David Madden: Otolithia and The Tragedy of the Commons, July 27, 2019

NOAA Teacher at Sea

David Madden

Aboard NOAA Ship Pisces

July 15-29, 2019

Mission: South East Fishery-Independent Survey (SEFIS)

Geographic Area of Cruise: Atlantic Ocean, SE US continental shelf ranging from Cape Hatteras, NC (35°30’ N, 75°19’W) to St. Lucie Inlet, FL (27°00’N, 75°59’W)

On board off the coast of North Carolina – about 45 miles east of Wilmington, NC (34°18’ N, 77°4’ W)

Pisces Route
Pisces Route as of July 27, 2019

Date: July 27, 2019

Weather Data from the Bridge:

Latitude: 34°18’ N
Longitude: 77°4’ W
Wave Height: 3-4 feet
Wind Speed: 6.68 knots
Wind Direction: 42°
Visibility: 10 nm
Air Temperature: 28.0°C 
Barometric Pressure: 1022.4 mb
Sky: Partly cloudy

Science and Technology Log

Today, with the help of friends Zeb and Todd, I’d like to take a deep dive into the mission of this cruise.  Starting with the fish work up process aboard Pisces, first explained in blog #3.  Below is a picture flowchart I drew up to help visualize what’s going on. 

NOAA Fish Protocol (color)
NOAA SEFIS Fish Survey Protocol

This sequential process is rather straight forward following steps 1-8, rinse (the gear) and repeat. It’s the before and after; what comes before step 1 and after step 8, that’s important; How and where is the data used.  If you follow along into steps 9, 10, 11… you start with the laboratory analysis of the biological samples – otoliths and gonads – used to age the fish, and determine reproductive activity and spawning seasons, respectively.  This information is vital to proper management of fisheries.  Here’s why. 

This cruise, and SEFIS in general, originally came into existence because of red snapper.  Scientists determined around 2009 that the red snapper population in the SE Atlantic was at historically low levels.  Strict regulations were put in place to help the species rebound.  This on its own was a good measure, but only one step.  In order to assess the effect of the regulations, scientists would have to monitor the abundance of red snapper in the region.  However, charting changes in abundance would not be enough with this species (or with many others) due to the nature of its life cycle and reproduction.  See, all populations have a natural age structure balance.  This includes species specific traits – like its survivorship curve (how likely it is for an individual to die at different points in their life – for red snapper and many other reef-associated species it’s incredibly high at their larval and juvenile stages).  It also includes pertinent developmental characteristics such as when the species is reproductively mature.  Like many similar fish, older, mature red snapper have greatly increased reproductive potential, also known as fecundity.  So while the population has been bouncing back in terms of numbers, the number of older, mature, more fecund fish is still considerably lower than historical levels; thus the population is still recovering.  *this information is gathered from the data collected by scientist here on our SEFIS mission, and others like them. 

SEFIS survey site locations
SEFIS survey site locations.

The next step is to share this data with other scientists who will then, in conjunction with other information on the species, analyze the data and bring the results and conclusions of their analyses to policy makers (FYI, the government is moving towards making governmentally gathered scientific data available to the public).  Discussion ensues, and climbs the political decision-making-ladder until allowable catch regulations are determined.  Florida fishers, check here for your current snapper regulations or maybe this Fish Rules app will help.  Fish safe, my friends!

Morning Crew
Morning crew: Mike, Dave, Brad, Me, Todd, Oscar the Octopus, Mike, Zeb
Macabre medieval cutlery? Or otolith extraction gear?

Ultimately this is a tricky and tangled issue of sustainability.  Commercial fishermen are understandably upset, as this can threaten their livelihood.  Although real, this concern is inherently short sighted, as their long term earnings depend on healthy and robust populations, and ecosystems.  The difficult part is to gather the necessary scientific data (very challenging, especially for marine organisms) and marry that to the many financial, social, and political concerns.  Comment below with thoughts and suggestions.  And while you’re at it, here’s a lovely and quick (fish-related) tutorial overview of this situation in general – the tragedy of the commons – and the challenges of managing our resources. 

A quick note about otoliths.  Within the fish processing protocol (above) – the most satisfying part is otolith extraction.  On board competitions abound: people vie for first chair (the spot in the lab that’s the coolest and best lit) and for the sharpest knives and scissors.  Much like a wild west showdown, most important is fastest extraction times.  Dave H opts for the classic chisel-through-the-gills technique, while the rest of us opt for the saw-through-the-skull-with-a-knife-and-crack-the-head-open-just-behind-the-eyes technique.  While Brad looks to perform the “double-extraction” – both otoliths removed in the tweezers at the same time, I look to perform the please-don’t-slice-my-hand-open extraction.  The quest for otoliths is usually straight forward.  But sometimes an ill-sliced cut can leave you digging for the tiny ear bones forever. 

This leaves us with: Why otoliths?  These tiny little ear bones help function in the fish’s vestibular system.  That’s a fancy way of saying the balance and orientation system of the fish.  They help vertebrates detect movement and acceleration, and they help with hearing.  These little bones help you determine your head and body orientation – turn your head sideways, it’s your otoliths who will send the message.  All vertebrates, including you, gentle reader, have them.  This makes me wonder if folks with exceptional balance and proprioception and court awareness have bigger otoliths?  Fish requiring more balance, those that sit and wait to hunt vs. those that swim predominantly in straight lines, have bigger otoliths. 

Otoliths are made of layered calcium carbonate (side question – does ocean acidification impact otolith formation?  Like it does with other calcium carbonate structures in the ocean?)  The fish secretes new layers as it ages: thicker layers during good times, thinner layers during lean times – correlated with summer and winter seasonality – just like with tree rings.  Once you dig out the otoliths, they can be analyzed by on-shore scientists who slice ‘em in half and take a really thin slice, deli-meat-style.  Voila! You can then count up the rings to tell how old the fish is. 

Fish Otolith
From Andrews et al 2019, published in the Journal of Marine and Freshwater Research: Illustration of a red snapper (top right), a photo of a red snapper otolith (top left), and an image of a cross-section of that otolith (bottom) http://www.publish.csiro.au/MF/fulltext/MF18265
cod otolith
From Hardie and Hutchings 2011, published in the journal Arctic: A cross-section of the sagittal otolith of an Atlantic cod.

Retrieved from https://www.researchgate.net/publication/255711740_The_Ecology_of_Atlantic_Cod_Gadus_morhua_in_Canadian_Arctic_Lakes

Black sea bass otoliths
Black sea bass otoliths with fingers for size comparison. Photos from Dave Hoke
Fish Count July 25th
Yesterday’s Fish Count.

Personal Log:

I’ve been continuing my work aboard the Pisces.  Lately the focus has been on conversations with scientists and ship personnel.  The source of most of today’s blog came primarily from conversations with Zeb and Todd.  They were both super helpful and patient in communicating the goals and mission of this cruise and SEFIS.  I’m also trying to contribute some things that might be useful to the NOAA scientists after the cruise is completed, and things that will be helpful to my students now and during the school year – like the drawings and diagrams, along with some upcoming videos (topics include: CTD color and pressure, Underwater footage featuring a tiger shark and hammerhead shark, Waves, All Hands on Deck, and a general cruise video). 

The food and mood of the cruise continues to be good.  * note: my salad eating has taken a hit with the expiration of spinach and leafy greens – it’s amazing they lasted as long as they did – the stewards, Rey and Dana, are amazing! 

General Updates:

  1. The other night I had my first bit of troubled sleeping.  The seas were roaring!  Actually, just about 6 feet.  But it was enough to rock the boat and keep me from falling asleep.  It was almost a hypnic jerk every time the ship rolled from one side to the other.  Special sensations for when my head dipped below my feet. 
  2. Two more book recommendations:  a. Newberry Book Award Winner: Call it Courage, by Armstrong Sperry.  I loved this book as a little boy.  I did a book report on it in maybe the 2nd or 3rd grade.  I spent more time drawing the cover of the report than I did writing it.    B.  A few years ago I read The Wave, by Susan Casey.  Great book about the science of waves and also the insane culture of big wave surfers. 
  3. I haven’t seen all that much lately in terms of cool biodiversity.  The traps did catch some cute swimming crabs, a lionfish, and a pufferfish.   * more below.
  4. Zeb won the Golden Sombrero Award the other day.  This is a momentous achievement awarded to a chief scientist after six consecutive empty fish traps!
  5. Lauren crafted us an extra special tie-dye octopus named Oscar.  He’s wearing the Golden Sombrero in the photo above.     
  6. Only 2.5 days till I’m back home.  Can’t wait to see my family. 


Neato Facts =

Back to general update #3 and today’s neato fact.  Both lionfish and pufferfish are toxic.  But are they poisonous? Or venomous?  Wait.  What’s the difference?  Both poisons and venoms are characterized as toxins, and often they are used interchangeably.  The distinction lies in the means of entry into your body.  Venoms get into you via something sharp – you’re either bitten with fangs or stung with stingers or spines.  Examples include our friend the lionfish, snakes, and bees.  Poisons, conversely, get into you when you eat it.  Examples include pufferfish, poison dart frogs,

Here’s a simple way to remember: Injection = Venom, Ingestion = Poison.  Click these links for interesting lists of poisonous animals, poisonous plants, and venomous animals

Pufferfish from today’s fish trap.
Lionfish and Pufferfish
Lionfish (Venomous) and Pufferfish (Poisonous). Injection = Venom, Ingestion = Poison http://www.peakpx.com/487337/lion-fish-and-blue-puffer-fish

Please let me know if you have any questions or comments. 

Sandra Camp: A Day in the Life of a Marine Biologist, June 17, 2015

Lookout fish!

NOAA Teacher at Sea
Sandra Camp
Aboard NOAA Ship Hi’ialakai
June 14 – 24, 2015

Mission: Main Hawaiian Islands Reef Fish Survey
Geographical area of cruise: Hawaiian Islands, North Pacific Ocean
Date: June 17, 2015

Weather Data: mostly cloudy, showers, visibility > 7 NM (nautical miles), winds east 10-15 KT (knots), air temperature 80° F, water temperature 80° F

Science and Technology Log

Days at sea begin early for the scientists aboard the Hi’ialakai. There are push-ups on the bow at 0630 (not mandatory), followed by breakfast at 0700. After breakfast, everyone meets outside on the deck at 0730 for a meeting about the day’s diving. Safety procedures are always reviewed during this meeting.

Morning Meeting
Morning meeting at 0730 in the fantail

Afterwards, the divers suit up, get their gear together, and get ready to board small boats, which will take them to the day’s scheduled diving sites. The way the small boats are lowered into the water with their passengers and gear from the larger ship is nothing less than a carefully orchestrated ballet of synchronized movement, line management, and communication.  The chief boatswain (“bosun” for short), the senior crewman of the deck department, is in charge of this process.  You can see him in the first photo, operating the crane.  Anyone on deck during this time must wear a hardhat for safety purposes.  You would not want to get hit in the head with moving cranes, hooks, or cables!

First, the small boats are lifted from the upper deck with a crane and lowered over the side of the ship.

Then, gear and passengers are loaded onto the boat, and it is carefully lowered into the water. Lines are released. and the boat drives away.

After that, the coxswain, the driver of the boat, takes the divers to the first survey site of the day. As we learn in class, a very important part of any scientist’s job is to gather evidence and data. Three to four groups of divers in separate small boats will gather data from 5-7 different sites each per day. After this project is complete, scientists will have gathered data from hundreds of different sites around the main Hawaiian islands.  At each site, they do fish counts and benthic (sea floor) analysis. They estimate the amount of coral present on the sea floor, and then list fish by their species and quantity. Each diver takes a clipboard with a waterproof piece of paper attached to it on which they record their data. They also carry waterproof cameras with them, as well as a small extra tank of oxygen called a RAS (Redundant Air System) that they can use in case their tank runs out of air.

After data is recorded for several different sites, the small boats return to the ship no later 1700, which makes for a very long day out on the water. Dinner is from 1700-1800, and afterwards, scientist divers head to the dry lab, where all the computer equipment is located, to enter the data they gathered on fish during their surveys.

Scientist Interview

While we were out at diving sites today, I had the opportunity to interview Jonatha Giddens, one of the divers on the boat. Jonatha is a graduate student at the University of Hawaii at Manoa. She has an undergraduate degree in coral reef fish ecology, and she is currently studying the effects of an introduced grouper (a species of fish that is not native to Hawaii) on the local marine ecosystem for her Ph.D.

Jonatha Giddens
Jonatha warming up after a dive

What are your primary responsibilities? Being part of the fish team, scuba diving, doing fish surveys, and entering the data collected during the day into computer systems at night.

What do you love most about your job? Being on the water!

What kind of education do you need to have this job? An undergraduate degree in marine biology

Do you have any advice for young people interested in your line of work? Get involved with research as early as possible. Find out what kind of research is going on in your area, and volunteer. Do summer internships at places that are farther away. You learn so much just by jumping into it.

Jonatha followed her passion and learned all she could about it. Now she has won an award from ARCS (Achievement Rewards for College Scientists) for her work in conservation ecology. ARCS is a foundation organized and run entirely by women to encourage female leadership in STEM careers. Go Jonatha!

Personal Log

Ninja Snorkeler
Don’t mess with this snorkeler!

I can sometimes go snorkeling while the divers are completing surveys, as long as I stay far enough away from them that I do not interfere with their work (they do no want me to scare the fish away).  I have to wear a knife strapped to my leg while snorkeling, in case I become tangled in fishing net or line (or in case there is a shark!).  Again, it is all about safety on the Hi’ialakai.

Did You Know?

The underwater apparatus held by Raymond Boland in the above photo is a stereo camera. It is composed of two separate cameras encased in waterproof housing. When a diver uses it to photograph a fish, two simultaneous pictures are taken of the fish. NOAA scientists calibrate the images using computers to get an accurate measure of the length of fish.

New Terms

chief boatswain – the person in charge of the deck department

coxswain – a person who steers a ship’s boat and is usually in charge of its crew.

benthic – relating to, or occurring on, the bottom of a body of water

Allan Phipps: Teacher from South Florida to Test the Waters in Alaska! June 29, 2012

NOAA Teacher at Sea
Allan Phipps
Soon to be aboard NOAA Ship Oscar Dyson
July 23 – August 10, 2012

Mission:  Alaskan Fisheries Walleye Pollock Survey
Geographic Area of Cruise:  Bering Sea Shelf
Date:  June 29, 2012

Introductory Log

Greetings from Washington, D.C. and from South Florida!  My name is Allan Phipps and I am a teacher from South Plantation High School’s Everglades Restoration and Environmental Science Magnet Program in Plantation, Florida (part of the greater Fort Lauderdale metropolis area).  I teach Advanced Placement Environmental Science, a course entitled Solar & Alternative Energy Honors, and serve as a senior research advisor.

Allan Phipps at Capital Building in DC
Einstein Fellow Allan Phipps at the Capital Building in DC

This year, I have had the distinct pleasure to serve as an Albert Einstein Distinguished Educator Fellow here in Washington, D.C. at the National Science Foundation.  While at the NSF, I have worked with both the Noyce Scholarship Program and the Math Science Partnership, both of which focus on improving the quality and quantity of highly qualified new STEM teachers in high-needs school districts across the country.  It has been a wonderful experience working at the NSF and with pre-service teachers.  I have also worked with the Presidential Awards for Excellence in Math & Science Teaching program that is operated through the NSF.  As a former PAEMST awardee, it was great to be able to work behind the scenes to reward outstanding teachers!  A highlight of my experience here in D.C. was when I spoke at the White House Environmental Education Summit!  I discovered the NOAA Teacher at Sea opportunity while here in Washington, D.C. working with the Einstein Fellows.

Solar Knight III racing at the Texas Motor Speedway

At South Plantation High, I am the sponsor of our Solar Knights Racing Team that has won 1st place in the nation twice in the past six years at the high school level Solar Car Challenge (see video below)!  We have been building and racing solar cars at the high school level for six years!  Two of the races we have competed in were cross-country, the latest of which went from Fort Worth, Texas to Boulder, Colorado over 7 days in July 2010.  Last year’s race was a track race at the Texas Motor Speedway.

Here I am with students helping deploy reef balls in south Florida.

I also sponsored our school’s Project ORB (Operation Reef Ball) and deployed thirty 500-1,500 lb concrete reef balls off the coast of

South Florida to encourage coral colonization and propagation to offset some of the damage done to our beautiful South Florida coral reefs.   Recently, I had the privilege of presenting a poster session about our Project ORB at the European Geophysical Union conference in Vienna, Austria!

One of my students, Carson Byers, takes the solar kayak out for a test drive.

One of my favorite senior projects was a solar-powered kayak, which would improve accessibility to the Florida Everglades as well as other coastal environments for persons with disabilities.  I really enjoyed this project as it blended my passion for alternative energy with my love for getting out on the water.  This project won the WOW Award at the Florida Solar Energy Center’s Energy Whiz Olympics!

Now, I am incredibly excited about the opportunity to sail aboard the NOAA Ship Oscar Dyson out of Dutch Harbor, Alaska!  This will officially be the furthest north I have ever traveled!  As we experience climate change, particularly in areas near the poles where the effects of climate change are more dramatic, it is important to study these changes and how they affect economically important species such as the Alaskan or Walleye Pollock (Theragra chalcogramma).  Walleye Pollock is said to be the largest remaining supply of edible fish in the world, and is the fish used in high quality breaded and battered fish products, fish sticks, and surimi (also known as “imitation crabmeat”).  Many fast food restaurants commonly use Walleye Pollock in their fish sandwiches.  It is important that this fishery be monitored and maintained so that harvest remains sustainable.  I hope that I may enlighten my students about their impacts on the environment when they decide what they will eat so they may become more conscientious consumers.

What’s Next?

I am getting ready to head out to sea and am really looking forward to working with the scientists on board the NOAA Ship Oscar Dyson!  While my blog will be geared towards my AP Environmental Science students, I hope that people of all ages will follow me along my journey as I learn about the science behind maintaining a sustainable fishery.  I also hope to inspire my own students, and others, about the career opportunities in STEM associated with NOAA.  Stay tuned!

Margaret Stephens, May 22-24, 2011

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 22-24, 2011

Weather Data from the Bridge as of 12:43 May 24, 2011
Wind Speed 9.67 knots
Wind Direction 147.00 º
Surface Water Temperature25.09 ºC
Air Temperature 24.20 ºC
Relative Humidity 83.00 %
Barometric Pressure 1016.30 mb
Water Depth 20.57 m
Skies: Clear

Acoustics team leader Warren Mitchell examines sonar display. Miami Dolphins “thinking cap”: optional.
Acoustics team leader Warren Mitchell examines sonar display. Miami Dolphins “thinking cap”: optional.

Science and Technology Log

The scientists’ work day never ends. Their scheduled twelve hour shifts routinely extend to fourteen, even eighteen hours, because they keep going until their tasks are completed, no matter how long they take. By night, beginning at 6 p.m., the acoustics team uses multibeam and split beam sonar to conduct mapping work needed to determine a course for the fish surveys the next day. Based on previous findings and the goals stated by Chief Scientist Nate Bacheler, the team sets up a mapping area and communicates it by ship’s radio to the bridge. The ship runs transect lines (similar to large grid lines, in a back and forth pattern) throughout the hours of darkness to gather information about the contours of the sea floor and translate it into three dimensional images to help visualize potential locations for setting fish traps.

Transect lines used for mapping sea floor.
Transect lines used for mapping sea floor.

Transect lines used for mapping sea floor.
Transect lines used for mapping sea floor.

Here’s where the “art” of science comes in. Because there are so many variables, Nate has to weigh what is known from previous surveys with the recent catches and video footage from the underwater cameras, the new data gathered, factor in wind and current conditions, distance between sites, and any other priorities, and use his best judgment to map a trapping route for the day that looks most promising to catch the target fish species. The entire operation is a delicate balance between science and art.

The videography team backs up all the footage recorded by the underwater cameras attached to the fish traps during the day. Christina spends four to six hours for each set of six traps to catalog and back up the video footage. Nate and Christina view some of the film immediately to look for signs of fish that may not have been trapped and clues to the type of bottom habitat.

Fish Survey

Fisheries scientists face an interesting challenge: their subjects of study—fish, of course—are mostly out of sight, underwater, mobile, often evasive, in scattered groupings, and sometimes smart or timid enough to avoid the enticement of baited traps. Yet to assess the health of fish populations and contribute information leading to sound stock management policies, scientists must first find the fish and then attempt to estimate their relative numbers from year to year. Sandy areas on the sea floor rarely harbor many fish of interest to this survey. Hardbottom provides a much more desirable habitat for fish to feed.

Historically, quantifying fish stocks has involved two principal methods:

Fishery dependent sampling – In this method, samples from commercial fish catches are used to estimate the population size of the species of interest. Because fishery dependent sampling relies on fish already caught by commercial fishers, it has the advantage of not requiring a large, expensive infrastructure of research ships and full

scientific teams. However, the data collected are affected by how fishers harvest their catch, including the areas fished, changing priorities of the market (i.e. if the market price for a particular species is up or down, the fishers are likely to go for more or fewer of them, accordingly), type of equipment used (nets, lines, traps, etc.), the experience and expertise of the fishermen, and seasonal or year-to-year changes in availability of the fish.

In fishery independent sampling, the method used on Pisces and other NOAA fish survey vessels, scientists use existing knowledge of species’ habitats along with statistical techniques to select areas to collect fish with traps, nets and other devices. The advantage is that the scientists can design the sampling area and method carefully, and the data collected are not directly affected by the kind of harvesting done by the fishing industry.

Baited chevron traps ready for deployment
Baited chevron traps ready for deployment

The survey work on Pisces involves positioning a set of six baited fish traps, known as chevron traps because of their shape, on the sea floor in an effort to capture red snapper and grouper for population assessment. The science team begins preparing the traps at 6 a.m. each day. They spear and cut whole menhaden, a plentiful fish common to the east coast and popular as bait fish, and suspend them from cords inside the traps. They attach two high-definition video cameras to the outside of each trap to capture images of the sea floor and fish communities that might not enter the traps, tag each trap with an identification number, and attach brightly colored buoys that float on the surface to mark the trap locations for easy spotting and to warn passing boats to avoid them.

The deck crew, directed by the Chief Scientist, releases each trap from the rear deck in the pre-selected position. Because the traps are weighted with heavy metal rods, they fall directly to the bottom and are left there to “soak” for ninety minutes. By the time the last trap in each set of six is in place, it is usually time for the ship to return to the first location to pick up the traps in sequence. The deck crew, guided by the operator of the “pot hauler” (a mechanized hoist and pulley system) sitting above, raises each trap and lifts it to the side deck, careful not to run over the trap lines or damage the cameras.

Then the real work begins. In some cases, the traps come up empty, save for the untouched bait. While a catch of “zero” may be disappointing, the zeroes provide important clues. The empty traps, together with the video images and sea floor mapping work, help the scientists assemble a better picture of the sea floor conditions and fish locations…or at least where they are not.

Crew member Kirk Perry observes as Investigators David Berrane and Dave Meyer empty catch of red snapper and black sea bass from chevron trap
Crew member Kirk Perry observes as Investigators David Berrane and Dave Meyer empty catch of red snapper and black sea bass from chevron trap

When the traps come up containing live fish, as they often do, the deck is abuzz with activity. The deck crew tips the traps open to slide a mass of jiggling, flopping, somewhat stunned sea life into awaiting large plastic containers. The science team begins sorting the catch by species, tossing each into separate bins. That is easier said than done, because the fish are slimy, slippery, and squirmy, and most have sharp spines. The fish handlers wear special high-grip gloves, waterproof fishing bibs and boots, but all protection that doesn’t prevent them from being decorated with fish scales on their hair and clothes and a decidedly fishy aroma by the end of the day. Water sprays about, and many a fish flops out of the containers and must be retrieved, over, under, or on top of lab tables and equipment. I learned the first day the danger of talking while this commotion was going on – unless one wants a mouthwash of fishy liquid, not too tasty at any time of day.

Non target species are released back into the water immediately. On this trip so far, the haul has included algae, octopus, sea stars, masses of sea jellies, and three moray eels. The sea creatures face some trauma from entrapment and being lifted up from the depths of thirty meters (approximately ninety-eight feet) or more, but the scientists make every effort to release the fish they don’t need for further study as soon as possible.

Many bony fish have swim bladders, balloon-like organs that help them control their position up and down in the water column by regulating buoyancy automatically, so they do not float or sink. The bladders allow gases such as oxygen and carbon dioxide in and out as the fish ascend or descend.

The gases in the swim bladder can over-expand when the fish are brought quickly from the bottom to the surface, as happens when they are reeled in on hooks and lines or captured in traps. When that occurs, the fish look like they are blowing bubble gum, as the pressure from the expanded swim bladders can push internal, sac-like tissue through their open mouths temporarily.

A team member places each container on a digital scale and calls out the weights loud enough for the data recorder to hear above the din of the equipment in the background. The team sets up in assembly line fashion to measure and record length of each fish. One or two people line up the still-lively fish while two stand at measuring boards, hold the fish flat to measure snout to tail, and then release them through a chute back into their ocean habitat. Only the individuals needed for further study are kept, frozen for later processing.

Measuring black sea bass in the wet lab
Measuring black sea bass in the wet lab

The NOAA team arranged to donate the fish catch to a local food bank program based in Jacksonville, part of the national Second Harvest initiative to assist families in need. The crew has gladly pitched in even after their long regular work shifts to fillet and package the fresh fish for donation. Since the market price for fillets of these species is $10 or more per pound, this represents a significant contribution of high-quality, protein-rich fresh fish.

Personal Log

After a few days working with the fish survey team, I began doing overnight shifts with the acoustics group. Much of their work is highly technical, requiring knowledge of fish habitats, geology, mapping, elements of ship’s navigation, Geographic Information Systems (GIS), sonar technology, and computer-based data management.

To the uninitiated (that would be me) the multiple computer screens displaying sonar, navigational information and models of the sea floor are overwhelming. Had I not been instructed otherwise, I might think I was in a high-tech hospital room, as the multibeam sonar projects an image akin to a medical ultrasound.

The acoustics team members, headed by Investigators Warren Mitchell and Todd Kellison, were unfailingly patient as they explained to me how all the elements of their complex system fit together and what I was to do.

My first assigned task was to mark points visible on the sonar screens representing changes in topography – ledges, mounds, and other contours that might be good potential habitat for our target species, red snapper and grouper. After the data are entered and processed, they are used to construct three dimensional images of the sea floor.

Challenge at Sea: Fatigue

Besides learning the basics needed to assist the team, a big challenge is staying awake and alert enough throughout the night to avoid making any costly errors. The other members of the team are better adjusted than I to sleeping during the day, although with all the work they do, they don’t get much rest. Try as I might, I haven’t managed to stay asleep for more than three or four hour stretches once the sun comes up, even after a couple of all-nighters and with the shades in the cabin fully drawn. I hate to miss all the activity on board, anyway, and I can catch up on sleep after returning to land.

Who said scientists don’t have fun? Although the acoustics work is mentally taxing, there is allowance for humorous banter and frequent foraging trips for midnight snacks. Warren labeled those mini-meals “re-dinners” and coined the verb form, “re-dinnering”. We each forage through the cupboards and refrigerators in the mess to assemble creative combinations. Among the highlights: English muffins with Nutella, monster salad with grouper and salmon, with and without wasabi, fruit and cake with ice cream, corn chowder and fresh baked bread. Somewhere between 2 and 4 a.m., it is usually time for a pre-breakfast bowl of cereal and a third or fourth cup of coffee for the night owls …. the ones who don’t have trouble sleeping during daylight hours!

Along with the eating and constant work, there are interludes for stretches, yoga and chin-ups from the well-placed overhead bars to keep oxygen flowing to our brains. I can certainly sympathize with people who work shifts, especially overnight, for long periods of time.

Fishy Humor?

Another custom on these research trips is to note any significant sayings or funny phrases that trip from anyone’s lips during the long days and nights.

Among the recent entries:

When the traps come up with no fish: “Zero is a number, too!”

When very few fish, or ones other than our subjects of study, are trapped: “Some is better than none.”

After the umpteenth trap haul containing nothing but black sea bass: “Black sea bass are fish, too.”

Every time someone expresses optimism about bringing in a big haul: “This is the one.”

To refer to just about anything that goes wrong: “It could be worse.”


A few times each day, the officer on deck announces something of note over the ship’s public address system.

“Safety first!” Chief Engineer Garet Urban with First Engineer Brent Jones
“Safety first!” Chief Engineer Garet Urban with First Engineer Brent Jones

“Attention Pisces: Sea turtles off port bow…: I rushed out to the deck just in time to catch a glimpse of two turtles.

“Attention Pisces: “Fish call. Fish call on rear deck.” When we are in a quiet period between operations or in transit to one research location to another, anyone who wishes to can use a rod and reel off the rear deck. Many of the crew members enjoy this pastime. So far, I haven’t seen any big catches.

I’m still waiting for the “Abandon Ship” drill. My required hat, long sleeved shirt and survival suit are ready to go as soon as the alarm sounds. I hope it is not during the few hours when I’m fast asleep!

Engineering Tour

I asked the Operations Officer, Lieutenant Tracy Hamburger, if it would be possible to have a tour of the ship’s engine room and other mechanical operations. Before I knew it, First Engineer Brent Jones appeared to lead me on a tour of the very impressive essential inner workings of Pisces. The ship’s engineering department keeps Pisces nearly self-contained with all the systems that support its safe operations, the science work, and the lives and comfort of the people aboard. The engineers maintain and repair everything, including the four engines, the fresh water supply system, refrigeration and air conditioning, trash incineration, sewage treatment and disposal, and all the lifts, hoists and other equipment used for scientific and other work.

Crew member Ryan Harris trying his luck during evening fish call
Crew member Ryan Harris trying his luck during evening fish call

Brent informed me that the ship’s trash is combusted at temperatures of 1200 degrees Fahrenheit or higher. Those high temperatures ensure a fairly complete combustion; nevertheless, there is a residue, or sludge, that must be cleared out regularly. The only materials prohibited from being placed in the incinerators are batteries and aerosol cans, which can explode at those temperatures and damage the system. Any hazardous materials such as paints, solvents, and other chemicals must be labeled and stored for disposal at specialized facilities once the ship returns to port.

Among the impressive other Pisces features and facts:

The ship, with a full complement of crew and scientists, generates about 1400 pounds of waste per day.

  • Special “quiet” controls make her four engines among the quietest in the NOAA fleet.
  • 360 degree thrusters provide force enough to make Pisces very maneuverable in all directions.
  • 1900 gallons or more of marine diesel fuel are consumed each day under normal operations.

Special Terminology

  • Fishery – In a resource management context, a fishery refers to a particular species of interest. For this Pisces research trip, the red snapper and grouper fisheries are of most interest.
  • Fisheries biologists – Scientists who study anatomy and physiology, life cycles, population dynamics, behavioral aspects, habitats, distribution and abundance of fish. They may be employed in academic research, government, education, or commercial sectors.
  • Menhaden – A bait fish commonly used for fisheries research. Menhaden are members of the clupeid family, which includes sardines and herrings. They are used here because they are abundant, relatively cheap, easy to catch and transport, the right size for the trap array and attractive to the target species in the snapper-grouper complex.
  • Hardbottom habitat – a sea floor type that allows for attachment of sponges, seaweed, and coral, which in turn support a diverse reef fish community. The target snapper-grouper complex fish species prefer hardbottom conditions, which are also known as “live bottom” or “live rock”.

Links & Resources

Margaret Stephens, May 19, 2011

NOAA Teacher at Sea: Margaret Stephens
NOAA Ship: Pisces
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 of log: Thursday, 19 May through Saturday, 21 May, 2011

Here I am with the CTD equipment
Here I am with the CTD equipment

Weather Data from the Bridge
Position: Latitude 27.87, Longitude -80.16
Wind Speed 11.06 kts
Wind Direction. 131.46 º
Surface Water Temperature 26.88 ºC
Surface Water Temperature
Air Temperature 27.10 ºC
Relative Humidity 78.00 %
Barometric Pressure 1015.50 mb
Water Depth 28.05 m
Sky conditions: clear

Science and Technology Log

General Description of the Scientific Work Aboard Pisces
While at sea, the ship’s operations and scientific crews work in shifts 24/7 – yes, that’s twenty-four hours, every day, with ship operations, maintenance, data collection and gear deployment continuing day and night.
The scientific team, headed by Chief Scientist, Dr. Nate Bacheler, includes researchers who are mostly marine biologists specializing in fisheries. Each team member has complementary specialized skills such as acoustics (use of sonar for sea floor mapping), physical or chemical oceanography, underwater video camera operations, data management and analysis, and many aspects of fish biology.

The main mission of this research cruise is to study red snapper and related grouper species, fish that are of great importance economically and to the marine ecosystem in near shore areas off the southeastern coast of the United States. In particular, the team is studying where the fish are likely to be found (their spatial distribution patterns) and their numbers, or abundance, and population dynamics (how the populations change over time).

This work expands the knowledge needed to guide decisions about how to protect and manage fisheries in a sustainable manner. Healthy, sustainable fish populations are essential to the economy, to the function of healthy ecosystems, and as high-protein (and tasty) food sources. In the past, many fish species have been overfished, resulting in dangerous declines in their populations.
The scientific work on board Pisces for this project is divided into three main areas. This log entry gives an overview of each of the three main areas of work, with a more detailed account of the acoustics, or mapping portion. Upcoming logs will describe the other phases in more detail.

  1. Acoustics – Using the science of sound with advanced sonar and computer technology, the acoustics team maps the sea floor and identifies areas likely to be good fish habitat.
  2. Fish survey – The survey team sets baited traps to catch fish, then collects them, identifies the species, and records essential data about the species of most interest.
  3. Underwater videography – The video team attaches cameras to the traps to view the kinds and activities of fish in the water and assess the type of sea bottom, such as sandy or hard, flat or “bumpy”, regular or irregular.
  4. After all this information is collected in the field, much of the painstaking, detailed analysis takes place back in the home labs and offices of the researchers.

Acoustics Work
Since acoustics is the first step used to identify specific sites to set traps for the fish survey, we’ll start here.
Throughout a long night shift, from 6 p.m. until the work is complete, often 7 a.m. or later the following day, the acoustics team uses sonar (SOund NAvigation and Ranging) and computer analysis to map the sea floor and identify promising areas to set traps for the fish survey. See a detailed description of the sonar equipment and procedures below.

Investigator Jennifer Weaver showing GIS model of sea floor contours
Investigator Jennifer Weaver showing GIS model of sea floor contours

At 5 a.m., the acoustics team meets with Chief Scientist Nate to report any sites they identified overnight and select the stations to sample with fish traps and underwater cameras during the day. The team then converts their data into a kind of route map that the helmsman (the ship’s “driver”) uses to steer the ship along the designated survey route.

The acoustics team members possess extensive knowledge about fish habitats, geography and geology of the sea floor, and computer and sonar technology. They also need to be aware of the interactions among wind, weather and currents and understand charts (marine maps) and ship’s navigation. They constantly communicate with the ship’s bridge via the internal radio network.

Fish survey team prepares baited traps at dawn
Fish survey team prepares baited traps at dawn

The acoustics lab houses work space large enough for five to ten people, banks of computer screens, servers, and large-scale display monitors projecting images from the sonar devices, real time navigation, and views from cameras positioned in work areas on deck.

Once the now-very-sleepy acoustics lab team wraps up its nocturnal work, the team members turn in for a day’s (or night’s?) sleep, just as the other teams’ daylight tasks begin in earnest.

Fish Survey Work
By 6 a.m., in the predawn darkness, the rear deck becomes a hub of concentrated activity, with sounds muffled by the early ocean haze and drone of the engines and generators. The four or more members of the fish survey team, still rubbing sleep from their eyes, assemble on the stern deck (rear of ship or fantail) to prepare the traps to catch fish for the day. Before the sun rises, floodlights illuminate the work of cutting and hanging menhaden, whole fish bait, in the traps, securing the underwater cameras in place, tagging each piece of equipment carefully and checking that everything is ready for deployment.

Chief Scientist Nate Bacheler directs trap deployment from the dry lab
Chief Scientist Nate Bacheler directs trap deployment from the dry lab

Chief Scientist Nate directs the deployment of the traps from the dry lab, where he faces a bank of computer screens displaying maps of the identified sampling route, the ship’s course in real time, and camera shots showing the personnel and operations on deck. By radio, Nate directs the deck crew to lower the traps at each of the designated sites.

The ship is steered along the sampling route, dropping traps in each of six locations. Each trap is left in place for approximately ninety (90) minutes. Once the last trap is lowered, the ship returns to the first location and raises the traps, usually following the same order. The deck crew members, together with the fish survey team, empty any catch and ready the traps for redeployment.
Chief Scientist Nate Bacheler directs trap deployment from the dry lab

Then the fish survey team, coordinated by Investigator Dave Berrane, sets to work sorting, weighing and measuring any catch and immediately releasing any fish not needed for further study.

Investigator Christina Schobernd views underwater video with Chief Scientist Nate Bacheler
Investigator Christina Schobernd views underwater video with Chief Scientist Nate Bacheler

Videography Work
As soon as the traps are hauled aboard by the deck crew, the wet lab team detaches and dries the cameras and hands them to the dry lab, where the videography team, headed by Investigator Christina Schobernd, removes the memory cards and transfers and makes duplicates of the video files on computer drives. All the teams take extreme care to label, catalog and back up everything carefully. Data management and redundancy are essential in this business. The scientists view some of the footage immediately to see if the cameras are working properly and to make any adjustments necessary. They also look for anything unusual or unexpected, any fish captured on camera other than those that made it into the trap, and they assess how closely the sea floor type matched what was expected from the acoustic team’s mapping work.

Christina works well into the night to back up and catalog all the day’s video recordings.

Detailed Description of Fisheries Acoustics Surveys

Multibeam sonar mapping the seafloor. Image courtesy of Jill Heinerth, Bermuda: Search for Deep Water Caves 2009.
Multibeam sonar mapping the seafloor. Image courtesy of Jill Heinerth, Bermuda: Search for Deep Water Caves 2009.

Fisheries Acoustic Surveys: Acoustic surveys help determine the relative abundance of target species and provide information to determine catch rates and guidance for fisheries management.

The equipment aboard Pisces includes two types of sonar devices that use sound waves to measure the water depth, shape or contours of the sea floor, and to a limited extent, fish groupings, or aggregations. Sonar operates using established knowledge about how fast sound travels in water under different conditions to develop a three-dimensional image of the shape of the sea floor. The first type is known as split-beam sonar, which uses sound waves at different frequencies to provide a picture of the underwater environment. Pisces has a Simrad EK60 echosounder.

The second, more sophisticated and expensive system involves Multibeam sonar mapping. Aboard Pisces is a Simrad ME70 device. Multibeam devices emit sound beams that forms an inverted cone, covering a larger area and providing a more complete picture of the sea floor than the series of vertical or horizontal sound signals that the split beam sonar provides. As described above, the bathymetric mapping surveys are conducted primarily during the night, from sundown until dawn, when fish sampling and other ship operations are not taking place. Ideally, this allows the science team to map out a route of sampling sites for the next day’s fish trapping work. At the end of the overnight shift, the acoustics team presents its findings to the Chief Scientist, who then coordinates the day’s activities with the fish team, the ship’s bridge, and the deck crew headed by the chief boatswain.

It’s called “multibeam” because unlike the first single-beam sonars, which sent out one signal or ping, multibeam sonar sends out a whole group of pings at once. Multibeam sonar can cover a larger area than a single beam can. Here’s a Quicktime movie of multibeam sonar: http://oceanservice.noaa.gov/education/seafloor-mapping/movies/multi_240.mov

Personal Log

I cannot say enough about how friendly and helpful everyone on board has been to this neophyte. It takes a while to adjust to any new environment, but being on a ship at sea has its own learning curve. Pisces, at 209 feet long, operates like a small town. Because it is out at sea for weeks at a time, all supplies and systems must be operating 24/7 to keep the ship and crew focused on the appointed mission and keep everyone on board safe, comfortable, and able to do their jobs.

I spent the first two days getting acclimated to the layout of the ship, safety practices, meeting the members of the scientific crew, adjusting to the rigorous schedule, and doing my best not to commit any grave offenses or make big mistakes that would make the work of this very patient group of dedicated professionals any more difficult than it is already.

Sleep Time Because the ship’s work continues round the clock, sleep time varies, depending on the person’s position and duties. It is important for everyone aboard to be mindful that at any hour of the day or night, it’s likely that someone is sleeping. The mapping crew began a 6 p.m. to 6 a.m. shift (or later, until the work is finished) on our second day at sea, and most of them will keep that difficult schedule for the entire cruise. Since I’m the lucky one to experience every aspect of the work, I’ll rotate through the various jobs and schedules. For the first few days, I’ll work with the fish survey team, from 6 a.m. until their work is completed, which may mean a break for supper at 5 p.m. followed by a few more hours of lab work to process all the day’s catch. My first day on the acoustics team, I’m scheduled to start at 4 a.m. assisting their nightly wrap up, as by the last few hours of their shift, they are quite tired.

Dining and Comforts Aboard Ship

Chief Steward/Chef Jesse Stiggens with a Pisces creation, a vegetable quiche.
Chief Steward/Chef Jesse Stiggens with a Pisces creation, a vegetable quiche.

Chief Steward Jesse Stiggens and Assistant Steward Michael Sapien create a terrific, appetizing menu for the three main meals and plenty of extras and snacks available at any hour.

The stewards are very accommodating, so anyone who will miss a main meal because of their work or sleep schedule can sign up in advance for the stewards to set aside a full plate of delicious food for them. The mess (dining room on a ship) is open all day and night, with coffee, cold beverages, an array of sandwich fixings, cereals and assorted leftovers kept chilled for anyone to microwave anytime they get a hankering for a nibble or a bigger bite. And…very important for morale … there’s a freezer stocked with ice cream, even Blue Bunny (a favorite in the South that I had not seen before) and Häagen-Dazs. There’s also a big screen television in the mess. The lounge area has computers, a conference or game table, a small library of books, a large screen television and several hundred movie titles, even new releases, for the crew to enjoy in their off time. Also available are wonderful reclining chairs, so comfortable, I wish I had time to use them. The one and only time I tried one out, the fire alarm went off for our first drill, and I haven’t had a free moment since.

Doomsday Came and Went: Saturday, 21 May, 2001….and Pisces work continues
CNN reports: After months of warnings and fear, the Day of Rapture, as predicted by apocalyptic Christian broadcaster Harold Camping, passed without apparent calamity. Judgment Day was to have started at 6 p.m., but as darkness fell on many parts of the world, it appeared that heaven could wait. At this writing, there have been no reports of people soaring upward to the skies, but plenty of folks are talking about it.

That includes those of us on Pisces. The possibility that Doomsday was approaching generated some good-natured kidding and gallows humor. We had some debate about when the end would begin. Since most of the ship’s instruments use Greenwich Mean Time (GMT) as a reference, we speculated that our end time might occur four hours later than east coast Daylight Savings Time (DST).

Everyone had their eyes on the clock and the horizon as first, the predicted doomsday hour of 6 p.m. DST came and went, and then, four hours later, 6 p.m. GMT passed without incident. Any apprehensions were put to rest, and now we have new fodder for discussion.

Special Challenges for Research at Sea
Many people have the idea that science is neat, pretty and conducted in sterile lab environments by other-worldly thinkers in clean white lab coats. That is decidedly not the case in fisheries work at sea. This section lists the special challenges (or, as, some optimists would say, “opportunities”) of conducting shipboard research. Each log will focus on or give examples of one or more challenges.

  • Limits of “shooting in the dark” – Imagine a vast, dark, deep, ever-changing, difficult-to-penetrate area, with living organisms moving about in and out, with all kinds of surface, bottom, and in-between conditions. That’s what underwater research involves. Examples: The mapping team thinks it has found great habitat for red snapper and grouper, so the survey team expects a bountiful trap. But up comes nothing but a trap still full of untouched bait. Or, the habitat conditions look promising, but the current is too strong to set the traps safely.
  • The Unexpected – It is often said that the only thing predictable in field research of this kind is unpredictability! You just never know….
  • Curiosity-seekers and just plain business – recreational and commercial boats – Not surprisingly, the areas of interest for NOAA fisheries research are often favorite fishing grounds for recreational fishermen, scuba divers, and active routes for commercial ships. Therefore, Pisces crew and helm (the person steering the ship) must always be on alert for other boat traffic. Example: On Saturday, a small recreational boat occupied by partiers pulled up nearly alongside Pisces. Despite polite cautions and requests from our bridge for the small boat to move away to a safer distance, the visitors just kept waving and cheering for a while.

Challenges to come in next logs:

  • Changing sea conditions, weather, waves and current
  • Fatigue
  • Limited daylight hours
  • Emergencies
  • More unpredictables

Links & Resources