Erica Marlaine: Oh, the Places You’ll Go! July 6, 2019

NOAA Teacher at Sea

Erica Marlaine

Aboard NOAA Ship Oscar Dyson

June 22 – July 15, 2019

Mission: Pollock Acoustic-Trawl Survey

Geographic Area of Cruise: Gulf of Alaska

Date: July 6, 2019

Weather Data from the Bridge:

Latitude: 55º 4.07N
Longitude: 156º 42 W
Wind Speed: 3.2knots
Wind Direction: 96º
Air Temperature:  10.3º Celsius
Barometric Pressure: 1025.7. mb
Surface Water temperature: 11.05º Celsius
Depth of water column: 1,057.6 meters

If you love science and exploring, consider a career in the NOAA Corps!

NOAA Corps

The NOAA Corps is one of our nation’s seven uniformed services (along with the Army, Marine Corps, Navy, Air Force, Coast Guard, and Public Health Service Commissioned Officer Corps). NOAA Corps officers are an integral part of the National Oceanic and Atmospheric Administration (NOAA), an agency of the U.S. Department of Commerce. NOAA and the NOAA Corps can trace their lineage to 1807 when President Thomas Jefferson signed a bill for the “Survey of the Coast.” The survey work was done by Army and Naval officers along with civilian men and women. The Coast Survey was actually the first federal agency to hire female professionals! Their duties included charting our nation’s waterways and creating topographic maps of our shorelines, which made our marine highways among the best charted in the world.

Today, the NOAA Corps is an elite group of men and women trained in engineering, earth sciences, oceanography, meteorology, and fisheries science. NOAA is comprised of the National Weather Service, National Marine Fisheries Service (NOAA Fisheries), Office of Oceanic and Atmospheric Research (NOAA Research), National Environmental Satellite, Data and Information Service, National Ocean Service, and the Office of Marine and Aviation Operations. NOAA Corps officers operate NOAA’s ships, fly aircraft, manage research projects, conduct diving operations, and serve in staff positions throughout NOAA.

NOAA Officer Spotlight

ENS Lexee Andonian
ENS Lexee Andonian

I had the opportunity to speak with Ensign (ENS) Lexee Andonian (although by the time this is published Ms. Andonian will have been selected for LTJG (Lieutenant junior grade)! ENS Andonian has been a member of NOAA Corps for almost 2 years, and loves her job, but it was not something she originally considered as a career (or even knew about). She first learned about NOAA while working at a rock climbing gym. A patron mentioned it to her, and offered to show her around a NOAA ship. She went home and googled NOAA. With her interest piqued, she decided to accept the patron’s offer, and went to Newport, Oregon to tour the NOAA Ship Bell M. Shimada (which is actually the sister ship of the NOAA Ship Oscar Dyson. A sister ship means they were based off the same blueprint and can serve similar projects.)

ENS Andonian applied for the NOAA Corps, but was waitlisted. NOAA is highly selective and accepts a very limited number of applicants (approximately 15-25 twice a year.) Undeterred, she applied for the next NOAA class, and was once again waitlisted, but this time she was accepted off the waitlist. After 5 months of training at the Coast Guard Academy, she was ready to begin her assignment onboard a NOAA ship, where additional hands-on training occurs non-stop. Each NOAA Corps member wears a multitude of “hats” while onboard. ENS Andonian is currently the Acting Operations Officer, the Navigation Officer, the Environmental Compliance Officer, and the Dive Officer. ENS Andonian loves that her job allows her to see unique places that many people never get to explore since they are not accessible by plane or car. Asked what she misses the most from home, she said, “Bettee Anne” (her dog).

Science and Technology Log

Today I was introduced to a few new species in the fish lab. Until now, most of the jellyfish have been Chrysaora melanasta, which are beautiful and can be quite large, but today I saw 2 egg yolk jellyfish, aptly named as they look like egg yolks.

Egg yolk jellyfish
Egg yolk jellyfish

I also saw a lumpsucker, which is the cutest fish I have ever seen. Lumpsuckers look like little balls of grey goo. He (or she) seemed to look right at me and kept opening and closing its mouth as if trying to say something. Lumpsuckers have a suction cup on their bottom which allows then to adhere to rocks or other surfaces.


Personal Log

As a teacher, I create experiences for my students that will take them out of their comfort zone so that they can realize just how much they are truly capable of. On the NOAA Ship Oscar Dyson, it is my turn to step outside my own comfort zone. If you would have told me a few months ago that I would feel comfortable being elbow-deep in live fish and jellyfish, or dissecting fish to see whether they are male or female, or slicing into a fish’s head to collect otoliths (ear bones), I would not have believed you, but that is how I spend every day onboard the Oscar Dyson, and after 2 weeks, it feels like something I have done all my life.  It is an experience I highly recommend to everyone!

Karah Nazor: The Glowing Dolphins of the Channel Islands and Interview with UCSC Graduate Student Ilysa “Ily” Iglesias, May 31, 2019

NOAA Teacher at Sea

Karah Nazor

Aboard NOAA Ship Reuben Lasker

May 29 – June 7, 2019

Mission: Rockfish Recruitment & Ecosystem Assessment

Geographic Area: Central California Coast

Date: May 31, 2019

Game Plan and Trawling Line: Channel Islands San Nicolas Line

I am up on the flying bridge and I just saw two humpback whales spouting, an albatross soaring and a large Mola Mola on the sea surface.  In this blog I will write about an amazing once in a lifetime experience that from last night- May 31, 2019. The first haul was called off due to an abundance of Pacific White-Sided Dolphins, Lagenorhynchus obliquidens, (as reported by the inside marine mammal watch prior to net deployment), so we motored on ahead to the second station, but dolphins chased the ship all the way there, too.  One strategy to encourage marine mammals to leave is for the ship to stop moving with the hope that the dolphins become disinterested and vacate the area. This pod was intent on having a party at the ship so Keith Sakuma encouraged everyone to just go outside to observe and enjoy the dolphins! 

Fishing on this survey takes place at nighttime (so the fish do not see the net) and Scripps graduate student Kaila Pearson and I stepped outside on the side deck into the darkest of dark nights. Kaila and I carefully placed one foot in front of the other because we couldn’t see our feet and where to step next. I was afraid I would trip. When I asked Keith Hanson if we should use a flashlight to safely make our way up to the top deck, he suggested that we stay in place for a few minutes to allow our eyes to adjust. Within 5 minutes or so objects around us started to present themselves to us within the black void.  We could eventually see our feet, each others faces, the dolphins, and even the finer features of the sea surface.

Within a few minutes Ily Iglesias reported seeing bioluminescence, a type of chemiluminescence that occurs in living things, such as the familiar green glow of lightening bugs in the Summer in the South.   This glow results from oxidation of the protein luciferin (present in photophore cells/organs) by the enzyme luciferase.  It its excited state, lucifern emits light.  This reaction is known to occur in some marine bacteria, dinoflagellates (single celled photosynthetic organisms), squid, deep sea fish, pyrosomes and jellyfish, and I am fortunate to have observed many of these creatures already on this research cruise (see photos below).  Some animals have photophore organs and generate their own luciferin, while others are hosts to bioluminescent bacteria.

deepsea longfin dragonfish
The large photo organ is a large green circle under the eye of the deepsea longfin dragonfish, Tactostoma macropus.
California lanternfish
California lanternfish, Symbolophorus californiensis, with photophores under the lateral line and the ventral surface.
California lanternfish photophores
California lanternfish photophores
Blue lanternfish
Blue lanternfish, Tarletonbeania crenularis, collected from a bongo net at 265 meters. Photophores line the ventral surface of the body.
Cranchia scabra
Cranchia scabra “baseball squid” with large photophores lining the eyes.
Chiroteuthis veranii squid
Chiroteuthis veranii squid

When dinoflagellates floating on the sea surface are agitated, they glow.  At first when I was trying really hard to see this, I noticed a couple of tiny flashes of green light, sort of like lightening bugs, but it wasn’t anything super obvious. In time, I noticed clouds of faint light, sort of like a glowing mist floating the water’s surface, that moved up and down with the swell.  I hypothesized that dinoflagellates on the sea surface were being agitated by the passage of waves through them and Ily suggested that it was caused by schools of anchovies.

Since the dolphins were intent on staying, we decided to head to the next station.  I knew that as the ship began to move that the bow would be breaking through surface water that had previously been undisturbed, and I predicted the bioluminescence would be much more intense.

As we took off, the dolphins began to bow surf and, as I predicted, the dinoflagellates were activated and this time their glow was a bright white.  As the dolphins surfaced to breath, their skin became coated with the glowing algal cells, creating an effect as if they were swimming in an X-ray machine.  The dolphins were literally glowing white swimming in a black sea! We were so entranced and excited by the beauty, we screamed in delight. I am sure the dolphins heard us cheering for them. They too, seemed excited and could see each other glowing as well.

Next we saw the faint cloud of dinoflagellates caused by Northern anchovies (Ily was right) up ahead of us. As the ship encountered the school of small (~ 3-6 inch) fish, they also started to glow really bright and it was easy to see all of the individual fish in the school. The dolphins could also see the glowing fish and split off in different directions to hunt them.  There were hundreds of fish that dispersed as they were being chased creating a pattern of short white glowing lines somewhat like the yellow lane markers on the highway.

The display was unlike anything I have ever witnessed. It was like the Aurora Borealis of the sea.  Despite our best efforts, our cell phone cameras were unable to pick up the bioluminescent signal, however, we do not need photos because the patterns of light will be forever embedded in our minds. The dolphins eventually tired from the surf and chase and departed. Ily said the experience was “an explosion of light that overwhelmed the senses” while Flora said it was “better than fireworks.”

With no marine mammal sightings at the third station, we completed a five minute haul in the deep channel and collected a huge white bin of anchovies (see photo of Keith Hanson with this catch below). In this catch we found a few Mexican lampfish, 3 king of the salmon, a lot of of large smooth tongues, a lot of salps, a few pyrosomes and one purple striped jellyfish.  The purple-striped jelly (Chrysaora colorata) is is primarily preyed upon by Leatherback turtles. Haul 2 was conducted over shallower water near San Nicolas Island and we only found salps and four small rockfish in the catch.  After these two hauls, we called it a night and wrapped up at 4:15 a.m.

Scientist Spotlight: Ilysa Iglesias, NMFS SWFSC FED/ University of California Santa Cruz (UCSC)

Ilysa “Ily” is a doctoral student who works in John Field’s Lab at UCSC.  She is studying the fish we are collecting on this cruise as part of her research. She is very knowledgeable about all of the survey research objectives. She is also one of the most positive and gregarious people I have every met. Ily grew up in Santa Cruz, CA, and enjoys surfing, hiking, gardening and raising chickens.   Ily is a fan of early marine explorer Jacques Cousteau, who often wore a red beanie/toboggan and a blue shirt. Ily came prepared and brought six red hats (that she knit herself) for each of the members of the sorting team. Ily’s favorite fish is the hatchetfish. She was thrilled when we found on in the catch!

Ilysa with hatchetfish
Ilysa Iglesias with deepsea marine hatchetfish
deepsea marine hatchetfish
A deepsea marine hatchetfish caught in the bongo which was deployed to depth of 265 meters.

Ily obtained a Bachelor’s degree from UC Berkeley in integrated biology and a Masters Degree from the University of Hawaii in Zoology with a specialization in marine biology.  Her thesis was on the function of intertidal pools as a nursery habitat for near-shore reef fish. She compared otoliths (fish bone ears) of fish reared inside and outside of tide pools and compared their growth rates.  Otoliths can be used to the age of the fish much like counting rings on a tree and stable isotope analysis reveals information about where the fish were reared.

Ily, Flora and Kristin have all used otoliths in their research and taught me how to locate and collect the sagittal otolith from anchovies and myctophids. It is a tiny ear bone (one of three) that is positioned near the hindbrain of fish.  See photos below of the otoliths we collected. This is a technique that I will definitely take back to my classroom and teach my McCallie students.

Otoliths we collected and observed under the dissecting microscope.
Photomicrograph of otoliths
Photomicrograph of otoliths we collected from blue lanternfish (top) and Northern Anchovy (bottom) and observed under the dissecting microscope.

After obtaining her masters degree, Ily was Conservation Fellow for the Nature Conservancy in HI and worked in octopus fisheries before returning home to join NOAA’s salmon team and then the rockfish team as a Research Associate.  Ily has just completed the first year of her doctoral work in the Field Lab and expects to complete the program within 5 years.

On this cruise, Ily is collecting small fish called Myctophids for her research. These are small bioluminescent fish that live at depths of 300 and 1,500 m in the bathypelagic zone. In this survey, we encounter these deep sea dwellers during their nightly vertical migration up to the edge of the photic zone at depths we are targeting.  They are likely chasing their prey (krill) on this upward journey. It is amazing to me they are able to withstand the pressure change. Mcytophids are also known as lanternfishes and have bioluminescent photophores dispersed on their bodies. The fish sorting team analyzes the position of these organs to help distinguish between the different species. There are 243 known species of myctophids, making these little fishes one of the most diverse vertebrates on Earth.  They are so abundant in the sea that they make up 65% of the ocean’s biomass, but most people have never heard of them!

In 2014- 2015 there was an anonymously high sea surface temperatures off of the Pacific Coast known as The Blob.  Marine scientists are still elucidating the effect of the hot water had on fish populations and ecosystems. Ily explains that “atmospheric forcing caused changes in oxygen and temperature resulting in variability in the California current.”  The water was less nutrient dense and caused a reduction in phytoplankton. This disruption of primary production propagated up the trophic cascade resulting in die offs of zooplankton, fish, marine mammals and birds.  

Ily is using the catch records and acoustics data from the rockfish survey to study changes in distribution and abundance of myctophids from before, during and after The Blob (2013-2019).  She aims to understand if and how their trophic position of myctophids was affected by the unusually high sea surface temperatures.   Using elemental analysis isotope ratio mass spectrometry to analyze the Carbon and Nitrogen atoms incorporated into fish muscle, Ily can determine what the myctophids were eating each year.

Kate Schafer: So Many Snappers… September 24, 2017

NOAA Teacher at Sea

Kate Schafer

Aboard NOAA Ship Oregon II

September 17 – 30, 2017


Mission: Shark/Red Snapper Longline Survey

Geographic Area of Cruise: Gulf of Mexico

Date: September 24, 2017

Weather Data from the Bridge:

Latitude: 28o 25.1’ N
Longitude: 94o 50.3’ W

Broken sky

Visibility 10 nautical miles

Wind speed 13 knots

Sea wave height 2-3 feet

Temperature Seawater 28.8 o Celsius

Science and Technology Log:

This is a shark and red snapper longline survey, and the sharks tend to steal the stage.  They are bigger (for the most part), more diverse and definitely have more of a reputation.  I have been surprised, however, by how much I’ve been drawn to the snappers.  They are a beautiful color, and tend to come up in groups that are pretty similar in size.

Red snapper (Lutjanus campechanus) ready to be measured

The Northern Red Snapper (Lutjanus campechanus) is commonly fished in the Gulf of Mexico, both recreationally and commercially.  It turns out that the commercial fishers get 51% of the catch quota and the recreational fishers get 49%.  The methods for dividing up those two basically equal pieces of the pie is different between the commercial and recreational fishers. In addition, the commercial fishing catch is monitored very closely, while the recreational fishing catch numbers are largely unknown.  Plus, the states have their own waters that extend out to different distances, depending on the state, and the federal waters extend from the state water boundary to 200 nautical miles offshore.  So, in other words, managing the fishery is quite complicated.

So, how do all these fishing rules and regulations get established and modified over time?  A law was passed in 1976, called the Magnuson-Stevens Fishery Conservation and Management Act, and one of the key parts of the act established eight regional management councils for regulating fishing in federal waters (more information on the act here:  It also established the 200 nautical mile extension of federal waters from land.  The Gulf of Mexico Fishery Management Council (GMFMC) is responsible for creating Fisheries Management Plans (FMPs) for fisheries within the U.S. federal waters of the Gulf of Mexico, from southern Texas, along Louisiana, Mississippi, and Alabama, and down the west coast of Florida.  This graphic shows the catch limits for red snapper and other species for 2017 set by the GMFMC.  For red snapper, the catch limit is close to 14 million pounds.

Annual Catch Limits as set by the Gulf of Mexico Fishery Management Council (

The data that we are collecting helps scientists and policy makers to determine what the annual catch limit for a particular season should be.  For each fish that we bring on board, we measure the fish length and weight, as well as the weight of the gonads.  In addition, we collect their otoliths (ear bones) and samples of the ovaries of females.  These both help managers to estimate the age and size of the population, and future populations as well.

Otoliths are calcium carbonate hardened structures and are present in the part of the inner ear that is responsible for balance.  Humans and other vertebrates have them too, and they can be used to tell the age of the fish.  The otoliths of Lutjanus campechanus are quite large.  There seems to be an overall relationship between the habitat of the fish species and the size of the otolith.  Species like Lutjanus campechanus that live along reefs and rocky structures have much larger otoliths than species like tuna that swim up in the water column.  Flying fish, which we’ve seen a lot of, also have large otoliths, given their body size, probably aiding them in knowing where they are as they glide through the air.

Otoliths taken from one of the red snappers we collected

Well, we have been collecting a lot of data over the past couple of days to help inform these policies in the future!  Each line we’ve pulled in lately has had a dozen or more snappers on it,  and they are a lot of extra work as compared with the sharks, due to all the samples we have to collect once we’re done.  A couple times, we’ve barely finished before it was time to start baiting lines again.

Personal Log:

As I mentioned earlier, I’ve really come to love the red snappers.  Their eyes are the same color as their skin and I’m just awed by their size.  I am used to snappers that I’ve watched on coral reefs, and even the largest species I’ve seen on reefs are nothing compared with these guys.

Red snapper (Lutjanus campechanus) eyes

I’ve also adjusted to the shift in my day, as evidenced by the fact that I’m finishing this up at 1 a.m.  It has been a long time since I’ve been on this kind of late night schedule.  I’m enjoying it, especially because I know when I return to California, I’ll be getting up at 5:30 a.m. again.


Did You Know?

That snappers eat a wide variety of different foods, including fish and various types of crustaceans? Here are a couple of items we’ve found in the ones we’ve caught.  Can anyone identify them?  I studied the second group for my Ph.D. dissertation!

Mystery snapper food

More snapper food






Kimberly Scantlebury: Sharks, Snappers, and Sealegs, May 2, 2017

NOAA Teacher at Sea

Kimberly Scantlebury

Aboard NOAA Ship Pisces

May 1-May 12, 2017

Mission: SEAMAP Reef Fish Survey

My beautiful home for two weeks.

Geographic Area of Cruise: Gulf of Mexico

Date: May 2, 2017

Weather Data from the Bridge

Time: 11:25

Latitude: 2808.4978 N, Longitude: 09329.9347 W

Wind Speed: 18.69 knots, Barometric Pressure: 1015.6 hPa

Air Temperature: 27.4 C, Water Temperature: 24.4 C

Salinity: 35.9301 PSU,  Conditions: sunny, no clouds, small waves

Science and Technology Log

There are several ways data is collected for the SEAMAP Reef Fish Survey in order to have a more complete understanding of the reef system. One of them is fishing with vertical long lines with Bandit reels. We are fishing for snapper species (Lutjanus sp.), grouper species (Serranidae sp.), and certain species of amberjack (Seriola sp.). There are three reels mounted on the vessel’s starboard side. The fishing works by dropping a weighted line with ten mackerel-baited hooks per reel, which then ends with an orange float. The boat is kept as still as possible and we wait a designated period of time before reeling up the lines.

I fished with deckhand James and Texas A&M graduate student, Jillian. The other lines were fished by NOAA scientists Joey, Kevin, John, and other deckhands. Our first try we caught two large spinner (Carcharhinus brevipinna) sharks that escaped back to sea. The other lines caught smaller sharks and a couple red snappers. We ended up catching and returning six sharks.

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Even though we were not aiming to catch sharks, they are part of the ecosystem and the data is collected. The data is written down on paper first and then transferred to computer databases. Some of the sharks required wrangling and less data was collected before releasing them live to prevent harm to shark and people.

The red snappers were weighed, measured in different ways, sexed, the sexual development was determined, and then retained, meaning we kept the fish. The otoliths (ear bones) and gonads (reproductive parts) were also weighed, labeled with an unique bar code, and stored for later analysis down at the Panama City Lab.

Determining variability of fish ages is possible due to this important work. Otoliths work similar to aging tree rings. Under a microscope you can clearly read each year. By comparing fish size to gonads, it has been determined a thirty-year-old red snapper can produce more eggs than 30 one year old red snappers. It is easy to see the research conducted on NOAA Ship Pisces is vital to managing and protecting our nation’s seafood supply.

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Personal Log

The movement aboard a ship this size is different than smaller vessels I’ve been on such as a ferry, lobster boat, and other research vessels. Right now we are expecting to not work Thursday due to high seas and wind. The NOAA Ship Pisces’s 208 feet sways in every direction-up, down, all around. The adjustment period for acclimating to this unpredictable movement is referred to as, “getting your sealegs.” This is also an apt metaphor for my time adapting to life on board.

Other than research protocols, Teachers at Sea need to learn what to do in case of emergencies. The science staff, including myself, received a safety briefing before leaving port.  Each person is assigned a muster station where they are to report if there is a Fire or Man Overboard. A separate location is assigned for Abandon Ship. Each emergency has a designated series of short or long horn blasts from the ship so it is clear to all what is happening.

It’s Gumby suit time!

Later, the whole ship drilled Abandon Ship. As fast as possible, we each carried our personal flotation device (PFD) and survival suit (referred to as a Gumby suit) to our life raft station. I then practiced how to get the suit on in less than a minute.

Did You Know?

As a New Englander, I talk faster than most people on NOAA Ship Pisces, whose home port is Pascagoula, Mississippi.

There are a lot of oil rigs in the Gulf of Mexico. We have not seen any other vessels out here, but can often see a half dozen rigs at a time. In fact, NOAA Ship Pisces was recognized for, “outstanding and successful emergency mobilization by providing acoustic monitoring survey operations under hazardous and arduous navigation conditions in support of the Deepwater Horizon Oil Spill recovery efforts.” 

Oil rigs in sight as equipment is brought back aboard.

David Walker: Equilibrium at Sea (Days 6-9), July 3, 2015


NOAA Teacher at Sea
David Walker
Aboard NOAA Ship Oregon II
June 24 – July 9, 2015

Mission: SEAMAP Bottomfish Survey
Geographical Area of Cruise: Gulf of Mexico
Date: July 3, 2015

Weather Data from the Bridge

Weather Log 7/2/15
NOAA Ship Oregon II Weather Log 7/2/15

Weather has fortunately continued to be calm.  The only main deviation from clear skies has been haziness (symbolized “HZ” on the above weather log from 7/2/15).  On 7/2/15, sky condition varied from FEW (3-4 octas) in the very early morning, to SCT (3-4 octas) and BKN (5-7 octas) at midday and afternoon, to SCT (3-4 octas) in the evening and night.  Swell waves have varied throughout the past couple of days, from less that 1 meter to around 3 meters in height.

Science and Technology Log

The past few days honestly blend completely together in my mind.  I feel as though I have reached an equilibrium of sorts on the boat.  The night shift has proceeded normally – station to station, trawl to trawl, CTD data collection at each station, plankton collected periodically throughout the shift.  Certain trawl catches have been exceptionally muddy, which poses a further task, as the organisms must first be separated from all of the mud and cleaned, before they can be identified.

In addition, on Day 6, the trawl net was damaged on a couple of occasions.  I’ve realized that a trawl rig is quite the complicated setup.  The trawling we are doing is formally called “otter trawling”.  Two boards are attached at the top of the rig to aid in spreading out the net underwater.  To allow the net to open underwater, one of the two lead lines of the net contains floats to elevate it in the water column.  A “tickler chain” precedes the lead lines to stir fish from the sea floor and into the net.  The fish collected by the net are funneled into the terminating portion of the net, called the “cod end”.  FMES Warren Brown is an expert when it comes to this entire rig, and he is in charge of fixing problems when they arise.  On Day 6, Warren had to fix breaks in the net twice.  With help from Lead Fisherman Chris Nichols and Skilled Fisherman Chuck Godwin, new brummel hooks were attached to the head rope for one of the door lifting lines, and a new tickler chain was installed.

I also learned a lot more of the specifics involved in the workup of the plankton catch.  The dual bongo contains two collection nets in parallel.  Plankton is removed from the cod ends of these nets, but not combined.  The plankton from the left bongo is transferred to a mixture of formaldehyde (10% v/v) and sea water for preservation.  The plankton from the right bongo is transferred to 95% ethanol.  The reason for this is that different solvent mixtures are needed to best preserve different parts of the plankton in the sample.  The formaldehyde solution is best for fixing tissue, yet it tends to dissolve hard parts (for example, otoliths, discussed below).  The ethanol solution is better for preserving hard parts (bones, cartilage, etc.).  This explains the need for two bongos.  Workup of collected plankton from the Neuston net is similar, except many non-plankton species are often collected, which have to be removed from the sample.  Highlight non-plankton species from the past couple days have been sailfin flyingfish (Parexocoetus brachypterus) and a juvenile billfish (Istiophoridae).  Neuston-collected plankton is transferred to 95% ethanol.  This solvent is the only one needed here, as only DNA analysis and stock assessment are conducted on Neuston-collected plankton.  All plankton is shipped to Poland, where a lab working in collaboration with NOAA will analyze it.  Samples are broken down according to a priority species list sent by NOAA.

The CTD survey is coming along nicely.  Progress through July 1 is shown on the below bottom dissolved oxygen contour.  Similar trends to those commented on in my last blog post continue to be observed, as a further area of hypoxia has been exposed near the coastline.  You can see that our survey is progressing east toward Mississippi (we will finish this leg in Pascagoula, MI, though the survey will continue on to the Florida coast during Leg 3).

A couple of other distinct memories stand out in my mind from the past couple of days:

  • Sexing “ripe” fish. Sometimes, certain species of fish are so fertile over the summer that certain individuals are deemed “ripe”.  Instead of cutting into these fish, they can be more easily sexed by applying pressure toward that anus and looking for the expression of semen or eggs.  One of the species for which this technique is most often applied this time of year is the Atlantic cutlassfish (Trichiurus lepturus).  One must be careful, however, for as I found out, the gametes sometimes emit from the anus with much force, shooting across the room.  It only takes wiping fish semen off of your face once to remember this forever.
  • Flying fish. I saw my first flyingfish (Exocoetidae) during a plankton collection with the neuston net.  The net would scatter the fish, and they would fly for cover, sometimes 10-15 meters in distance.  Amazing.
  • Preparing sand dollars. Interestingly, the sand dollars we caught (Clypeaster ravenelii) looked brown/green when they came out of the ocean.  Sand dollars are naturally brownish, and in the ocean, they are most often covered in algae.  We kept a couple of these organisms to prepare.  To prepare, we first placed the sand dollars in a dilute bleach solution for awhile.  We then removed them and shook out the sand and internal organs.  We then placed them back in the bleach for a little longer, until they looked white, with no blemishes.  The contrast between the sand dollar, as removed from the ocean, and this pure white is quite remarkable.

  • Otoliths.  Fisheries biologist Kevin Rademacher showed me a nifty way to remove the otoliths from fish.  Otoliths, “commonly known as ‘earstones,’ are hard calcium carbonate structures located behind the brain of bony fishes,” which “aid fish in balance and hearing” (Florida Fish and Wildlife Conservation Commission).  When viewed under microscope and refracted light, otoliths show a pattern of dark translucent zones (representing period of quick growth) and white opaque zone (representing periods of slower growth).  By counting the white opaque zones (called “annuli”), fisheries biologists can estimate the age of the fish.  Granted, this process differs for different fish, as different fish species have different otolith size.  Accordingly, a species standard is always prepared (usually a fish raised from spawn, from which the otoliths are taken at a known age) to estimate the growth time associated with one whole annulus for the particular species.  Sample otoliths are compared to the standard to estimate age.  Otolith analysis also allows scientists to estimate “growth rates,…age at maturity, and trends of future generations” (Florida Fish and Wildlife Conservation Commission).  On this survey, we only take otoliths from fish that are wanted for further laboratory analysis, but are too large to store in the freezer.  On some surveys, however, otoliths are removed from all fish caught.  I got to remove the otoliths from a large red snapper (Lutjanus campechanus).  The first step is to make an incision to separate the tongue and throat from the lower jaw.  The hand is then inserted into the hole created, and using a fair bit of force, the throat and gills are ripped away from the head to expose the vertebrae.  The gills are then cut from the base of the vertebrae, to expose the bony bulb containing the sagittal otoliths.  Diagonal cutters are then used to crack open the boney bulb containing the sagittal otoliths, and the otoliths are removed using forceps.

Personal Log

I am still feeling great on the boat.  The work is quite tiring, and I usually go straight to the shower and the bed after my shift ends.  Interestingly, I think I’m actually gaining quite a bit of weight.  The work is hard and the food is excellent, so I’ve been eating a bunch. I’ve been getting 7-8 hours of sleep a night, which is more than I normally get when I am at home, especially during the school year.  One thing I have been noticing ever since the trip started is that I have been having quite nightmarish dreams every night.  This is rare for me, as I usually either don’t have dreams or can’t remember the ones that occur.  I initially thought that this might be due to the rocking of the boat, or maybe to the slight change in my diet, but I think I’ve finally found the culprit – Dramamine®.  Research has indicated that this anti-motion sickness drug can cause “disturbing dreams” (Wood, et al., 1966), and I have been taking this medication since the trip started.  This hypothesis is consistent with the observation that my nightmares lessened when I reduced my daily Dramamine® dose from 2 pills to one. I finished Everything is Illuminated and have begun a new novel (Tender is the Night, by F. Scott Fitzgerald). I am now well into the second week of my trip!

Did You Know?

Earrings can be made from fish otoliths (ear stones).  These seem to be quite popular in many port cities.  Check out this article from the Juneau (Alaska) Empire Newspaper.

Notable Species Seen

Spencer Cody: Science at Sea, June 1, 2014

NOAA Teacher at Sea

Spencer Cody

Aboard NOAA Ship Pisces

May 27 – June 11, 2014

Geographical Area of Cruise:  Gulf of Mexico
Mission:  SEAMAP Reef Fish Survey
Date:  June 1, 2014

Observational Data:

Latitude:  27˚ 50.503 N
Longitude:  93˚ 46.791 W
Air Temp: 26.3˚C (79.3˚F)
Water Temp: 23.3˚C (73.9˚F)
Ocean Depth:  126.8 m (416 ft.)
Relative Humidity:  84%
Wind Speed:  7.8 kts (9.0 mph)
Barometer:  1,009.5 hPa (1,009.5 mbar)

Science and Technology Log: 

It was not until the Pisces arrived at its first survey area off the coast of Texas that I was able to appreciate the volume of scientific data collection that this vessel could collect.  It took most of the 27th and all of the 28th to arrive at our initial survey area.  While in transit, the Pisces is constantly collecting data.  Data such as air temperature, wind direction, relative humidity, wind speed, and barometric pressure are recorded and periodically reported back to NOAA and the National Weather Service and from other marine vessels to improve data on meteorological events in the Gulf and weather forecasts.

In addition to collecting meteorological data, the Pisces uses a fishery acoustics system called the ER-60 to track depth and various sea floor features.  This system can also be used to monitor biomass such as fish, coral, and even plankton.  Once we arrived at our initial survey area within the SEAMAP survey grid, the amount of science conducted increased dramatically.  In the survey areas, the camera array is dropped to the sea floor to survey fish populations.  In most cases we are looking at fish habitat from 50 to 120 m deep.  Video and still photos are taken of fish attracted to the bait bag filled with squid.  To ensure that sampling is both consistent and unbiased for the survey, pictures and video are pulled at random from all four cameras on the camera array.  It is important that the same procedures are carried out throughout the SEAMAP survey gird concerning data collection in order to be able to reliably compare different survey areas and track species development and abundance.

In order to assist the camera array in obtaining accurate information about precisely how deep the camera array is when it is recording fish population data, a Temperature Depth Recorder or TDR is attached to the camera array to compare position in the water column to what the ship’s fishery acoustics system is displaying.  This is necessary in case the camera array has fallen off an underwater cliff or is hung up on some other topographic feature.

The Conductivity Temperature and Depth or CTD submersible probe can measure the salinity of the water, temperature, pressure, plankton concentrations, dissolved gases, and water samples at different depths.

The Conductivity Temperature and Depth submersible aids the ship’s acoustic equipment in determining an accurate depth of the ocean bottom.  Since sound travels at different velocities in water that has different densities and temperatures, information regarding the salinity and temperature of the water must be fed into the ship’s fishery acoustics system to calibrate the system for it to accurately read the bottom depths.  If temperature or salinity are not taken into account, the depth will either be too shallow or too deep compared to the true value.

The Pisces not only has the ER-60 for fishery acoustics, but it also has a state of-the-art multi-beam echo sounder, the ME-70, that has 27 transducers that are aligned in a configuration allowing for scans of wide swaths of the ocean bottom.  In fact, the Pisces has engines that are specifically designed to run quietly enough to accommodate such advanced acoustic equipment.  The ME-70 is used for mapping various sample areas of the SEAMAP survey.

While the camera array can be used to measure the length of some of the fish viewed, it cannot reliably determine characteristics such as age or sex.  Determining age or sex just through appearance can be very tricky in the Gulf and is frequently unreliable.  Many species of fish will grow at different rates depending on available forage and other environmental factors.  This is an issue that is also commonly encountered among freshwater fish in South Dakota.  Complicating fish characteristics even further, many reef fish are one or the other sex at different phases of their lives.  They are not strictly male or female but change roles depending on complex physical or environmental factors.  With so many factors complicating these characteristics, live catches are necessary to determine the full story of what is going on with reef fish in the Gulf.

For live catches we use bandit reels.  Bandit reels are similar in concept to a standard fishing rod and reel except they are built for heavy duty sea fishing.  The reel and rod are attached to the side of the ship.  One hundred pound test line is used with a five pound sinker weight.  Each line for the bandit reels has ten hooks, a small float that keeps the hooks in a vertical column, and a large float that keeps the ten hooks just above the ocean bottom. 

  Again, in order to guard against bias in the results, we use the bandit reels with a set procedure.  For our survey we are using three bandit reels at a time each with ten hooks.  The bandit reel stations are in radio communication with the dry lab, where the chief scientist is coordinating the sampling, and the bridge, which is keeping the ship in position for the lines preventing lines from running under the ship.  Since we want to be as objective as possible without contributing to any type of bias in the sampling, each line was in the water for exactly five minutes.  Even though it may have went against every natural inclination of most fishermen and fisherwomen, we were not allowed to jig our lines or do anything that might attract more fish to our bait.  In addition to standardizing the number of hooks and the length of time spent fishing, three different sizes of hooks are used and rotated out from each bandit reel station; consequently, one of each of the three hook sizes is always being used for each survey area.

White, nickel-sized disk-like structures called otoliths can reliably age fish. They are inner ear structures that grow in size as a fish ages allowing calcium carbonate deposits to form over the course of its life. Scientists can read these calcium carbonate deposit rings like rings in a tree to determine the age of the fish.  Credit Harriet Nash for the photo.

After all the measurements are taken of the fish and their otoliths and gonads have been sampled, the information must be added to the database for use in the SEAMAP Survey. Credit Adam Pollack for the photo.

After five minutes of fishing, the lines are brought up and fish are tagged one through ten to keep fish identified with a specific hook and depth.  The tagged fish are then taken to the wet lab for measurement readings.  In the wet lab, fish length, weight, sex, and phase of reproductive development are recorded.  Since reproductive development, and sometimes even sex, can be difficult to determine, a sample of each fish’s gonads (ovaries or testes) are removed and placed in a labeled specimen vial for confirmation in the lab back on land.  The otoliths (inner ear bones) are removed from the fish, as well, in order to reliably age the fish back in the lab.  Once the measurements are recorded, they need to be added to the database to be compiled with the gonad and otolith specimens.  This is just a small piece of the monitoring that is occurring in the Gulf through NOAA.  The Gulf of Mexico is a remarkably diverse expanse of ocean and requires significant scientific research in order to understand and track fish populations and the habitat and forage that sustain them.  Without these types of intensive scientific studies on the ocean, we could not possibly manage or attempt to conserve a natural resource that we would, otherwise, have little to no understanding of.

Personal Log:

Since we had arrived off the coast of Texas a couple of days ago, we have been slowly back tracking to Pascagoula as we go through our survey areas.  The weather has been beautiful the last couple of days; however, sea swells do cause the boat to jostle around a bit.  Each day we see more species on the surface of the water and through our camera array under the water.  Since the science log is rather long for this post, I will talk more about life at sea and the different types of organisms we are encountering in future posts.

Did You Know?

Fish identification can be a tricky business in the Gulf of Mexico.  Many species of Gulf fish alter their physical appearance depending on their reproductive development, environmental factors, or phase of physical development.  Fish will even appear to have different patterns depending on whether they are viewed under our out of water.

Chris Henricksen: Standing My First Watch, May 8, 2014

NOAA Teacher at Sea

Chris Henricksen

Aboard NOAA Ship Henry B. Bigelow

April 29–May 10, 2014

Geographical area of cruise: Gulf of Maine

Mission: Spring Bottom Trawl & Acoustic Survey

Date: May 7, 2014

Air Temp: 9.1°C (48.38°F)

Relative Humidity: 73%

Wind Speed: 10.83mph

Barometer: 1011.7mb



Science and Technology Log

My section stands watch from midnight to noon–twelve hours on, twelve hours off.  Today I stood my first watch, acting as one of three “recorder” on the fish sorting line.  A recorder’s role is to assist his assigned “cutter” by entering requested measurement data (e.g., length, weight, etc.) of individual fish into a computer database.  The cutter processes fish by identifying the species, then performing any number of actions (i.e., cuts, as in, with a knife) in order to retrieve information about particular fish for later use by scientists.  Such data will consist of measuring, weighing, and sexing the fish, as well as checking the contents of its stomach.  Other particular data may be gathered, such as collecting otoliths (ear bones) from the head of the fish.

photo of net prep
Preparing the net for our first trawl

After getting underway, the captain called a series of drills, one of which was abandon ship.  During this exercise, I reported to the aft deck of the ship, donned a “Gumby” survival suit, which is bright orange/red, keeps you warm while in the water, and helps you to stay afloat.  Following that, we had a collision drill.  In a disaster scenario, everyone has a muster station, so that we can be counted, and then help control the situation, if need be.

photo of abandon ship drill
Abandon Ship Drill

Today was my first of about a dozen watches I will stand.  It went smoothly, but there was considerable down time.  The first stations (the areas in which the nets are lowered and trawling begins) were about 25 nautical miles from one another, so it took a couple of hours to steam from one station to the next.  During this time, I was able to relax, grab a bite, or hang out with other members of my watch. Personal Log The food aboard ship is very good, and there is plenty of it. Between mealtimes, the cook makes sure that plenty of drinks and snacks are available, so there is no reason to go hungry aboard the Henry B. Bigelow. The ship has a huge library of DVDs with many new movies.  We can also watch TV thanks to a satellite connection (DirectTV). The only things I am not allowed to do are 1) re-enter my stateroom after going on watch, as there is always an off-watch shipmate trying to catch some shuteye, and 2) make a surprise appearance on the bridge, which is where the NOAA officers navigate and steer the ship.  That’s for safety, and I am sure they would welcome me, as long as I called ahead first. I am tired, but feeling pretty good.  I boarded the ship wearing an anti-motion sickness patch, fearing that, after twenty years of not being at sea, I might be susceptible to seasickness.  The medicine made me feel awful, so I took it off, and now feel much better!  I had almost forgotten how much I enjoy the rocking of a ship.  It’s an especially good way to fall asleep–gently rocking…

2014-05-06 deck selfie
Deck Selfie!

Liz Harrington: The Temporary Lull in the Action, August 21, 2013

NOAA Teacher At Sea
Liz Harrington
 Aboard NOAA Ship Oregon II
August 10 – 25, 2013

Mission : Shark/Red Snapper Bottom Longline
Geographical area of cruise: Western Atlantic Ocean and Gulf of Mexico
Date: August 21, 2013

Weather: current conditions from the bridge:
Partly cloudy
Lat. 29.18 °N  Lon. 84.06 °W
Temp. 75 °F (24 ° C)
Wind speed  10-15  mph
Barometer  30.04 in ( 1017.3 mb)
Visibility  10 mi

Science and Technology Log:

It has been just over a week now since I’ve been aboard the Oregon II.  The catch has not been as abundant as it was the first couple of days of fishing, but that tells the scientist something as well. So far I’ve experienced three water hauls – not one fish on any of the 100 hooks!  Even though we are not catching many fish (for now), the fishing will continue until it is time to return to port.  Don’t get me wrong, we are still catching fish, just not as many as we had been.  Occasionally we pull up something other than fish, like eels, skates, crabs or sea stars. This is called the bycatch. In the previous blog I explained how the line was set. In this one I’ll explain about the catch.

“Fish On”. A Sandbar Shark is brought alongside the ship to be cradled.

crab as bycatch
This crab, part of the bycatch, wouldn’t let go of the bait.

preparing for haul back
Lead Fisherman Chris Nichols (right) and Fisherman Buddy Gould prepare to retrieve the high flyer.

Hauling in the line is similar to setting it out.  The fisherman handle the line and the science team process the fish. Our team includes a person manning the computer to keep track of the hook numbers and the condition of any remaining bait;  a person “racking” (carefully but quickly returning the gangions into the storage barrels); and a “data” person to write down information about each fish, and the rest of the team will be “wranglers” (those who handle the catch).  We all rotate through the jobs.  I like to be a wrangler, but the racker and computer folks get a nice view of the fish being brought on board.  Everything we catch is brought on board, weighed and measured.

tagging Tiger Shark
The Day Team tagging a Tiger Shark

Many species of sharks are tagged and a fin clip is taken to obtain its DNA.  They are given an injection of a chemical which will help to age the shark if it is caught again.  The entire process only takes a few minutes because they are trying to get the sharks back into the water as soon as possible. The scientists and crew are all very conscientious about doing what is best for the marine life.  What’s really nice is that we all take turns tagging the sharks.  It is just so exciting to be up close to them, especially the big ones. You can feel the strength and power beneath that sandy skin.

weighing a shark
Sometimes sharks are too heavy for the handheld scale, so they are hoisted up to be weighed. Notice the scientist to the right to get sense of its weight.

processing fish
Kristin and Cliff find otoliths at the end of the rainbow.

The boney fish that are caught are also weighed and measured. After the haul back (when the line is in, gangions are stored, high flyers returned and deck hosed down), they are brought to the back of the ship to have otoliths removed and tissue samples taken. The otoliths are boney structures in the fish’s inner ear which are sensitive to gravity and acceleration. As the fish grows, each year a new layer is added to the otoliths – similar to tree rings. By examining the otoliths under a microscope its age can be determined. I was taught how to remove the otoliths, so now (given enough time – I need plenty) I can help process the fish. Learn more about the procedure here.

Personal Log

I have the bottom bunk in stateroom #5

It has been easy for me to acclimate to life aboard the ship because all of the people are so friendly and interesting.  The ship is always rocking but I don’t even notice it any more. It actually lulls me to sleep at night, along with the constant sound of the engine and particularly the gurgling sound of the water moving along the hull (frame of ship). I was a little worried that I might get seasick in the beginning of the cruise, but I didn’t. The only problem I had was that reading or working on the computer made me queasy, but that only lasted for a couple of days.  Quarters are tight, but they make good use of all of the space. Most of the bedrooms (called staterooms) sleep two people. We all eat in a room called the galley. It only holds twelve people at a time, so when we are done eating we leave to make room for someone else. The food on board is delicious and abundant. The chief steward, Walter Coghlan, does a great job providing a variety of choices. There is literally something for everyone.  If we have free time, there is a lounge area with a huge selection of movies.

I like to spend my free time out on the decks, if I can find a place in the shade and the breeze. I love to look out over the water. And the sky stretches from horizon to horizon in all directions, something I don’t see in the mountains of Vermont.  The cumulus clouds develop during the day and I can usually see a thunderstorm somewhere by late afternoon. It’s a beautiful view.  Yesterday we were visited briefly by a small group of dolphins. Their acrobatics were very entertaining. They were here and then gone. That seems to be the continuing theme here; you never know what you are going to see.

Dolphin visit
A small group of dolphins swim along side the ship.

A distant passing thunderstorm.

Did you know?  The ship makes it own fresh water from the sea water.  There is a reverse osmosis desalination system located down in the engine room. The fresh water is stored in large tanks, so it is always available.

volunteers await a haul
Volunteers Micayla, Daniel, David and Cliff waiting to do some wrangling.

New Term

Foul Hook – when a fish is hooked in a place other than its mouth (ie -fin or body)

More examples of bycatch.

clearnose skate
Clearnose Skate

little tunny
Micayla holds a Little Tunny (yes, that’s it’s real name)

yellowedge grouper
Yellowedge Grouper ready for processing

sea star
Sea Star

Amie Ell: Fireworks, Fish, and Flukes, July 6, 2013

NOAA Teacher at Sea
Amie Ell
Aboard NOAA Ship Oscar Dyson (NOAA Ship Tracker)
June 30 – July 21, 2013

Mission: Alaska Walleye Pollock Survey
Geographical Area: Gulf of Alaska
Date: July 6th, 2013

Location Data from the Bridge:
Latitude: 55.29.300 N
Longitude: 156.25.200 W
Ship speed:   10.7 kn

Weather Data from the Bridge:
Air temperature: 8.6 degrees Centigrade
Surface water temperature: 8.6 degrees Centigrade
Wind speed:  14 kn
Wind direction: 210 degrees
Barometric pressure: 1008.5 mb

Science and Technology Log:

The Oscar Dyson is equipped with several labs to accommodate the researchers on board.  In this blog post I will describe to you what is happening in the wet/fish lab.  This is where I have experienced quite a bit of hands-on data collection.

Pollock being separated on the conveyor belt.
Pollock being separated on the conveyor belt.

Basket full of pollock.
Basket full of pollock.

After a trawl, the crew dumps the load of  fish into a bin.  Inside the lab we can raise or lower this bin to control the amount of fish coming onto a conveyor belt.  Once the fish are on the belt the scientists decide how they will be separated.   We separate the pollock according to age into baskets.  They are categorized by size; under 20 cm (age 1), under 30 cm (age 2), and any larger than 30 cm

A lumpsucker

A basket full of small squid
A basket full of small squid

At this time we also pull out any other sea creatures that are not pollock.  So far we have pulled up quite a few jelly fish, la lumpsucker, shrimp, squid, eulachon, and capelin.  These are also weighed, measured, and in some cases frozen per request of scientists not currently on board.

Larger squid.
Larger squid.

After organizing the pollock into appropriate age groups, we then measure and record their weight in bulk.  Scientists are using a scale attached to a touch screen computer with a program called CLAMS to record this information.  The pollock are then dumped into a stainless steel bin where their sex will be determined.  In order to do this the fish must be cut open to look for “boy parts, or girl parts”.   After the pollock are separated into female and male bins we begin to measure their length.

This is the tool used for measuring length of the fish.
This is the tool used for measuring length of the fish.

The tool used to measure length is called the Ichthystick.  This tool is connected to the CLAMS computer system.  The fish is placed on the Ichthystick and a pointer with a magnet in it is placed at the tail end of the fish.  There are three different types of length measurement that can be done: fork length, standard length, and total length.  When the magnetic pointer touches the Ichthystick it senses that length and sends the information to the CLAMS computer system.

Northern shrimp

One of these bins of fish is placed aside for individual weighing, length measurements, and removal of otoliths.  You may recall that I mentioned otoliths in the last blog post.  These ear bones are sent to a lab and analyzed to determine the age of each of these individually measured fish.  The Alaska Fisheries Science Center has created a demonstration program where you can try to determine the age of different types of fish by looking at their otoliths. Click here to try it yourself! (I will add hyperlink to:

Personal Log:

Ben and Brian in fire gear  with flares.
Ben and Brian in fire gear with flares.

One afternoon while waiting for the fishermen to bring up the trawl net, I watched a group of porpoises swimming behind the ship.  Another day I was able to see whales from up on the bridge.  These were pretty far out and required binoculars to see any detail.  I observed many spouts, saw one breach, and some flukes as well.

There is quite a bit of downtime for me on the ship while I am waiting in between trawls.  I get to read a lot and watch movies in my free time.  I have had the opportunity to talk with different members of the crew and learn about their roles a bit.  The chief engineer gave me a tour of the engine rooms (more about this with pictures in a future post.)

The 4th of July fireworks show on the Oscar Dyson was like no others I have ever experienced.  Two of our crew, Ben & Brian, dressed in official fire gear shot expired flares off the ship into the sea.  America themed music was played over the PA system.  I have attached a video of our fireworks display.  Happy Independence Day everyone!

Rita Salisbury: More on the Mission, April 23, 2013

CDTs record conductivity, depth,  and temperature
CDTs record conductivity, depth, and temperature

NOAA Teacher at Sea
Rita Salisbury
Aboard NOAA Ship Oscar Elton Sette
April 14–29, 2013

Mission: Hawaii Bottomfish Survey
Geographical Area of Cruise: Hawaiian Islands
Tuesday, April 23, 2013

Science and Technology Log

CDT being lowered over the starboard side
CDT being lowered over the starboard side

A few days ago we dropped the CDT, an apparatus that collects data on the conductivity, the depth, and the temperature of the sea water in which the acoustic survey is taking place. All of these three things impact how quickly sound travels underwater. The scientists collect the information and then use it to figure out an accurate rate of speed for the sound waves. Once they have that information, they can determine how far a target is from the ship.I was able to ride along in a small boat to Maui to pick up parts for the AUV. While in the Maui harbor, I had the opportunity to visit the Huki Pono, a small boat working on this survey that is using BotCams to survey the fish population. The palu, or bait, that I help make every day is frozen and then transferred to the fishing boats. It is frozen in a shape that fits into a cage on the BotCam located near the camera. As the bait breaks up, fish are attracted to it and come close enough to the BotCam to be visually recorded. There is a lot of video to go through so Dr. Kobayashi says they won’t have the data from the BotCams for a while.  But the other three fishing boats assigned to this project turn their survey information in every evening and I get to add it to a spreadsheet to help keep track of what section the boats were in and what they found while they were there.

BotCam on the deck of the Huki Pono
BotCam on the deck of the Huki Pono

Chris Demarke, Jamie Barlow, and Bo Alexander retrieving a BotCam aboard the Huki Pono with Maui in the background
Work continues with the ROV and AUV. The scientists are always working on them, trying to make them run as smoothly as possible. We worked on calibrating the acoustics again this morning for the same reason. The better the information you have when you start a project, the better chance you have of having a successful outcome.

As I mentioned before though, not everything we are doing is high tech. We fish off the side of the ship in the evenings, dropping our lines all the way to the bottom so they are on the sea floor. The scientists running the acoustics tell us if they see fish and then we do our best to catch a representative sample.  Here are two of the fish I caught off the bottom: an opakapaka and a taape. The observers that ride in the small boats every day spend the night on the Sette. That way, they can turn their logs in and I can record the data. As a bonus, a few of them are expert fishermen and are a huge help to us as we fish from the ship.

Opakapaka and ta'ape
Opakapaka and ta’ape

Personal Log
I’m really enjoying my time on the Sette. In addition to learning new things that I can apply in my classroom, I’m making new friends. Everyone is exceptionally friendly and they go out of their way to explain things to me. Most of them call me “Teach” or “Taz” and almost all of them have sailed with a Teacher at Sea before.

Did You Know?
You can tell the age of a fish by their otoliths? The picture has the otoliths from an opakapaka, an ehu, and a hogo. Otoliths are a fish’s “ear bones” and they have growth lines in them much like a tree has growth rings.


Additional Section

Why are these bottom-dwelling fish red?

Red fish?
Red fish?

Allan Phipps: Show Me the Data! August 2, 2012

NOAA Teacher at Sea
Allan Phipps
Aboard NOAA Ship Oscar Dyson
July 23 – August 11, 2012

Safety first!

Mission: Alaskan Pollock Mid-water Acoustic Survey
Geographical Area: Bering Sea
Date: August 2, 2012

Location Data
Latitude: 61°12’61” N
Longitude: 178°27’175″ W
Ship speed: 11.6 knots (13.3 mph)

Weather Data from the Bridge
Wind Speed: 11 knots (12.7 mph)
Wind Direction: 193°
Wave Height: 2-4 ft (0.6 – 1.2 m)
Surface Water Temperature: 8.3°C ( 47°F)
Air Temperature: 8.5°C (47.3°F)
Barometric Pressure: 999.98 millibars (0.99 atm)

Science and Technology Log

At the end of last blog, I asked the question, “What do you do with all these fish data?”

The easy answer is… try and determine how many fish are in the sea.  That way, you can establish sustainable fishing limits.  But there is a little more to the story…

Historically, all fisheries data were based on length.  It is a lot easier to measure the length of a fish than to accurately determine its weight on a ship at sea.  To accurately measure weight on a ship, you have to have special scales that account for the changes in weight due to the up and down motion of the ship.  Similar to riding a roller coaster, at the crest of a wave (or top of a hill on a roller coaster), the fish would appear to weigh less as it experiences less gravitational force.  At the trough of a wave (or bottom of a hill on a roller coaster), the fish would experience more gravitational force and appear to weigh more.  Motion compensating scales are a more recent invention, so, historically, it was easier to just measure lengths.

One of the motion-compensating scales onboard the             Oscar Dyson.

For fisheries management purposes, however, you want to be able to determine the mass of each fish in your sample and inevitably the biomass of the entire fishery in order to decide on quotas to determine a sustainable fishing rate.  So, you need to be able to use length data to estimate mass. Here is where science and math come to the rescue!  By taking a random sample that is large enough to be statistically significant, and by using the actual length and weight data from that sample, you can create a model to represent the entire population.  In doing so, you can use the model for estimating weights even if all you know is the lengths of the fish that you sample.  Then you can extrapolate that data (using the analysis of your acoustic data – more on this later) to determine the entire size of the pollock biomass in the Bering Sea.

How do they do that?  First, you analyze and plot the actual lengths vs. weights of your random sample and your result is a scatter-plot diagram that appears to be an exponential curve.

Scatterplot showing observed Walleye pollock weights and lengths for a sample of the population.

Then you create a linear model by log-transforming the data.  This gives you a straight line.

Linear regression of the Walleye pollock length and weight data.

Next, you back-transform the data into linear space (instead of log space) and you will have created a model for estimating weight of pollock if all you know are the lengths of the fish.  This is close to a cubic expansion which makes sense because you are going from a one-dimensional measurement (length) to a 3-dimensional measurement (volume).

Observed weight and length data showing the model for predicting weight if all you know are lengths.

Scientists can now use this line to predict weights from all of their fish samples and then extrapolate to determine the entire biomass of Walleye pollock population in the Bering Sea (when combined with acoustic data… coming up in the next blog!) when the majority of the data collected is only fish lengths.

Another interesting question… How does length change with age?  Fish get bigger as they get older, all the way until they die, which is different from mammals and birds. However, some individual fish grow faster than others, so the relationship between age and length gets a little complicated.  How do you determine the age distribution of an entire population when all you are collecting are lengths?

Several age classes of Alaskan pollock (Theragra chalcogramma).  Can you tell which one is youngest?                Are you sure???

Just like weight, you can determine the age from a subset of fish and apply your results to the rest. This works great with young fish that are one year old.  The problem is… once you get beyond a one-year-old fish, using lengths alone to determine age becomes a little sketchy.  Different fish may have had a better life than others (environmental/ecological effects) and had plenty to eat, great growing conditions, etc and be big for their age relative to the rest of the population.  Some may have had less to eat and/or unfavorable conditions such as high parasite loads leading them to be smaller…   There are also other things to consider such as genetics that affect length and growth rate of individuals.  Here is where the collection of otoliths becomes important.  By collecting the otoliths with the lengths, weights, and gender data, the scientists can look at the age distributions within the population.  The graph below shows that if a pollock is 15 cm long, it is clearly a 1 year old fish.  If a pollock is 30 cm long, it might be a 2 year old, a 3 year old, or a 4 year old fish, but about 90% of fish at this length will be 3 years old.  If a fish is 55 cm long, it could be anywhere from 6 to 10+ years old!

Graph showing age proportions of the Walleye pollock population when compared to length data.

Collection of otoliths is the only way to accurately determine the age of the fish in the random sample and be able to extrapolate that data to determine the estimated age of all the pollock in the fishery.  Here is a photo comparing otolith size of Walleye pollock with their lengths.

    A comparison of otolith sizes. These otoliths were taken from fish that were 12.5cm, 24.5cm, 30.5cm, 39.0cm, 55.5cm, and 70.0cm counter clockwise from top, respectively.
A comparison of otolith sizes. These otoliths were taken from fish that were 12.5cm, 24.5cm, 30.5cm, 39.0cm, 55.5cm, and 70.0cm counter clockwise from top, respectively.

If we wanted to find out exactly how old each of these fish were, we would need to break the otoliths in half to look at a cross section.  Below is what a prepared otolith looks like (courtesy of Alaska Fisheries Science Center).  You can try counting rings yourself at their interactive otolith activity found here.

Cross section of Walleye pollock otolith after being prepared (courtesy of the Alaska Fisheries Science Center).

All of these data go into a much more complicated model (including the acoustic-trawl survey walleye pollock population estimates) to accurately estimate the total size of the fishery and set the quotas for the pollock fishing industry so that the fishery is maintained in a sustainable manner.

Next blog, we will learn about how the various ways acoustic data fit into this equation to create the pollock fishery model!

Personal Blog

Ok, so here is a long overdue look at the NOAA Ship Oscar Dyson that I am calling home for three weeks.  I was pleasantly surprised when I saw my state room.  It is bigger than I thought it would be and came with its own bathroom.  I was also pleasantly surprised to learn I would be sharing my state room with Kresimir Williams, one of the NOAA scientists and an old college friend of mine!  Here is a picture of our room.

My state room on the Oscar Dyson. The curtains around each bunk help block out light.

The room has a set of bunk beds.  Thankfully, my bed is on the bottom.  I do not know how I would have gotten in and out of bed in the rough seas we had over the last couple of days.  If I do fall out of bed, at least I will not have far to fall.  Last year, the ship rocked so hard in rough seas that one of the scientists fell head first out of the top bunk!  The room also had two lockers that serve as closets, a desk and chair, and our immersion suits (the red gumby suits).  The bathroom is small and the shower is tiny!  Notice the handles on the wall.  These are really handy when trying to shower in rough seas!

The bathroom in my state room. Notice the essential handles.

Next, we have the Galley or Mess Hall.  This is where we have all of our meals prepared by Tim and Adam.  Notice that all of the chairs have tennis balls on the legs and that each chair has a bungee cord securing it to the floor!  There are also bungee cords over the plates and bowls.  Everything has to be secured for rough seas.

The Mess Hall, also known as “The Galley.”

The chairs in the galley have tennis balls on their feet and have bungee cords holding them down so they will not move during high seas.

The coffee bar and snack bar in the galley.

The Mess Hall also has a salad bar, cereal bar, sandwich fixings, soup, snacks like cookies, and ice cream available 24 hours a day.  No one on board is going hungry.  The food has been excellent!  We have had steaks, ribs, hamburgers and fish that Tim has grilled right out on deck.  Here is a picture of my “surf and turf” with a double-baked potato.

“Surf and Turf” meal, courtesy of Stewards Tim and Adam. Yummy!

Most of my work here on board (other than processing fish) has been in the acoustics lab, also known as “The Cave” since it has no windows.  This is where the NOAA scientists are collecting acoustic data on the schools of fish and comparing the acoustic data with the biological samples we process in the fish lab.

The acoustics lab, also known as “The Cave” since it has no windows.

I also spend some time up on the Bridge.  From the Bridge, you can see 10 to 12+ nautical miles on a clear day.  This morning, we saw a couple of humpback whales blowing (surfacing to breathe) about 1/4 mile off our starboard side!  A couple of days ago (before the weather turned foul), we spotted an American trawler.

An American Trawler spotted in some foggy weather.

Today, we got close enough to see the Russian coastline!  Here is a picture of a small tanker ship with the Russian coastline in the background!

Land Ho! A small tanker off the Russian coastline.

Here are some pictures of the helm and some of the technology we have onboard to help navigate the ship.

The “helm” of the Oscar Dyson.

Radar showing numerous Russian fishing vessels near the Russia coastline.

I have also spent some time in the lounge.  This is where you can go to watch movies, play darts (yea, right!  on a ship in rough weather???), or just relax.  The couch and chairs are so very comfy!

The Lounge aboard the Oscar Dyson.

When you have 30 people on board and in close quarters, you better have a place to do laundry!  Here is a picture of our very own laundromat.

The onboard laundry facilities.

All for now.  Next time, I will share more about life at sea!

Allan Phipps: Fish heads, fish heads, rolly polly fish heads…. July 31, 2012

NOAA Teacher at Sea
Allan Phipps
Aboard NOAA Ship Oscar Dyson
July 23 – August 11, 2012

Mission: Alaskan Pollock Mid-water Acoustic Survey
Geographical Area: Bering Sea
Date: July 31, 2012

Location Data
Latitude: N 61°39’29”
Longitude: W 117°55’90”
Ship speed: 11.7 knots (13.5mph)

Weather Data from the Bridge
Wind Speed: 26 knots (30mph)
Wind Direction: 044°
Wave Height: 4 meters (12 ft)
Surface Water Temperature: 8.2°C ( 46.8°F)
Air Temperature: 7.4°C (45°F)
Barometric Pressure: 994 millibar (0.98 atm)

Science and Technology Log:

Last blog, we learned about the different trawl nets and how the NOAA scientists are comparing those nets while conducting the mid-water acoustic pollock survey.  We left off with the fish being released from the codend onto the lift table and entering the fish lab.  Here is where the biological data is collected.

Walleye pollock on the sorting table. Various age groups are seen here, including one that is 70cm long and may be over 12 years old! Most are 2 to 4 year olds.

The fish lab is where the catch is sorted, weighed, counted, measured, sexed, and biological samples such as the otoliths, or earbones,  are taken (more about otoliths later in this post).  First, the fish come down a conveyor belt where they are sorted by species (see video above).  Typically, the most numerous species (in our case pollock) stay on the conveyor and any other species (jellyfish and/or herring, but sometimes a salmon or two, or maybe even something unique like a lumpsucker!), are put into separate baskets to weigh and include in the inventory count.  In the commercial fishing industry, these species would be considered bycatch, but since we are doing an inventory survey, we document all species caught.  Here are some pictures of others species caught and included in the midwater survey.

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The goal of each trawl is to randomly select a sample of 300 pollock to measure as a good representation of the population (remember your statistics!  Larger sample sizes will give you a better approximation of the real population).  If more than 300 pollock are caught, the remainder are weighed in baskets and quickly sent back to sea.  All of the catch is weighed so the scientists can use the length and gender data taken from the sample to extrapolate for the entire catch.  This data is combined with the acoustics data to estimate the size of the entire fishery (more on acoustic data in a future post). Weights are entered via touch screen into a program (Catch Logger for Acoustic Midwater Surveys – CLAMS) developed by the NOAA scientists onboard.

The CLAMS display showing that I am “today’s scientist.”

The 300 pollock are sexed to determine the male/female ratio of this randomly selected portion of the population.  Gender is determined by making an incision along the ventral side from posterior to anterior beginning near the vent.  This exposes the internal organs so that either ovaries or testes can be seen.  Sometimes determining gender is tricky since the gonads look very different as fish pass through pre-spawning, spawning, or post-spawning stages.  When we determine gender, the fish are put into two separate hoppers, the one for females is labeled “Sheilas” and the hopper for males is labeled “Blokes.”

Making incision to determine gender on pollock sample.

Hopper for female pollock ready to be measured with the Ichthystick and entered into CLAMS.

We use an Ichthystick to then measure the males and females separately to collect length data for this randomly selected sample.  Designed by NOAA Scientists Rick and Kresimir, the Ichthystick very quickly measures lengths by using a magnet placed at the fork of the fish’s tail (when measuring fork-length).  This sends a signal to the computer to record the individual fish’s length data immediately into a spreadsheet and the software creates a population length distribution histogram in real-time as you enter data.

The Ichthystick with fingertip magnet used to quickly measure and enter length data into CLAMS.

A randomly selected subset of 40 pollock get individually weighed, length measured, sexed, evaluated for gonadal maturity and have the otoliths removed.  Otoliths (oto = ear, lithos = bone) are calciferous bony structures in the fish’s inner ear.  These are used to determine age when examined via cross-section under a dissecting scope.  The number of rings corresponds to the age of the pollock, similar to rings seen in trees. The otoliths are taken by holding the fish at the operculum and making an incision across the top of the head to expose the brain and utricle of the inner ear.  The otolith is found inside the utricle.  Forceps are used to extract the otoliths, which are then washed and put in individual bar-coded vials with glycerol-thymol solution to preserve them for analysis back at the Alaska Fisheries Science Center.

Incision across the skull revealing the otoliths on either side of the brain stem.

One otolith from a Walleye pollock.

Watch this short video to see what the entire process of data collection looks like.

So… why collect all of this data?  How is this data analyzed and used?  Stay tuned to my next blog!

Personal Log:

Well, I can officially say… the honeymoon is over.  The Bering Sea had been so extremely kind to us with several days of great weather while we had a high pressure system over us.  We enjoyed spectacular sunrises and sunsets, cloudless days and calm seas.

Sunny skies and calm seas on the Oscar Dyson.

Now… we have a low pressure system on top of us.  Last night, we experienced 35 knot winds and 12 foot seas.  I have spent a lot of time in my room in the past 24  hours…  Late this morning, the sun came out and the winds calmed down, but the barometric pressure was still very low (around 990 mbars) which basically meant we were in the center of the low pressure system (similar to the eye of a hurricane, but not as strong… thank goodness!).  We had a few hours relief, but we are back to pounding through the waves as the wind picks back up.  It will be another long and sleepless night for this landlubber…

On a positive note, we did see two Laysan Albatrosses (Phoebastria immutabilis) from the Bridge as the winds began to kick up.  They seemed to really enjoy the high winds as they soared effortlessly around the ship.  The Officer on Deck (OOD) also said he saw a humpback breaching, but by the time I got up to the Bridge, it had moved on…

Next blog, I will share pictures of my room, the galley, “the cave,” the Bridge, etc.  Right now, I am just trying to hold on to my mattress and my stomach…

Carmen Andrews: Transforming Fish into Data, July 15, 2012

NOAA Teacher at Sea
Carmen Andrews
Aboard R/V Savannah
July 7 – 18, 2012

Mission: SEFIS Reef Fish Survey
Location: Atlantic Ocean, off the coast of Cape Canaveral, Florida
Date: July 15, 2012

Latitude:      28 ° 50.28   N
Longitude:   80 ° 26.26’  W       

Weather Data:
Air Temperature: 28.6° C (83.48°F)
Wind Speed: 18 knots
Wind Direction: from the Southeast
Surface Water Temperature: 27.6 °C (81.68°F)
Weather conditions: Sunny and Fair

Science and Technology Log

How are fish catches transformed into data? How can scientists use data derived from fish to help conserve threatened fish species?

The goal of the Southeast Fishery-Independent Survey or SEFIS is to monitor and research reef fish in southeast continental shelf waters.  Marine and fisheries scientists have developed sophisticated protocols and procedures to ensure the best possible sampling of these important natural resources, and to develop fisheries management recommendations for present and future sustainability.

During the cruise, important commercial fish in the snapper and grouper families are caught over as wide an area as possible; they are also taken in large enough numbers that they can be worked up into statistically reliable metrics. In addition to counts and measurements, biological samples are also taken at sea for future analysis in land-based research labs.

Gag grouper ready for its work up
Gag grouper ready for its work-up

Scientists strive to render an informative snapshot of reef fish stocks in a given time interval. Reports that analyze and summarize the data are submitted to policy-makers and legislators to set fisheries rules, restrictions and possible quotas for commercial and sports fishermen.

After fish are caught and put on ice, processing includes several kinds of measurement that occur on deck. This data is referred to as ‘Length Frequency’. Tag information from the trap follows the fish through all processing.  Aggregate weight measurements for all the fish of one species caught in a trap are made and recorded in kilograms.

David is weighing the gag grouper, with Adam P. looking on
David is weighing the gag grouper, with Adam P. looking on

The length for each fish in the trap is noted, using a metrically scaled fish board. Not all fish are kept for further processing.

David measuring the length of the gag grouper
David measuring the length of the gag grouper

Species-specific tally sheets randomly assign which fish from the catch are kept and which ones are tossed back into the ocean. These forms, which specify percentages of fish identified as ‘keepers’, are closely consulted by the data recorder and the information is shared with the scientist who is measuring the catch.

Shelly is recording length frequency measurement data
Shelly is recording length frequency measurement data

Length frequency data entries
Length frequency data entries

Red Porgy keep/toss percentage sheet
Red Porgy keep/toss percentage sheet

Kept fish are put in a seawater and ice slurry. The others are thrown over the side of the boat.

Age and reproductive sampling are done next in the wet lab.

Small yellow envelopes are prepared before fish work up can begin. Each envelope is labeled with cruise information, catch number, fish number, and the taxonomical name of the fish, using  binomial nomenclature of genus and species.

Adam P. and Shelly labeling envelopes and plastic specimen containers
Adam P. and Shelly labeling envelopes and plastic specimen containers

A small color-coded plastic container (the color indicates fish species tissue origin), with the fish’s source information riveted at the top, is also prepared. This container will store fish tissue samples.

The fish trap catch number is documented on another data form, along with boat and science team identification, collection method and other important information about the circumstances surrounding the fish catch.  Each species’ data is separately grouped on the data form, as individual fish in a catch are sequentially numbered down the form.

Me, transcribing fish weight & length data
Me, transcribing fish weight & length data

Each fish is weighed, and the weight is noted in grams. The scale is periodically calibrated to be sure the fish is weighed accurately.

Vermilion snappers and scamp, labeled and  ready for dissection
Vermilion snappers and scamp, labeled and ready for dissection

Three length measurements that are made: standard length (SL), total length (TL), and if the fish species has a fork tail — fork length (FL). The fish is laid, facing left on a fish board. The board is long wooden plank with a metric measuring scale running down the center.

Standard length does not include the caudal fin or tail. It begins at the tip of the fish’s head; then the fish measurer lifts the tail up slightly to form a crease where the backbone ends. Standard length measurement includes the fish’s head to end of backbone dimension only. Total length is the entire length of the fish, including the caudal fin. In fork-tailed species, the fork length measurement begins at the fish’s snout and ends at the v-notch in the tail.

Fish length measurements
Fish length measurements

Source: Australian Government – Department of Environment, Water, Population and Communities

Part of the dissection of every fish (except gray triggerfish) is the extraction of  otoliths from the fish’s head. An otolith is a bone-like structure made of calcium carbonate and located in the inner ear of fish. All vertebrates have similar structures that function as gravity, balance, movement, and directional indicators. Otoliths help fish sense changes in horizontal motion and acceleration.

To extract the otoliths, the scientist makes a deep cut behind the fish’s head and pulls it away from the body. The left and right otoliths are found in small slits below the brain. They must be removed carefully, one at a time with forceps. They can easily break or slip into the brain cavity.

Red snapper with removed otolith
Red snapper with removed otolith

Otoliths reveal many things about a fish’s life. Its age and growth throughout the first year of its life can be determined. Otoliths have concentric rings that are deposited over time. The information they show is analogous tree ring growth patterns that record winter and summer cycles. Other otolith measurements can determine when the fish hatched, as well as helping to calculate spawning times in the fish’s life.

The oxygen atoms in calcium carbonate (CaCO3) can be used to assay oxygen isotopes. Scientists can use these markers to reconstruct temperatures of the waters the fish has lived in. Scientists also look for other trace elements and isotopes to determine various environmental factors.

Each pair of otoliths is put into the small labeled yellow envelope.

The otoliths on the gray triggerfish are too small to be studied, so the spine from its back is collected for age and growth analysis.

Spine removed from a gray triggerfish
Spine removed from a gray triggerfish

The last step standard data collection is determining the sex and maturity of the fish. The fish is cut open at the belly, similar to preparing the fish as a filet to eat it.

Making a cut into a vermilion snapper
Making a cut into a vermilion snapper

If the fish is big, the air bladder must be deflated. The intestines are moved or cut out of the way. The gonads (ovaries and testes) are found, and the fish can be identified as a male or female. (Groupers can be hermaphroditic.) The fish’s stage of maturity can also be determined this way.  Maturational stages can be classified with a series of codes:

U = undetermined

1 = immature virgin (gonads are barely visible)

2 = resting (empty gonads – in between reproductive events)

3 = enlarging/developing (eggs/sperm are beginning to be produced)

4 = running ripe (gonads are full of eggs/sperm and are ready to spawn)

5 = spent (spawning has already occurred)

Dissected gonad specimens are removed from the fish and placed in a plastic containers, snapped shut and stored in a formalin jar to preserve them. These preserved samples will be analyzed later by histology scientists. Histology is the science of organ tissue analysis.

Dissected fish gonads
Dissected fish gonads

Red snappers have their fins clipped to provide a DNA sample. They may also have their stomachs removed and the contents studied to better understand their diets.

Video data from the underwater cameras is downloaded in the dry lab. This data will be analyzed once scientists return to their labs on land.

Personal Log

Many different kinds of echinoderms and other invertebrates have been pulled up in the fish traps. Several are species that I’ve never seen before:

Basket Star
I am holding a basket star. It is a type of brittle star in the echinoderm phylum.

A red sea star
A red sea star

Spikey sea star
Spikey sea star

Small crab, covered in seaweed, shell and sand
Small crab, covered in seaweed, shell and sand

We also catch many unusual large and small fish in the traps and on hooks. Several of these have been tropical species that I’ve only seen in salt water aquariums.



Hooked blacktip shark
Hooked blacktip shark

Scrawld Filefish
Scrawld Filefish

Spotted butterflyfish
Spotted butterflyfish

Jack knife fish
Jack knife fish

Lesley Urasky: Setting Sail from St. Croix, June 16, 2012

NOAA Teacher at Sea
Lesley Urasky
Aboard the NOAA Ship Pisces
June 16 – June 29, 2012


Mission:  Caribbean Reef Fish Survey
Geographical area of cruise: St. Croix, U.S. Virgin Islands
Date: Saturday, June 16, 2012

Latitude: 17.6395
Longitude: -64.8277

Weather Data from the Bridge:
Air Temperature: 29°C (84°F)
Wind Speed: 15.76 knots (18.1 mph)
Relative Humidity: 79%
Barometric Pressure: 1,012.7 mb
Surface Water Temperature: 29°C (84°F)

Personal Log

My trip to meet the Pisces and become a Teacher at Sea was a two-day process.  I traveled from my home in Sinclair, Wyoming to Denver, Colorado to catch the first of three flights.  The first flight was from Denver to Dallas/Ft. Worth International Airport; after a two-hour layover, I then flew to Miami.  Originally, I was to travel the entire way in one day.  However, I didn’t want to arrive in St. Croix at 10:00 p.m. and have to make my way to the pier, pass through security, board the ship, find my stateroom, and hopefully meet some of the crew and scientists late at night.  Instead, I spent the night in Miami and flew to St. Croix the next morning.

Trip to St. Croix from Sinclair, Wyoming
Google Earth view of my trip to St. Croix.

Once I landed at the Frederiksted Airport on St. Croix, I took a taxi to the cruise ship pier.  The taxi driver was very concerned about taking me there, because no cruise ships were docked; he was doubtful that any ship was there.  After convincing him that a NOAA ship was indeed docked, he moved aside the sugar cane in the back, loaded my bags, and took me to the pier.  Breaking my trip into two pieces turned out to be the best plan because once I got to the security gate, there was no approved members list at security and they wouldn’t accept my travel document.  They called the ship and the Commanding Officer (CO) came down the pier to meet me at the gate and escort me to the ship.  After a quick tour of the ship, I took some time to settle into the stateroom I’m sharing with the Operations Officer, Kelly Shill.  The rest of the afternoon was spent exploring Frederiksted.

The Pisces viewed from Frederiksted, St. Croix

On Friday, June 15th, I went to Christiansted with some of the ship’s crew members.  Kelly Schill, Operations Officer; Chris Zacharias, Junior Engineer; Peter Langlois, 3rd Mate; and I went shopping for souvenirs, had lunch, and fed the resident school of tarpon outside of Fort Christian Brew Pub.  Later that evening, we went to a beachside restaurant and watched a performance by some modern dance fire dancers.

Hungry tarpon waiting for tidbits.

Modern fire dancers
Fire dancers

Today we left port and embarked on the third Leg of the Caribbean Reef Fish Survey.  The first leg was when the Pisces traveled from Pascagoula, Mississippi to San Juan, Puerto Rico; here the ship picked up the scientific crew.  The second leg was from San Juan, Puerto Rico to St. Croix; during this time period, they collected data about the ocean and the fish along the reef system.  I joined the scientists and crew of the Pisces at Frederiksted, St. Croix in the U.S. Virgin Islands.  The Pisces was in port at St. Croix for three days for personnel change, resupply of the galley, and to give the crew a rest. During this leg, we will be traveling back to San Juan, Puerto Rico taking samples around St. Croix and St Thomas islands.  In addition to the reef fish survey, the Pisces will be deploying the base (anchor and chain) for another buoy to collect oceanographic data 3 nautical miles (nm) south of Saba, which is located between St. Croix and St. Thomas.  The University of Virgin Islands is working in conjunction with NOAA to accomplish this goal.  Once back in San Juan, the scientists will leave the ship, returning home with the data.  On the fourth leg, the Pisces will return to Mayport, Florida, retrieving a buoy that is adrift along the way.  Commander Fischel is kindly allowing me to remain aboard during the cruise back to port!

Science and Technology Log

Here is a quick overview of all equipment the survey will use to collect data. There is an array of four video cameras that is baited with frozen squid.  The array is lowered over the side of the ship at each sampling site, and allowed to rest on the bottom for 40 minutes.  The cameras cannot be deployed during the night because there are no lights on the array. Therefore, viewing is dependent upon the availability of sunlight penetrating the water column.  Because of the need for natural light, the cameras are only used during daylight hours; the array cannot be deployed earlier than one hour after sunrise and must be retrieved from the bottom of the continental shelf or shelf edge one hour before sunset.

After the camera array is deployed, a cluster of instruments called a CTD is lowered to collect data on the ocean environment.  CTD is an acronym for Conductivity, Temperature, and Depth. Conductivity is used to determine the salinity (the amount of salts dissolved in the water).  Water conducts electricity (this is why you shouldn’t use electrical appliances while in or around water, and why the lifeguard tells you to get out of the pool during a thunderstorm).  As the salinity increases, conductivity increases.  Temperature is a very straight forward measurement.  I’m sure you’ve measured the temperature of several different things ranging from air temperature (to see how hot it is outside) to the internal temperature of a roasting chicken.  These measurements are related to specific depths within the water column. The depth the instrument is at in the ocean is calculated from measuring the hydrostatic pressure (how much pressure the overlying water exerts on the instrument).  The CTD instrumentation cluster collects huge amounts of data – 8 measurements per second!  These are averaged and compressed into “bins” covering 1 meter segments.

The CTD and camera array waiting deployment.

In addition, the instrument cluster also measures the amount of oxygen dissolved (DO) in the water column.  As you probably already know, most organisms require oxygen to live (carry out cellular respiration).  The amount of oxygen dissolved in the water is directly correlated to how much life the water can support.  More oxygen = more life.  When water is warmer, it loses its ability to “hold onto” oxygen; cold water will contain more dissolved oxygen.  This is one reason why climate change and warming aquatic environments are of great concern.

Victor, Joey, and Joe deploying the camera array

After both the camera array and CTD have been deployed and retrieved, the final step at each site is to collect fish through the use of bandit reels located at three sites on the ship.  All three are located on the starboard (right hand) side of the ship.  Reel #1 is starboard (S), Reel #2 is starboard aft (SA), and Reel #3 is starboard stern (SS) at the back of the ship.  Reel #3 is where I helped the attempts to collect fish.  Each bandit reel has ten hooks of the same size (8/0, 11/0, and 15/0) attached to a 300-lb test monofilament.  Each of the hook sizes are rotated around the stations throughout the day.  These hooks are baited with slices of frozen Atlantic mackerel.  A 10 pound weight is attached to the end of the line, the baited hooks attached, and the line let out until it hits bottom.  Then, a float is attached and the line is left for five minutes before being reeled back in.

Any fish that are caught are identified and have their length and mass measured.  Afterwards, the fish’s otoliths are removed and it is opened to determine its gender and have its reproductive stage assessed.  More on the fish specifics to come!

Marian Wagner: From Fishing to Dissecting in the Wet Lab, August 22, 2011

NOAA Teacher at Sea
Marian Wagner
Aboard R/V Savannah
August 16 — 26, 2011

Mission: Reef Fish Survey
Geographical Area: Atlantic Ocean (Off the Georgia and Florida Coasts)
Date: Monday, August 22, 2011

Science Team on R/V Savannah Aug 16-26, 2011: Back row: Chief Scientist Warren Mitchell, Christina Schobernd, Katie Rowe, Mike Burton. Front row: Shelly Falk, Stephen Long, Sarah Goldman, Marian Wagner, David Berrane.

Weather Data from the Bridge (the wheelhouse, where the controls of the ship are)
S-SW Wind at 15 knots
(This means wind is travelling 15 nautical miles per hour, 1.15 statute miles = 1 nautical mile)
Sea depth today ranged from 45 meters to 74 meters
Seas 3-4 feet in the morning, 2-3 feet in the evening (measure of the height of the back of the waves, lower the number = calmer seas and steadier boat)

Science and Technology Log

In my last blog, I explained what I am doing on the  first half of my shift (noon to around 6:00pm/dinnertime) and how we conduct our research on the aft deck of the boat: we drop chevron traps to the ocean floor with cameras attached and then pick up the traps with fish sample collections.  The fish we trap and the cameras recording the activity around the traps help us estimate the fish populations.  We finish up this segment of our work on the deck of the boat by recording this data in a systematic data collection sheet called “Length Frequency”.  If we didn’t record the data the same way every time, it would be impossible to compare the thousands of samples in the past and into the future and understand what is happening to the populations of fish over time.

Length Frequency Data Recording

Here is a picture of us recording the weight and length of the fish and the frequency (how many we caught) in a systematic way,  always keeping track of where the fish were caught as well.  Because we catch large numbers of certain fish species (such as Vermillion Snapper, Red Porgy, Gray  triggerfish, and Black Sea Bass), we do not keep all of them for further research.  When recording/reporting “toss” or keep” got monotonous, I found ways to communicate creatively—how many words can you think of that rhyme with “toss” and “keep”? I got 11 for toss and 16 for keep.  David, Katie, and Stephen were such sports for going along with my silly games!

After this point in the day, the fish are in bags and put on ice, and we wash up for dinner.

After dinner, our work moves into the wet lab, where we prepare biological samples for further research.  For the rest of this log section I describe more about how and why we
use the biological samples.

Dissecting vermillion snapper in wet lab, in search of otoliths and gonads.

We use the biological samples to obtain and report important biological measures such as age, length, weight, feeding habits, and genetics.  In order to know specific ages of the fish, we take out a small bone in the fish called the OTOLITH, which is located in the inner ear. An otolith is a reliable source to obtain the age of a fish. They show age in rings similar to how trees show their age in their growth rings.  We also take the GONADS from the fish to give important information about reproductive development.  Here is a picture of me dissecting a vermillion snapper and taking out the otolith (right hand) and gonads (left hand) to send to the lab back in Beaufort, North Carolina, where scientists work.

Here I just reeled in a gray triggerfish, one of our target species for hook and line catch.

Sometimes after dinner we had time to fish with hook and line in the stunning sunset.  This method of catching fish provided us with fish samples to study that did not have stomachs full of bait like the rest of our fish samples caught in traps. We did this so we could study their stomach contents and learn about what they are eating and get information about the ecosystem they are dependent upon. We were targeting vermillion snapper and gray triggerfish, fish that are known to really gorge on bait in the traps.  Sarah was dissecting the stomach of scamp grouper and found an octopus beak!

Sarah dissecting stomach of scamp grouper and finds octopus beak!

When Sarah was dissecting the stomach of a scamp grouper, she found an octopus beak, the last part of the octopus to be digested. Exciting find!!

When fishing becomes chaotic, teamwork is key.

Here is one of my favorite pictures of all, captured during one of our hook and line battles, and a testament to the incredible teamwork of the scientists and crewmen. How many people does it take to catch a fish? Here, 5 of us were working on the same task.  Lines from 4 reels were tied up from a strong fish swimming in circles, and it took an intense team effort to unravel them in a critical moment. Success was sweetly earned.

Click here for more info on the fish we are studying for stock assessments.

Personal Log

I’m on a boat!  This phrase has been repeated many times and it captures my enthusiastic awe (with a touch of humor) that I have had many privileges, and the fortune to be around some remarkable people, day in and day out. I took the opportunity to interview a few of them so I could share it here.  (Next blog: Interview with Captain Raymond Sweatte)

Richard's showing me how to tie the speed bowline knot, see to learn this knot.

Interview with Richard Huguley, engineer

Marian: When you were a kid, would you have imagined yourself here now?
Richard: Yes. In Mobile, Alabama, where I grew up, I played with wooden boats, making them go up and down the creek, and spent time catching crawfish. I could see this as where I’d be.
M: How often did you play outside?
Richard: From sun-up to sun-down.  I skipped out to the woods all day some days.  I was never afraid to be in the woods. I played with snakes, frogs, had a baby pet squirrel I kept in my pocket.  It poked its head out to eat, and then crawled back into my pocket.
M: How did you become prepared for work as an engineer on a boat?
Richard: I have worked in all different fields required of an engineer: electrical, metal manufacturing-welding, automotive, building race cars and motor cycles, etc.  I always had the interest to take a challenge someone else wouldn’t take—not a challenge that just required physical strength, but more of intellectual puzzle.  It takes lots of time.  I took the time to figure the challenges out.  I can visualize math.  My dyslexia is a strength I use to my advantage.  I see people struggling with something, and it’s like I see it from the opposite end.  I do it without thinking about it.  Jigsaw puzzles are good for this kind of challenge.  It would be good for your students to try doing a jigsaw puzzle with the pieces upside down so they build the puzzle from the angles of the edges.
Thank you, Richard, for taking the time to talk and share your stories and the many skills you taught me. You are one-of-a-kind and I hope you can come visit my classroom someday!

Katie Rowe on the deck of the aft.

Interview with Katie Rowe, scientist and scuba diver/instructor

Marian: What do you like about working in a lab?

Katie: Lab work is about exploration, you don’t know entirely what you’ll find. We’re looking for otoliths, etc, but there is a possibility to find anything!

M: What makes the best partnerships in the lab?

Katie: I like working with people who are organized and efficient, people who can interpret and know what needs to be done next.  It takes an organized system for people to work like this, like we work here.  The system works well here so everyone knows what they are doing, and what happens next so we can all step in and do what needs to be done.

M: What’s your favorite animal?

Katie: Bull shark, Carcharhinus leucas, because they are adaptable.  They can survive in fresh water.  In Nicaragua, one was found in fresh water going after fish to eat, and they thought it was a new species, but then realized it was the bull shark.  They have the highest testosterone of any animal in the world, so they are bad-tempered, but I still love them.  I named my cat Leucas after the bull shark’s Latin name.

Thanks Katie!  It was great to work with you day in and day out!  You are a tough gal and make an excellent partner, very organized and efficient!

Tossing grappling hook to "catch" buoys attached to fish traps.

Fun extra:  How do we retrieve the buoys and pull up the fish traps?  I got to try my hand at this new sport, the grapple hook toss.  I am so grateful to have had the chance to try my hand at so many different roles.  Thanks for the opportunity!

Jennifer Goldner: Still Learning! August 22, 2011

NOAA Teacher at Sea
Jennifer Goldner
Aboard NOAA Ship Oregon II
(NOAA Ship Tracker)
August 11 — August 24, 2011

Mission: Shark Longline Survey
Geographical Area: Southern Atlantic/Gulf of Mexico
Date: August 22, 2011

Weather Data from the Bridge
Latitude: 27.56 N
Longitude: 83.73 W
Wind Speed: 5.95 kts
Surface Water Temperature: 30.50 C
Air Temperature: 31.60 C
Relative Humidity: 66.00%

Science and Technology Log

Okay, so I admit, I can’t learn enough.  I just THOUGHT I was doing my last post, but I have to share with you some more information I learned toward the end of our journey.  So if you want to learn some “cool facts,” today’s post is for you!

Cool Fact #1:  Sargassum This is a type of seaweed we saw in the ocean today alongside the ship.  It mats together in large clumps and serves as a refuge for larval fish.  It also is a type of “floating community” with lots of fish, such as mahi mahi, congregating around it.  Newly hatched sea turtles find refuge in sargassum.

Sargassum off the starboard side of NOAA Ship Oregon II
Sargassum off the starboard side of NOAA Ship Oregon II

Sargassum- courtesy of bing images
Sargassum- courtesy of bing images

sargassum fish
Sargassum fish

Cool Fact #2:  Shark skin samples and fin clips — All week long I have seen shark skin samples and fin clips taken, but today I found out from two of the scientists on our survey, Dr. Trey Driggers and Adam Pollack, what is done with these.  The skin sample is done so the shark can be identified down to the species.  For example, there are 3 species of smooth dogfish in the Gulf of Mexico.  They all look the same externally.  Keep in mind, the smooth dogfish shares the same genus (Mustelus), but the species differs.  One of the ways to tell them apart is to look at their skin sample under a microscope.  For this reason, every shark that is caught has a small sample of skin taken that is placed in alcohol for preservation.

Fin clip
Fin clip

When it gets to the lab, the scientist looks at the dermal denticles (scales) under a microscope.  If the denticle has 1 point, its species is either canis (common name– smooth dogfish) or norrisi (common name–Florida smooth dogfish).  If it has 3 points, its species is sinusmexicanus (common name- Gulf smooth dogfish).

The fin clip is collected and archived and later a DNA analysis is performed.  They are compared to fish of the Gulf of Mexico to tell if they are genetically different or similar.  This information is used for stock management.

Cool Fact #3: Otoliths– I have been assisting the scientists this week in getting the otoliths from various fish, such as red grouper, yellowedge grouper, and blueline tilefish.  Today I got to take the otoliths out myself.  By “myself,” I mean with the help of skilled scientist, Adam!    It was neat!  So what are otoliths?  They are the ear bones of fish.  They tell the age of the fish, much like the annual rings of a tree trunk do.   These are collected and put in an envelope with the identification number in order to be observed under a microscope in the lab.

Removing the otoliths-  Thanks to Adam, Scientist, for teaching me how to do this!
Removing the otoliths- Thanks to Adam, Scientist, for teaching me how to do this!

Otoliths, courtesy of Google images
Otoliths, courtesy of Google images

Otoliths removed
Otoliths removed

Personal Log

Last night after our shift ended at midnight, by the light of the moon we watched a pod of about 25 dolphins chase flying fish and play in the wake of the boat.  I sure will miss all the sights the sea has to offer.  I will especially miss the people.

I mentioned in an earlier post that NOAA Ship Oregon II is like a city.  It has everything needed on board to run smoothly.  There are people with numerous kinds of backgrounds. Each and every one of these individuals is needed in order to successfully complete a NOAA mission, whatever it may be.

So now I’m talking to you kids.  Have you ever thought about what you want to be or do when you grow up?  How about starting now?  How about you adults, have you ever thought about trying to do something new and exciting?   I have a question for you (and I would like for you to put your answer in the poll):  If you could choose any job on this ship, what would it be?

If you will notice from my posts, I did not just cover the science end of this ship.  There are so many other careers going on to make these surveys work.  It’s a team effort.  Under the leadership of Cap Nelson, that’s exactly what you have here on NOAA Ship, Oregon II: a team effort.  And that’s what makes this ship a model for any team to follow.

Walter Charuba: Red Skies at Night: July 21st, 2011

NOAA Teacher at Sea
Walter Charuba
Aboard R/V Savannah
July 18 — 29, 2011

Mission: Reef Fish Survey
Geographical Area: Southeast Atlantic Ocean
Date: July 21, 2011

Science and Technology Log

There is an old sailor’s proverb: “Red Sky at night, it will be bright” or “sailors take flight“ or something like that. I just know that I live by this saying and it has caused many a captain to throw away their weather charts. There was a beautiful red sunset last night and I stood at the bow or stern (I am down to two boat locations now) in complete admiration. However, when I started my shift in the morning there was a front moving in with rain clouds and lightning. I must admit I have been pretty calm most of the trip and this has not been due to the Dramamine. Seeing these clouds caused my imagination to get the better part of me, which of course would be the part that includes my brain.  I had images of “The Great Wave” by Hokausai racing in my head.  This outlook was ridiculous because there weren’t even white caps on the waves. The storm never hit us and the day turned out to be excellent.

Dolphins chasing flying fish at night

Another reason last night was special was because I was able to view some dolphins at a very close distance.  First Mate, Michael Richter, made it quite clear that no one was supposed to walk around the boat alone at night, especially the dark upper deck , and especially on the railings. So after daylight, we are limited to the lighted lower deck.  As I was reviewing my constellations, the light seemed to attract these flying fishes. I do not know if this is true, because correlation isn’t always causation, but it looked true.  As I was staring at the flying fishes, a large splash startled everyone. It was a spotted dolphin and a calf jumping for the flying fishes. The dolphins jumped around for about twenty minutes until we took off to our next destination. It was kind of like our own little Sea World, except natural. It was a perfect way to end the night.

Here I am (right) preparing to help with the trap collection

Morning was the time to not only see, but capture, new creatures. My last blog described the deployment of traps, but now I will write about the retrieval of traps. Science Watch Chief, David Berrane termed this “action time.”  The two flotation buoys we drop are significant because, after “soaking” a trap for 90 minutes, the boat returns to these devices and a crew member has to throw a grappling hook at a line between the buoys. We then quickly pull the buoys in next to the boat.  The buoys are lifted up, the line is connected to a “hauler,” and a trap is pulled on board. This may sound simple but it is actually a five person task. The task is very intense and focused because people may trip over the buoys or ropes, or the trap’s line can snap due to weight or current. Hopefully the trap will be filled with fish and the cameras will record useful data from depths ranging from 25 to 83 meters. As soon as the trap is brought on board, the fish are collected and the cameras are disconnected.

The cameras used on the fish traps

The video survey of the reef is just as important as capturing fish, as cameras can assess the population of species that do not go in traps. Zeb Schobernd, the video watch commander, and I do salute him, downloads all the data on board for further viewing during the off season. Imagine all the viewing that has to be done? For instance fifteen videos were taken in one day of our ten day cruise, and there are four or five missions a year. To avoid reef video insanity, the data is viewed in thirty second intervals which is still a great deal of work.

Fish brought on board are immediately classified to species, and then measured individually. Measurement data are called “length frequency,” and hundreds of fish could be measured from one trap. According to a random tally sheet, certain fish are kept to collect “age and growth” data. Again, this could be hundreds of fish. In the ship’s “wet lab,” fish are then dissected. Most fish have a pair of “otolith” bones (i.e., ear stones) in their head.  Otoliths are collected at sea, but sent to a lab where they will be examined under a microscope.  When otoliths are cut by a delicate saw, visible rings tell the age of a fish, similar to how the rings visible on a tree stump can tell the age of a tree. Fish are further dissected to check the condition of their reproductive systems.

In the next blog I will I write about the “CTD” device.

Cathrine Fox: Issue Six: Alaska, impossibly big and impossibly green

JULY 24 – AUGUST 14, 2011

Mission: Walleye Pollock Survey
Location: Kodiak, Alaska
Date: July 27, 2011

Weather Data from the Bridge
True Wind Speed: na
Air Temperature: 14° C dry/12° C wet
Air Pressure: na
Latitude: 57.44° N, Longitude: 152.31° W
Ship heading: n/a
(Limited data, as ship is in port)

Scientific Log:

I’ve received an in-depth tour of the ship and labs, and I am starting to piece together how the “Acoustic Trawl Survey” works. Basically, NOAA is responsible for monitoring the populations of walleye pollock and accomplishes this task in several ways. The acoustic trawl survey is one part of how this is done.

Net Reels
Net Reels

The science team identifies particular transect areas in the Gulf of Alaska. The ship travels to that area, then transmits acoustic signals about once per second as it travels along each transect. The returning echo gives scientists an initial measurement of the abundance of organisms in the water below the ship. Just “listening,” however, is not enough. We also have to sample populations physically to determine the ages, sizes, and species of the organisms. The ship trawls for these additional data.

A trawl is a large net towed behind the ship to catch fish and other organisms. The individuals (of all species) in the catch are identified and counted. Cameras (three) are mounted inside the back of the trawl (codend) to collect images as they pass through the trawl. From this larger catch, a sample of the walleye pollock (about 300 individuals) are dissected to determine sex, diet, measured (length and weight) for size and aged by looking at (yes) their ear bones or otoliths. I’ll cover all of this in depth once I have been able to do it and see it in action, but that is the gist.

Personal Log:
I think first impressions are important. Alaska? Alaska is impossibly big and impossibly green. Too big, perhaps to describe with common adjectives. It took me about two days of travel from the 4-Corners to make my way up here: a Beechcraft 1900 from Cortez to Denver, then flights from Denver to Seattle and Seattle to Anchorage. I spent the night in Anchorage and wandered the city at midnight… …not that you can tell that it was so late from the pictures.

The next morning I took off from Anchorage and met up with the crew and scientific party onboard the Oscar Dyson in Kodiak, an island the size of Connecticut in the Gulf of Alaska

Adventures in a Blue World, Issue 6
Adventures in a Blue World, Issue 6

As for how ‘impossibly green’ Alaska is, I was thinking about the reasons Georgia O’Keeffe gave for moving from New York City to New Mexico in 1949. She said (and I paraphrase) that she wanted to use more vibrant colors in her palette of paints than just green. Ms. O’Keeffe would have it rough here in Alaska: greens, greys and blues abound. Adventures in a Blue World Issue 6 may not convince you of the colors of Alaska, but I hope it gives you a grasp of its size.

Kodiak, Alaska dock
Kodiak, Alaska dock

I’ve already settled in to the ship and my stateroom. My stateroom is small but comfortable, and I share it with a woman who is part of the scientific NOAA team. Interestingly, she worked for the same professor at the Rocky Mountain Biological Laboratory in Gothic, Colorado as an undergraduate that I did. Very Small World.

We are docked in Kodiak for a few more days than anticipated: we are awaiting the arrival of another deck-hand, and there are a few repairs that need to be made to the ship. Once we get started, I will be working the 4am-4pm shift, and taking part in whatever science is taking place. In the meantime, I get to ‘nose around’ Kodiak, go for hikes and runs, check out museums (see below), and eat as many salmonberries as I can stuff into my mouth.

Until our next adventure,

Anne Mortimer: Swell Sleeping, July 12, 2011

NOAA Teacher at Sea
Anne Mortimer
Onboard NOAA Ship Oscar Dyson
July 4 — 22, 2011 

Mission: Pollock Survey
Geographical area of cruise: Gulf of Alaska
Date: July 12, 2011

Weather Data from the Bridge
Conditions: Foggy and windy, changing to partly sunny and windy
Air Temperature: 10.1 ⁰C
Sea Temperature: 7.6 ⁰C
Wind direction: 237 ⁰C
Wind speed: 20 knots
Wave height: 2-3 ft.
Swell height: 5-6 ft.

Science and Technology Log

Last night we had a “splitter” catch. The scientists found an area that they couldn’t pass up fishing, so at about 9pm the trawl was put in the water. The 540 ft. long Aleutian wing trawl brought in lots of pollock and Pacific ocean perch, a type of red-colored rockfish.  A catch is called a splitter when it is so big it won’t all fit on the table. To get a weight of the whole catch, the deck crew use a crane to weigh the net, then empty it out.  Then the catch is dumped into a bin that is split in two parts. Only one part of the bin is then raised, putting a sub-sample on the table to be worked-up. It took a long time to process all of the catch. We separated the species on a conveyor belt system, then the messy stuff happens. I mentioned that otoliths and stomachs are collected, but I don’t think I emphasized just how gross this can be. To sex the fish, we use a scalpel to slice the fish down the side, then look for larger pink-colored ovaries or a stringy, twisted looking testes. To collect otoliths, the fish skull is cut just behind the eyes and cracked open. The otoliths are then picked put with tweezers. If you are really good at pulling otoliths, you can pull both at once, which can be very challenging. My double-take record is only 2 in a row, but I’ve pulled both at once at least 5 times now!  The last messy thing is stomach collection. You can imagine what this entails, I’m sure. I’m happy to say that I’ve only had to hold the baggie for the stomach, not cut any out! Processing this catch took several hours– we didn’t end until after 1am.

red rockfish
This red-colored fish is a pacific ocean perch, or P.O.P. to a fish biologist.

Pacific ocean perch

When I am not processing a trawl or on the bridge observing, I have been working to annotate some videos from the cam-trawl. The cam-trawl is a stereo-camera system that takes snapshots of whatever comes through the net. This cam-trawl was designed by several of the scientists on the pollock survey. They are hoping it will help lead to less actual fish samples needed if the images can accurately provide evidence of species, numbers, and sizes. Some trawls would still have to be taken aboard for sexing, weights, and otolith and stomach samples.  Annotating the images basically means that I click through the images, counting each species of fish or invertebrate (usually jellies) that I see. This can very tedious, but the whole idea of the project is very exciting. I’ll talk more about the cam-trawl and this technology in my next blog.

Personal Log

Yesterday was my first real encounter with rocking and rolling on the Oscar Dyson. The winds were blowing at about 30 knots (that’s about 35 mph), and there was a lot of swell. Swell waves are long-wavelength surface waves that could have originated from a storm hundreds or thousands of miles away. The combination of these two made for a very rocky ride until we hid behind an island until sunrise. Since I go to bed at 4:30am, it wasn’t long before the boat was headed back out to unprotected waters, and I was rudely awakened by the swell. To say I didn’t have a swell sleep is an understatement. I had to take a nap this evening to compensate for my lost hours!

Kathleen Harrison: Fish Stick, Anyone? July 15, 2011

NOAA Teacher at Sea
Kathleen Harrison
Aboard NOAA Ship  Oscar Dyson
July 4 — 22, 2011

Location:  Gulf of Alaska
Mission:  Walleye Pollock Survey
Date: July 15, 2011

Weather Data from the Bridge
True Wind Speed:  34 knots, True Wind Direction:  284.43
Sea Temperature:  10.02° C, Air Temperature:  11.34° C
Air Pressure:  1014.97 mb
Latitude:  56.12° N, Longitude:  152.51° W
Sunny, Clear, Windy, 10 foot swells
Ship speed:  10 knots, Ship heading:  60°

Science and Technology Log

The Walleye Pollock is an important economic species for the state of Alaska.  It is the fish used in fish sticks, fish patties, and other processed fish products.  Every year, 1 million tons of Pollock  are processed in Alaska, making it the largest fishery in the United States by volume.  The gear used to catch Pollock is a mid-water trawl, which does not harm the ocean floor, and hauls are mostly Pollock, so there is very little bycatch.

table full of pollock
A sample of pollock that the Oscar Dyson caught for scientific study. A "drop" in a very large "ocean" of pollock industry.

Although Pollock fishermen would like to make as much money as they can, they have to follow fishing regulations, called quotas, that are set each year by the North Pacific Fishery Management Council (NPFMC).  The quotas tell the fishermen how many tons of pollock they can catch and sell, as well as the fish size, location, and season.  The NOAA scientists on board NOAA Ship Oscar Dyson have an important role to play in helping the NPFMC determine what the quotas are, based on the biomass they calculate.

The quotas are set in order to prevent overfishing.  Pollock reproduce and grow quickly, which makes them a little easier to manage.  When fishing is uncontrolled, the number of fish becomes too low, and the population can’t sustain itself.  Imagine being the lone human in the United States, and you are trying to find another human, located in Europe, only you don’t know if he is there, and all you have is your voice for communication, and your feet for traveling.  This is what happens when fish numbers are very low– it is hard for them to find each other.

There are many situations where uncontrolled fishing has cost the fishermen their livelihood. For example, in the early 1900s, the Peruvian Anchovy was big business in the Southeast Pacific Ocean.  Over 100 canneries were built, and hundreds of people  were employed.

anchovy catch graph
This graph shows how the Peruvian Anchovy catch rose to record heights in 1970, then collapsed in 1972. This could have been prevented by effective fishery management.

Scientists warned the fishermen in the 1960s that if they didn’t slow down, the anchovies would soon be gone.  The industry was slow to catch on, and the anchovy industry crashed in 1972.  The canneries closed, and many people lost their jobs.  This was an important lesson to commercial fishermen everywhere.

The Walleye Pollock (Theragra chalchogramm) is a handsome fish, about 2 feet long, and greyish – brown.  Most fishermen consider him the “dog” food of fish, since he pales in comparison to the mighty (and tasty) salmon.  Nonetheless, Pollock are plentiful, easy to catch, and thousands of children the world over love their fish sticks.

Besides calculating biomass, there are 2 other studies going on with the Pollock and other fish in the catch.  Scientists back at the Alaska Fisheries Science Center (AFSC) in Seattle are interested in how old the fish are, and this can be determined by examining the otoliths.

2 pollock otoliths
Here are 2 otoliths from a pollock. The one on the left shows the convex surface, the other shows the concave surface.

These are 2 bones in the head of a fish that help with hearing, as well as balance.  Fish otoliths are enlarged each year with a new layer of calcium carbonate and gelatinous matrix, called annuli, and counting the annuli tells the scientists the age of the fish.  Not only that, with sophisticated chemical techniques, migration pathways can be determined.  Amazing, right?  The otoliths are removed from the fish, and placed in a vial with preservative.  The scientists in Seattle eagerly await the return of the Oscar Dyson, so that they can examine the new set of otoliths.  By keeping track of the age of the fish, the scientists can see if the population has a healthy distribution of different ages, and are reproducing at a sustainable rate.

Another ongoing study concerning the Pollock, and any other species of fish that are caught during the Pollock Survey, deals with what the fish eat.

stomach being put into a bag for later study
A pollock stomach is put into a fabric bag, which will be placed in preservative. Scientists at the Alaska Fisheries Science Center will study the contents to determine what the fish had for lunch.

Stomachs are removed from a random group of fish, and placed into fabric bags with an ID tag.  These are placed into preservative, and taken to Seattle.  There, scientists will examine the stomach contents, and determine what the fish had for lunch.

Personal Log  

I learned about fishing boundaries, or territorial seas, today.  In the United States, there is a 12-mile boundary from the shore marked on nautical charts.  Inside this boundary, the state determines what the rules about fishing are.  How many of each species can be kept, what months of the year fishing can occur, and what size fish has to be thrown back.   Foreign ships are allowed innocent passage through the territorial seas, but they are not allowed to fish or look for resources.  Outside of that is the Economic Exclusion Zone (EEZ) which is 200 miles off shore.  The EEZ exists world-wide, with the understanding among all international ships, that permits are required for traveling or fishing through an EEZ that does not belong to the ship’s native country.

Everyone was tired at the end of the day, just walking across the deck requires a lot more energy when there are 10-foot swells.  Check out this video for the rolling and pitching of the ship today.

Anne Mortimer: Otoliths and more otoliths…, July 8, 2011

NOAA Teacher at Sea
Anne Mortimer
Onboard NOAA Ship Oscar Dyson
July 4 — 22, 2011 

Mission: Pollock Survey
Geographical area of cruise: Gulf of Alaska
Date: July 8, 2011

Weather Data from the Bridge
Air temperature: Sunny, 10°C
Sea temperature: 9.1°C
Wind direction: SW; 318 degrees
Wind Speed: 24.1 knots
Barometric pressure: 1012.12 mbar

Science and Technology Log

On my last 12 hour shift, a beautiful, sunny day, we started by pulling in, sorting, counting, and weighing fish caught in a mid-water trawl.  The scientists were also testing out a new “critter cam” that was attached to the net. The trawl net has a special device called a M.O.C.C. which stands for Multiple Opening and Closing Cod-ends. The net has three separate nets that can be opened and closed by the M.O.C.C. when the scientists reach the desired depth or location for catching, this keeps the catches from different targeted depths from mixing together. The three separate nets are called cod-ends. Each cod-end catch is processed separately. In this trawl, we saw multiple jellies, juvenile pollock, krill, juvenile squid, juvenile Pacific sandlance, capelin, juvenile flatfish, and juvenile cod.

Capelin from our trawl covered the deck of the boat.

MOCC entering the water
The Multiple Opening and Closing Cod-end, or MOCC, and net being released to the water for a mid-water tow.

Later, we trawled a 2nd time for about an hour. The trawl net used is called the AWT or Aleutian Wing Trawl because the sides of the net are like wings. After the net is in the water, two large steel doors are dropped in the water and help to pull the net open wide. You can see them in the picture above, they are the giant blue steel plates attached to the very stern (end) of the ship. During this trawl, only one cod-end was opened, and the catch was several hundred pounds of Pollock, with some eulachon, capelin, squid and jellies also.

Because pollock are the target fish of this survey, each was sexed and counted, and a smaller number were measured for length and weight, and the stomachs and otoliths were removed. The stomachs are being preserved for another research project back in Seattle, and as I mentioned previously about otoliths, they tell the age of the fish.

Personal Log

Today I was happy to have beautiful sunshine and 2 trawls to sort through. The skies and surrounding islands were absolutely stunning. I can understand why people are drawn to this place. It’s wild and rugged and looks like it probably did hundreds of years ago.

Scenery of the Shumigan Islands.

Dusk in the Shumigan Islands.

Species List

humpback whale (just one today!)


tufted puffin


arrowtooth flounder




Pacific sandlance


juvenile flatfish

juvenile cod

sea gulls


Thought for the day… if I was a blubbery whale, I would live in the Gulf of Alaska. If I was a pollock, I’d try not to get into a net, they can give you a splitting headache.

Steven Wilkie: July 4, 2011

JUNE 23 — JULY 4, 2011

Mission: Summer Groundfish Survey
Geographic Location: Northern Gulf of Mexico
Date: July 4, 2011

Ship Data

Latitude 29.31
Longitude -94.79
Speed 0.00 kts
Course 172.00
Wind Speed 4.99 kts
Wind Dir. 268.67 º
Surf. Water Temp. 30.60 ºC
Surf. Water Sal. 24.88 PSU
Air Temperature 30.70 ºC
Relative Humidity 68.00 %
Barometric Pres. 1014.50 mb
Water Depth 10.40 m

Personal Log

My final watch ended last night with what was one of our largest catches of the trip.  The knowledge that it was our last trawl–well mine at least–and the Oregon II will head back out in a few days for its final leg of the ground fish survey, allowed us to knock it out in no time.

Our final (and one of our largest) catches waiting to be sorted.

It is amazing how similar my experience has been on this trip to the experiences I have with my students in my classes at school.  They come in “green” on the first few days of class: some of them have a some background knowledge, some of them have little, but slowly but surely as we build on their existing knowledge they get to a point where they are confident enough to speak up about issues and content that we have been discussing.  Towards the end of the year, they can link the ideas of what was talked about at the beginning of the year to what we discussed the week before final exams.  Everything is connected.

I feel now, how I hope my students feel on their last few days of my classes.  A sense of understanding, a battery of skills that I didn’t have when I started now at my disposal, and an appreciation for what it is that the people who taught me know and do on a daily basis.  In all of my years of professional development, summer workshops and the like, I can say that none has been as enjoyable or rewarding as this experience.

With the help of chief scientist Michael Hendon, I remove the otiliths (ear bones) from a snapper. These bones can be used to help determine the age of a fish.

I came into the Teacher at Sea program with a good sense of the marine environment, and I have relied heavily on NOAA’s resources for years to help my students better understand the ocean and its processes.  But to see firsthand how some of that information is gathered and to get a sense of how hard these scientists work to ensure their data and procedures are valid is both commendable and reassuring, as I am consistently telling my students how good procedures will lead them to good data, and will, in turn, allow them to draw well-supported conclusions.

I pride myself on the hands-on approach I bring to science in my classroom, and nothing is more hands on then being elbow deep in 600 croakers flopping on the deck!  Everyone learns differently. I am a learn-by-doing kind of guy, and I try to provide as much of that in my classroom as possible, but even doing something doesn’t guarantee that you will understand it–that often requires a good teacher.  The Oregon II’s crew is the epitome of good teachers in action.  I have to personally extend a thank you to Brittany Palm, my watch leader, and Michael Hendon the chief scientist on board.  Both of these gifted scientists helped me go from a fumbling, taxonomically challenged amateur, to a less fumbling, taxonomically appreciative assistant in training!  Their patience as we butchered scientific names and misidentified organisms allowed us to slowly but surely get a better understanding of the procedures until we could practically work up a catch on our own. Well, we left the fish we couldn’t identify for them, but none the less….

I am happy to be heading home to my family and to a more regular work day (12 hour shifts are tough), but I do think I will miss the experience and the camaraderie among the people on the ship, and the soothing rhythm of the ship’s engines and the waves.  I hope those of you that read this get a sense of what an awesome experience this is, as well as take away the importance of the work that NOAA does, and the need for it!

My watch on our last day, notice how happy we are! From left Michael Hendon (chief scientist), me, Amy Schmitt, Kristin Foss, Brittany Palm (watch leader).

The Oregon II docked in Galveston

John Taylor-Lehman, June 29, 2011

NOAA Teacher at Sea 
John Taylor-Lehman 
Onboard R/V Savannah 
June 24 – July 1, 2011 
NOAA Teacher at Sea: John Taylor-Lehman 
Ship: R/V Savannah 
Mission: Fisheries Survey
Geographical area of the cruise: Continental Shelf off of Florida
Date: Wednesday, 29 June 2011

Weather Data from the Bridge 
Longitude. 80.15
Latitude 29.08
Salinity 36.343
Temperature 27.25
Barometric pressure 32.00
Depth 47.7 m
Winds S,SW 26 knots

Science and Technology Log 

We continue to bait and deploy traps during the daylight hours. Three sets of 6 traps are typically deployed at one location. On Tuesday, 4 sets were deployed because of the low number of fish caught on the previous 3 sets.

There is an art to selecting sites and retrieving traps. Some traps can get hung-up on the ledges they were meant to be resting upon. Our Chief Scientist, Nate Bacheler, must communicate with the winch operator and captain with gestures to subtly move the tether in the hopes of freeing the trap. In rare events, a trap can be lost.

Here I am getting ready to deploy a fish trap.  On the right is the camera that goes on the front of the trap.
Camera on top of the fish trap.

Here I am getting ready to deploy a fish trap. On the right is the camera that goes on the front of the trap
Here I am getting ready to deploy a fish trap. On the right is the camera that goes on the front of the trap

Mounted on each trap are 2 video cameras. They record the habitat and activity in the vicinity of the trap. The resolution on the videos is remarkable! During the winter months the films will be viewed and the fish species identified and counted.

What Happens to the Data? 

Eric taking measurements on a Red Snapper
Eric taking measurements on a Red Snapper

The data collected on these cruises allows scientists to create an “index of abundance” for each species of interest. This information is combined with information from other sources and in-put to an existing assessment (population) model. The South Atlantic Fisheries Management Council then looks at the output from the model to decide on management regulations. They’ll decide on loosening or strengthening harvesting rules for each species.

So What Happens Once the Fish Are Caught? 

There is a great deal of information collected on each fish caught. For example: site location, weight, species, total length, length to fork in tail, and length before the tail. Select fish are later dissected to collect their otoliths (a bone in the head that can be used to determine age) and gonads (for maturity and sex determination). All fish are kept on ice in a large cooler until they are processed. Some of the fish are filleted, wrapped and frozen to ultimately be given away to charity.

Personal Log 

I no longer see the placid Atlantic under the ship. Strong winds (40 knots) have been blowing and stirring up the surface, creating 3-4 ft. waves and at times 4-5 ft. My stomach has noticed the change in conditions so I have been trying to keep busy and my mind distracted. Tried chewing some ginger, a remedy many people have suggested. Later, as the seas calmed and/or the ginger took effect, my stomach settled.

The weather conditions have stimulated much discussion among the science staff and crew. It was decided that conditions were ok to deploy the traps but too “sketchy” to retrieve them safely.

Zeb , David and Nate, members of the science crew
Zeb , David and Nate, members of the science crew

The chief scientist seems to have many contingency plans for when the weather does not cooperate. Decisions can be made at a moment’s notice to head to another site or cancel the trap drops. The fall back plans maximize the productivity of the research with the limited time at sea. The “down” time has given me some extra time to interview the science staff and crew. They are all very interesting people.

Zeb , David and Nate, members of the science crew

New animal sightings: (birds) brown boobies, yellow-throated warbler, Wilson’s storm-petrel, royal terns, (fish) reticulated moray eel, purplemouth moray, and red porgy.

Here I am holding a Red Snapper
Here I am holding a Red Snapper

John Taylor-Lehman, June 26, 2011

NOAA Teacher at Sea 
John Taylor-Lehman 
Onboard R/V Savannah 
June 24 – July 1, 2011 
NOAA Teacher at Sea: John Taylor-Lehman 
Ship: R/V Savannah 
Mission: Fisheries Survey
Geographical area of the cruise: Continental Shelf off of Florida
Date: Monday 26, June 2011

Weather Data from the Bridge 
South West Winds 10-15 knots
Barometric Pressure 29.73

Science and Technology Log 

I assisted in deploying and retrieving 6 “chevron” fish traps at a time. This was done several times at designated sites. The traps are pushed off the back of the boat (fantail) and winched up along the starboard side. Two buoys are attached to each trap. The traps rest on the bottom of the Atlantic between 45 and 230 ft. deep. Locations are determined before the cruise but can be changed if necessary. Ideal locations have hard bottom with some relief.

Here I am (left) getting traps ready with the crew

Traps are baited with 24 “menhaden”, which is a type of fish. Some of the bait is suspended in the trap while other rests on the bottom. The traps “soak” for 90 minutes before being retrieved. There is great anticipation as each trap is being winched aboard the ship. We are all hoping for large numbers of our target fish: grouper and snapper.

This collection technique has been used for 22 years, which allows valid comparisons of data over time. The fish found in the traps thus far are: gag grouper, Warsaw grouper, red snapper, vermillion snapper, sand perch, black sea bass, gray triggerfish.

Personal Log 

Flying Fish
Flying Fish

The entire science staff and ship crew have all been very kind and helpful to me, the novice. They have readily answered all my questions, whether it is about the ship operations or the research being conducted. They have gone out of their way to bring to my attention items or events they think would be of interest to me.

Last evening we spent the last hours of our shift processing black sea bass. I learned how to remove the otoliths from the skull and the reproductive organs from the body cavity. The former can be used to age the fish and the latter to determine maturity and sex.

This is called an oyster toad fish
This is called an oyster toad fish

While walking on the back of the boat last night I heard a great deal of splashing in the water. The lights from the ship were bright enough to illuminate the water below me, so in I was able to see 6 dolphins in the water. They were feeding on the many flying fish that were attracted to the ship’s lights. I imagine a few of the fish were able to escape because the dolphins remained for at least 1.5 hours. Some of the dolphins were able to grab the fish out of the air.

Unusual sights: 4 cruise ships heading south, a double rainbow, oyster toad fish

Tammy Orilio, My First Pollock Trawl, June 20, 2011

NOAA Teacher at Sea: Tammy Orilio
NOAA Ship Oscar Dyson
Mission: Pollock Survey
Geographical Area of Cruise: Gulf of Alaska
Date: 20 June 2011
Weather Data from the Bridge:
Latitude: 54.29 N
Longitude: -165.13 W
Wind Speed: 12.31 knots
Surface Water Temp: 5.5 degrees C
Water Depth: 140.99 m
Air Temp: 6.1 degrees C
Relative Humidity: 97%

Science & Technology Log: walleye pollock, which is an important fish species here in Alaska. Walleye pollock make up 56.3% of the groundfish catch in Alaska (, and chances are you’ve eaten it before.  It’s a commonly used fish in all of the fast food restaurants, in fish sticks, and it’s also used to make imitation crab meat.

Our first catch had a little over 300 walleye pollock, and we processed all of them. Three hundred is an ideal sample size for this species. If, for example, we had caught 2,000 pollock, we would only have processed 300 of the fish, and we would have released the rest of them back into the ocean.  Check out the photos/captions below to see how we process the catch.

Conveyer belt

Gender Box

Length Station
After sexing, we then measured the length of each fish. There’s a ruler embedded in the lab table, and we laid each fish down on the ruler. Then we put a hand-held sensor at the caudal (tail) fin of the fish, and the total length was recorded on a computer.

At the sexing station, cutting open pollack.
At the sexing station, cutting open pollack.

We also removed and preserved 20 stomachs from randomly selected fish in order to (later) analyze what they had been eating prior to them being caught. One of the last things we do is collect otoliths from each of those 20 fish. Otoliths are ear bones, and they are used to determine the age of a fish- they have rings, similar to what you see in trees.

Here’s a look at some of the bycatch in our nets:

Basket Star.  Marine 1: What phylum are sea stars in?
Basket Star. Marine 1: What phylum are sea stars in?

Arrowtooth flounder.
Arrowtooth flounder.

The reason(s) WHY they're called ARROWTOOTH flounder.
The reason(s) WHY they’re called ARROWTOOTH flounder.

Animals Spotted:
walleye pollock
chum salmon
arrowtooth flounder
basket star
Northern Fulmars
Albatross (couldn’t tell what kind)
* I did spot some kind of pinniped yesterday, but have no idea what exactly it was!

Personal Log:
I was very excited that we finally got to fish today!!  As an added bonus, we caught 2 salmon in the trawl, which means we’re having salmon for dinner tonight!  We we supposed the have teriyaki steak, but the cook has changed it to teriyaki salmon instead 🙂  I didn’t get any pics of them because my gloves were covered in fish scales, blood, and guts by that point and I didn’t want to get any of that funk on my camera 🙂
We passed by Dutch Harbor yesterday- it should sound familiar if you watch Deadliest Catch.  We didn’t go into the Harbor, so no, I didn’t see any of the crab boats or any of the guys from the show!  Below are some pics of the Aleutian Islands that I’ve see thus far…many more to come, since we still have another 13 days (give or take) of sailing left!


  • The Aleutian Islands were formed at the boundary where the North American and Pacific Plates are coming together.  The Pacific Plate is denser than the North American Plate, so it slides underneath the North American Plate.  What is this type of plate boundary called (where plates move towards each other), and what is it called when one plate slides underneath another?
  • One thing we’re doing on this trip is trawling for fish.  We are conducting both mid-water and bottom trawls.  Describe one advantage and one disadvantage to trawling in order to gather scientific data.

Margaret Stephens, May 25-27

NOAA Teacher at Sea: Margaret Stephens
NOAA Ship:
Mission: Fisheries, bathymetric data collection for habitat mapping
Geographical Area of Cruise: SE United States continental shelf waters from Cape Hatteras, NC to St. Lucie Inlet, FL
Dates: May 25-27, 2011

Weather Data from the Bridge 

View from the Pisces bridge: calm seas
View from the Pisces bridge: calm seas

As of 11:43 May 27, 2011
Latitude 29.94
Longitude 80.29
Wind Speed 0.60 knots; calm
Wind Direction 167.50 º
Surface Water Temperature 26.60 ºC
Air Temperature 25.70 ºC
Relative Humidity 81.00 %
Barometric Pressure 1013.70 millibars (mb)
Water Depth 54.59 m
Skies: clear to partly cloudy

Science and Technology Log 

I struggle to measure a squirmy black sea bass, Centropristis striata.
I struggle to measure a squirmy black sea bass, Centropristis striata.

Previous logs describe in some detail the three principal components of this research work aboard Pisces: overnight mapping using acoustics (SONAR) technology; daytime fish trapping; and underwater videography. The nighttime mapping is used to identify the hardbottom habitats favored by red snapper and grouper species and helps the science team determine where to set traps the next day. The videography provides additional visual clues to the contours and composition of the sea floor, water clarity, and marine life in the area.

Scientific research at sea is far from neat, clean and predictable. Messy, hot, smelly, sometimes frustratingly unpredictable – and not for the weak-stomached– are better descriptors. The work goes on as long as it takes, well past the scheduled twelve hour shifts. The “wet” lab could just as well be called the “fishy” lab. For good reason, the seasoned researchers wear special waterproof bibs and boots and clothing they don’t mind getting dirty. A distinctly fish-infused aroma fills the air and embeds skin, hair and garb. The best laid plans go awry. Equipment and instruments are checked, double- and triple-checked; nevertheless, they don’t always function properly or yield the expected results. Despite using high-tech SONAR to locate what appear to be promising locations, and baiting traps with the most appetizing bait imaginable (dead menhaden), the fish move around and are not always lured into the traps we set so carefully. While this project has been graced so far with unusually calm seas, the currents, other boat traffic, threatening weather and other factors can cause the ship to deviate from its appointed path.

These scientists seem to thrive as they meet the challenges of the ever-changing seascape, solving problems and continuing the hard work day and night.

Todd Kellison (l) and Warren Mitchell (r) confer at sunrise as their long night’s acoustics lab work continues past dawn. Photo credit: David Berrane
Todd Kellison (l) and Warren Mitchell (r) confer at sunrise as their long night’s acoustics lab work continues past dawn. Photo credit: David Berrane

After spending the first few days south of Cape Canaveral, mapping and trap sampling, calibrating and making adjustments to the instruments and deployment procedures, we headed north, because strong currents and turbid (cloudy) waters were limiting the team’s ability to deploy traps and capture useful underwater video images. When the currents are too strong (>2.5 – 3 knots, or nautical miles per hour), the moving water tends to drag the traps, making it very difficult to position them in the desired locations on the sea floor. In addition, the currents swirl sediments around, reducing visibility and yielding video images that are less than revealing. Since moving north of Cape Canaveral, the currents have been less of a problem, and the water clarity has improved.

The mapping, trapping, and video procedures all went more smoothly after the team made adjustments guided by the first days’ experiences. The acoustics team leaders, Warren Mitchell and Todd Kellison, have worked assiduously throughout the taxing, tiring overnight shifts to produce useful bathymetry maps with the ship’s state-of-the-art ME70 multibeam sonar unit. Investigator Jen Weaver has applied her expertise with GIS and mapping software to help Warren and Todd translate the sonar data into three dimensional maps most useful for Nate Bacheler, the Chief Scientist, to plan the trapping routes.

Sonar image shows ledges and outcrops. Photo credit: Christina Schobernd
Sonar image shows ledges and outcrops. Photo credit: Christina Schobernd

By the second and third nights on the acoustics team, I was getting better at recognizing the features on the sonar screen displays, such as ledges and rocky outcroppings, that are indicative the hardbottom habitats we were seeking. Chief Scientist Nate has perfected the timing and communications with the deck crew so that the traps are released off the stern deck at just the right time, sinking to the bottom in the desired locations. Radio transmitter in hand, Nate studies an array of monitors displaying the sonar images of the sea bottom mapped the night before, the navigation system with the ship’s position and path, and a live video feed showing the crew awaiting instructions on the deck. The helmsman alerts Nate that the ship is approaching the next drop point and slows the ship.

Nate issues a series of commands to the deck crew by radio:

Crew deploys baited trap above guard rail on
Crew deploys baited trap above guard rail on

Ready the cameras. Ready the cameras.” – A few minutes before the ship approaches each trap point, a team member activates the two video cameras attached to the trap.

Crew deploys baited trap above guard rail on

Go on standby; stand by to deploy trap.”- The deck crew positions the trap at the edge of the stern (back) deck and makes sure all the lines are clear.

Deploy trap; deploy trap.” The deck crew pushes the trap over the edge of the stern and lets the line attaching it to the ship run free. Once the line goes slack, indicating the trap has reached the bottom, the crew releases the bright orange buoys to float on the surface, marking the trap locations to warn other ships to steer clear and facilitate retrieval.

The deck crew then positions the next trap, and the helmsman, Nate and crew repeat the choreographed sequence until all six traps in each set are in place. Soon after, the helmsman maneuvers the ship for the deck crew to retrieve the traps and their contents one by one using a pothauler, a special hoist.

Technical/Logistical Challenges 

We ran into some initial difficulties with the video cameras attached to the traps when they turned off and failed to record. As good scientists, the team observed the procedures closely and determined that the force of the cameras hitting the water upon release was probably causing them to shut off. At first, the traps with cameras attached were being pushed off the stern above a fixed guard rail, which sits about 1.5 meters above the deck, with three removable guard wires below the rail. A simple adjustment seems to have fixed that problem – instead of releasing the traps above the guard rail, the crew lowered the traps to the deck floor and pushed them off more gently from there. This modified procedure seems to have done the trick, as the cameras have not shut off since.

Science team adjusts camera-trap arrays on stern deck
Science team adjusts camera-trap arrays on stern deck

We are constantly reminded of the ship’s mantra, “Safety first!”, as anyone working on deck while machinery is in operation is required to wear a hardhat and personal flotation device (PFD). He or she who forgets to do so is quickly alerted by others. Because the change in the trap release procedure necessitated removing the three safety wires below the stationary guard rail, leaving a gap large enough for a person to slip overboard, the crew members tied themselves to tethers attached to the deck. Falling off the stern of the ship is dangerous, not least because the propellers turn rapidly and create a backwash effect that could draw a person underwater, even one wearing a PFD.

After each set of six traps is collected, the crew and wet lab team prepare them for redeployment. They empty any fish caught from the traps into bins, separate them into species, then weigh, measure, and release or preserve them for further study. With the help of the deck crew, two or three members of the science team stay on the side deck, dressed in waterproof bibs, boots, life vests and helmets. They detach and dry the cameras and hand them to the dry lab video coordinator, Christina Schobernd, who immediately removes the memory cards, sets up the video to view, and readies the cameras for the next trapping sequence. Occasionally, a camera tilts out of alignment, possibly in the jolt of travel or by hitting something underwater or on the bottom. Each time that happens, Christina meticulously assesses the situation and adjusts the cameras’ attachments.

Under these conditions, working with expensive equipment, it is crucial to anticipate possible problems and build redundancy into the operations as much as possible. This year, the team added a second, high-definition camera to the video array, and each camera is attached to the trap frames with at least six heavy-duty plastic ties and a tether wire and clip. That tether has been a camera-saver, as in one instance the cameras somehow broke free and would have been lost without it.

Fish measuring “assembly line” in the wet lab
Fish measuring “assembly line” in the wet lab

Thanks to good planning, enhanced by a measure of good luck, so far we have not lost any traps or equipment. It is not unheard of to have a trap break free from impact, from a boat propeller running over and cutting the line, or for some other reason. If a trap breaks loose in a place that’s too deep for human divers to search, or if the ship is not equipped with diving capability or a ROV (remote operating vehicle), the trap must be given up for lost.

Once the traps’ fishy contents are brought in and separated by species, three to four people in the wet lab process the fish in assembly-line fashion, as described in the previous log. With traps containing one hundred fifty (150) fish or more, we have to work fast and furiously to weigh, measure and release them before the next haul is aboard. The fish flop and squirm and squirt, and as I learned the first time I handled them, the black sea bass have some mighty sharp spines that can penetrate even the heavy, protective gloves we wear.

To ready the array for the next trap set, the team then

  •  “freshens” the bait by taking out any fully or partially eaten bait and replacing it with the same number of whole menhaden fish;
  •  reattaches the cameras;
  • lines up the numbered traps on deck, ready to go again.

Sometimes, the interim between trap sets coincides with the ship’s lunch time: 11 a.m. If so, the science team takes a short break to refuel with Steward Jesse Stiggens’ tasty culinary creations. If not, the stewards leave the lunch buffet available for whenever the team can get away for a few minutes. While the traps are “soaking” (sitting on the sea floor for the required ninety minute intervals), the science team keeps busy viewing video from the previous haul, processing fish specimens, tidying the deck and lab area, speculating about what the next trap might yield, and telling fish stories from past field work. As anyone who has spent time around fishers (the gender-neutral form of fishermen) knows, fishing stories always get better with time!

Processing and Collection of Biological Samples 

Otolith showing age rings Photo source:
Otolith showing age rings Photo source:

To assess fish stock and population trends, scientists must do more than identify species and catch, weigh and measure fish. They also determine the sex, size and ages of fish and genetic diversity within the populations studied. Connecting size and age can help determine the fishes’ growth rates, where they are in their reproductive cycles, and how likely they are to spawn, or reproduce.

Why is it important to determine the age of fish? By knowing the age of fish, fisheries managers can better understand and monitor how fish populations change over time, and how they are affected by environmental stresses or disturbances, including environmental changes, storms, pollution, commercial and recreational fishing, natural mortality, predation, and changes in the availability of food. The age information helps inform policies promoting fishing practices that protect the fish resources for sustainable, long-term benefit.

David Berrane removes otoliths from red snapper, Lutjanus campechanus Photo credit: Christina Schobernd
David Berrane removes otoliths from red snapper, Lutjanus campechanus Photo credit: Christina Schobernd

To determine fish age most accurately, the scientists remove otoliths, two bones located on either side of fish’s skull that are analogous to the human ear bone. The otoliths show annual growth rings, so the technique used is similar to counting tree rings. You may clickhere to try aging a sample fish.

On board Pisces, the experienced scientists remove the otoliths from dead fish with a sharp knife and scalpel, then place the otoliths in small envelopes, labeled with the date and location caught, ready to be analyzed back in laboratories on land. At the same time, they preserve tissue samples used for DNA/genetic analysis. They may also remove the gonads, or egg sacs, of female fish, if they are needed for further study. They can approximate how close the fish are to spawning based on the condition of the egg sac. The closer they are to spawning, the fuller and larger the sacs become.

Removing egg sacs from female black sea bass, Centropristis striata
Removing egg sacs from female black sea bass, Centropristis striata

Through laboratory analysis using DNA from tissue samples, scientists can evaluate the genetic diversity within each species and other population dynamics. Genetic diversity among fish populations, as in other animal and plant species, is desired because more genetically diverse populations are generally more resilient, more resistant to disease and more able to withstand changes in environmental conditions, availability of food, and other stresses.

Personal Log 

We’ve been fortunate to have had a stretch of unusually fine weather and calm seas. Thank goodness, not a single person has shown a hint of sea sickness. It may be bad luck to say this while we are still out on the water, but I have never been seasick, and I certainly would not want this to be the first time. I’ve seen people who literally turned green and felt absolutely miserable while traveling on rough seas. Some of the crew members who served in the United States Navy or on commercial vessels told me that they had been violently sick every day for weeks when they first went to work at sea. Most eventually get over that. I cannot imagine how debilitating and horrible it must be to feel so wretched. There’s no place to go once you are on a ship — you cannot just jump overboard and swim home through long distances and possibly shark-infested waters, although if you are sick enough, that prospect might seem a welcome relief!

Significant events 

Late one afternoon, I noticed that we had changed direction. We had been heading south, and then turned back north. Since this was not the planned route, I thought perhaps I had missed or misunderstood something, so I went up to the bridge to investigate. Commander Jeremy Adams (the CO = Commanding Officer) informed me that he had turned the ship around in response to a radio call from the Coast Guard, the branch of the armed services of the United States in charge of monitoring the coasts for navigation, safety and law enforcement. The radio call was a Pan-pan alert, one step short of the emergency Mayday call that mandates immediate action. A Pan-pan is urgent but not imminent, and ships in the area are not required to respond. In this case, the Coast Guard announced that they had received a report of a partially submerged small boat with possible man overboard/missing. Since Pisces was the closest vessel to the reported location, CO Adams made the decision to deviate from the planned course and redirect her at nearly full speed, approximately fourteen knots (nautical miles per hour), to search and assist if necessary. As Captain Jerry put it, even though he was not obligated to respond, he would not have been able to rest knowing there was a possibility the ship under his command could have helped. While en route there, another radio relay from the Coast Guard canceled the Pan-pan, because the initial report was apparently a false alarm. The CO informed me that false alarms of this kind occur all too often. Sometimes disgruntled or troublemaking recreational boaters, perhaps annoyed with the Coast Guard’s vigilance or just pulling a prank, call in alarms. These are akin to and at least as dangerous as intentionally false bomb scares or fire alarms on land. Such maliciously false reports take emergency personnel and resources away from true emergencies, cause tremendous waste of public funds, and can put emergency responders and others at risk. At sea, if the perpetrators are caught, they can be fined heavily and held responsible for all the costs incurred.

Devastation in Joplin, Mississippi 

On Sunday, May 22, news of the catastrophic tornado in Joplin, Mississippi reached Pisces. One of the crew members watched the news feed in horror, as the images of an elementary school that had been completed flattened played over and over again on the large screen in the mess. His friend lived just two blocks from that same school and had probably been at home when the powerful twister hit. The crew member tried in vain to call her cell phone or reach anyone who might have heard from her.

In the next hours, we learned that this NOAA ship’s crew is like family. The CO authorized the crew member to take personal leave and arranged for Pisces to meet a Coast Guard vessel the next morning to transport the young man to shore, so he could catch a flight and drive to Mississippi to search for his friend. Since he is also a certified medic, he would be allowed in to the town, despite any official restrictions.

We all felt for him and waited anxiously for word from Joplin. Thankfully, a day later, the ship received a message that his friend was alive and physically intact, although her home and entire neighborhood were destroyed, and so many other residents were critically injured, missing or dead.

It would be terrible to be isolated at sea in such circumstances and feel utterly helpless. I was reminded of the sacrifices so many service members make. As other crew members who had served in the U.S. Navy and other military branches know all too well, home leave, even in emergencies, is not always possible. Many of them had missed key personal events and tragedies while they were away from home on active duty.

Links & Resources

Rebecca Kimport, JULY 14, 2010 part2

NOAA Teacher at Sea Rebecca Kimport
NOAA Ship Oscar Dyson
June 30, 2010 – July 19, 2010

Mission: Summer Pollock survey
Geograpical Area:Bering Sea, Alaska
Date: July 14,  2010

Weather Data from the Bridge

Time: 1500
Latitude: 57.34N
Longitude: 173.35W
Cloud Cover: 2/8
Wind: 10 knots
Air Temperature: 8.50 C/ 470 F
Water Temperature: 8.10 C/ 470 F
Barometric Pressure: 1021.4 mb

During this trip, it has been amazing how the days have blended into each other. There are times when it has been hard to even remember what we did in the morning (before breakfast) by the time lunch rolls around. In some ways, a “day” is not a useful unit of measurement for time. Instead, things happen in moments.

Sightings of mammals and birds require you to be at the right place at the right time. Yesterday, during dinner, a call came into the mess hall from the flying bridge — sperm whales and killer whales off the port bow. Within seconds, everyone hustled into gear, shoveling down the last bites of food, clearing their plates and heading up to see the whales. I went all the way up to the flying bridge and was able to see three different sperm whales catching their breath before diving back to the depths. Ernesto also showed me the killer whales through the big eyes. As sperm whales can be down for 45-50 minutes, it is very exciting to catch them at the surface as we are moving to fast to see them on their next trip up.

Ready to dig out otoliths

In addition, timing is important to ensure that operations on the ship continue smoothly. For example, fishing operations involve three teams (officer on deck, the deck crew and the scientists) all working together to ensure that the fish we spot get in the net, on the boat, and processed as quickly as possible. As Katie, Michele and I became more familiar with processing, we were able to move through the hauls much faster. On Tuesday, we completed three hauls in our shift and still had time to catch up on emails, learn about the Aleutian volcanoes and attempt to master some old-school knots.

Katie eats the jellyfish

While we’re on the subject of timing, I have to mention the crew’s and scientists’ comedic timing. I can’t tell you how much time I have spent laughing and joking while on this cruise. It could be as simple as a funny face someone makes when confronted by a huge jellyfish or as nerdy as when someone uses the word of the day in a sentence. As the trip comes to a close (we will be in port by 9 am on Friday), I have started to think about how I will take this experience back to my classroom and to my friends and family. In addition to the science and the amazing sights I have seen, I will definitely take the memories of how often we fell out of our chairs laughing.

Michele Brustolon, July 12, 2010

NOAA Teacher at Sea
Michele Brustolon
Onboard NOAA Oscar Dyson
June 28 – July, 2010

NOAA Teacher at Sea: Michele Brustolon
NOAA Ship Oscar Dyson
Mission: Pollock Survey
Geographical area of cruise: Eastern Bering Sea (Dutch Harbor)
Date: July 12, 2010

Weather Data from the Bridge

Time: 1500
Latitude: 61.18N
Longitude: 175.22W
Cloud Cover: 8/8
Wind: 16 knots
Air Temperature: 70 C/ 450 F
Water Temperature: 6.90 C/ 450 F
Barometric Pressure: 1014 mb

Science and Technology Log

The floating city
A modern city has a network of companies that provide us with modern conveniences (water, electricity, sewage, and trash removal). A NOAA research vessel provides those same conveniences to its crew through a complex engineering network. We wouldn’t be able to eat, drink, take showers, or conduct research without the expertise of our engineers.

Jerry (1st Engineer) over the sea chest

Lots of drops to drink

Sea water is taken in by an intake valve about 6 m below the surface. It goes through a variety of cleaning processes to filter, distill and purify the water for human consumption. First, small sea creatures are removed by a filter known as the “sea chest.” Next, the water is distilled using the heat from the engine under a vacuum to remove dissolved ions. The water is then purified using bromine and UV light before it is pumped into the piping system (running throughout the ship in pipes labeled “potable water”). The water is so pure that we have to add salt for the espresso machine to recognize the water level (the science of the espresso machine will have to wait for a later entry).

Contents of the sea chest

Lights, Camera, Acoustics

The Oscar Dyson requires electricity to run the ships instruments, the scientific equipment and the lights which allow us to keep the ship operational 24/7. Our power is generated by the engines which also propel the ship forward. The Oscar Dyson runs on diesel fuel and uses larger, more powerful versions of the engines we find in cars. We use about 110 gallons of fuel each hour to maintain scientific and navigational operations.

One of the Dyson’s engines

Taking out the Trash

Kitchen and food waste are the main sources of trash on the Oscar Dyson. Trash is sorted and disposed of based on how it breaks down. Food, which decomposes, is released into the ocean to re-enter the ecosystem. Combustible items (such as paper, napkins, etc) are burned in the ship’s incinerator which is run every night.  Non-combustible items, such as aluminum cans, are recycled and brought back to land.

The Dyson’s incinerator

And out the other end

Although a less than pleasant topic to discuss over dinner, it is important to remember that a ship must track its human waste as well. Per NOAA regulations, human waste is treated through a complex process before being released into the ocean (to re-enter the eco-system). This process, like those of water treatment plants and septic systems on land, break down the waste through multiple steps involving biological, physical and chemical reactions. Ask me for more information if you really want the dirty details.

Who’s watching the engines?

The Oscar Dyson employs an engineering staff of seven, who have specialized training and job responsibilities to ensure proper functioning and maintenance of the vessel. Like all good engineers, they usually work behind the scenes so it was great to get an inside look at the inter-workings of the ship.

Personal log

Day 13 of my twelve hour shifts; still no rough seas, but we have found the fish! Fishing has definitely picked up over that last few days. Unfortunately we are approaching the last days of Leg II. Both shifts have been fishing more and we are seeing different sizes of pollock in different catches. Although I am not yet an expert, I feel as though I have seen enough fish to determine that the smaller ones (1-2 years old) are much harder to work with because they are not as developed (you can ask me for details later). On the other hand, the larger pollock are smellier and messier. Yesterday after we fished, we immediately did a Methot trawl and found the tiniest squid I have ever seen. It even inked! In the afternoon when we fished, we had 2 herring in our catch. It has become a goal of mine to see something new everyday which happens often in the Bering Sea.

Pollock on the table-ready to be processed

Letting the teacher part of us take over, Rebecca and I decided that we would like to take some samples of otoliths back home with us. After we fished for the last time yesterday, we measured various sizes of male and female pollock and then took their otoliths. (insert picture of otoliths here)Because everyone has been patient with us, this entire trip has been filled gaining experience with different types of equipment and procedures on board a research vessel. This allowed Rebecca and me to actually get what we needed on our own; a small side project if you will. I’m not exactly sure how I will incorporate them into my lessons, but it had to be done. I can figure out the logistics later- I have some ideas!

Taking otoliths (ear bones) from a pollock

After dinner I decided to head up to the Flying Bridge to see what the mammal observers were up to. There are five cetaceans (killer whales, Dall’s porpoises, fin whales, minke whales, and humpback whales) that are typically seen in the Eastern Bering Sea along the shallow part of the shelf. I have only seen killer whales and Dall’s porpoises so naturally I was on a mission to add to my list. While looking through the “Big Eye,” Paula Olson saw spouts from whales in the distance and took the time to help direct me. After watching along the horizon, I was able to see the blow holes of 2 fin whales. Fun fact…fin whales are the second largest mammal on Earth. Like I said…there is always something new to see. It was around 2000 hours at this point, but that means off to bed for a decent night’s sleep because 0315 roles around fast.