Leah Johnson: Fish Identification & Pisces Farewell, August 1, 2015

NOAA Teacher at Sea
Leah Johnson
Aboard NOAA Ship Pisces
July 21 – August 3, 2015

Mission: Southeast Fishery – Independent Survey
Geographical Area of Cruise: Atlantic Ocean, Southeastern U.S. Coast
Date: Saturday, August 1, 2015

Weather Data from the Bridge:
Time 12:13 PM
Latitude 033.995650
Longitude -077.348710
Water Temperature 24.37 °C
Salinity 36.179 ppt
Air Temperature 27.4 °C
Relative Humidity 83 %
Wind Speed 15.95 knots
Wind Direction 189.45 degrees
Air Pressure 1012.3 mbar

Science and Technology Log:
I am still amazed at the wealth of data collected aboard the Pisces on this survey cruise. I am getting better at identifying the fish as they are hauled up in the traps, as well as when I see these fish on video. Because of light attenuation, many fish look very different in color when they are underwater. Light attenuation refers to the gradual loss of visible light that can penetrate water with increasing depth. Red light has the longest wavelength on the visible light spectrum, and violet has the shortest wavelength. In water, light with the shortest wavelength is absorbed first. Therefore, with increasing depth, red light is absorbed, followed by orange, then yellow. Fish that appear red in color at the surface will not appear red when they are several meters below the sea surface where they are captured on camera.

For example, we hauled in some blackfin snapper earlier this week. At the surface, its color is a distinct red like many other types of snappers, and it has a black spot near the base of its pectoral fin. When I looked at the videos from the trap site, I did not realize that all of the fish swimming around with yellow-looking tails were the very same blackfin snappers that appeared in the traps! When I remembered that red light is quickly absorbed in ocean water and noticed the black spot on the pectoral fin and shape of the dorsal fin, it made more sense.

Top: Blackfin snapper collected from trap.
Bottom: Video still of blackfin snappers swimming near trap.

I tell my geology students every year that when identifying minerals, color is the least reliable property. I realize now that this can also apply to fish identification. Therefore, I am trying to pay closer attention to the shape of the different fins, slope of the head, and relative proportions of different features. The adult scamp grouper, for example, has a distinct, unevenly serrated caudal fin (tail) with tips that extend beyond the fin membrane. The tip of the anal fin is elongated as well.

scamp grouper

Scamp grouper

Another tricky aspect of fish identification is that some fish change color and pattern over time. Some groups of fish, like wrasses, parrotfish, and grouper, exhibit sequential hermaphroditism. This means that these fish change sex at some point in their lifespan. These fish are associated with different colors and patterns as they progress through the juvenile phase, the initial phase, and finally the terminal phase. Some fish exhibit fleeting changes in appearance that can be caught on camera. This could be as subtle as a slight darkening of the face.

The slight shape variations among groupers can also lead groups of scientists to gather around the computer screen and debate which species it is. If the trap lands in an area where there are some rocky outcrops, a fish may be partially concealed, adding another challenge to the identification process. This is no easy task! Yet, everyone on board is excited about the videos, and we make a point to call others over when something different pops up on the screen.

warsaw grouper

We were all impressed by this large Warsaw grouper, which is not a common sight.

I have seen many more types of fish and invertebrates come up in the traps over the past week. Here are a few new specimens that were not featured in my last “fish” post:

Did You Know?

Fish eyes are very similar to those of terrestrial vertebrates, but their lenses that are more spherical.

lens from fish eye

Lens from fish eye

Personal Log:

I love being surrounded by people who are enthusiastic about and dedicated to what they do. Everyone makes an extra effort to show me things that they think I will be interested to see – which I am, of course! If an interesting fish is pulled up in the trap and I have stepped out of the wet lab, someone will grab my camera and take a picture for me. I continue to be touched by everyone’s thoughtfulness, and willingness to let me try something new, even if I slow down the process.

me, standing on the deck at the stern

Me, on the deck of the ship. We just deployed the traps off the stern.

As our cruise comes to an end, I want to thank everyone on board for letting me share their work and living space for two weeks. To the NOAA Corps officers, scientists, technicians, engineers, deckhands, and stewards, thank you for everything you do. The data collection that takes place on NOAA fishery survey cruises is critical for the management and protection of our marine resources. I am grateful that the Teacher at Sea program allowed me this experience of a lifetime. Finally, thank you, readers! I sincerely appreciate your continued support. I am excited to share more of what I have learned when I am back on land and in the classroom. Farewell, Pisces!

Joan Le, Touchdown for TowCam, August 8, 2014

NOAA Teacher at Sea
Joanie Le
Aboard NOAA Ship Henry B. Bigelow
August 5 – 16, 2014

Mission: Deep-Sea Coral Research
Geographic area of the cruise: Off the coast of Assateague Island, Virginia
Date: August 8, 2014

Weather information from the Bridge:
Air Temperature: 24° C
Wind Direction: 320° at 5 knots
Weather Conditions: Partly Cloudy
Latitude: 37° 49.460′
Longitude: 74° 03.380′

Science and Technology Log

Recording “zero winch” time (when TowCam splashes down). Photo credit Dr. Martha Nizinski.

After arriving at our first dive location yesterday at 16:00, we successfully completed our first dive. In the water for almost 8 hours, we collected 2,946 high resolution pictures and lots of data.

Deployment is a team effort, and everyone is on high alert. With steel toe shoes, hard hats, and life vests in place, the crew carefully raises TowCam off the deck by a winch wire and gently into the water below. Though I’m getting used to it, the bobbing of the ship while it holds position for deployment is noticeable. Keeping an eye on the horizon goes a long way to settle the stomach.

Because shorter wavelengths can’t reach our eyes through the moving water, you can see the yellow net on TowCam appear to turn green as it submerges.

As TowCam descends into the water, it is hard not to be impressed by the depth beneath us. For almost half an hour, the winch pays out cable at a rate of 35 meters per minute. Fuzzy images of the water column begin to arrive, and adds to the abyssal sensation of the water below.

Dr. Lizet Christiansen monitors the location of TowCam as images stream back to the lab

Finally, TowCam sends visual of the bottom, and logging of observations begins. At first, only a few images of soft sediment appear–one after the other, 10 seconds apart. And then, a red crab. Then a fish. I felt not unlike an astronomer receiving those first black and white images from Mars’s Curiosity. It was that exciting. We note the time, location, features of the seafloor, and tentative ids of the organisms we see. Later, we’ll match these up with the high-res images inside TowCam.

Chief Scientist Dr. Martha Nizinski monitors low resolution images as they stream from TowCam.

After about 8 hours, TowCam returns the way it arrived–slowly back up the water column. It’ll stay on deck just long enough to charge batteries and download the precious images while we make our way to the next dive location. Then, back to the drink it goes.

"Burping" TowCam's batteries.

“Burping” TowCam’s batteries to remove excess air. Photo credit Matt Poti.

An Unlucky Passenger

The TowCam is a pretty amazing instrument, but we didn’t know how alluring it might appear to the fish that come and go. Unfortunately for this little guy, he never did manage to leave until it was too late. Evolved to withstand life under pressure, this unlucky swimmer lost his innards while TowCam returned home.

Personal Log

The Moon rises over the water at the beginning of my shift at midnight.

The Moon rises over the water at the beginning of my shift at midnight.

The first watch was pretty exciting. It was strange to wake up at 11 PM and get ready for work, but the commute was sweet! Instead of my usual hour-long metro ride (okay, I usually just drive) I simply walked downstairs and greeted the folks that had just spent the previous 12 hours logging and monitoring the submerged TowCam. They were in surprisingly good spirits.

I also must say that not much can top the wonderfully eerie feeling of moving steadily along through the ocean in a moonlit night. The light from the deck makes the water a velvety blue, and if you’re lucky you can see dolphins slipping quietly by as the Sun begins to peek up over the horizon.

Marla Crouch: Pitch and Roll, June 24, 2013

NOAA Teacher at Sea
Marla Crouch
Aboard NOAA Ship Oscar Dyson
June 8-26, 2013 

Mission:  Pollock Survey
Geographical area of cruise:  Gulf of Alaska
Date: June 23, 2013

Weather Data from the Bridge: as of 2100
Wind Speed 6.30 kts
Air Temperature 11.7°C
Relative Humidity 73.00%
Barometric Pressure 1,004.20 mb

Latitude:  56.42N   Longitude: 158.20W

Science and Technology Log

Who can tell me the direction longitudinal and transverse waves move?  Think about the electromagnetic spectrum; what is the relationship between wavelength and frequency?  The physics of these wave actions are experienced in fields other than earthquakes (seismic), and light (optics) and sound (audio).

Picture provided by NOAA NWS Prediction Center

Picture provided by NOAA NWS Prediction Center

There are two different types of water waves that mariners regularly encounter, wind waves and swell waves.  An analogy for wind waves and swell is a wind wave is to weather as swell is to climate.  In other words, wind waves are local and swell occurs over a great distance.

Waves are formed when repeated disturbances move through a medium, such as, air, earth and water.  As the wind moves or blows across the open waters, energy is transferred from the friction of the moving air particles to the waters’ surface creating wind waves.  The speed, and fetch (unchanged direction) of the wind, and the distance the wind has traveled unimpeded; influence the amplitude and frequency of the waves.  As wind speed picks up so does the amplitude of the waves.  Wind waves can be identified by their white caps.  Wind waves have short wave lengths.

Graphic courtesy of Tammy Pelletier, WA State Dept. of Ecology http://www.vos.noaa.gov/MWL/apr_06/waves.shtml

Graphic courtesy of Tammy Pelletier, WA State Dept. of Ecology

Swells are a formation of long wavelength surface waves, which travel farther and faster than short wavelength wind waves.  Swells can be formed by storms that occurred somewhere else in the ocean.  For example, Tropical Storm Leepi formed off the China coast south of Japan, and was active June 17 – 19, 2013.  The energy from Leepi’s 40 mph winds and rain radiates outward from the storm, like the ripples that form when you drop a rock in a puddle of water, creating swells.  Swells can travel in a multitude of directions as they bounce off landmasses back into the open waters.

Wind waves and swells transfer energy to ships, such as the Oscar Dyson.  The energy causes ships to pitch, roll and yaw.

Pitch, roll, and yaw are three dynamic ways crafts, such as airplanes and ships move in a fluid.  In my “Surf your Berth” blog I used a teeter totter as an example of pitch.  If you think about the way energy moves in waves, pitch is a longitudinal wave where the energy is moving front to back, so that the bow of the ship goes up and down.  Roll is a transverse wave, the energy is moving side to side, rolling the ship from port to starboard (left to right).  To describe yaw, think about sitting in a chair that swivels.  Yaw is the swiveling action of you in the chair moving in the chair or a ship rotating around a vertical axis.  Watch the horizon in the video to get an idea of what pitch looks like from the vantage point of the bridge of the Oscar Dyson.

If you turn your field of view 90°, so you are looking either port or starboard and see the same motion that is roll.

The officers of the Oscar Dyson work to navigate through both the wind and swell waves to give us the smoothest ride possible.

Personal Log 

Recently we experienced sustained wind speeds between 30 and 40 kts.  Needless to say, we were a pitchin and a rollin.  Chiachi Island afforded us calmer seas, as we reached the lee (wind shadow) side of the island.  I noticed something different in this last encounter with rough seas, instead hearing the water race past the hull, this time the water slammed into the side of the Oscar Dyson.  The crashing transformed some of the wave’s kinetic energy into thunderous claps of sound…BAM!…BAM!  What caused the difference, I’m not sure, maybe we were in a convergent zone, before reaching the lee, where wind and seas raced around the island creating a collision akin to clapping your hands together that buffeted the Dyson from both sides.

What do we do aboard ship to cope with the pitch and roll?  We anchor ourselves.  Chairs at our work stations, do not have casters and are tethered to the desk with a cord.  The dressers in our berths have straps to keep the draws shut and the closet doors lock into their closed position.

On a ship the dining hall is called the Mess.  Here the chairs are tethered to the floor.

Amanda Peretich: Awesome Acoustics, July 13, 2012

NOAA Teacher at Sea
Amanda Peretich
Aboard Oscar Dyson
June 30, 2012 – July 18 2012

Mission: Pollock Survey
Geographical area of cruise:
Bering Sea
July 13, 2012

Location Data
Latitude: 59ºN
Longitude: 174ºW
Ship speed: 11.7 knots (13.5 mph)

Weather Data from the Bridge
Air temperature: 7.3ºC (45.1ºF)
Surface water temperature: 7.6ºC (45.7ºF)
Wind speed: 4.3 knots (4.9 mph)
Wind direction: 12ºT
Barometric pressure: 1010 millibar (1.0 atm, 757.5 mmHg)

Science and Technology Log

How sonar works: energy (sound) waves are pulsed through the water. When it strikes an object, it bounces back to the receiver. (from http://www.dosits.org/)

How sonar works: energy (sound) waves are pulsed through the water. When it strikes an object, it bounces back to the receiver. (from http://www.dosits.org/)

Before stepping onto the Oscar Dyson, I wasn’t quite sure about much of the science going on. Did they just put the nets in the water every so often and hope to catch some fish? Carefully lean over the side of the ship saying “here fishy fishy” with the hope that the pollock would find their way into the net? Neither of these scenarios is correct (good thing I’m not actually a fisherman!). So today’s lesson is going to be all about what the chief scientist actually uses to find fish: hydroacoustics (hydro meaning water and acoustics meaning sound). This also involves SONAR, which is short for SOund Navigation And Ranging.

Fishfinding Basics

Fishfinding basics.

If you’ve ever been on a smaller boat, yacht, fishing vessel, or the like, you may have seen something called a fishfinder. The basic concepts are the same as what is happening on the Oscar Dyson. An echosounder sends a pulse of energy waves (sound) through the water. When the pulse strikes an object (such as the swim bladder in fish), it is reflected (bounced) back to the transducer. This signal is then processed and sent to some sort of visual display.

Swim Bladder

Swim bladder in a fish.
(from https://www.meted.ucar.edu/)

The Oscar Dyson uses acoustic quieting technology where the scientists can monitor fish populations without altering their behavior. The Scientific Sonar System and various oceanographic hydrophones (underwater microphones) are raised and lowered through the water column beneath the ship on a retractable centerboard. This is important so that the transducers can be lowered away from the flow noise generated by the hull, which in turn will improve the quality of data collected. In addition, there is a multibeam sonar system located on the forward hull. Ultimately the hydroacoustic data is all used as one piece to the puzzle of measuring the biomass of fish in the survey area.

OD acoustics

The different sonar signal transmitter/receivers (transducers) used on this leg of the pollock survey and their location on the ship.

Neal at work

Chief scientist Neal working away in the Acoustics lab. The second screen from the left on the upper row is showing the information from the ME70 multibeam.

So how does this all work when we are looking for fish? The chief scientist (Neal on the 0400-1600 watch) or another scientist (Denise on the 1600-0400 watch) will spend a lot of time analyzing the various computer screens in the acoustics lab, which has been affectionately termed the “cave” (no windows). They are looking at the information being relayed from both the multibeam and the EK60.

What is a multibeam? The Oscar Dyson has the Simrad ME70 scientific multibeam echosounder. It is located on the hull (underside) of the ship on the front half and sends 31 sonar beams per second down to the bottom of the sea floor.


Multibeam echosounder.
(from http://www.simrad.com/)

Aft of the multibeam (on the centerboard) are the five Simrad transducers. It may seem confusing, but hopefully I can walk you through a teensy little bit of how it works when we are looking to trawl for fish.

EK60 Transducer

Information from the EK60 transducer at 18kHz (top) and 38kHz (bottom).

Information from the EK60 echosounder is displayed on the far left screen in the acoustics lab while information for the ME70 multibeam is displayed on the next screen. The darker patches are showing that there are fish in that area. When the scientist first starts to see a good amount of fish, they will “mark” it and keep watching. If the screen fills up with fish (as in the EK60 image), the scientist will call upstairs to the bridge and tell them where to head back to on the transect line to start trawling. Depending on the location of the fish in the water column, it may be a bottom trawl (83-112 net), a midwater trawl (AWT net), or a methot trawl. Side note: the 83-112 midwater comparison trawl that I’ve mentioned before is done almost immediately after an AWT midwater trawl to compare the fish caught in a common area.

ME70 Multibeam

Information from the ME70 multibeam. You can determine the sea floor depth and there are five narrow beam slices from the mid-section of the multibeam (of the 31 different beams that span 120 degrees) displayed on screen.

Neal on bridge

Chief scientist Neal up on the bridge.

Then the scientist will head upstairs as the deck crew is preparing the net. One of the many sensors attached to the net is called the FS70 fishsounder or “the turtle”, and it is only used during trawls (because it is attached to the headrope). The scientist can “watch” the fish swimming under the ship using the EK60 information combined with the information from the fishsounder. The yellow “turtle” on the right in the image shows how the FS70 is flying in the water. You want minimal pitch and roll and for the front of it to be facing the back of the ship. This way, we can “see” the fish as they are going through the net. The officer of the deck and lead fisherman or head boatswain can adjust various things to keep the turtle in the right orientation. The middle image below is constantly changing on the screen in the bridge as the sonar is sweeping back and forth, so you can almost watch the individual fish enter the net. It was interesting to watch the delay between when you would see the fish from the EK60 (on the left) and when you saw them with the FS70 (middle).

Trawl Fishsounder

Display screens on the bridge used during a trawl.

Once the scientist is satisfied that enough fish have been caught for a sufficient sample size, the net will be hauled back and the acoustics work is done for just a little bit (giving Neal some time to grab some well-deserved coffee and the rest of us time to get our rain gear on to process the fish).

So some of the questions I had asked (that don’t really fit nicely in the information above):

Why do we use different frequencies in the acoustic studies?

Frequency Wavelength

Relationship between frequency and wavelength. (from http://emap-int.com)

This ties right back in to chemistry (and other sciences) with an equation and the relationship between frequency and wavelength (yay!). Basically there is an inverse relationship which means that at a high frequency there is a smaller or shorter wavelength (wavelength is the distance for peak to peak of a wave). At a low frequency, there is a higher or longer wavelength.

At a low frequency, you will see only see things that are larger, like pollock, whereas you will see very small things like krill and zooplankton at higher frequencies. Having information from both types of frequencies is necessary to complete the scientific research on the Oscar Dyson.

Single Fish

Traveling at 1 knot, showing single fish from EK60 sonar.

Is it possible to see a single fish?
Yes! From sunset to sunrise, the Oscar Dyson doesn’t actually travel the transect lines. This is because the pollock behave differently during darkness than during the day. So instead of traveling between 11 and 12 knots (which is what happens between trawls), it’s almost like the boat is just sitting around for a couple of hours. But during this time, since the boat isn’t moving along quickly, it’s possibly to see individual fish on the sonar as shown in the image.


Hydroacoustic surveys can involve any number of different types and locations of the transducers. (from http://btechgurus.blogspot.com/2012/06/sonar.html)

Personal Log
Today is Friday the 13th but it was far from unlucky – I finally saw something out in the water other than fog: a boat! Again, all good sightings seem to come from up on the bridge, so I’m thankful for Lieutenant Matt for allowing me to ask a billion questions while I’m up there and teaching me more than I ever thought my brain could hold. He has all of the qualities of a great teacher, which is nice to see.


The ship we saw up on the bridge this morning from about 5 nautical miles away (left), on the sonar (middle), and through the binoculars (right).

Dancing in the fish lab on the Oscar Dyson

Neal and I dancing while waiting for the fish!

Highlight from the other day? Chief scientist Neal finally dressed out in his Grundens (rain gear) and came to help process a catch in the fish lab! While waiting, he even took a quick second to dance in the doorway (we were “Dougie”-ing) to my music that was playing over the speaker system.

NOAA Oscar Dyson flier
NOAA Oscar Dyson Ship Electronics Suite
HTI Sonar
Wikipedia: Sonar