows seawater to be collected via a hole in the hull that feeds directly to the Chem Lab.

Table 1. Sample depths for eDNA. Two independent samples should be taken at each depth. The total ocean depth of location for the CTD cast determines the depths at which water samples will be collected. The rows of the table are labeled Sampling Depth (m) and the columns are labeled Topography depth of CTD cast. — Table 1 in Protocol manual, written by Chem Lab member and eDNA scientist Abi Wells.

While the rosette descends, data is recorded from multiple sensors and are later used by scientists to compare with Acoustic and Wet Lab data and compile and categorize new information from the survey. Pressure, depth, temperature, conductivity, salinity, oxygen, fluorescence, and turbidity were all being recorded during this leg of the survey mission.

photo of a computer screen displaying data. two graphs depict depth (m) on the y-axis and salinity or dissolved oxygen on the x-axes. — Program displaying data collected from the CTD rosette in real time.

Environmental DNA: eDNA

During the day, Hake stay in deeper waters, averaging around 200-350m, but at night the nocturnal feeders start their daily migration through the water column to shallower depths. They feed primarily on zooplankton, shrimp, myctophids (Lanternfish), and even young Hake at this depth. As Hake move throughout the water column, they leave behind DNA in the water that can be collected later as sort of a signature of their presence in that location. The collection, filtering, and preservation of sampled water in the ocean environment is categorized as collecting eDNA. This environmental DNA can be in the form of gametes (reproductive cells), fish scales, feces, etc.

Collecting water samples at different depths in the same vertical column can show what marine life was present at that location, and what depth they were at. I relate it to reviewing school security cameras or talking to other teachers at the end of the school day, to determine where a student was at a certain time and why.

Chem Lab member and eDNA scientist Abi Wells collecting a 2.5L water sample from a Niskin bottle after a successful CTD deployment.

When the rosette is back on deck, scientists use gloves and new collection bags called Whirlpacks, to collect approximately 2.5L of water from each 10L Niskin bottle. This process is conducted with a great emphasis on sterility, including wiping the bottle spigot with DNAway to remove any contaminants, using new materials, and not allowing fingers or the spigot to touch the collection bag.

White paper is taped down on a bench in the wet lab. On it are rows of water filtering cups mounted on gray horizontal pipes attached to hoses. Each filter cup is topped with a paper filter. Two have funnels attached; additional funnels, still sealed, line the workbench behind the filtering cups. — Sterile work site being set up to pour water samples into the cups and strain through the filters.

blue gloved hands pour water from a clear plastic bag into a funnel attached to a filtering cup. nearby, three plastic pitchers serve as holders for open plastic bags will filled with water. — Sterile work site being set up to pour water samples into the cups and strain through the filters.

Once the collection bags are filled and brought to the Chem Lab, filtration occurs using 1.0 micron filters. Although this size of filter, compared to smaller filters, allows some cells to pass through and not be collected, it is faster and results in less breakage of cells and loss of DNA. After 2.5L of the water sample is poured through individual filters for each depth sample, they are placed in pre-labeled (location and depth information) tubes with 2mL of preservative buffer. The tubes are stored at room temperature and away from UV light until NOAA Ship Bell M. Shimada is back in port and the samples can be further researched in on-land laboratories. Results from additional studies help to compile lists of marine life that was present in the water column and can be compared to acoustic data and species caught and logged in the Wet Lab.

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Personal Log

So, there you have it. Three Labs onboard that conduct very different research, but fit together in the puzzle of Hake development, migration, diet, niches, ecosystem, biomass, and supporting sustainable commercial fisheries. Each additional piece of data; whether it be echo sounds, physical samples, eDNA, or CTD information, strengthens the others and helps to create a cohesive summary of the data.

This was a lot to learn in the first few days, but as I’ve said before, all of the crew has been welcoming, supportive, and educational. Having a strong team that works together is priceless, and thoroughly noticed and appreciated.

A few days into the mission my Mom asked me what the best part of my day was. I had three answers and haven’t had a day yet with only one answer. I replied that it was the great salmon dinner, clean clothes, and seeing Risso’s Dolphins for the first time.

Video taken by me of Risso’s Dolphins surfacing for air. (Plays on loop)

We are now a little more than halfway through the mission and it has truly flown by. We’ve shared riddles and daily Final Jeopardy questions. We’ve laughed over daily experiences and the faces Hake fish make. We’ve played music and watched baseball during dinner. We enjoy watching marine life and breathe in the salt air while strengthening our sea legs. Sometimes we just drink coffee and snack and enjoy this opportunity with each other, and that makes every part of the day the best part.

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Did You Know?

Although Hake are occasionally cannibalistic, they are not at the top of their food chain. Humboldt Squid (Remember those 15 foot long tentacles in my Wet Lab post?), Dogfish Sharks, and marine mammals are all predators, as well as commercial fishing.
Today well over 100 Spiny Dogfish Sharks were inadvertently caught in the trawl, in the same location as the baskets of Hake we sampled from.
Maybe there were baby Hake fish in the sharks’ stomachs… we didn’t attempt to find out.

a white plastic basket of small sharks — Basket one of Spiny Dogfish

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New Terms/Phrases

Although I had learned the terms a few days earlier, I got to help Wet Lab Lead Ethan Beyer collect otolith and stomach samples for the first time from a sub-sample of Hake the other day.

I watched and learned, then helped scan barcodes of otolith sample bottles, add 95% ethanol that is diluted 50/50 with water, and delicately pick up the ear bones with tweezers and place them in the bottle.

Additionally, each Hake in the sub-sample has its weight recorded, along with length, sex, and developmental stage. From that sub-sample, five stomachs are removed for later analysis, and five have their stomachs opened and their diet is recorded. We often find Lanternfish (Myctophids), Krill (Euphausiidae) and small Hake.