sample sorting – NOAA Teacher at Sea Blog

August 26, 2022August 30, 2022

George Hademenos: A Day in the Life…of a Marine Science Researcher, August 25, 2022

NOAA Teacher at Sea

George Hademenos

Aboard R/V Tommy Munro

July 19 – 27, 2022

Mission: Gulf of Mexico Summer Groundfish Survey

Geographic Area of Cruise: Eastern Gulf of Mexico

Date: August 25, 2022

In this post, I would like to walk you through my interactions and observations with the science research being conducted aboard the R/V Tommy Munro, in particular, the steps that were taken during a trawling process. The entire process involved three stages: Preparing for Sampling, Conducting the Sampling, and Analyzing the Sampling with each stage consisting of six distinct steps.

View the following steps in an interactive tour here: Trawl Sampling Process (Genially)

I. Preparing for Sampling

Step 1: The ship travels to designated coordinates for sampling sites as determined for the particular leg of the Survey by SEAMAP (Southeast Area Monitoring and Assessment Program).

screenshot of a computer screen showing the path that R/V Tommy Munro traveled among sampling sites. The ship's path is a bold blue line connecting sample sites marked in yellow. It's superimposed on an electronic nautical chart. This survey occurred southeast of Florida's Apalachicola Bay and St. George Island. — **Ship Transport to Sampling Site**

Step 2: Once the ship reaches the site, a Secchi disk is attached to a cable and lowered into the water off the side of the ship to determine visibility. When the disk can no longer be seen, the depth is recorded and the disk is raised and secured on ship.

a scientist wearing a life vest stands on a small grated platform that has folded down off the fantail of R/V Tommy Munro. With his left land, he grasps a cable hanging from an A-Frame that extends out of the photo. The cable is attached to a white disk, about the size of an old record, with a weight underneath. — **Deployment of Secchi Disk**

Step 3: A CTD (Conductivity, Temperature, and Depth) unit is then prepared for deployment. It is a rectangular chamber with sensors designed to measure physical properties of the water below including dissolved oxygen, conductivity, transmissivity, and depth.

a conductivity, temperature, and depth probe, mounted inside a rectangular metal cage about 1 foot square and about 3 feet high, sits on deck. a crew member wearing white shrimp boots hooks a cable onto the top of the CTD frame. Another person, mostly out of frame, touches the CTD frame with their right hand, covered in a blue latex glove. — **Preparation of CTD Unit**

Step 4: The CTD unit is powered on and first is submerged just below the surface of the water and left there for three minutes for sensors to calibrate. It is then lowered to a specified depth which is 2 meters above the floor of the body of water to protect the sensors from damage.

the CTD unit, attached to a cable, sinks into dark blue water. — **Deployment of CTD Unit**

Step 5: Once the CTD unit has reached the designated depth, it remains there only for seconds until it is raised up and secured on board the ship.

a science team member, wearing a blue hat, a blue life vest, and blue latext gloves, stands on the deployment platform out the back of R/V Tommy Munro. He grasps the top of the CTD frame as a cable lifts it back out of the water. — **Recovery of CTD Unit**

Step 6: The CTD unit is then turned off and the unit is connected through a cable to a computer in the dry lab for data upload. Once the data upload is completed, the CTD unit is flushed with deionized water using a syringe and plastic tubing and then secured on the side of the ship.

the CTD unit sits on deck, now connected to a computer via a cable to upload the data it collected. — **Data Upload from CTD Unit**

II. Conducting the Sampling

Step 1: The trawling process now begins with the trawl nets thrown off the back of the ship. The nets are connected to two planks, each weighing about 350 lbs, which not only submerges the nets but also provide an angled resistance which keeps the nets open in the form of a cone – optimal for sampling while the ship is in motion.

a view of the fantail of R/V Tommy Munro, from an upper deck. we are looking through the rigging of the trawl frames. two large planks rest on the lower deck, connected to ropes and lines. the trawl net, connected to the planks, extends out the back of the fantail. It is just visible below the surface, a turquoise-colored cone submerged in a blue sea. — **Preparation of the Trawling Process Part 1**

another view of the fantail of R/V Tommy Munro from an upper deck, through extensive rigging and frames. the trawl net is further extended; now the large planks are lowering off the back deck as well, suspended by lines connected to a pulley in an A-frame. it is a clear day and the water is very smooth. — **Preparation of the Trawling Proces**s Part 2

Step 2: Once the trawl nets have been released into the water from the ship, the ship starts up and continues on its path for 30 minutes as the nets are trapping marine life it encounters.

a view of the fantail of R/V Tommy Munro from an upper deck. the trawl net is fully deployed and no longer visible. a crew member sweeps the deck. — **Onset of the Trawling Process**

Step 3: After 30 minutes has transpired, a siren sounds and the ship comes to a stop. The two weighted planks are pulled upon the ship followed by the trawl nets.

a view of the A-frame at the fantail R/V Tommy Munro as the trawl net rises from the ocean. The two spreader panels are suspended from separate lines running through the central pulley. behind those, the top of the trawl net is visible above the water. a crew member guides the spreader doors with his left hand, holding the lines with his right hand. — **Conclusion of the Trawling Process** Part 1

the spreader doors are now resting on the fantail deck again. two crewmembers, wearing life jackets, pull the trawl net back on board. — **Conclusion of the Trawling Process** Part 2

Step 4: The trawl nets are raised and hoisted above buckets for all specimens to be collected. Then begins the process of separation. In the first separation, the marine life is separated from seaweed, kelp and other debris. The buckets with marine life and debris are then weighed and recorded.

a crewmember (only partially visible) empties the contents of the trawl net into a blue plastic basket. it looks like it's mostly sargassum. — **Content Collection from the Trawl** Part 1

four plastic baskets on deck hold the sorted contents of the trawl. one has larger fish; another contains only a single fish; a third is a jumble of seaweed and sargassum, and may represent the remainder to sort; the contents of the fourth are not visible. a crewmember wearing a life vest and gloves leans over the baskets. another crewmember, only partially visible, looks on. — **Content Collection from the Trawl** Part 2

Step 5: The bucket(s) with marine life are emptied upon a large table on the ship’s stern for separation according to species.

a pile of fish on a large metal sorting table. we can see snappers, a trigger fish, and many lionfish. a stack of white sorting baskets rests adjacent to the pile. — **Separation Based on Species** Part 1

a gloved hand reaches toward the pile of fish on the metal sorting table. (this photo was taken from the same vantage point as the previous one.) — **Separation Based on Species** Part 2

Step 6: Each species of marine life is placed in their own tray for identification, examination, and measurements inside the wet lab.

two gloved crewmembers sort fish into smaller white baskets on a large metal sorting table. the table is on the back deck of the ship, and we can see smooth ocean conditions in the background. the crewmember in the foreground considers a small fish he has picked up from the remaining unsorted pile. the other crewmember looks on. — **Species Sorted in Trays** Part 1

a close-up view of the sorting basket containing only lionfish. — **Species Sorted in Trays** Part 2

III. Analyzing the Sampling

Step 1: After all species were grouped in their trays, all trays were taken into the wet lab for analysis. Each species was positively identified, counted, and recorded.

a direct view of three fish of different species, lined up on the metal sorting table. the third is a spotfin butterflyfish. — **Tray Transport to Wet Lab**

Step 2: Once each species was identified and counted, the total number of species was weighed while in the tray (accounting for the mass of the tray) and recorded on a spreadsheet to a connected computer display system.

a view of a scale. — **Total Weight Measurements**

Step 3: For each species, the length of each specimen was recorded using a magnetic wand with a sensor that facilitated the electronic recording of the value into a spreadsheet.

two hands, wearing latex gloves, measure a small lionfish on the electronic measuring board. the scientist holds the fish against the board with his left hand and with his right hand marks the length with the magnetic stylus. — **Individual Length Measurements**

Step 4: Weights of the collected species were recorded for the first sample and every fifth one that followed.

the gloved arm places the small lionfish on the scale behind the fish measuring board. — **Individual Weight Measurements**

Step 5: If time permitted between samplings, the sex of selected specimens for a species was determined and recorded.

gloved hands cut into a small lionfish to remove the fish's gonads. — **Individual Species Sex Identification**

Step 6:Once the entire sampling was analyzed, selected samples of specimens were placed in a baggie and stored in a freezer for further analysis with the remaining specimens returned to a larger bucket and thrown overboard into the waters. The separation table was cleaned with a hose and buckets were piled in preparation for the next sampling.

view out the fantail of R/V Tommy Munro from the lower deck. the trawl net and spreader doors lay on the deck, not currently in use. the sun shines on calm seas. — **Finalize Process and Prepare for Next**

In this installment of my exercise of the Ocean Literacy Framework, I would like to ask you

to respond to three questions about the fifth essential principle (The ocean supports a great diversity of life and ecosystems.), presented in a Padlet accessed by the following link:

https://tinyurl.com/427xp9p3

Remember, there are no right or wrong answers – the questions serve not as an opportunity to answer yes or no, or to get answers right or wrong; rather, these questions serve as an opportunity not only to assess what you know or think about the scope of the principle but also to learn, explore, and investigate the demonstrated principle. If you have any questions or would like to discuss further, please indicate so in the blog and I would be glad to answer your questions and initiate a discussion.

July 21, 2015August 21, 2021

Michael Wing: How to Sample the Sea, July 20, 2015

NOAA Teacher at Sea
Michael Wing
Aboard R/V Fulmar
July 17 – 25, 2015

Mission: 2015 July ACCESS Cruise
Geographical Area of Cruise: Pacific Ocean west of Marin County, California
Date: July 20, 2015

Weather Data from the Bridge: 15 knot winds gusting to 20 knots, wind waves 3-5’ and a northwest swell 3-4’ four seconds apart.

Science and Technology Log

On the even-numbered “lines” we don’t just survey birds and mammals. We do a lot of sampling of the water and plankton.

Wing on Fulmar — Wing at rail of the R/V Fulmar

We use a CTD (Conductivity – Temperature – Depth profiler) at every place we stop. We hook it to a cable, turn it on, and lower to down until it comes within 5-10 meters of the bottom. When we pull it back up, it has a continuous and digital record of water conductivity (a proxy for salinity, since salty water conducts electricity better), temperature, dissolved oxygen, fluorescence (a proxy for chlorophyll, basically phytoplankton), all as a function of depth.

We also have a Niskin bottle attached to the CTD cable. This is a sturdy plastic tube with stoppers at both ends. The tube is lowered into the water with both ends cocked open. When it is at the depth you want, you clip a “messenger” to the cable. The messenger is basically a heavy metal bead. You let go, it slides down the cable, and when it strikes a trigger on the Niskin bottle the stoppers on both ends snap shut. You can feel a slight twitch on the ship’s cable when this happens. You pull it back up and decant the seawater that was trapped at that depth into sample bottles to measure nitrate, phosphate, alkalinity, and other chemical parameters back in the lab.

When we want surface water, we just use a bucket on a rope of course.

We use a hoop net to collect krill and other zooplankton. We tow it behind the boat at a depth of about 50 meters, haul it back in, and wash the contents into a sieve, then put them in sample bottles with a little preservative for later study. We also have a couple of smaller plankton nets for special projects, like the University of California at Davis graduate student Kate Davis’s project on ocean acidification, and the plankton samples we send to the California Department of Health. They are checking for red tides.

We use a Tucker Trawl once a day on even numbered lines. This is a heavy and complicated rig that has three plankton nets, each towed at a different depth. It takes about an hour to deploy and retrieve this one; that’s why we don’t use it each time we stop. The Tucker trawl is to catch krill; which are like very small shrimp. During the day they are down deep; they come up at night.

A mass of krill we collected. The black dots are their eyes.

What happens to these samples? The plankton from the hoop net gets sent to a lab where a subsample is taken and each species in the subsample is counted very precisely. The CTD casts are shared by all the groups here – NOAA, Point Blue Conservation Science, the University of California at Davis, San Francisco State University. The state health department gets its sample. San Francisco State student Ryan Hartnett has some water samples he will analyze for nitrate, phosphate and silicate. All the data, including the bird and mammal sightings, goes into a big database that’s been kept since 2004. That’s how we know what’s going on in the California Current. When things change, we’ll recognize the changes.

Personal Log

They told me “wear waterproof pants and rubber boots on the back deck, you’ll get wet.” I thought, how wet could it be? Now I understand. It’s not that some water drips on you when you lift a net up over the stern of the boat – although it does. It’s not that waves splash you, although that happens too. It’s that you use a salt water hose to help wash all of the plankton from the net into a sieve, and then into a container, and to fill wash bottles and to wash off the net, sieve, basins, funnel, etc. before you arrive at the next station and do it all again. It takes time, because you have to wash ALL of the plankton from the end of the net into the bottle, not just some of it. You spend a lot of time hosing things down. It’s like working at a car wash except with salty water and the deck is pitching like a continuous earthquake.

The weather has gone back to “normal”, which today means 15 knot winds gusting to 20 knots, wind waves 3-5’ and a northwest swell 3-4’ only four seconds apart. Do the math, and you’ll see that occasionally a wind wave adds to a swell and you get slapped by something eight feet high. We were going to go to Bodega Bay today; we had to return to Sausalito instead because it’s downwind.

The sea state today. Some waves were pretty big.

We saw a lot of humpback whales breaching again and again, and slapping the water with their tails. No, we don’t know why they do it although it just looks like fun. No, I didn’t get pictures. They do it too fast.

Did You Know? No biologist or birder uses the word “seagull.” They are “gulls”, and there are a lot of different species such as Western gulls, California gulls, Sabine’s gulls and others. Yes, it is possible to tell them apart.

May 4, 2015August 21, 2021

Emily Whalen: Station 381–Cashes Ledge, May 1, 2015

NOAA Teacher at Sea
Emily Whalen
Aboard NOAA Ship Henry B. Bigelow
April 27 – May 10, 2015

Mission: Spring Bottom Trawl Survey, Leg IV
Geographical Area of Cruise: Gulf of Maine
Date: May 1, 2015

Weather Data from the Bridge:
Winds: Light and variable
Seas: 1-2ft
Air Temperature: 6.2^○C
Water Temperature: 5.8^○C

Science and Technology Log:

Earlier today I had planned to write about all of the safety features on board the Bigelow and explain how safe they make me feel while I am on board. However, that was before our first sampling station turned out to be a monster haul! For most stations I have done so far, it takes about an hour from the time that the net comes back on board to the time that we are cleaning up the wetlab. At station 381, it took us one minute shy of three hours! So explaining the EEBD and the EPIRB will have to wait so that I can describe the awesome sampling we did at station 381, Cashes Ledge.

This is a screen that shows the boats track around the Gulf of Maine. The colored lines represent the sea floor as determined by the Olex multibeam. This information will be stored year after year until we have a complete picture of the sea floor in this area!

Before I get to describing the actual catch, I want to give you an idea of all of the work that has to be done in the acoustics lab and on the bridge long before the net even gets into the water.

The bridge is the highest enclosed deck on the boat, and it is where the officers work to navigate the ship. To this end, it is full of nautical charts, screens that give information about the ship’s location and speed, the engine, generators, other ships, radios for communication, weather data and other technical equipment. After arriving at the latitude and longitude of each sampling station, the officer’s attention turns to the screen that displays information from the Olex Realtime Bathymetry Program, which collects data using a ME70 multibeam sonar device attached to bottom of the hull of the ship .

Traditionally, one of the biggest challenges in trawling has been getting the net caught on the bottom of the ocean. This is often called getting ‘hung’ and it can happen when the net snags on a big rock, sunken debris, or anything else resting on the sea floor. The consequences can range from losing a few minutes time working the net free, to tearing or even losing the net. The Olex data is extremely useful because it can essentially paint a picture of the sea floor to ensure that the net doesn’t encounter any obstacles. Upon arrival at a site, the boat will cruise looking for a clear path that is about a mile long and 300 yards wide. Only after finding a suitable spot will the net go into the water.

Check out this view of the seafloor. On the upper half of the screen, there is a dark blue channel that goes between two brightly colored ridges. That's where we dragged the net and caught all of the fish! — Check out this view of the seafloor. On the upper half of the screen, there is a dark blue channel that goes between two brightly colored ridges. We trawled right between the ridges and caught a lot of really big fish!

The ME70 Multibeam uses sound waves to determine the depth of the ocean at specific points. It is similar to a simpler, single stream sonar in that it shoots a wave of sound down to the seafloor, waits for it to bounce back up to the ship and then calculates the distance the wave traveled based on the time and the speed of sound through the water, which depends on temperature. The advantage to using the multibeam is that it shoots out 200 beams of sound at once instead of just one. This means that with each ‘ping’, or burst of sound energy, we know the depth at many points under the ship instead of just one. Considering that the multibeam pings at a rate of 2 Hertz to 0.5 Herts, which is once every 0.5 seconds to 2 seconds, that’s a lot of information about the sea floor contour!

This is what the nautical chart for Cashes Ledge looks like. The numbers represent depth in fathoms. The light blue lines are contour lines. The places where they are close together represent steep cliffs. The red line represents the Bigelow’s track. You can see where we trawled as a short jag between the L and the E in the word Ledge

The stations that we sample are randomly selected by a computer program that was written by one of the scientists in the Northeast Fisheries Science Center, who happens to be on board this trip. Just by chance, station number 381 was on Cashes Ledge, which is an underwater geographical feature that includes jagged cliffs and underwater mountains. The area has been fished very little because all of the bottom features present many hazards for trawl nets. In fact, it is currently a protected area, which means the commercial fishing isn’t allowed there. As a research vessel, we have permission to sample there because we are working to collect data that will provide useful information for stock assessments.

My watch came on duty at noon, at which time the Bigelow was scouting out the bottom and looking for a spot to sample within 1 nautical mile of the latitude and longitude of station 381. Shortly before 1pm, the CTD dropped and then the net went in the water. By 1:30, the net was coming back on board the ship, and there was a buzz going around about how big the catch was predicted to be. As it turns out, the catch was huge! Once on board, the net empties into the checker, which is usually plenty big enough to hold everything. This time though, it was overflowing with big, beautiful cod, pollock and haddock. You can see that one of the deck crew is using a shovel to fill the orange baskets with fish so that they can be taken into the lab and sorted!

You can see the crew working to handling all of the fish we caught at Cashes Ledge. How many different kinds of fish can you see? Photo by fellow volunteer Joe Warren

At this point, I was standing at the conveyor belt, grabbing slippery fish as quickly as I could and sorting them into baskets. Big haddock, little haddock, big cod, little cod, pollock, pollock, pollock. As fast as I could sort, the fish kept coming! Every basket in the lab was full and everyone was working at top speed to process fish so that we could empty the baskets and fill them up with more fish! One of the things that was interesting to notice was the variation within each species. When you see pictures of fish, or just a few fish at a time, they don’t look that different. But looking at so many all at once, I really saw how some have brighter colors, or fatter bodies or bigger spots. But only for a moment, because the fish just kept coming and coming and coming!

Finally, the fish were sorted and I headed to my station, where TK, the cutter that I have been working with, had already started processing some of the huge pollock that we had caught. I helped him maneuver them up onto the lengthing board so that he could measure them and take samples, and we fell into a fish-measuring groove that lasted for two hours. Grab a fish, take the length, print a label and put it on an envelope, slip the otolith into the envelope, examine the stomach contents, repeat.

Cod, pollock and haddock in baskets waiting to get counted and measured. Photo by Watch Chief Adam Poquette.

Some of you have asked about the fish that we have seen and so here is a list of the species that we saw at just this one site:

Pollock
Haddock
Atlantic wolffish
Cod
Goosefish
Herring
Mackerel
Alewife
Acadian redfish
Alligator fish
White hake
Red hake
American plaice
Little skate
American lobster
Sea raven
Thorny skate
Red deepsea crab

Goosefish. Does this remind you of anyone you know?

Mackerel. Possibly the best looking fish in the sea.

I think it’s human nature to try to draw conclusions about what we see and do. If all we knew about the state of our fish populations was based on the data from this one catch, then we might conclude that there are tons of healthy fish stocks in the sea. However, I know that this is just one small data point in a literal sea of data points and it cannot be considered independently of the others. Just because this is data that I was able to see, touch and smell doesn’t give it any more validity than other data that I can only see as a point on a map or numbers on a screen. Eventually, every measurement and sample will be compiled into reports, and it’s that big picture over a long period of time that will really allow give us a better understanding of the state of affairs in the ocean.

Sunset from the deck of the Henry B. Bigelow

Personal Log

Lunges are a bit more challenging on the rocking deck of a ship!

It seems like time is passing faster and faster on board the Bigelow. I have been getting up each morning and doing a Hero’s Journey workout up on the flying bridge. One of my shipmates let me borrow a book that is about all of the people who have died trying to climb Mount Washington. Today I did laundry, and to quote Olaf, putting on my warm and clean sweatshirt fresh out of the dryer was like a warm hug! I am getting to know the crew and learning how they all ended up here, working on a NOAA ship. It’s tough to believe but a week from today, I will be wrapping up and getting ready to go back to school!

April 30, 2015August 21, 2021

Emily Whalen: Trawling in Cape Cod Bay, April 29, 2015

NOAA Teacher at Sea
Emily Whalen
Aboard NOAA Ship Henry B. Bigelow
April 27 – May 10, 2015

Mission: Spring Bottom Trawl Survey, Leg IV
Geographical Area of Cruise: Gulf of Maine
Date: April 29, 2015

Weather Data:
GPS location: 42^○51.770’N, 070^○43.695’W
Sky condition: Cloudy
Wind: 10 kts NNW
Wave height: 1-2 feet
Water temperature: 6.2^○C
Air temperature: 8.1^○C

Science and Technology Log:

On board the Henry B. Bigelow we are working to complete the fourth and final leg of the spring bottom trawl survey. Since 1948, NOAA has sent ships along the east coast from Cape Hatteras to the Scotian Shelf to catch, identify, measure and collect the fish and invertebrates from the sea floor. Scientists and fishermen use this data to assess the health of the ocean and make management decisions about fish stocks.

What do you recognize on this chart? Do you know where Derry, NH is on the map? — This is the area that we will be trawling. Each blue circle represents one of the sites that we will sample. We are covering a LOT of ground! Image courtesy of NOAA.

Today I am going to give you a rundown of the small role that I play in this process. I am on the noon to midnight watch with a crew of six other scientists, which means that we are responsible for processing everything caught in the giant trawl net on board during those hours. During the first three legs of the survey, the Bigelow has sampled over 300 sites. We are working to finish the survey by completing the remaining sites, which are scattered throughout Cape Cod Bay and the Gulf of Maine. The data collected on this trip will be added to data from similar trips that NOAA has taken each spring for almost 60 years. These huge sets of data allow scientists to track species that are dwindling, recovering, thriving or shifting habitats.

At each sampling station, the ship first drops a man-sized piece of equipment called a CTD to the sea floor. The CTD measures conductivity, temperature and depth, hence its name. Using the conductivity measurement, the CTD software also calculates salinity, which is the amount of dissolved salt in the water. It also has light sensors that are used to measure how much light is penetrating through the water.

While the CTD is in the water, the deck crew prepares the trawl net and streams it from the back of the ship. The net is towed by a set of hydraulic winches that are controlled by a sophisticated autotrawl system. The system senses the tension on each trawl warp and will pay out or reel in cable to ensure that the net is fishing properly.

Once deployed, the net sinks to the bottom and the ship tows it for twenty minutes, which is a little more than one nautical mile. The mouth of the net is rectangular so that it can open up wide and catch the most fish. The bottom edge of the mouth has something called a rockhopper sweep on it, which is made of a series of heavy disks that roll along the rocky bottom instead of getting hung up or tangled. The top edge of the net has floats along it to hold it wide open. There are sensors positioned throughout the net that send data back to the ship about the shape of the net’s mouth, the water temperature on the bottom, the amount of contact with the bottom, the speed of water through the net and the direction that the water is flowing through the net. It is important that each tow is standardized like this so that the fish populations in the sample areas aren’t misrepresented by the catch. For example, if the net was twisted or didn’t open properly, the catch might be very small, even in an area that is teaming with fish.

Do you think this is what trawl nets looked like in 1948? — This is what the net looks like when it is coming back on board. The deck hands are guiding the trawl warps onto the big black spools. The whole process is powered by two hydraulic winches.

After twenty minutes, the net is hauled back onto the boat using heavy-duty winches. The science crew changes into brightly colored foul weather gear and heads to the wet lab, where we wait to see what we’ve caught in the net. The watch chief turns the music up and everyone goes to their station along a conveyor belt the transports the fish from outside on the deck to inside the lab. We sort the catch by species into baskets and buckets, working at a slow, comfortable pace when the catch is small, or at a rapid fire, breakneck speed when the catch is large.

If you guessed 'sponges', then you are correct! — This is the conveyor belt that transports the catch from the deck into the wetlab. The crew works to sort things into buckets. Do you know what these chunky yellow blobs that we caught this time are?

After that, the species and weight of each container is recorded into the Fisheries Scientific Computing System (FSCS), which is an amazing software system that allows our team of seven people to collect an enormous amount of data very quickly. Then we work in teams of two to process each fish at work stations using a barcode scanner, magnetic lengthing board, digital scale, fillet knives, tweezers, two touch screen monitors, a freshwater hose, scannable stickers, envelopes, baggies, jars and finally a conveyor belt that leads to a chute that returns the catch back to the ocean. To picture what this looks like, imagine a grocery store checkout line crossed with an arcade crossed with a water park crossed with an operating room. Add in some music playing from an ipod and it’s a pretty raucous scene!

The data that we collect for each fish varies. At a bare minimum, we will measure the length of the fish, which is electronically transmitted into FSCS. For some fish, we also record the weight, sex and stage of maturity. This also often includes taking tissue samples and packaging them up so that they can be studied back at the lab. Fortunately, for each fish, the FSCS screen automatically prompts us about which measurements need to be taken and samples need to be kept. For some fish, we cut out and label a small piece of gonad or some scales. We collect the otoliths, or ear bones from many fish.

It does not look this neat and tidy when we are working! — These are the work stations in the wet lab. The cutters stand on the left processing the fish, and the recorders stand on the right.These bones can be used to determine the age of each fish because they are made of rings of calcium carbonate that accumulate over time.

Most of the samples will got back to the Northeast Fisheries Science Center where they will be processed by NOAA scientists. Some of them will go to other scientists from universities and other labs who have requested special sampling from the Bigelow. It’s like we are working on a dozen different research projects all at once!

Something to Think About:

Below are two pictures that I took from the flying bridge as we departed from the Coast Guard Station in Boston. They were taken just moments apart from each other. Why do you think that the area in the first picture has been built up with beautiful skyscrapers while the area in the second picture is filled with shipping containers and industry? Which area do you think is more important to the city? Post your thoughts in the comment section below.

Rows of shipping containers. What do you think is inside them?

Downtown Boston. Just a mile from the shipping containers. Why do you think this area is so different from the previous picture?

Personal Log

Believe it or not, I actually feel very relaxed on board the Bigelow! The food is excellent, my stateroom is comfortable and all I have to do is follow the instructions of the crew and the FSCS. The internet is fast enough to occasionally check my email, but not fast enough to stream music or obsessively read articles I find on Twitter. The gentle rocking of the boat is relaxing, and there is a constant supply of coffee and yogurt. I have already read one whole book (Paper Towns by John Greene) and later tonight I will go to the onboard library and choose another. That said, I do miss my family and my dog and I’m sure that in a few days I will start to miss my students too!

If the description above doesn’t make you want to consider volunteering on a NOAA cruise, maybe the radical outfits will. On the left, you can see me trying on my Mustang Suit, which is designed to keep me safe in the unlikely event that the ship sinks. On the right, you can see me in my stylish yellow foul weather pants. They look even better when they are covered in sparkling fish scales!

Seriously, they keep me totally dry! — Banana Yellow Pants: SO 2015! Photo taken by fellow volunteer Megan Plourde.

Seriously, do I look awesome, or what? — This is a Mustang Suit. If you owned one of these, where would you most like to wear it? Photo taken by IT Specialist Heidi Marotta.

That’s it for now! What topics would you like to hear more about? If you post your questions in the comment section below, I will try to answer them in my next blog post.

August 8, 2014August 21, 2021

Kacey Shaffer: Fish Scales. Fish Tales. August 8, 2014

NOAA Teacher at Sea

Kacey Shaffer

Aboard NOAA Ship Oscar Dyson

July 26 – August 13, 2014

Mission: Walleye Pollock Survey

Geographical Location: Bering Sea

Date: August 8, 2014
Weather information from the Bridge:

Air Temperature: 11° C

Wind Speed: 27 knots

Wind Direction: 30°

Weather Conditions: High winds and high seas

Latitude: 60° 35.97 N

Longitude: 178° 56.08 W
Science and Technology Log:

If you recall from my last post we left off with fish on the table ready to be sorted and processed. Before we go into the Wet Lab/Fish Lab we need to get geared up. Go ahead and put on your boots, bibs, gloves and a jacket if you’re cold. You should look like this when you’re ready for work…

This is the gear you'll need in the Wet Lab. It can get pretty slimy in there! (Photo Credit: Emily) — This is the gear you’ll need in the Wet Lab. It can get pretty slimy in there! (Photo Credit: Emily)

The first order of business is sorting the catch. We don’t have a magic net that only catches Pollock. Sometimes we pick up other treats along the way. Some of the cool things we’ve brought in are crabs, squid, many types of jellyfish and the occasional salmon. One person stands on each side of the conveyor belt and picks these other species out so they aren’t weighed in with our Pollock catch. It is very important that we only weigh Pollock as we sort so our data are valid. After all the Pollock have been weighed, we then weigh the other items from the haul. Here are some shots from the conveyor belt.

Kacey lifts the door on the table so the fish will slide down onto the conveyor belt. This is when other species are pulled out. (Photo Credit: Sandi)

At the end of the conveyor belt, Pollock are put into baskets, weighed and put into the sorting bin. (Photo Credit: Sandi)

Not every single fish in our net is put into the sorting bin. Only random selection from the catch goes to the sorting bin. The remaining fish from the haul are returned back to the sea. Those fish who find themselves in the sorting bin are cut open to determine their sex. You can’t tell the sex of the fish just by looking at the outside. You have to cut them open, slide the liver to the side and look for the reproductive organs. Males have a rope-like strand as testes. Females have ovaries, which are sacs similar to the stomach but are a distinctly different color.

This is the sorting bin. Can you guess what Blokes and Sheilas means?

The white, rope-like structure is the male reproductive organ.

The pinkish colored sac is one of the female's ovaries. It contains thousands of eggs! — The pinkish colored sac is one of the female’s ovaries. It contains thousands of eggs!

Kacey uses a scalpel to cut the fish. She slides the liver out and looks for the reproductive organs. Is it a male or female? (Photo Credit: Darin)

Okay, no more slicing open fish. For now! The next step is to measure the length of all the fish we just separated by sex. One of the scientists goes to the blokes side and another goes to the sheilas side. We have a handy-dandy tool used to measure and record the lengths called an Ichthystick. I can’t imagine processing fish without it!

The Ichthystick is used to record the length of fish. A special tool held in the hand has a magnet inside that makes a connection with a magnet strip inside the board. It automatically registers a length and records it in a computer program called Clams

Kacey measures the length of a male with the Ichthystick. She holds the tool in her right hand and places it at the fork in the fish’s tail. A special sound alerts her when the data is recorded. (Photo Credit: Darin)

That is the end of the line for those Pollock but we still have a basket waiting for us. A random sample is pulled off the conveyor belt and set to the side for another type of data collection. The Pollock in this special basket will be individually weighed, lengths will be taken and a scientist will determine if it is a male or female. Then we remove the otoliths. What are otoliths? They are small bones inside a fish’s skull that can tell us the age of the fish. Think of a tree and how we can count the rings of a tree to know how old it is. This is the same concept. For this special sample we remove the otoliths, which are labeled and given to a lab on land where a scientist will carefully examine them under a microscope. The scientist will be able to connect the vial containing the otoliths to the other data collected on that fish (length, weight, sex) because each fish in this sample is given a unique specimen number. This is all part of our mission, which is analyzing the health and population of Pollock in the Bering Sea!

Kacey scans a barcode placed on an otolith vial. Robert is removing the otoliths from each fish and Kacey places them in the vial. It is important to make sure the otoliths are placed in the vial that corresponds to the fish Robert measured. (Photo Credit: Emily)

Kacey removes an otolith from a fish Robert cut open. The otoliths are placed in the vial Kacey is holding. (Photo Credit: Emily)

At this point we have just about collected all the data we need for this haul. Each time we haul in a catch this process is completed. As of today, our survey has completed 28 hauls. Thank goodness we have a day shift and a night shift to share the responsibility. That would be a lot of fish for one crew to process! For our next topic we’ll take a look at how the data is recorded and what happens after we’ve completed our mission. By the way, “blokes” are males and “sheilas” are females. Now please excuse us while we go wash fish scales off of every surface in the Wet Lab, including ourselves!

Personal Log:

Just so you know, we’re not starving out here. In fact, we’re stuffed to the gills – pun completely intended. Our Chief Steward Ava and her assistant Adam whip up some delicious meals. Since I am on night shift I do miss the traditional breakfast served each morning. Sometimes, like today, I am up for lunch. I’m really glad I was or I would have missed out on enchiladas. That would have been a terrible crisis! Most people who know me realize there is never enough Mexican food in my life! Tacos (hard and soft), rice and beans were served along with the enchiladas. Each meal is quite a spread! If I have missed lunch I’ll grab a bowl of cereal to hold me over until supper. I bet you’ll never guess we eat a lot of seafood on board. There is usually a fish dish at supper. We even had crab legs one night and fried shrimp another. Some other supper dishes include pork chops, BBQ ribs, baked steak, turkey, rice, mashed potatoes, and macaroni and cheese plus there are always a couple vegetable dishes to choose from. We can’t forget about dessert, either. Cookies, cakes, brownies or pies are served at nearly every meal. It didn’t take long for me to find the ice cream cooler, either. What else would one eat at midnight?!

Ava and Adam are always open to suggestions as well. Someone told Ava the night shift Science Crew was really missing breakfast foods so a few days ago we had breakfast for supper. Not only did they make a traditional supper meal, they made a complete breakfast meal, too! We had pancakes, waffles, bacon, eggs, and hashbrowns. It was so thoughtful of them to do that for us, especially on top of making a full meal for the rest of the crew. Thanks Ava and Adam!

There are situations where a crew member might not be able to make it to the Mess during our set serving schedule. Deck Crew could be putting a net in or taking it out or Science Crew could be processing a catch. We never have to worry, though. Another great thing about Ava and Adam is they will make you a plate, wrap it up and put it in the fridge so you have a meal for later.

Like I said, we’re not going hungry any time soon! Here are some shots from the Mess Deck (dining room).

Mess Deck on the Oscar Dyson. Can you guess why there are tennis balls on the legs of the chairs?

There are always multiple options for every meal. If you’re hungry on this ship you must be the pickiest eater on Earth!

Did you know?

Not only are otoliths useful to scientists during stock assessment, they help the fish with balance, movement and hearing.