David Knight: Work Out and Work Up: Part I, July 17, 2018

NOAA Teacher at Sea

David Knight

Aboard NOAA Ship Pisces

July 10-23, 2018


Mission: Southeast Fishery-Independent Survey

Geographic Area: Southeastern U.S. coast

Date: July 17, 2018

Weather Data from the Bridge:

Latitude: 30° 30.2 N
80° 15.6 W
Sea wave height:
1-2 ft
Wind speed:
15 kts
Wind direction:
10 nm
Air temperature:
30.1 °C
Barometric pressure:
1014.7 mB
Broken Clouds

Science and Technology Log

Warning!!! Great Science Ahead…

Part I.

Waiting to see
Waiting to see what the traps have brought up this time… (photo by David Knight)

As fish traps begin to be brought up by the deck crew, scientist wait to see what may be in the trap. I’ve actually found that I am looking over the deck in anticipation of new fish that may have been caught, or to see how many fish will need to be “worked up.” Once the fish have been removed from the trap and emptied into a large bin, they are then sorted by species into 17-gallon bins to determine the total weight of all fish.  Moving 17 gallons worth of fish up to the lab bench to the scale can be quite a “work out.” There have been a couple of hauls that have captured so many fish of a particular species that more than one bin has to be used. After the fish have been weighed, the total length of each fish is determined to get a length frequency of the entire catch.  For species like Tomtate (Haemulon aurolineatum), every fish is measured and then returned to the ocean. For some species, a pre-determined percentage are kept for a more detailed work up that may include the extraction of otoliths, removal of gonads, or a collection of stomach contents. The data collected from each fish will then be used by scientists in a number of different agencies and in different states to better understand the growth and reproduction of the particular species. All of this data is then used to create management plans for economically and ecologically important fish as well as to gain a better understanding of its life history.

Work Up


Measuring fish
Measuring the length of each, individual fish. (photo taken by Nate Bacheler)

One may assume that a very long fish is also very old, but that is not necessarily the case. The length of a fish is not a good way to determine the age of a fish because factors such as temperature and food availability may alter the growth rate. Many fish grow very rapidly early on, but then slow their growth, so it is possible that a fish that is twelve years old is the same size as a fish that is three years old. Because many fish demonstrate logistic growth rates in terms of length, it is important to use additional pieces of data to determine their age.


In the head of ray-finned fish, one can find small, bone-like structures called otoliths. These structures have a variety of sensory functions that include detection of sound vibrations in water, movement, and its orientation in the water. As fish age, calcium carbonate will be added to the otolith, forming ring-like structures that can be used to determine the age of a fish, much like a tree will add new tissue each season forming tree rings.  Otoliths are the best way to determine the actual age of a fish.

Otoliths. [left to right: Black Sea Bass, Red Snapper, Jackknife fish] (photo by David Knight
For the fish that we were sampling, we remove the sagittal otoliths which are located beside the brain just about level with the eyes. To extract them, a cut is made on the dorsal side of the fish with a sharp knife to gain access to the skull case.  To extract otoliths from some very “hard-headed” fish, a saw is used, while others take little effort. After a few hours of otolith extraction, I feel as though I am getting the hang of it, although I am nowhere near as fast as the biologist on board! I’ve been collecting otoliths from Black Sea Bass (Centropristis striata) and Vermillion Snapper (Rhomboplites aurorubens) to bring home with me to create a lab for my class and to post on the NOAA Teacher-at-Sea website.

Extracting otolith
Looking for a perfect extraction of otolith from Vermilion Snapper. (photo taken by Nate Bacheler)

Be sure to check back for Part II. Gonads, Diet and DNA

Personal Log

The motion of the ship has not been a problem so far and I stopped taking any motion sickness pills after the first day. As I have been removing otoliths from fish, I cannot help but think about the similarities in how both fish and humans perceive their spatial environment and maintain balance. In our vestibular system, we too have otoliths that help to sense acceleration in a vertical and horizontal direction. Of course my thoughts then go to a dark place…what if someone were removing my otoliths to determine my age?


Did You Know?

The longest known life span in vertebrates is found in the Greenland Shark (Somniosus microcephalus). It is estimated that the Greenland shark grows less than 1 cm per year. Since sharks do not have otoliths, scientist have to analyze proteins found in the lens of their eye.  In 2016, scientist from the University of Copenhagen collected a 5 m shark that was estimated to be about 392 years old, but may be anywhere from 272 to 512 years old.

Reference: Eye lens radiocarbon reveals centuries of longevity in the Greenland shark (Somniosus microcephalus). Science  12 Aug 2016: Vol. 353, Issue 6300, pp. 702-704

Kaci Heins: Shoreline Verification and Auroras, September 27-29, 2011

NOAA Teacher at Sea
Kaci Heins
Aboard NOAA Ship Rainier
September 17 — October 7, 2011

Heading Back to the Rainier After Shoreline Verification

Mission: Hydrographic Survey
Geographical Area: Alaskan Coastline, the Inside Passage
Date: Thursday, September 29, 2011

Weather Data from the Bridge

Clouds: Overcast/Drizzle/Rain
Visibility: 2 Nautical Miles
Wind: 15 knots
Dry Bulb: 8.2 degrees Celsius
Barometer: 1001.1 millibars
Latitude: 55.42 degrees North
Longitude: -133.45 degrees West

Science and Technology

Waterfall on Shore

When we are out on a launch acquiring data there are so many beautiful shorelines to see.  From far away they look inviting, but in reality there are usually numerous boat hazards lurking below or on the shoreline.  I have written a lot about the hydrographic survey aspect of this mission and how it is important to ships so that they can navigate safely.

However, when we are out on a survey launch the first priority is safety of the crew, the boat, and the technology.  This means that we normally do not go anywhere that is shallower than about eight meters.   Consequently, this leaves areas near the shore that is not surveyed and leaves holes in the chart data.  This is where shoreline verification comes in using single beam sonar.  However, since the launch with the single beam is not operational at this time we have been using the multibeam instead.  The Marine Chart Division (MCD) gives the Rainier specific items that need to be identified because they are considered Dangers to Navigation,  or they need to be noted that they do not exist.  The MCD compiles a priority list of features that come from numerous sources such as cruise ships, aircraft pilots, and other boats that have noted that there may be a danger to navigation in a certain area.  Many of these charts have not been updated since they were created in the early 1900’s or never charted at all!

Before we leave the Sheet Manager and the Field Operations Officer (FOO) come up with a plan for what shoreline they want to verify for the day.  A plan must be made because there is a small window to acquire the information needed to satisfy the requests of the Marine Chart Division.  The shoreline verifications must be done at Mean Low or Low Water.  This means that it has to be done when the average low tide of each day comes around, which has been in the early morning and afternoon for us.

Shoreline 4 Meter Curve

Using the launches we head up to what is called the four meter curve.  This curve is the limit to where we can go during meal low or low water.  If we get any shallower or move closer to the shore then we will put everyone and everything in danger on the boat.  We bring with us  a camera to document the features, a clinometer, which allows us to document headings and angles, a laser range finder, charts that they can draw and note features on, and their computer software.   Once we get underway and arrive to our first rock that we have to document, the officers make sure they maintain good communication with the coxswain, or boat driver.  We make sure we circle everything in a counterclockwise motion so that he can see everything off to his starboard, or right side as we move.  We can see the rock become exposed as the waves move over it, but the tricky part is getting as close to it as possible without hitting it.  This is so we can get a precise location as possible for the chart.  Our coxswain was very experienced so we were able to get right next to it for photos, the heading, and to drop a target, or the location, in the software.

Notes Documenting Various Features

The rest of our shoreline verification was a lot less intense as we confirmed that there was a lot of kelp around the rocks, the shoreline, and specific rocks were in the correct place.  LT Gonsalves, the Hydrographer-in-Charge (HIC),  showed me how he draws some of the features on his chart and makes notes about whether the features are there or not.  I took photos and noted the photo numbers for the chart, as well as the range and height of various features.  Shoreline verification is very important for nautical charts so that ships and their passengers know exactly where dangers to navigation lie.  It takes 120 days from the final sounding for all the data to get submitted to the Hydrographic Survey Division.  From there the information gets looked over by numerous agencies until about 2 years later the updated chart is available.  This is quite a long time to wait for changes in dangers to navigation.  To be safe, the chart stays the same even if there is not a dangerous rock lurking around at mean low or low water.  It is best to just avoid the area and err on the side of caution.  There is still a lot of work to be done in Alaska that will take many, many years to complete.  However, it is thanks to hydrographic ships like the Rainier and its crew that get the job done.

Personal Log

NASA SOHO Image of Solar Wind and the Magnetic Field

Tonight was very special because we could actually see an aurora, or the northern lights,  in the night sky.  An aurora is a natural light display in the arctic and antarctic, which is caused by the collision of charged particles in the upper atmosphere.  Auroras start way back about 93 million miles (or 1 astronomical unit– AU) at the sun.  When the sun is active, usually due to coronal mass ejections, it releases energetic  particles into space with the very hot solar wind.  These particles travel very quickly over those 93 million miles until they reach the Earth’s magnetic field.   Most of these energetic particles are deflected around the Earth, but some get trapped in the magnetic field and are moved along towards the polar regions until they strike the atmosphere.  We knew there were possibilities to see an aurora while we were anchored, but usually it has been cloudy at night so we couldn’t see the stars.  However, on the 27th Officer Manda came through saying he had seen the lights.  Low and behold there was a green glow in the sky behind some clouds and a couple of times some of the energized particles made bands across the sky.  If there hadn’t been so many clouds I think it would have been even more spectacular, but I was so glad I did get to see them.  Very quickly, more clouds moved in and it was just a green glow on the horizon.  I also was able to see the milky way in all its glory and the brightest shooting star I have ever seen.  These amazing photos of the aurora were taken by Ensign Manda and I am very grateful he was willing to share.

Aurora and Shooting Star Courtesy of Ensign Manda
Aurora in Alaska Courtesy of Ensign Manda

Click HERE for a link to a neat animation of how an aurora is formed.

Student Questions Answered

Animals Spotted!

Seal On a Rock We Were Documenting

Seals – species unknown









Question of the Day

Maureen Anderson: Data and Measurement, July 31, 2011 (Post #4)

NOAA Teacher at Sea
Maureen Anderson

Aboard NOAA Ship Oregon II (NOAA Ship Tracker)
July 25 — August 9, 2011

Mission: Shark Longline Survey
Geographical Area: Southern Atlantic/Gulf of Mexico
Date: Sunday, July 31, 2011

Weather Data from the Bridge
Latitude:  30.39 N
Longitude: -080.41 W
Wind Speed: 13.67 kts
Surface Water Temperature: 29.50 C
Air Temperature:  29.10 C
Relative Humidity: 78 %
Barometric Pressure:  1016.43 mb
Water Depth: 37.10 m

Science and Technology Log

A part of any good experiment or survey is the careful collection of data. We know that without a good data collection plan, our results may have error or be open to wide interpretation. The shark longline survey has been going on for the past 17 years in order to understand the abundance of shark species in this area.  It has standard procedures and protocols that we must follow so that each survey is consistent.  Hmm…that sounds similar to what we do in science class!

Every time we reach a “station” (a pre-designated spot) our team collects data on the characteristics of that area. One piece of technology we use to do this is called a CTD (which stands for conductivity, temperature, and depth). This instrument is placed overboard with the help of a winch and takes measurements for several minutes. Conductivity tells us information about the salinity (amount of salt) of the water. The device also reads the temperature, depth, levels of  chlorophyll, dissolved oxygen, and can give us water samples. This is important because every time we change stations, we want to know about the conditions of that area. The data from the CTD is then sent electronically to a data room and graphed.

Here is the CTD which measures conductivity, temperature, and depth

We also collect data on the color of the ocean water, the wave height, and the percentage of cloud cover. This last one is a bit tricky because it is so subjective.

It is also important to collect data consistently. There are two shifts aboard the boat – the day shift (which I am on) and the night shift. Each shift is 12 hours long. We collect data even in the middle of the night. What do you think would happen if we only collected data on sharks during the day time?

CTD graph
This is a graph of data from the CTD. The temperature is in blue, salinity is red, and depth is on the left vertical axis.

There are several measurement tools we use. The measuring board allows us to place a small shark on the board and read its length in millimeters. We take two readings – one for the length from the snout to the fork where the tail splits, the other for the entire length of the shark from end to end. The spring scale is used to measure the shark’s weight in kilograms. If the shark is too big for either of the above tools, we will take measurements in the cradle. We use a flexible tape measure for length, and record weight through a scale on the cradle. We know the cradle’s weight, so all we have to do is record the total weight of the cradle with the shark in it and subtract (see kids, math in the real world!)

cloud cover
Can you guess the percentage of cloud cover here?
We tag some sharks with a Roto clip and/or an identification marker.  All of the data is written down on a clipboard and then entered into a database.  Pictures are also taken with a camera so that we can photo-document the catch.  Each picture is renamed with the corresponding ID number of the tag so that we have a database of images.

Personal Log

I mentioned earlier that we have satellite TV access on the  boat.  Actually there are three – one in the lounge and two in the galley.  Funny enough, we have the perfect program to watch this week on the Discovery channel…happy Shark Week everyone!  Yesterday, we had to postpone doing our longline survey at one station due to a distress call from a small boat that was 10 miles away.

spring scale
In this photo, I'm using a spring scale to weigh a sharpnose shark.
The crew aboard our ship got ready to perform a search and recovery operation by getting the Zodiac rescue boat ready.  But as it turned out, another vessel was able to aid them faster, and we resumed our work.  I was amazed to see the crew jump into action and be ready so fast.

Species Seen Today
Atlantic Sharpnose Shark
Sandbar Shark
Mutton Snapper
Tiger Shark

cradle with sandbar shark
This sandbar shark is too large to bring on deck. It is measured in the cradle.
Rescue boat
This is the Zodiac rescue boat ready for deployment.
fin tips
These fin tip samples will help with shark identification.
Tools to Tag
This roto tag (small yellow clip) and identification marker are used to tag the shark.
Tiger shark with Roto tag
This very small, young Tiger shark now has a Roto tag on its fin
half sharpnose
Something was hungry for the other half of this Atlantic sharpnose.

Kevin McMahon, August 7, 2004

NOAA Teacher at Sea
Kevin McMahon
Onboard NOAA Ship Ronald H. Brown

July 26 – August 7, 2004

Mission: New England Air Quality Study (NEAQS)
Geographical Area:
Northwest Atlantic Ocean
August 7, 2004

Weather Data from the Bridge
Lat. 42 deg 33.05 N
Lon. 68 deg 23.03 W
Heading 349 deg
Speed 0 kts
Barometer 1007.91 mb
Rel Humidity 83.96 %
Temp. 16.68 C

Daily Log

0800 hours. The past evening was spent steaming to this point where we are on station. The ship will remain here for all of the morning and part of the afternoon. We will await a fly over by the J31 as well as the NASA DC8. Many of the scientists onboard will also set their equipment with the use of a satellite due to pass overhead in the early afternoon.

My morning was spent helping Dan Wolfe, one of the NOAA meteorologists repair an electrical problem which had disabled the sensors that relay air temperature and relative humidity to computers aboard ship. As you can see from the photos, this was not something you would find in the job description for meteorologists. To solve the problem Dan had to climb up to a crows nest like platform on the masthead near the bow of the ship and then perform a diagnostic test on the electrical circuitry for the systems.

It was finally discovered that a switch box had allowed moisture to enter through leaky gasket. In all, the task it took several hours to complete.

During the time we were engaged with the repair we started to notice a small school of dolphins moving closer to the ship. At first they seemed to keep a distance of about 100 yards but after time, small pods of four or five would move in closer to the ship and investigate our presence in their world. I believe that this type of dolphin is known as the Atlantic White Sided Dolphin. As we were stationary in the water, a flock of shearwaters could be seen loitering off our stern and starboard side. They are a wonderful seabird to watch as they seem to effortlessly propel themselves through the air with a continuous glide, using a ground effect air flow created by an updraft of the sea waves. The dolphins would at times glide under the floating shearwaters and make them alight from the water. They seemed to enjoy this form of teasing as they repeated the act over and over.

During the afternoon I helped Drew Hamilton take more sun readings with his Sunphotometer. As I stated in yesterdays log, the sunphotometer measure the intensity of the suns direct radiation. Because we had a couple of aircraft fly over us today, the J31 and the DC8, and because those platforms contain the same equipment as that aboard the ship, we were able to validate our readings.


Why is it important to have standardized equipment when conducting the same types of experiments by different people in different locations?