Justin Garritt: Paired Trawling, X-raying, and The Galley Master: September 11, 2018

NOAA Teacher at Sea

Justin Garritt

NOAA Ship Bell M. Shimada

September 1-14, 2018

Mission: Hake Research

Geographical area of cruise: Seattle, Washington to Newport, Oregon

Date: September 9-11, 2018: Day 7-9

Location: West of the Columbia River and Astoria, Oregon

 

Where Are We? After fishing off of the Straits of Juan de Fuca on Friday and Saturday, we headed south.  We ended up west of the Columbia River off the coast of Astoria, Oregon and continued to fish for a few days.

 

The fishing and sampling continues: A typical day consists of the scientists waking up before sunrise to begin scouting for fish. We use the information from the acoustic transducer to find fish.

Chief Scientist Rebecca Thomas

Chief Scientist Rebecca Thomas spots signs of fish on the sonar

sonar from the acoustic transducer

The sonar from the acoustic transducer showing signs of fish

Paired Trawling: Last week I wrote about our goals of the cruise. One of them was to perform paired trawls to determine net size impact to evaluate the differences between the US 32mm net liners and the Canadian 7mm net liners. A paired trawl is when we fish approximately the same location and depth two times using two different size liners. Data is collected on the size, characteristics, and species of fish being caught to eliminate the possibility that there is bias in the data between the two liners. Below are pictures of the nets being sent in and brought back based on information from the sonars. This typically happened 2-4 times per day (1-2 paired trawls).

 

Sorting the Fish Aboard:

rockfish photo shoot

A rockfish photo shoot 🙂

How We Collect Data:

When fish come aboard we follow this flow chart to determine what analysis needs to be done on the catch.

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Our instructional chart for how we analyze the hake and other species

Hake is the majority of the fish we catch. It is also the main species we are researching this cruise.

A random sample of 250 are set aside and the rest are sent back in to the ocean. Of the approximately 250 random hake, 30 are dissected for enhanced sampling (length, weight, sex, maturity, and other projects).

220 are set aside for sex/length analysis. All other species of fish must be logged into the computer and some are kept for special research projects. See pictures below:

Male vs. female hake distinction:

Determining the length of the hake:

Enhanced sampling (length, weight, sex, maturity, and other projects):

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Dissecting the hake to enhance sample

Special Projects: There are also a number of special projects going on aboard:

Fish X-ray: Scientist Dezhang Chu x-rays samples of fish occasionally. The x-ray is used to determine the volume of the swim bladders in certain species of fish (see picture below). The volume of different species’ swim bladders affects the observed acoustics. I spoke to him about the purpose of this study. He said that the present acoustic transducers are great to capture whether fish are present below the ship’s surface but are still not able to classify the type of species being observed. He is working on a team that is trying to use x-ray’s from multiple species to solve that problem. When asked how long he thought it may take for there to be an acoustic system advanced enough to better predict the species onscreen, he said, “People have and will continue to spend their entire careers on improving the system.” If we have more scientists like Dr. Chu on this project, I predict it will be much sooner than he leads on.

"Super Chu"

“Super Chu” and I with his new apron I made him for x-raying

Filming the Catch: Melanie Johnson leads the science team’s visual analysis. During each trawl a camera is placed securely on the net. The purpose of the net is to analyze approximately which depth and time certain fish enter the net.

fish entering the net

Camera footage of fish entering the net

———————————————————————

Getting to know the crew: As promised in other blog posts, here is another interview from the incredible crew aboard  NOAA Ship Bell M. Shimada who continue to make my journey such a rich experience:

Mr. Arnold Dones, Head Chef

Arnold Dones is our head chef or what I like to call him, “Master Chef.” Since the minute I’ve been aboard I quickly noticed the incredible work ethic and talent of our chef. To be clear, every meal has incredible! When I spoke to my mom a few days into the cruise my exact words were, “The food aboard is better than a buffet on a cruise ship. I expected to come aboard for two weeks and lose a few pounds. Well that’s not going to happen!”

Chef Arnold

Chef Arnold and his incredible food artwork

Arnold was born in the Philippines and his family migrated here when he was twenty. When he first got here he knew very little English and worked hard to learn the language and the American culture. He worked a few odd and end jobs until he joined the United States military as a chef. During his first years in the military, he showed so much promise as a chef that he enrolled in “A School” which allowed him to learn how to be a master chef in the military. He spent more than a decade working on military vessels. His last ship placement was aboard the USS Ronald Reagan where he and his team prepared meals for 6,000 soldiers per meal. Two months ago he joined the NOAA Ship Bell M. Shimada family as head chef.  Arnold has two children and a wife who live back in San Diego.

After a tour of the galley with Arnold, I learned how much work it takes to pull 42 meals in 14 days for over 40 crew members without a supermarket nearby. A few weeks out, Arnold has to create his menu for the next cruise leg (typically two weeks). He then has to order the food required to make the meals and do so by staying under a strict budget. When the ship ends a leg and pulls in to port, a large truck pulls up and unloads all his ordered food in large boxes. He then organizes it in the order he plans to prepare it in his large freezer, refrigerator, and store rooms. The trick is to be sure his menu is organized so nothing spoils before it is used.  Arnold’s day begins at 05:00  (5am) and goes until 19:00 (7pm) with a short break after lunch. The only days off he has is a day or two once every two weeks when the boat is in port.

Here is a sample menu for the day:

Breakfast (7-8am)- Eggs benedict, blueberry pancakes, french toast, hash browns, scrambled eggs, oat meal, cut fresh fruit, and breakfast danish.

Lunch (11-12pm)- Bacon wrapped rockfish, chicken wings, Chinese noodles, brussel sprouts, bread, a large salad bar, homemade salads, avocado, bean salad, homemade cookies, and ice cream.

Dinner (5-6pm)-  Stuffed pork chops with spinach and cheese, fine braised chicken thigh, baked salmon, Spanish rice, oven potatoes, peas, dinner rolls, a large salad bar, homemade salads, homemade apple pie, and ice cream.

Snack (24/7)- Soup, crackers, ice cream, and salad/fruit bar

We dock in Newport, Oregon on Friday, September 14, 2018. My final post will be on Friday. Thank you for continuing to follow along in this journey. I am grateful for your support and for the amazing people I have met aboard.

Justin

 

Kimberly Godfrey: Creature Feature, June 8, 2018

NOAA Teacher at Sea

Kimberly Godfrey

Aboard NOAA Ship Reuben Lasker

May 31 – June 11, 2018

 

Mission: Rockfish recruitment and assessment survey

Geographic Range: California Coast

Date: June 8, 2018

 

Data from the Bridge

Latitude: 36° 43.508′ N

Longitude: 121° 52.950′ W

Wind: 30.87 knots from the SE

Air Temperature: 12.7°

Waves: 2-3 feet with 6-8 foot swells

 

Science and Technology Log

We moved up north to continue with our trawls. The first night we trawled just north of Monterey Bay. It was a good thing we did because outside the bay, the wind and swells are rough. We saw lots of jellyfish and lots of krill in our catches. However, I would like to talk a little about a very specific group of fish, rockfish. If you read the mission above, you will recall that rockfish are the primary focus of this survey. Therefore, I think they need a moment in the spotlight to themselves.

While this number may vary, NOAA has over 60 species of rockfish listed on the West Coast. They are an intriguing group of fish for many reasons. First, it is important to note that they are extremely significant to their food web because they are a prey species, but they are also important as a food and income source for humans. Species like the bocaccio rockfish and the yelloweye rockfish are species of concern due to over fishing, and populations are slow to recover. That is enough reason to learn as much possible about these fish.

Yelloweye Rockfish

Yelloweye Rockfish

Bocaccio

Bocaccio

What we know about rockfish species is they can live for a long time. Many can live over 50 years, some can even live over 100 years of age!  Their growth rate is relatively slow, and very few make it to adulthood because they are prey for other fish. During the first year (sometimes more depending on the species), they spend much of their time in the pelagic realm (open water). If they live long enough, they can grow to a size that allows them to settle in the benthic zone (ocean floor). For many species, 60 mm is a large enough size to settle. This is what the term “recruitment” refers to. Once rockfish settle out of the pelagic zone, they have a higher chance of reaching reproductive maturity.

YOY Rockfish

Various species of YOY (Young Of the Year) rockfish caught in one of our trawls. Photo Credit Keith Sakuma

NOAA Fisheries has been surveying the West Coast for rockfish since 1983. They first started in a smaller region from Monterey Bay to Point Reyes, CA. The survey area expanded in 2004 and by 2013 it covered the entire coast of California. The success of the local ecosystem and the commercial fisheries depend on healthy fish populations. The survey tries to collect at least 100 specimens per species of rockfish and take them back to the lab (on land).  Back at the lab the species identifications are determined as many rockfish are difficult to identify to species at this life history stage without using a microscope.  In addition, their size is recorded and tissue samples taken for genetic studies. Then, on select species, otoliths are removed to age the specimens. The otolith is an ear bone. In fish, the ear bone deposits layers of bone in rings. It happens daily and these daily rings can be counted using a microscope to learn how old the fish is. These ages are used by scientists not only to learned how old the fish are, but they can compare this information to the size data collected and estimate the expected size of a fish at any given age.

I had a chance to talk to everyone from the night shift science team about what they do and how they came to work for NOAA:

Keith Sakuma has been working with the survey since 1989. He is the chief scientist and team leader of the night crew. He works hard to make sure we are all focused and efficient because it is a fast-paced work environment. In between hauls, he enjoys the company of his team and a few Dragon Ball episodes. He was born and raised in Hawaii, and went to University of Hawaii for his Bachelor’s degree in Zoology.  In his younger years, Keith worked for the Division of Aquatic Resources, where he spent his days walking up and down the beach to count fisherman and interview them about their catches for the day. He also did snorkel surveys doing fish counts in fisheries management areas.  In addition, he worked on a team that implemented fish aggregating devices, buoys that attract fish for the local fisherman.

While at the University of Hawaii, he was part of the Marine Option program where they teach you various marine skills and connect you with marine research activities. Through this program he completed his scientific diving training, and then participated in two diving surveys. Both surveys documented the impacts of tourism on the reef systems on the island of Lanai Island and Molokini, which is a tiny islet off Maui. On Molokini, tourist traveling to the islet by boat, dropping anchor in the reef, caused a significant amount of damage to the reef. Mitigation included the addition of moorings so boats could tie up and not have to drop anchor, destroying more of the reef.

For his Master’s, he attended San Francisco State University.  His major advisor just returned from a 2-year sabbatical, working with the National Marine Fisheries Service (NMFS) [also known as NOAA Fisheries] on the mid water trawl survey, and suggested that Keith do his Master’s Thesis on the data he collected on the survey. While finishing his Master’s degree, he was offered a full-time position working with NMFS, and has been here ever since. That means he has 29 years put into this work.

Growing up in Hawaii near the ocean definitely influenced his decision to pursue Marine Science. He used to say to others how much he loved the ocean and that the ocean loved him back. He couldn’t wait to spend time at the beach in the water. And while today this remains true, he has mentioned that that cold waters of Pacific Coast are not as affectionate as the warm waters of Hawaii.  The water around the islands is so clear, allowing one to see at a distance the beauty that lies beneath. Here, you must pick the right day at the right time to find tolerable temperatures and some visibility. The murkiness makes it hard to see anything, but that murkiness is what contributes to the productivity of the region.

Even after 29 years, Keith still very much enjoys being at sea. He doesn’t get sea sick, so he can spend time working in the field with real specimens and real-time data rather than just analyzing data collected by other people. He enjoys seeing new people come on and get excited about the work. For anyone interested in pursuing Marine Biology and any research science, it is important to have a strong background in math and statistics, especially in today’s world. He also mentioned how important it is to have computer skills and programming skills. The software used to process and analyze data requires one to read and write programming language. Having these skills make one a stronger candidate when applying for research positions. It also gives one more validity when having to speak about and defend the analysis of the research.

That’s Keith, the Chief Scientist, in a nutshell. I also got to learn more about the rest of the team. Thomas Adams has been working with this survey for 5 years now. He started as a volunteer with NMFS, analyzing marine chlorophyll samples. He always had an interest in Marine Biology, and already had a connection to someone working in a NOAA lab. He was invited to work on the rockfish survey because he was known for being a knowledgeable and efficient worker. He too is very enthusiastic and really enjoys being at sea with Keith and the rest of the team. He is the main provider of Dragon Ball, and the Simpsons, which the team enjoys in between trawls. He recently completed his Bachelor’s degree and plans to go for his Master’s in Marine Biology in the near future.

Melissa Monk is a Research Mathematical Statistician, and is responsible for fisheries stock assessments for West Coast near shore ground fish. She also participates in research related to improving fisheries. Her schedule is on a bi-annual cycle. One year is devoted to stock assessment, and the next year is devoted to research.  During stock assessment years, there is a mad dash that happens around September to learn anything and everything about your assigned species. At the end of the assessment season, there is a week-long panel review of all the data gathered during the assessment. Once the assessment is approved, the information is used for species management and harvest regulations. She received her undergrad in Wildlife Sciences with a minor in Statistics. Her Master’s was in fisheries. She spent half her year monitoring the sea turtle populations in North Carolina, and the other half of the year in classes. She did a lot of quantitative work, research, and recruitment training for her Master’s. She also had a connection to NOAA because her PhD advisor at LSU used to work for NOAA. She learned that NOAA trained people to become stock assessors, and pursued fisheries as a career. Her favorite part about working for NOAA is that her work directly impacts fisheries success.

Rebecca Miller is a GIS Specialist, works on a variety of projects at the Santa Cruz NOAA lab. One project is the spatial mapping of rockfish and other marine species. She maps California fisheries catches in both time and space, and is able to analyze this data as far back as the 1930’s. Her Master’s degree is from Oregon State University in Fisheries Sciences with a minor in Geography. She knew since 6th grade that she wanted to be a Fisheries Biologist. She participated in internships and part-time summer jobs in freshwater salmon fisheries, marine intertidal work, and geodatabase management. She loves the people she works with, and the fact the work is so diverse. There is a lot of field work, lots of data analyses, and different projects to work on. She too enjoys knowing that her work helps to sustain fisheries to be both utilized and conserved.

Stephanie Oakes is from NOAA Fisheries Office of Science and Technology (OST). She got her Ph D. in Marine Sciences, and worked on Antarctic krill in an ecosystem context.  The rockfish survey is similar in the sense the it also surveys species in an ecosystem context.  Being able to participate in surveys like this is important to her because she gets to experience first had what happens during the surveys and how the team operates.  Her personal gratification is that she gets her hands in the catch, in the field like she did for her Ph.D.  NOAA Fisheries OST is there to advocate and ensure sound scientific basis for NOAA Fisheries science programs and resource conservation and management decisions.

Did you know…

Here are some of the species we found during our trawls:

  • Adult and young of year (YOY) anchovy
  • Adult and YOY sardine
  • Jack Mackerel
  • Northern Lamp fish
  • Mexican lamp fish
  • California Lamp fish
  • Blue lantern fish
  • Northern smoothtongue
  • Black smelt
  • Pacific Hake
  • Pacific Sanddab
  • Speckled Sanddab
  • CO Turbot
  • Black-bellied dragon fish
  • High fin dragon fish
  • Barracuddina
  • King-of-the-salmon
  • Market squid
  • Gonatus squid
  • Boreal squid
  • Octopus
  • Electric Ray
  • Wolf Eel
  • Pacific Sea Nettle
  • Purple striped jelly
  • Moon Jelly
  • Krill
  • Pelagic Red Crabs
Pacific Sanddab

Young of Year (YOY) Pacific Sanddab

King of the salmon

King-of-the-Salmon

Krill

Krill. There is mostly one species of krill here, but we’ve seen multiple species in our catches.

Barracudina

Barracudina

Adult Anchovy

Adult Anchovy

Myctophids

Blue lantern fish

Pelagic Red Crab

Pelagic Red Crab

Chryasora colorata

Purple Striped Jelly

Boreal Squid

Boreal squid

Octopus

Octopus

Wolf eel

Juvenile wolf eel Photo Credit Wyatt Sebourn

Dawn White: Finally Fishing! June 27, 2017

NOAA Teacher at Sea

Dawn White

Aboard NOAA Ship Reuben Lasker

June 19 – July 1, 2017

 

Mission: West Coast Sardine Survey

Geographic Area of Cruise: Pacific Ocean; U.S. West Coast

Date: June 27, 2017

 

Weather Data from the Bridge

Date: June 27, 2017                                                         Wind Speed: 28.9 kts with gusts
Time: 9:15 p.m.                                                                 Latitude: 4828.20N
Temperature: 13.4oC                                                      Longitude: 12634.66W

Science and Technology Log

White_Lasker route 6-27

The red line indicates the route of NOAA Ship Reuben Lasker transiting along the coast of Vancouver Island

We finally reached the tip of Vancouver Island on Sunday evening, June 25. It would be our first night of fishing.  The red line indicates the route taken by the Reuben Lasker as we transited along the coast to the northernmost tip of the island.  The blue lines indicate the path to be taken for regular interval acoustic monitoring for schools of fish.  Based on the acoustics results, a decision would be made as to where the fishing would occur at night.

 

 

 

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Crew deploying the fishing net

The photo at left shows the crew completing the deployment of the fishing net.  You can see the large winch that will release and retrieve the main body of the net.  The net will be set out for about 45 minutes.  During this time there are many variables that will be monitored.  Sensors attached to the net will collect data on time spent at each depth.  Other factors being monitored include temperature, wind speed, swell size,  and lat/long of trawl. In addition, there are four water-activated “pingers” attached to the net that emit sounds at frequencies known to disturb larger mammals in an effort to reduce accidental captures.

Once the net has been retrieved, the scientists collect the catch in large baskets and begin the process of weighing and sorting.  The first night’s catch was primarily made up of a very unique colonial type of organism called a pyrosome. The side nets and codend (mesh covered end of the main net where most of the catch is collected) were packed with these the first couple of trawls.

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Many pyrosomes were mixed in with the catch.

You can see many pyrosomes mixed in with the rest of the catch here.  They are the pink colored cylindrical organisms.  They have been increasing in population over the past couple of years as well as appearing further north than ever observed before.  A nice overview of the pyrosome influx and volumes observed was recently reported in an article published by Environment entitled “Jellied sea creatures confound scientists, fishermen on U.S. Pacific Coast”. You can review the article here.

The trawl net being used was part of the research project, as it possessed modifications aimed at capturing and quantifying organisms that made it through an apparatus called the extruder door.  The purpose for this opening is to allow for larger mammals and non-target organisms to pass through the net relatively unharmed should they get caught.  Two additional pocket nets had been added to the main net for the specific purpose of monitoring what made it through the mesh.

This far north, the researchers were expecting to find mostly juvenile herring and salmon.  On our second night of fishing we actually had several species of fish and other marine animalia to i.d. The amount and type of data collected depended on the species of organism.  In some cases, we collected just the mass of the group of organisms as a whole.  For other species, we collected mass, lengths, presence/absence of an adipose fin, DNA samples from a fin clip, and more.  Certain species were tagged, bagged, and frozen for further study in a land-based lab.  It’s so interesting to see the variety we pull out of the net each trawl!

Some of the species collected can be seen below:

Extension question for my students reading this:

What traits could you use to differentiate between the juvenile salmon and Pacific herring?

 

Personal Log:

White_scientists collecting data

Here are some of the scientists making sure the correct data is collected and recorded from one of our catches.

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Here I am (in yellow) with some of the scientists (L to R: Emily, Amy, and Angela) getting ready to receive the evening’s catch.

First trawl starts as close to sunset as possible, which for this latitude has been somewhere between 9:30-10:00 p.m. There is always this air of anticipation as we wait for the net to be emptied.  It has been enlightening to work with the science staff as they evaluate each sample.  The number of reference sheets and data recording forms is incredible.  It seems like you would need to take a course in data management just to ensure you were familiar enough with the requirements to not overlook some detail of importance.

The photo of the group above was taken about 11:00 p.m.  I was worried initially that I would not be able to flip my sleep schedule to match the work schedule, but it has been much more doable than I thought it would be.  Our staterooms are dark and quiet, so going to bed in the morning really doesn’t feel any different that at night.  Thanks to the extensive movie collection and my ability to keep downloading books to read on Kindle, I have had plenty of filler for downtime and that “reading before bed” I always do.

Time to go to work…..

 

Did You Know?

There are 36 species of dolphin worldwide, including 4 species of river dolphins.  Quite a few of the Common Bottlenose Dolphin followed the ship out of the harbor in San Diego, riding along on the wake produced by the ship.  On the way up the coast of California I saw a couple of Dall’s Porpoises (not in the dolphin family, but quite similar in appearance).  Then as we traveled south along Victoria Island there were a couple of Pacific White-Sided dolphins enjoying games along-side the ship. It is so exciting to see these animals out in their native habitat!

Every night before the ship drops the fishing net, a member of the science team is sent to the bridge to perform a 30-minute mammal watch.  The surrounding waters are observed closely for any signs of these and other larger species.  The investigators do their best to ensure that only the small fish species intended for capture are what enters the net.  Should there be a sighting, the ship moves on another 5 miles in an effort to avoid any accidental captures.  The scientists and crew work very hard to minimize the impact of their studies on the surrounding ecosystems.

David Amidon: The Night Shift, June 4, 2017

NOAA Teacher at Sea

David Amidon

Aboard NOAA Ship Reuben Lasker

June 2 – 13, 2017

Mission: Pelagic Juvenile Rockfish Recruitment and Ecosystem Assessment Survey

Geographic Area of Cruise: Pacific Ocean off the California Coast

Date: June 4, 2017

 

Science and Technology Log

All of the work for the Juvenile Rockfish Survey is completed at night – we probably will not even get going  most nights until after 9 PM. Wonder why so late? Any guesses?

This is a night time operation because we are focused on collecting prey species – we are not catching full grown rockfish, only juveniles which are less than a years old (YOY = Young of the Year). As Keith Sakuma, the Chief Scientist for the Reuben Lasker, explained – this survey gathers information about the juvenile rockfish so that NOAA can pass information onto the states in order to establish a sustainable fishery. This could lead to changes in fishing regulations based on the abundance of the juvenile stocks, which would be adults down the road. They trawl at night for two main reasons- during the day time, the rockfish would simply see the net and swim away. Also, many of the other creatures being catalogued are prey species that hide in the depths during the day to avoid predators, rising to the surface as the night moves on.

The night shift includes the science personnel and the crew of the boat. The boat crew not only operates the ship, but the fisherman also send out the trawl net and bring it back in. While the boat crew rotates on a specified schedule, the night-time science group keeps going until the work is done. However, these two groups are very much in sync and really work well together.  This blog entry will be my introduction into the procedures and initial results of our work from the first couple nights. I will provide much more detail in later posts.

The science personnel for this leg of the voyage includes myself and Chief Scientist Sakuma as well as Cherisa and Ryan, who are members of the NOAA Corps; Thomas, an undergrad student from Humboldt State; Rachel, a PhD student at UC-Santa Cruz; and Maya, a Hollings undergraduate scholar from UNC-Wilmington.

Pink shrimp 7

The Night Crew at work separating species during the shrimp haul. Photo by Keith Sakuma.

The Juvenile Rockfish Survey, boiled to its simplest terms, consists of a midwater trawling net behind the ship, meaning it does not float and it never touches the bottom. Anything caught will be sorted and analyzed by the science crew. In reality, it is a bit more complicated.

First of all, net operations take place at specified stations that the ship revisits periodically and have been used for some time. The stations for a night run on the same latitude line, running west away from the coast.

Before sending the net out, we need to run a Marine Mammal Watch from the bridge for 30 minutes. If a marine mammal, such as a sea lion, dolphin or whale, is spotted, then they make efforts to avoid getting them tangled in their nets, or alter their behavior in any way. Sometimes the trawl for that station has to be abandoned due to wildlife activity, although we have not seen any marine mammals during our investigation so far.

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Getting ready for my shift on the Marine Mammal Watch

Once the ship arrives at a station, the boat crew sends out the net. After it reaches the depth of 30m, they trawl for a 15 minute interval. A science crew member is also sent outside on deck to continue the marine mammal watch for the duration of the trawl. Finally, after the time is up, they bring in the net and empty its contents into buckets, which are then transferred to the science crew.

This is when our work began. While we are on the lookout for rockfish, we actually found very few of these. A majority of our catch consisted of pyrosomes and krill. The science crew employed a number of measures to estimate the numbers of these creatures, as counting them one-by-one would have taken a long, long time to do. We did volume approximations and analysis of representative samples for these creatures. When we found fish or other species of note, we would pull the individuals out, classify them and record their lengths. Samples were frozen for use by researchers working at other locations on the West Coast.

IMG_1368

Measuring the mantle of a Market Squid. Photo by Rachel Zuercher.

Some examples of the species we collected:

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Juvenile Rockfish collected off the “Lost Coast”

IMG_1375

Sample of other species collected and catalogued, including: Medusa Fish, Gonatus Squid, Thetys and California Headlight Fish

We worked solid through four stations on the first night, wrapping up just before 6 AM. We will be at it again, if weather permits, every night of the voyage.

Personal Log

Thursday, June 1st

This was a very long day. I left my house in Syracuse, NY at 6 AM, flying out of the airport around 8 AM. After a quick transfer in Chicago, I flew in a Boeing 737 all the way to San Francisco. I then made it to Eureka, California around 4 PM (West Coast time) for an overnight stay. Fortunately, I met up a few of the science personnel for dinner who were also headed to the Reuben Lasker in the morning. Eureka was beautiful, surrounded by oceans and redwoods.

IMG_1282

Sunset in Eureka, CA

Friday, June 2nd

In the morning, we caught a transfer boat at the public marina out to the Reuben Lasker, anchored a few miles away off the coast. Once the passage was done, we settled in and met some of the crew. I even shared a coffee with the CO- or Commanding Officer. Everyone onboard has been so open and welcoming – you can tell they enjoy their work.

IMG_1287

Transfer boat that to us to the Reuben Lasker

After dinner, we finally got down to sciencing. (That’s my word – I’m sticking to it.) I was impressed by how different the catch was from each station, even though they are only a few miles apart. You can try to start telling a story right there. That’s kind of the point to this whole survey. To try to tell a story about the overall health of the pelagic ecosystem based on representative samples. Piece by piece, year by year, data points can turn into meaning when connections are made. I think it is science in the purest form -gathering data for the sake of having information. By having a long-term data base of information about all of the other creatures collected, not just the rockfish, we can decipher meaning by analyzing population trends and collating them with other phenomena, such as weather, fishing or pollution. 

Saturday, June 3rd

I am getting adjusted to the day/night pattern of the Night Shift. I got to sleep around 6:30 AM and woke up close to 2 PM. I was able to grab a quick cereal from the Galley and then started in on some work. Dinner was served at 5 PM – filet mignon with crab legs? The cooks, or stewards, Kathy & Patrick do an amazing job. They also save meals for people running the late schedule. For the next week and change, lunch is served around midnight and breakfast will be close to 6 AM, before we head to sleep.

Today, the wind picked up and the waves kicked up with it. We cruised around the “Lost Coast” and ran two stations at night. We were scheduled for more, but the waves got larger the further the ship is off the coast. Today’s word is shrimp – we hauled in more shrimp than you could count. We also found a number of rockfish in one of the stations, although there were very few found in our second trawl.

Did You Know?

… that there are over 85 species of krill?

http://www.krillfacts.org/1-krill-facts-center.html

Nichia Huxtable: These ARE the Fish You’re Looking For, May 4, 2016

NOAA Teacher at Sea

Nichia Huxtable

Aboard NOAA Ship Bell M. Shimada

April 28 – May 9, 2016

Mission: Mapping CINMS

Geographical area of cruise: Channel Islands, California

Date: May 4, 2016

Weather Data form the Bridge: 0-2ft swells, partly cloudy, slightly hazy

Science and Technology Log:

We’ve been waiting for you, rockfish. We meet again, at last. You might wonder why scientists need to know the location and population densities of rockfish in the Channel Islands National Marine Sanctuary. Well, rockfish are tasty and commercially important, plus they are an important component of healthy marine ecosystems.  To estimate how many there are and where they’re at, you’ll need lots of equipment and fisheries biologist, Fabio Campanella.

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Fabio Campanella and Julia Gorton getting some fresh air. Breaks are important to help them stay on target.

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Monitor showing the EK60 in action. Your eyes can deceive you…watch out for the acoustic dead zone!

First, let’s start with the equipment. Shimada has an EK60, which is essentially a fish finder: the computer’s transducer sends out sonic “pings” that become a single acoustic “beam” in the water. It covers about 7° at one time, so think of it as taking a cross section of the water column. The beam bounces off any solid object in the water and returns to the transducer. The size and composition of the object it hits will affect the quality of the returning pings, which allows Fabio to discern between seafloor, small plankton, and larger fish, as well as their location in the water column. One drawback of this system is the existence of an acoustic dead zone, which is an area extending above the seafloor where fish cannot be detected (think of them as sonar blind spots).

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Do. Or do not. There is no try. Fabio Campanella hard at work in Shimada‘s Acoustic Lab.

 

Starry rockfish (Sebastes constellatus)

It’s a trap! Nope, it’s a starry rockfish (Sebastes constellatus) found in the CINMS.

Ideally, acoustic data collection is done simultaneously with ground truthing data. Ground truthing is a way to verify what you’re seeing. If you think the EK60 is showing you a school of herring, you can run nets or trawls to verify. If it’s in an area that is untrawlable, you can use ROVs or stationary cameras to identify fish species and habitat type. Species distribution maps are also useful to have when determining possible fish species.

 

EK60 data shown on the bottom; ME70 data on top right; 3-D visualization of the school on the top left.

EK60 data shown on the bottom; ME70 data on top right; 3-D visualization of the school on the top left. Witness the power of this fully operational Echoview software.

If Fabio finds something especially interesting on the EK60, such as a large school of fish, he can refer to the data simultaneously collected by the ME70 multibeam sonar to get a more detailed 3-D image. Since the ME70 uses multiple beams and collects 60 degrees of data, he can use it to (usually) get a clear picture of the size and shape of the school, helping him identify fish species and density. So why does he use the EK60 first if there is so much more data provided by the multibeam? Well, the amount of data provided by the ME70 is incredibly overwhelming; it would take weeks of data analysis to cover just a tiny section of the marine sanctuary. By using the EK60 to cover large areas and the ME70 to review small areas of specific interest, he is able to create fish distribution and density maps for the largest areas possible.

After collecting data from the two sonars, it needs to be processed. The method you use to process the data depends on your goal: biomass, population densities, and fish locations are all processed differently. Since rockfish are found close to hard, rocky seafloor, data analysis becomes quite complicated, as it becomes difficult to discriminate the fish from the seafloor. Hard bottoms also introduce a lot of bias to the data; for these, and other, reasons there are very few hard bottom studies for Fabio to refer to.

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Cleaned data. I’ve got a good feeling about this.

But back to the data analysis. Once data is collected, it is loaded into Echoview software. Fabio then removes the background noise coming from other equipment, averages the data to reduce variability, and manually modifies the seafloor line (rocky bottoms with lots of pinnacles give incorrect bottom data). This last step is crucial in this mission because the focus is on rockfish who live close to the bottom.

 

 

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School of fish shown on the right of the screen and the frequency response shown on the left. Fish are not lost today. They are found.

The clean echogram is then filtered for frequencies falling in the suitable range for fish with swimbladders (a gas-filled organ used to control their buoyancy). Object with a flat response at all frequencies (or slightly higher at low frequencies) will most likely be fish with swimbladders, whereas a high response to high frequencies will most likely not be fish (but it could be krill, for example). Once Fabio has made the final fish-only echogram, he exports the backscatter and uses it to create biomass or density estimates. All of these steps are necessary to complete the final product: a map showing where rockfish fish are in relation to the habitat.

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Krill shown on the right and frequency response shown on the left. Judge them by their size, we do.

 

 

 

 

 

 

 

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The final product. When making accurate maps of rockfish, there is no such thing as luck.

Personal Log:

It seems I overpacked sunscreen…12 hours of my day are spent in the acoustics lab staring at monitors, with brief breaks every so often to look for whales and other wildlife. This mission is so technical. I am grateful for the hours spent asking the scientists questions and having them explain the details of their work. Lately, the big screen TV in the lab has been turned on with some great movies playing. So far we’ve watched, Zootopia, Deadpool, LoTR, and, of course, The Force Awakens. May the 4th be with you…always.

Word of the Day: Holiday.

A holiday is an area in your bathymetry map that does not include any data (think of it as “holes in your data”). It’s like you’ve painted a picture, but left a blank splotch on your canvas.

 

Andrea Schmuttermair, Bottom’s Up!, July 15, 2015

NOAA Teacher at Sea
Andrea Schmuttermair
Aboard NOAA Ship Oscar Dyson
July 6 – 25, 2015

Mission: Walleye Pollock Survey
Geographical area of cruise: Gulf of Alaska
Date: July 15, 2015

Weather Data from the Bridge:
Latitude: 56 42.2N
Longitude: 153 46.5W

Sky:  Overcast; foggy

Visibility: 6nm
Wind Direction: 173 degrees

Wind Speed: 14 knots
Sea wave height: 2ft

Swell wave: 4-5ft

Sea water temp: 12.3C
Dry temperature: 11.5C

 

Science and Technology Log

In my last post we talked about the Aleutian Wing Trawl (AWT), the mid-water trawling net we use to take samples of pollock. There are two other types of nets we may use during our cruise, although not as frequently as the AWT.  Sometimes the echogram shows a large concentration of fish closer to the ocean floor. In this instance, we might use a bottom trawl net, known as the Poly Nor’easter (PNE), to “go fishing”. The process for putting out the net is similar to putting out the AWT, except that it is extended to just above the ocean floor in order to catch fish that are congregated towards the bottom. In our recent bottom trawl, we caught a lot of Pacific Ocean perch, or rockfish, and very few pollock.

It has been fascinating to see how scientists “do science” out here. Patterns and observations are important skills for scientists, and analyzing patterns and behaviors of fish help scientists to make informed decisions about whether they are seeing pollock, krill, rockfish, or something else entirely on the echogram. For example, acoustically, pollock and rockfish have the same reflectivity (and therefore are difficult to differentiate based solely on acoustics), but their behaviors are different. When we recently put out a bottom trawl net, we anticipated catching mostly rockfish because of the location we were at, and their schooling behavior close to the ocean floor. Rockfish are also usually found lower in the water column than pollock. Our first bottom trawl yielded quite a few rockfish, some jellies, several flatfish, and a few other types of fish. Just as we did with the pollock, we weighed, sexed and measured a sample of rockfish. These fish were a little more difficult to handle as they have sharp spines in several places.

There is a third type of net we deploy on this survey is called a Methot net. It’s named after Dr. Rick Methot, a famous fisheries modeler. This net has an opening of 5 square meters, and has a finer mesh than the AWT or the PNE at 2x3mm. At the end of the net is a small codend where the sample is taken from. This net is typically used to catch krill and macrozooplankton that would normally escape the larger nets. From the acoustic display, we would anticipate about 100-200 times more than what is actually caught in the net. Back scatter could be one reason for this. Scientists have worked to try and decrease this discrepancy by using strobe lights mounted on the net. The abundance tends to agree better with strobes on the net, with the hypothesis being that the organisms are blinded and don’t realize they’re going into the net.

Meet the Scientists

Kresimir smelling a capelin (smelt)- they smell like cucumbers!

Kresimir smelling a capelin (smelt)- they smell like cucumbers!

Chris, one of the scientists on board

Chris, one of the scientists on board

During one of our shifts, I had the opportunity to interview 2 of the scientists on our night watch team, Kresimir Williams and Chris Bassett. Their enthusiasm and passion for their work is evident in the discussions we have had and the work they are doing. It is great to work with scientists who are so knowledgeable and also patient enough to explain what we are doing here. Let’s meet them!

What is your educational background?

Kresimir:  I received my undergraduate degree in marine science from Samford in Birmingham, Alabama. During this time, I spent summers at Dauphin Island. I received my Master’s Degree in fisheries and aquaculture from Auburn (also in Alabama), and finally received my PhD in fisheries from the University of Washington.

Chris: I went to the University of Minnesota for my undergraduate degrees in mechanical engineering and Spanish. I then went on to receive both my Master’s & PhD in mechanical engineering at the University of Washington.

How long have you been working at the AFSC lab in Seattle?

Kresimir:  I have been working at the lab for 13 years as a research fisheries biologist.

Chris: I am currently working with both AFSC and the Applied Physics Lab at the University of Washington as a post-doctoral research associate.

What do you most enjoy about your work as a scientist?

Kresimir: I enjoy doing the research, discovering new things, and conducting field experiments.

Chris: The work that I do allows me to learn by playing with big kid toys in beautiful places; for example, the EK80, one of the broadband acoustic scattering systems brought on this ship

What has been a career highlight for you?

Kresimir:  The development of the CamTrawl (what we are currently using on our nets here on the Dyson). I have seen this project from development to operationalization.

Chris: Using broadband acoustics systems in a 4 month long lab experiment to detect crude oil spills under sea ice.

What does it mean to you to “do science”?

Kresimir: It means following a set of rules, and discovering things that can be repeated by other people. Remembering that data leads you to the answers rather than using it for something you want to prove.  Research generally generates more questions.  Finally, it means learning how the little piece of the world you are interested in works.

Chris: It means looking around and seeing what knowledge exists and where we can advance knowledge in that field and how we can do so. It’s understanding that often identifies more new questions than it answers.

What message would you give students who want to pursue a career in (marine) science?

Kresimir: Do your math homework! There are very few biologists out there discovering new things, so you need to bring something else to the table such as coding or geosciences. There is a lot of quantitative modeling and interplay between other sciences such as physics and chemistry.

Chris: Do your math homework! Having skills in a little bit of everything – all of the sciences come into play. You also need good writing skills.

What is your favorite ocean creature?

Kresimir:  I love all kinds of fish because I can find something unique about each one of them.

Chris: Bluefin tuna

Thanks for the interview gentlemen!

Personal Log

The Oscar Dyson runs for 10 months out of the year, more than most of the other ships in the NOAA fleet. Many of the people on this ship are here almost year-round, and call the Dyson their home. Having places where they can relax and feel at home is important. Besides up on the bridge or out on the deck, another place to spend some free time is in the lounge. Equipped with beanbag chairs, a large couch, and some comfy chairs, the lounge encourages people to hang out, watch a movie, play video games, or just relax after their shift.  We have a large selection of movies, and have access to some of the most recent movies as well. We recently watched Mockingjay, the third movie in the Hunger Games series. It was a good movie, but not as good as the book.

I am really enjoying my time so far on the Oscar Dyson, mostly because I am being challenged to learn new things. We’ve had a bit of downtime the last couple nights, and it has been a good opportunity for me to learn the game of the ship, cribbage. This is a popular game amongst the scientists, and you can typically find some of them playing a quick round in between shifts or as a break from work. I’m by no means great at it yet, but I expect by the end of this trip I’ll be a lot better.

Filleting some rockfish

Filleting some rockfish

Fileting Rockfish

Fileting Rockfish

When I first got on board the Dyson, I remember talking to one of the scientists about filleting fish. I’m not too sure how we got on that subject, but it occurred to me that I had never actually filleted a fish myself. I used to fish as a kid, but we left the cleaning and filleting to my dad (thanks, dad). What could be a better time to learn this skill than on a boat full of experienced fishermen? We ate a rockfish ceviche that Robert, one of the scientists, had made the first night I was on the ship, and it was delicious. When we pulled in our bottom trawl of rockfish, it was the perfect time to learn how to fillet a fish. Rockfish are a bit tricky, as they have several sharp spines covering them. We had to be careful so as not to get stabbed by one of them- it wouldn’t feel very good! I had a busy evening helping to fillet about 14lbs of rockfish. I was by no means quick (our lead fisherman filleted 3 rockfish to my 1), but I had lots of time to practice.

Did you know? Pacific Ocean Perch (POP), or rockfish, were overfished in the 1970’s. Today, Pacific Ocean perch have recovered to the extent that they support a sustainable fishery in Alaska. Read more about the POP.

This POP bears a striking resemblance to the scorpionfish, one of the species we brought up in the SEAMAP Summer Groundfish Survey in the Gulf of Mexico in my TAS trip in 2012. Guess what? These two fish, while living thousands of miles apart, are actually related! They both belong to the family Scorpaenidae.

Pacific Ocean Perch (rockfish)

Pacific Ocean Perch (rockfish)

Scorpionfish we pulled up in a bottom trawl from the Gulf of Mexico (TAS2012)

Scorpionfish we pulled up in a bottom trawl from the Gulf of Mexico (TAS2012)

Kainoa Higgins: Preparing to Set Sail! June 15, 2014

NOAA Teacher at Sea

Kainoa Higgins

(Almost) Aboard the R/V Ocean Starr

June 18 – July 3, 2014

Mission: Juvenile Rockfish Survey

Geographical Area of Cruise: Pacific Coast

Date: June 15, 2014

Personal Log

Aloha from the great Pacific Northwest!  My name is Kainoa Higgins and although I was born and raised on the island of O’ahu, Hawai’i, I have spent the last 10 years calling Tacoma, Washington home.  I am incredibly excited to have been selected as a 2014 NOAA Teacher at Sea and can’t wait to climb aboard the R/V Ocean Starr in a matter of hours!  I will be participating in two legs of research during my two and half weeks on ship.

During the first leg, I will be assisting scientists with conducting a Juvenile Rockfish Survey as they examine groundfish populations off the coast of the Western Seaboard of the North America.  Though I have been attempting to get caught up to speed, I currently only understand the program at a general level.  There are many species of rockfish, all of which are commercially valuable, and keeping track of their populations and distributions is essential for conscious management.  Having spoken with my Chief Scientist for this leg, Ric Brodeur, on several occasions leading up to my departure, I understand that my job will entail any, some or all of the following: mammal/bird observational surveys and plankton analysis by day followed by sorting of trawled collections analysis of the catch in the wet lab by night.  I’ll be able to share more as the adventure unfolds.

In the second leg, I will connect with Laurie Weitkamp who will take over as chief scientist with a fresh research team and research focus.  In a recent e-mail Laurie explained that this leg will be “experimental”.  In short, we will be trying a variety of modifications to a marine mammal excluder device to see how it fishes and influences the catch.  I’m not sure, exactly, how the MMED is used, but I would be willing to take a guess at it’s purpose.  I imagine it has something to do with an attempt to maintain commercial fishing operations without the interruption of marine mammals (dolphins, porpoises, seals, whales, etc.) in close proximity.  Through some sort of “deflection”, its goal would also be reduce unintentional by-catch.  Once again, I’ll know more concretely a bit further down the road.  According to Laurie, in addition to help work up the catch, I will be helping with “marine mammal watch” before and during fishing.  Since we will use a surface trawl during the day, it is possible that we could catch a marine mammal (e.g., seals and dolphins). To minimize this risk, I will help serve as a lookout  before we set and when the trawl is out, and are required to immediately stop fishing if any are spotted nearby.  I look forward to spending some time on the bow scanning the horizon for marine mammals.

Plankton

One of my favorite pics of marine diatoms (phytoplankton) from the Puget Sound. Taken with iphone camera though microscope eyepiece.

A bit more about myself and the school I represent.  I grew up loving the ocean.  Much of my life as a child was spend in or around it.  Whether snorkeling, surfing or fishing my brother and I were raised to respect and appreciate all that the ocean had to offer.  After all, my name, Kainoa, means “free as the sea”.  There is a saying in the islands, Malama ‘aina, Malama i ke kai, meaning ‘to care for the land and care for the ocean’.  After graduating from Punahou School  in Honolulu, Hawaii I headed for the great Northwest to attend the University of Puget Sound.  I participated in Athletics, Lu’au, Senior Theatre Festival and even Greek Life.  I studied Biology and spent a semester abroad in Christchurch, New Zealand.  Even though I took Marine Biology in one of the most amazing diverse systems in the world, my favorite class had to be “The Diversity of Algae”.  It opened my eyes up to the beauty and importance of micro life for the first time.  This led to my passion for – and borderline obsession with – plankton.

After earning a Master’s in the Arts of Teaching from UPS, I began my career at the Tacoma School of the Arts teaching entry level biology.  After my second year, I was asked to join our recently founded sister school, the Tacoma Science and Math Institute (SAMI) located in Point Defiance Park on the North Tacoma peninsula.  SAMI  is built around a particular vision: we believe that students make the most of their learning when they take ownership of their education—when students intentionally choose to take on the challenge real learning entails. We further believe that this ownership most naturally develops within a learning community, encouraged by others who share that commitment.  We theme our curriculum around the math and science and emphasis the integration of disciplines and staff collaboration all the while perpetuating the pillars on which the schools were founded: community, empathy, thinking and balance.  SAMI has allowed me to pursue my passion for marine science.  We are a two minute walk to the waterfront which makes the learning opportunities for myself as students invaluable.  Between this field resource and collaborations with the University of Washington in the High School program and the University’s School of Oceanography I am in a position to offer my students a world-class learning experience.

I think it is important that teachers are always looking for opportunities to improve their practice and better educate themselves in ways that will better prepare their students for the world ahead of them.  The Teacher at Sea opportunity is an incredible way to engage myself as a life-long learner and will help me to better engage and inspire my students.  I look forward to designing and offering lessons derived from real-time science and experiences.  I am very grateful for this opportunity and can’t wait to share it with you.

See you soon,

Kainoa

 

SAMI Students

SAMI Students reflecting on a trip to Dungeness Spit, WA.

Pups

The men of the house in my absence

Sandys

A relationship founded on respect