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

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