Martha Loizeaux: Cool Science Tools and Drifter Buoy! August 26, 2018

Amanda Dice: Ending Week 1 at Line 8, August 26, 2017

NOAA Teacher at Sea

Amanda Dice

Aboard Oscar Dyson

August 21 – September 2, 2017


Mission: Juvenile Pollock Fishery Survey

map cropped
Oscar Dyson moves across the Shelikof Straight to collect the Line 8 samples

Geographic area of cruise: Western Gulf of Alaska

Date: August 26, 2017

Weather Data: 13.2 C, cloudy with light rain

Latitude 57 36.6 N, Longitude 155 .008 N



Science and Technology Log

As part of this survey, the scientists onboard collect data from what is known as “Line 8”. This is a line of seven sampling stations, positioned only a few miles apart, near the southern opening of Shelikof Straight between Kodiak Island and the Alaskan Peninsula. Water samples are taken at different depths at each sampling station to measure several different properties of the water. This study is focused on profiling water temperature and salinity, and measuring the quantities of nutrients and phytoplankton in the water.

The CTD rosette is lowered into the water using a winch – as seen from above.

To collect this data, a conductivity and temperature at depth (CTD) instrument is lowered into the water. This instrument can take water samples at different depths, by using its eleven canisters, or Niskin bottles. The water collected in the Niskin bottles will be used to determine the nutrient quantities at each station. The rosette of Niskin bottles also has sensors on it that measure phytoplankton quantities, depth, temperature, and how conductive the water is. Scientists can use the readings from conductivity and temperature meters to determine the salinity of the water.

Each Niskin bottle has a stopper at the top and the bottom. The CTD goes into the water with both ends of each Niskin bottle in the open position. The CTD is then lowered to a determined depth, depending on how deep the water is at each station. There is a depth meter on the CTD that relays its position to computers on board the ship. The survey team communicates its position to the deck crew who operate the winch to raise and lower it.

Niskin bottles are lowered into the water with the stoppers at both ends open.

When the CTD is raised to the first sampling depth, the survey crew clicks a button on a monitor, which closes the stoppers on both ends of Niskin bottle #1, capturing a water sample inside. The CTD is then raised to the next sampling depth where Niskin bottle #2 is closed. This process continues until all the samples have been collected. A computer on board records the depth, conductivity and temperature of the water as the CTD changes position. A line appears across the graph of this data to show where each sample was taken. After the Niskin bottles on the CTD are filled, it is brought back onto the deck of the ship.

They let me take control of closing the Niskin bottles at the sampling depths!
CTD screen cropped
I used this screen to read the data coming back from the CTD and to hit the bottle to close each Niskin bottle. The purple horizontal lines on the graph on the right indicate where each one was closed.

Water is collected through a valve near the bottom of each Niskin bottle. A sample of water from each depth is placed in a labeled jar. This study is interested in measuring the quantity of nutrients in the water samples. To do this it is important to have samples without phytoplankton in them. Special syringes with filters are used to screen out any phytoplankton in the samples.

Screen Shot 2017-08-26 at 8.28.56 PM
Syringes with special filters to screen out phytoplankton are used to collect water samples from the Niskin bottles.

The “Line 8” stations have been sampled for nutrient, plankton, and physical water properties for many years. The data from the samples we collected will be added to the larger data set maintained by the Ecosystems and Fisheries-Oceanography Coordinated Investigations (Eco-FOCI), Seattle, Washington. This NOAA Program has data on how the marine ecosystem in this area has changed over the last few decades. When data spans a long time frame, like this study does, scientists can identify trends that might be related to the seasons and to inter-annual variation in ocean conditions. The samples continue to be collected because proper nutrient levels are important to maintaining healthy phytoplankton populations, which are the basis of most marine food webs.


Collecting water samples from a Niskin bottle.

Personal Log

As we travel from one station to the next, I have some time to talk with other members of the science team and the crew. I have really enjoyed learning about places all over the world by listening to people’s stories. Most people aboard this ship travel many times a year for their work or have lived in remote places to conduct their scientific studies. Their stories inspire me to keep exploring the planet and to always search for new things to learn!

Did you know?

Niskin bottles must be lowered into the water with both ends open to avoid getting an air bubble trapped inside of them. Pressure increases as depth under water increases. Niskin bottles are often lowered down below 150 meters, where the pressure can be intense. If an air bubble were to get trapped inside, the pressure at these depths would cause air bubble to expand so much that it might damage the Niskin bottle!

DJ Kast, Pre-Cruise, May 18, 2015

NOAA Teacher at Sea
Dieuwertje “DJ” Kast
Aboard NOAA Ship Henry B. Bigelow
May 19 – June 3, 2015

Mission: Ecosystem Monitoring Survey
Geographical area of cruise: East Coast

Date: May 18, 2015 (Pre-cruise)

Personal Log

Chris Melrose picked me up from the hotel and really helped me get a grasp of life aboard a research vessel. I learned all about Narragansett Bay and the lab here in Rhode Island.

I then met Jerry Prezioso, the Chief Scientist for the voyage, who gave me a great tour of the Narragansett Bay Lab. I learned what an XBT (expendable bathythermograph) was and how it measures temperature at various depths.

XBT  Photo by: DJ Kast
Photo by: DJ Kast


I learned how a Niskin bottle works and how many Niskin bottles lined up in a circle to make a piece of equipment called a rosette. The Niskin bottle is like a hollow tube with a mechanism that closes the tube at a specific depth that will then bring a water sample indicative of that depth. They apparently cost $400 each.  I am already making plans on how to make a DYI one for the classroom.

Niskin Bottle Photo by: DJ Kast
Niskin Bottle
Photo by: DJ Kast
This is a Rosette with 12 niskin bottles. Photo by: DJ Kast
This is a Rosette with 12 niskin bottles. Photo by: DJ Kast

With Jerry, I also met Ruth Briggs who works for the Narragansett Bay Apex Predators division and she showed me the shark tags that she has citizen scientists put onto sharks on the base of their dorsal (top) fin that they catch. When the sharks are caught again, the information she requests is sent back to her and includes species, size, sex, location to shore, and weight. She even let me borrow a decommissioned tag to show to my students in California.

Decommissioned shark tag from the Narragansett Bay Apex Predators Division Photo by: DJ Kast
Decommissioned shark tag from the Narragansett Bay Apex Predators Division
Photo by: DJ Kast


I saw a drifter buoy that I will be decorating with all of my programs (USC, JEP, YSP and NAI) logos.

Jerry also sent me the map of all the stations that we will be visiting on our ship and at each station we are projected to measure salinity, depth, temperature, nutrients and plankton! I am so excited! We are expected to go as far south as North Carolina and as far north as the Bay of Fundy in Canada (International Waters!!!).

TAS and the NOAA Ship Arrival

My stateroom is amazing! My roommate and I even have our own head (bathroom) in our room with sink, shower and all. There are two beds in a bunk bed format, and since I showed up about 6 hours before the other scientists I chose the bottom bunk and the cabinet I wanted for my stuff. I unpacked (and gladly didn’t over pack) and managed to fit it all in the closet that was given to us. I feel so fortunate to have such amazing accommodations like this.

Important People who Keep the Ship Afloat and on Course

Today I met the Operations Officer, Laura, who showed me the ropes and introduced me to people on the ship at dinner at the bowling alley on the naval base here in Newport, RI. She also showed me the buoy yard filled with lots of different buoys that indicate different paths of travel and safe/unsafe waters for ships coming into port.

I entered a yard of buoys on the Newport Naval Base and here I am for a size comparison. They are HUGE!
I entered a yard of buoys on the Newport Naval Base and here I am for a size comparison. They are HUGE!
Here is a look at what happens when  a buoy is freshly painted and when its being fouled by marine organisms and algae (RUST!) Photo by: DJ Kast
Here is a look at what happens when a buoy is freshly painted and when its being fouled by marine organisms and algae (RUST!) Photo by: DJ Kast


Important Ship Personnel
CO: Commanding Officer
XO: Executive Officer
CME: Chief Marine Officer
OO or Ops: Operations Officer= Laura
NO: Navigational Officer or Nav= Eric
CB: Chief Boson or Deck Boss= Adrian
AB: Able Seaman or a Deckhand = Roger

Meal Schedule
I also learned about food times (Very important).
7AM- 8 AM or 0700-0800 hours= Breakfast
11- 12 PM or 1100-1200 hours= Lunch
5- 6 PM or 1700-1800 hours = Dinner

Roommate in Stateroom 2-22


DJ Kast on the Gateway Photo by: DJ Kast
DJ Kast on the Gangway
Photo by: DJ Kast
Here I am boarding the NOAA Henry B. Bigelow Photo by: DJ Kast
Here I am boarding the NOAA Henry B. Bigelow
Photo by: DJ Kast


I met my amazing roommate Megan and she is a master’s student at the University of Maine. We will sadly have opposite schedules for most of the trip because I will be on the 12 PM- 12 AM shift and she will be on the 12 AM- 12 PM shift. We have a lot of things in common including our love of the ocean, geology and Harry Potter. She will be looking at dissolved nutrients in the water and she will be monitoring the instruments that measure conductivity, temperature and depth or (CTD) and requesting water samples while at various stations.

Kate DeLussey: TowCam Anyone? July 11, 2012

NOAA Teacher at Sea
Kate DeLussey
Onboard NOAA Ship Henry B. Bigelow
July 3 – 18, 2012

Mission:  Deep-Sea Corals and Benthic Habitat:  Ground truthing and exploration in deepwater canyons off the Northeast
Geographical area of cruise: Atlantic Ocean, Leaving from Newport, RI
Date:  Wednesday, July 11, 2012

Everyone works at sea. Here I am helping with the pre-deployment checklist.   (See how wet Lowell is!  He has been to the ocean floor many times.)

Latitude:  39.8493°
Longitude: -69.5506 °

Weather Data from the Bridge:
Air Temperature: 19.30° C
Wind Speed: 20.74 knots  5  on the Beaufort  wind scale
Relative Humidity:  88.00%
Barometric Pressure: 1,020.80 mb
Surface Water Temperature: 21.39° C

Science and Technology Log

High winds, moderately rough seas, and difficulties with the ship’s positioning system all contributed to the delay of the first scheduled launch of TowCam on our midnight shift.  Even though the necessary decision meant a loss of precious underwater time, it is better to delay than risk losing  expensive equipment.

When the seas calmed down we were able to launch TowCam, but first we had to go through the pre-launch checklist.  I helped Lizet as she prepared TowCam.

Did you guess that Batteries power the components of TowCam?          Lizet must test the batteries  before and after each launch.

The batteries are under very high pressure when TowCam goes to the ocean floor so we have to push out the air before each trip.   I help by tightening the battery caps.  Every time I am on deck I must put safety first.  I always wear a hard hat and the life vest.

One of my jobs is to help with TowCam.

When everything has been checked and double checked, the operator gives the signal, and the deck crew of the Bigelow use the winch and tag lines to launch TowCam on its next mission.

The winch swings TowCam off the deck and lowers it into the ocean.

Look at the picture carefully.  The deck crew always wear their safety equipment too!  They hook themselves to the ship by their belts, and they wear safety vests and hardhats.  The deck crew on Bigelow also make sure everyone follows the safety rules.

As soon at TowCam is in the water, everyone wants to view the images sent by the camera, but the TowCam operator must keep an eye on the monitors.

These are six of the monitors used to control and guide TowCam.

TowCam operators watch eight different computer monitors to control TowCam’s movements.  With the help of mathematic modelers and previously collected data about the structure of the ocean floor, the scientists choose  locations where they think they will find corals. These locations are called “stations.”

This map from the NOAA web site shows the track of the Bigelow. The places where the lines cross over one another are some of the stations where the scientists looked for coral

The ship must make very small movements to get the camera in the correct place on station. The operator will say something like, “Lab to Bridge- move 10 m to the North please.”… Then they watch the camera and the monitors to see if TowCam moves to the correct position.   Sometimes TowCam floats right past the spot scientists want to see, and then the operators have to try to get it back into position to take the pictures.  Not every station has the corals the scientists hope to find.  But even knowing where corals are not is important information.  After several hours of picture taking, we move on the next station.

I sit next to the TowCam operator and keep the logs.

Even in calm seas controlling TowCam is a challenging process.  Remember, TowCam hovers over the ocean floor  attached to the ship by a wire.   Fully loaded it weighs over 800 pounds in the air.  Since the ship moves TowCam by pulling it, it is not easy to follow the scientists’ plan.

However, when the perfect coral images appear on the screen, no one thinks about how hard they were to find.  We all crowd around the monitors and watch in amazement.  The scientists try to figure out  types of corals in the picture, and then they wait for the next picture to see if there are even more!  We have found corals at lots of stations!

Think about a time you tried to pull something tied to the back of  a rope.  Was it easy to steer?  Did it get stuck?  

Personal Log

We have talked a bit about how scientists find and try to study corals using the underwater camera and other sensors on TowCam.  On other missions scientists  sometimes use remote control underwater vehicles ROVs.   Unlike TowCam which is dragged behind the ship, these vehicles are more versatile because they are driven and controlled remotely using a joy stick similar to the ones you use for computer games.    Sometimes scientists even go to the ocean floor and drive themselves around using submersibles.  One thing is certain,  you have to get under the water to study corals.

Scientists go to all this trouble because corals are important to our Earth’s oceans. They are very old, and they provide habitat for other animals. 

As you grow, it will be your job to find ways to study and protect corals and all other living things in the oceans. 

Who knows how corals could help us in the future!

Polyps are extended from deep-sea coral colony.
Photo from NOAA Undersea Research Program.

Kate DeLussey: Lowell Searches Beneath the Ocean, July 8, 2012

NOAA Teacher at Sea
Kate DeLussey
Onboard NOAA Ship Henry B. Bigelow
July 3 – 18, 2012

Mission:  Deep-Sea Corals and Benthic Habitat:  Ground truthing and exploration in deepwater canyons off the Northeast
Geographical area of cruise: Atlantic Ocean, Leaving from Newport, RI
Date:  Sunday, July 8, 2012

Latitude:  38.9580 °
Longitude: -72.4577 °

Liz thought we needed our school mascot on the mission. When she went to the store, she brought back Lowell the Lion.

Weather Data from the Bridge:
Air Temperature: 24.60° C
Wind Speed: 4.5 knots
Relative Humidity:  88.00%
Barometric Pressure: 1,010.30 mb
Surface Water Temperature: 24.49° C


Science and Technology Log

Look who went to the bottom of the ocean on TowCam.  No you silly students…not me!  TowCam is exploring the deep ocean between the twilight zone and the midnight zone, and it is not possible for people to travel in deep water without very special equipment.

Our mascot Lowell Lion accompanied TowCam as it was deployed for Tow 2.

At this location, TowCam reached a depth of over 1900 meters below the surface of the ocean.  That is more than one mile-straight down!  It was a good mission.  The camera was sending some very interesting images back to the ship.  As I was doing my job logging, I was watching these first images.  I was able to see hard bottom- the best habitat for corals.  I also saw fish and sea stars, and then I saw the corals! They looked like little fuzzies on the rocks. The scientists had the ship hold position right over of the corals so they could take lots of pictures.  The TowCam operator used controls on the ship to raise and lower TowCam to get close to the corals without touching the cliffs where the corals were living.

Students:   Can you imagine using remote controls to move the TowCam?  I bet you would be good at it.  Perhaps the video games you play will help prepare you to fly TowCam when you finish college. 

Doesn’t Lowell look proud?  He survived his first dive and brought some interesting friends back with him.

Well, when TowCam came back on the ship, Lowell was very wet, but he handled the cold, dark high pressure very well.   Thanks to Greg and Lizet, Lowell stayed on the TowCam Sled!

Once TowCam was secured on the deck. We went out to take care of TowCam.   What a big surprise to find other creatures hitchhiking on TowCam.   Lowell the Lion must have made some friends.

This sea star was hidden on TowCam

The first deep sea visitor was a spiny orange sea star.

The orange sea star was found on TowCam deployment #2.

Isn’t it beautiful?  We all rushed to see it.  Dr. Nizinski carefully examined and measured the sea star.   She used her tweezers to pick up a tiny sample the sea star leg, and she put the sample into a little bottle with a label.  She will use the sample to test the DNA to help classify the sea star.  She will find the sea star’s “family.”

It was exciting to find the sea star, but when we looked further one of the scientists saw a piece of coral tucked in a hiding place on TowCam.   Dr. Martha took care of the coral also.  The coral will become a permanent record that reminds us that this type of coral lives here.

   These corals were hidden in the batteries after Tow 2. July 8, 2012


Do you see how carefully the sample is documented?  Some of the things we do in school like labeling and dating our illustrations and our work prepare you to be a scientist.  

Many years from now someone can look at the coral in this picture and see that the sample was collected on the Bigelow TowCam #2, on July 8th.  The ruler in the picture helps everyone know the approximate size.

One of the components on TowCam we have not talked about yet is the slurp.  


TowCam slurp

Try to find the Slurp on TowCam.              

The “slurp” is really an underwater vacuum cleaner that sucks up water, sediment, and sometimes small creatures.  When TowCam is in deep water, the scientists watch the images to decide when it is a good time to trigger the slurp.   They have to choose carefully because the slurp can be done only once on each trip to the bottom.

The scientists used the slurp on Tow #2.  The collection container looked like it just had “mud” and water.   It was emptied through a sieve to separate the “mud” and other things from water.  The scientists carefully examined what looked like regular mud but tiny organisms like bivalves, gastropods, and small brittle stars were found in the sieve.  These animals were also handled very carefully.

This brittle star was found with mud and sediment slurped from the ocean bottom.

This brittle star was found with mud and sediment that was slurped from the ocean bottom.

Can you find any other living things in this picture?


You never know what is hiding in the mud.  I bet we could do this kind of exploring right in our school’s courtyard.  What do you think we could find if we examined our mud?


Kate DeLussey on the Bigelow July 12

Personal Log

I think we should talk about the ocean today.  Many of us have had some experience with the ocean.  Maybe you have been to the beach, and maybe you have even seen some of the cool creatures that can be found on the beach.  I have seen crabs, horseshoe crabs, clams, and plenty of jellyfish, but the scientists on Bigelow are working in a very different part of the ocean.

If you visit the beach, you are only swimming in a teeny tiny part of the ocean.  Maybe you are allowed in the ocean up to your knees to a depth of 20 inches (about 1/2 a meter), or maybe you are brave and are able to go in the ocean with an adult up to your waist to a depth of 30 inches (about 3/4 a meter).  Even if you have been crabbing or fishing in the Delaware Bay where the average depth is 50 feet (15.24 meters) you have been in only the most shallow part of the ocean.  TowCam has been down as far as 1.2 miles (2000 meters).  That is not even the deepest ocean!  The ocean is divided into zones according to depth and sunlight penetration.  I learned about the top three zones.

  • The sunlight zone– the upper 200 meters of the ocean are also called the euphotic zone.  Many fish, marine mammals like dolphins and whales, and sea turtles live in this band of the ocean.  At these depths there is light, plants, and food for creatures to survive.  Not much light penetrates past this zone.
  • The twilight zone– this middle zone is between 200 meters and 1000 meters and is called the disphotic zone.  Because of the lack of light, plants cannot live in this zone.  Many animals like bioluminescent creatures with twinkling lights do live in this zone.  Some examples of other creatures living in this zone includes: crabs, gastropods, octopus, urchins, and sand dollars.
  • The midnight zone– this zone is below 1000 meters and is also called the aphoticzone has no sunlight and is absolutely dark.  At these depths the water pressure is extreme, and the temperature is near freezing.  90% of the ocean is in the midnight zone.So you can see that when you are at the beach, you are never in the “Deep Ocean.”  You are still in a great place to find many amazing creatures.  Keep your eyes open!  Be curious! Make sure you do some exploring the next time you visit this important habitat.  Then write and tell me about the things you find. Try to draw and label the three zones of the ocean.  Be sure to draw the living things in the correct zone.
  • Next time:  Someone will be working on deck getting TowCam ready for deployment.  Hint:   It will not be Lowell. : )

Kate DeLussey: Underway and Under the Sea, July 7, 2012

NOAA Teacher at Sea
Kate DeLussey
Onboard NOAA Ship Henry B. Bigelow
July 3 – 18, 2012

Mission:  Deep-Sea Corals and Benthic Habitat:  Ground truthing and exploration in deepwater canyons off the Northeast
Geographical area of cruise: Atlantic Ocean, Leaving from  Newport, RI
Date:  Monday, July 7 , 2012


Here I am on the bridge of Henry B. Bigelow.  ENS. Zygas put me to work looking up changes for navigational charts.

Latitude:  39.29 °
Longitude: -72.25°

Weather Data from the Bridge:

Air Temperature: 23.40° C
Wind Speed: 15 Kts
Relative Humidity:  90.00%
Barometric Pressure: 1,011.99 mb
Surface Water Temperature: 23.66° C

Science and Technology Log

At 7:00 pm last night the Henry B. Bigelow left Pier 2 from the Newport Naval Base.  Narragansett Bay was crowded with sailboats, yachts, and even a tall ship, but once we passed under the bridge, we knew we were really on our way.  Now that we are at sea, everyone onboard will begin his or her watch.  I will be working 12 am to 12 pm along with some of the scientists.  Even though I never worked night work before, I was excited to learn about my jobs!

One of our jobs is to keep track of the “TowCam” when it is in the water.  Every ten minutes while the TowCam is deployed (sent underwater) we log the location of the ship using Latitude and Longitude. We also have to keep track of other important data like depth.  The information is logged on the computer in a spreadsheet and then the points are plotted on a map.  A single deployment can last 8 hours.  That is a lot of data logging!  These documents provide back up in case something were to happen to the data that is stored electronically.   I will have other jobs also, and to get ready for those duties, Lizet helped me get to know the TowCam better by explaining each component.

Students:  See if you can find each part Lizet showed me on the picture of the TowCam in my last blog.


The camera on TowCam faces down to capture images in the deep ocean

Camera– The camera is the most important part of the TowCam.  You need a very special camera that will work in cold deep water.  When the TowCam is close to the ocean floor this digital camera takes one picture every 10 seconds. The thumbnails or samples of the pictures are sent to computers on the ship by the data link. The camera operator described the thumbnails like the picture you see when you look at the back of your camera. When I look at the thumbnails I don’t usually see much in the picture.  The scientists know what they are looking for, and they can recognize hard bottom on the ocean floor and corals.  They see fish and other sea creatures too, and when they see a picture they like, they will ask the ship navigator to “hold the setting” so they can take more pictures.  Remember, the scientists are trying to find corals, or places where corals might live.  If they have a picture, they have proof that these special animals live in a certain habitat that should be protected.

Strobe light– There are two strobe lights on the TowCam.  The deep ocean does not have

Strobe light illuminates the darkness of the deep ocean

natural lighting because the sunlight does not reach down that far.  The strobe light flashes each time a picture is taken.  If the TowCam did not have these special lights, you would not be able to see any of the pictures from the camera.  These lights are tested every time the TowCam is deployed.

The CTD measures Conductivity, Temperature, and Depth

      CTD- The CTD is an instrument that has sensors to measure Conductivity, Temperature, and Depth in a certain water column.  It is attached to the TowCam and the information from the CTD is sent to the computers through the datalink.  This information gives the scientists a better understanding about the ocean water and the habitat for the creatures they are looking for.  Look for more components on the TowCam.  How do you think the TowCam gets its power?


Personal Log

I am getting adjusted to life at sea.  For the first few days, when we were still on the dock I did not have much to do.  ESN Zygas gave me a job and let me find updates for the navigational charts that are stored on the bridge.  The charts are maps of the oceans and waterways that help the NOAA Corps team steer the boat, and these charts get updated when markers like buoys are moved or when the water depths and locations change.  Up-to-date charts keep the ships safe.  I was glad to do a job that helped keep us safe.  Now that we are at sea, I have been working my watch.  The work varies.  We have hours of watching TowCam on the bottom of the sea and charting the positions of the ship. Then we have the excitement when the camera comes on-board with pictures and samples that need to be processed.

One of the best things about this experience is that I am the student just like my students at Lowell.  I am excited to learn all of the new things, but I am frustrated when I don’t understand.  Sometimes I am embarrassed when I have to ask questions.  Yesterday I was working with some of the images and I was looking for fish. All I had to do was write “yes” there is a fish in this photo.  Well, I had to ask Dave (one of the scientists) for help.  I had to ask, “Is this a fish?”  Can you imagine that?  A teacher like me not knowing a fish!  It was like finding the hidden pictures in the Highlight magazine!

So instead of being frustrated, I am open to learning new things.  I keep practicing and try not to make mistakes, but when I do make those mistakes, I just try again. By the time we go through the thousands of pictures I may not be a pro, but I will be better.  I can see that I am improving already.  I can find the red fish without zooming in -the red color probably helps!

Next time:  Wait until you see who went to the bottom of the ocean on TowCam.  You won’t believe what they brought back with them.

Until next time:)

Wes Struble: Analysis of Water Samples, March 4, 2012

NOAA Teacher at Sea
Wes Struble
Aboard NOAA Ship Ronald H. Brown
February 15 – March 5, 2012

Mission: Western Boundary Time Series
Geographical Area: Sub-Tropical Atlantic, off the Coast of the Bahamas
Date: March 4, 2012

Weather Data from the Bridge

Position:30 deg 37 min North Latitude & 79 deg 29 min West Longitude
Windspeed: 30 knots
Wind Direction: North
Air Temperature: 14.1 deg C / 57.4 deg F
Water Temperature: 25.6 deg C / 78.4 deg F
Atm Pressure: 1007.2 mb
Water Depth:740 meters / 2428 feet
Cloud Cover: 85%
Cloud Type: Cumulonimbus and Stratus

Science/Technology Log:

In the previous log I described a CTD cast in detail from start to finish. Now that the CTD platform is on the deck of the Ron Brown the actual sampling process can begin. The CTD has a number of Niskin bottles holding a little more than 10 liters of water each. Water samples from each bottle must be collected and analyzed for various parameters which could include: Salinity, Oxygen content, Inorganic carbon, and others. On this cruise most of the CTD casts were sampled for both salinity and dissolved oxygen.

The first step in measuring salinity involves a careful rinsing of the sample bottles. After a standard three rinses, the bottle is filled and the depth from which the water was sampled is recorded for each bottle.

As a beautiful western Atlantic sunset falls on the Ron Brown another night of CTD's begins
I prepare a water sample for dissolved oxygen analysis after a CTD Cast at 2:00 am
The dissolved oxygen analysis lab station in one of the science labs on the Ron Brown

The full sample bottles are then either taken to the dissolved oxygen lab station or the Salinity lab station for analysis.

A close-up of the amperometric titration apparatus for analysis of dissolved oxygen in one of the science labs on the Ron Brown. A solution of Manganese Chloride and a combination of Sodium Hydroxide/Sodium Iodide is added to the water sample to sequester the oxygen and then when the temperature is stable the solution is amperometrically titrated with thiosulfate.
The Ron Brown off the starboard stern from the workboat
The "climate airlock" leading to the salinity analysis lab. The airlock helps keep the water samples under constant temperature and humidity conditions.
The two Autosals in the Salinity lab. These are precision instruments for measuring the salinity of seawater
A east-west cross-section across the eastern Atlantic Ocean. The eastern US coast is at left. The diagram illustrates north (reds)-south (blues) movement of the Antilles and Deep Western Boundary Current. Vertical scale in meters horizontal scale in 100,000 meter units (100 kilometers)

Wes Struble: What in the World Is a CTD Cast? March 2, 2012

NOAA Teacher at Sea
Wes Struble
Aboard NOAA Ship Ronald H. Brown
February 15 – March 5, 2012

Mission: Western Boundary Time Series
Geographical Area: Sub-Tropical Atlantic, off the Coast of the Bahamas
Date: March 2, 2012

Weather Data from the Bridge

Position: 26 degrees 19 minutes North Latitude & 79 degrees 55 minutes West Longitude (8 miles west of Florida’s coast)
Windspeed: 14 knots
Wind Direction: South
Air Temperature: 25.4 deg C / 77.7 deg F
Water Temperature: 26.1 deg C / 79 deg F
Atm Pressure: 1014.7 mb
Water Depth: 242 m / 794 feet
Cloud Cover: none
Cloud Type: NA

Science/Technology Log:

There are four different ship’s stations that are involved in a CTD (Conductivity, Temperature, & Depth) operation: the bridge, the survey team, the winch operator, and the computer room. The bridge is responsible to keep the ship on position and stable over a predetermined latitude and longitude. The survey team is responsible for preparing the CTD platform for deployment and securing it back on deck at the completion of the cast. The winch operator controls the actual motion of the CTD platform by the use of a hoist.  The computer lab relays commands to the winch and survey team in reference to testing and sampling depths, and when to start and stop the ascent and descent of the platform. The CTD platform can carry many types of instruments depending upon the nature of the research being conducted. During this cruise our platform usually contained two each of a temperature gauge, conductivity gauge (from which you can obtain salinity), and oxygen gauge.  In addition there is one pressure gauge and a transmissometer (that measures the turbity of water which is an indicator of the phytoplankton), 23 Niskin water sampling bottles, and two Acoustic Doppler Range finders – one pointing toward the surface and one pointing at the sea floor.

The CTD (Conductivity, Temperature, & Depth) platform on the Ron Brown. The long grey cylinders are the water sampling Niskin bottles, the yellow and blue device at the bottom in the Acoustic Doppler Current Profiler (for measuring distance to the sea floor) for measuring the distance to the sea floor during descent phase of a cast, the grey cylinders are weights, and the green cylinder is the power supply.
A Niskin Bottle with my Nike shoe for scale
The CTD platform being lowered over the side for start of another cast.
The "downlooking" ADCP (Acoustic Doppler Current Profiler mounted on the CTD.
The "up-looking" ADCP (Acoustic Doppler Current Profiler) mounted on the CTD
The Niskin Bottle trigger release. This device is used to remotely close the Niskin bottles at depth
The bridge of the Ron Brown during a CTD cast

     A CTD cast begins when the ship arrives at prearranged coordinates of latitude and longitude. The bridge will announce that we are “on station”.

A photo of the Ron Brown off the coast of Grand Bahama Island

   The survey team acknowledges and then raises the CTD platform and places it is the water at the surface for a minute or two. Then after receiving a signal from the computer operator that all functions are operating within normal parameters the platform is lowered to 10 meters and held there for two minutes to allow the instruments to stabilize.

Here I am starting my midnight to 6 :00 am shift at the CTD computer control station in the computer lab of the NOAA Ship Ronald H Brown
The "brains" of the CTD. This device also contains the pressure sensor.

   After the two minute hold at 10 meters the entire platform is brought back to the surface and the log is started as the package is lowered. The descent begins at about 30 meters/minute and eventually reaches 60 meters/minute. Many of the deep water casts on this cruise were between 4000 m and 5500 meters (about 13000 ft and 18,000 ft) and take over an hour to reach the bottom. While the descent takes place all the instruments are recording data which is stored and plotted in real time at the computer monitor.   When the CTD platform is 10 meters from the bottom the descent is stopped and the first water sample is collected by sending a signal that closes the first Niskin bottle. At this point the CTD slowly begins its climb back to the surface (another hour or more) stopping at designated depths to collect water samples.After the last Niskin bottle is closed at the surface, the CTD platform is brought back on deck, the water samples are removed, and the entire platform is prepared for the next cast.

Here I am on the weather deck in my favorite chair on the ship. I enjoy relaxing here in the sun in the morning after a night shift at the CTD computer station.
Another beautiful western Atlantic pre-sunset. I enjoyed many of these during the cruise.
The early sun rising in the east off the stern of the Ron Brown brings another night of CTD's to an end.

Nathan Pierantoni, Thursday 4.7.11

NOAA Teacher at Sea: Nathan Pierantoni

University of Miami Ship R/V Walton Smith

South Florida Bimonthly Hydrographic Survey

Florida Bay, in transit from Dry Tortugas to Key West.

Thursday, April 7 2011

Weather Data from the Bridge

1400 hrs Local Time

Barometric pressure = 1017 Millibars

79 F

78% Humidity

Visibility = good

Wind SE 16 knots

Science and Technology Log

Dr. Neslon was very gracious and gave me free reign to learn as much as I could while aboard the R/V Walton Smith. Water sampling requires the most manpower and it is most common thing we are doing for this cruise, and therefore I have been involved in many vertical casts of the CTD. CTD stands for Conductivity, Temperature, and Depth, and when I refer to “the CTD” I am referring to the hefty apparatus that is pictured below, sitting on the fantail (the open deck at the stern of the ship). The procedure is as follows: as we get to our stations along our survey route, the boat stops and the we don our hardhats and life jackets and go out to the fantail,. We then lower the safety lines and prepare for a cast. Next, the captain goes to the stern of the upper deck where there is a winch cabin, from where he can pilot the ship and control the cast. The CTD is attached to a cable and is raised and lowered via an A-frame. The scientists give signals to the captain, and together, the device is lowered into the water where it does its work.

The CTD is actually a dual-purpose piece of equipment. It has sensors that measure conductivity (salinity), temperature, depth, chlorophyll, and dissolved oxygen. These sensors are built into a unit at the base of the apparatus and are protected by a metal cage.Above the sensor array is a rosette of tubes, which are able to collect water samples. Each tube holds 10 L of water, and our CDT has 12 tubes, called Nisken Bottles. The whole thing is electronically linked to the science deck through its cable, and in addition to the 2 scientists on deck who deploy the device, there is a CTD operator inside who monitors water parameter changes as the CTD goes from the surface to the bottom. This scientist is in communication with the captain in the winch cabin, and as the device returns to the surface the scientist is able to fire the Niskin bottles so that they fill with water. For example, we just finished a 340m CDT sample, and Nelson fired the CTD at three depths, 338 m, 70m, and 2 m. On the way down he was able to determine ‘where’ in the water column he wanted to collect his samples, because he was able to ‘watch’ the water parameters change on his computer monitor as the data from the CTD’s sensors streamed in. Interestingly, they fire two bottles at each depth in case one of them fails. It’s just another way to prevent against errors that would be too time consuming and thus too costly to fix. Once at the surface, the scientists and the winch operator guide the CTD back aboard the ship, and secure it to the deck.

While data from the sensors is logged and converted electronically to graphs, the chemical oceanographer begins her work. Cheryl Brown, aka ‘CB’ is an ocean scientist who I have had the pleasure of working with on the day shift. Cheryl works for the Cooperative Institute for Marine and Atmospheric Studies, a University of Miami institute that receives funding through NOAA. She participates in a variety of water quality projects, and spends about 25% of her time at sea. The other 75% of her work is in the lab, where she has multiple responsibilities that include filtration, data processing, and plotting of the samples from her fieldwork. This is common to most areas of field science, where for every hour of fieldwork yields at least double the time in the lab. CB has a degree in marine science, and specialized in marine invertebrates before finding her way to Miami.

The responsibilities on the chemistry deck are numerous. For each CDT deployment, there are a variety of samples that must be prepared from the water collected by the CTD. Each of this same series of samples is required for each depth of water that has been tested. On average, three depths are sampled per CTD deployment, but on this cruise some casts have collected water from four depths, and some have only collected water from the surface. The water from each depth is transferred to a bottle, which has been rinsed three times to avoid contamination, and brought into the wet lab. From there, a nutrient samples, chlorophyll samples, and dissolved CO2 samples are taken.

A nutrient sample is a general measure of ocean health, and includes many of the same samples that might be taken in a home aquarium, like ammonia, nitrates, and nitrites. To prepare the sample, we manually filter 50 ml of seawater into a sterile container, and preserve it with chloroform. It is then placed into the lab cooler. Finally, the time, location, depth, sample number, and collection number are logged.

The next step is to prepare a chlorophyll sample, and this is done with another process. In order to increase accuracy, two-200 ml samples are filtered through a small pad that is connected to a vacuum system. The water passes through the filter and is discarded, but the dissolved chlorophyll stays behind. Both small filters are placed into one vial, and the vial is stored in a liquid nitrogen container on deck. Then the samples are logged.

At some of our stations we have collected dissolved CO2 samples. This measure is also an important measure of ocean health, because CO2 is important to the photosynthetic processes that many reef organisms require. To collect a CO2 sample, a sterile flask is filled to the top with seawater, and 2 microliters of Mercury Chloride (HgCl2) are added. These samples are also logged.

This entire process gets repeated for each depth of water that was brought up in the tubes on the CTD. In the end, a whole lot of lab methods are practiced in a very short amount of time. You can imagine that as the week has gone on, these tasks have become easier and easier. At first, we were running stations about every half an hour, and the seas were quite rough. The amount of work to do in short intervals was a little bit overwhelming, but Cheryl let us all know that is would get easier as the week went on, and we she was right! As I finish up this log and we steam from the Tortugas back to the Keys I am looking forward to perfecting my CTD technique before we finish off the week!

Personal Log

It’s been really inspiring to get to know more about the people I am working with. Everyone here is very passionate about the work they are doing, and it is clear that if it weren’t for the love of the job they wouldn’t be out here bobbing around in the ocean! It is also interesting to hear about the different routes that people have taken to get here. This morning during breakfast I had the chance to talk at length with Cheryl about her recent Peace Corps experience. She was sent to the South Pacific island nation of Vanuatu for 27 months to do environmental work and to help facilitate a bank that was going to make micro-loans to women in business. When she got there, plans changed, and she ended up living on a small island called Paama. The island was 2 miles x 7 miles and has 21 villages spread around the coast. What had been an environmental mission turned into an educational one, and she ultimately spent her time on Paama rebuilding a primary school that had been destroyed by a cyclone. She had a canoe specially built for her so she could move about roadless island, and while on Paama she had to adapt to the lifestyle that sounds a lot like backcountry camping to me! Ultimately she had to jump islands on small planes, bargain with shipping captains and work with the entire community to get the school completed.

As I listened to Cheryl tell her story, enthralled by the adventure and romance of her experience, I was reminded of how lucky we are in America to have the education system that we have. It is my hope for my students and colleagues that you all really take advantage of the resources, facilities, and especially the technology what we probably take for granted at times. As I learn more about the future of oceanography I have been especially interested in the direction it is moving, toward space. As more and more remote sensing capabilities are developed, the need for ground proofing will also increase. What is clear to me is that oceanography, like all fields of science, will require dedicated researchers who are passionate about their work and skilled in technology, math, and engineering. There is only one place to get these skills, and its at school, and it requires practice, time, and patience. Thanks to Cheryl’s work, students in that small village on the coast of Paama are able to work toward their education. I challenge everyone at Heights Middle School, myself included, to do their personal best to taking advantage of all of the resources we have in order that our students will become the problem solvers of tomorrow!

I’ll keep posting pictures when I can, and I’m excited to come back to school on Monday!

Here is a shot from the CTD monitor inside the ship. The operator can see what is going on on deck, and follow the ater parameters at the same time.

CTD Monitor inside the ship
CTD Monitor inside the ship

In this shot Cheryl and I are preparing to Launch the CTD. I am signaling the winch operator.

Launching the CTD
Launching the CTD

Another shot of the fantail, and you can see the CTD controlled by a cable via the A-frame.


Here is the CTD collecting a surface sample.

Collecting a Surface Sample
Collecting a Surface Sample

Here I am in the process of collecting water out of a Niskin bottle, so that I can take it inside for preparation. Notice the instrumentation on the bottom of the CTD.

Collecting Water
Collecting Water out of a Niskin bottle

Here is a shot of Cheryl getting started in the lab on the sample preparation.

Sample Preparation
Sample Preparation

I like this shot, it shows a clean filter pad and a ‘dirty’ one. The pad attached to the vacuum has just finished filtering 200 ml of seawater. The materials on the pad will be analyzed back in Cheryl’s lab on land.

Filter Pads
Filter Pads

Here is a shot of Nelson Melo. He has been operating the CTD during the day, and he is holding a graph that charted Chlorophyll, temperature, O2, and salinity. This CTD was launched to a depth of 340 m.

Nelson Melo
Nelson Melo

Nelson’s work (which I described in my Tuesday log) and the data Cheryl pulls out of the samples we’ve collected will help to refine scientist’s capabilities for remote sensing in oceanography. I think its pretty significant that the latest issue of the scientific journal

Oceanography Journal
Oceanography Journal

Oceanography has a satellite on it. This is the direction that ocean science has headed!

Nice Sunset! Almost as good as our New Mexico sunsets!


Wesley Struble, 19 July, 2010

NOAA Teacher at Sea
Wes Struble
Onboard NOAA Ship Ka’imimoana
July 8 – August 10, 2010

Mission: Tropical Atmosphere Ocean (TAO) cruise
Geographical area of cruise: Equatorial Pacific: 110 deg W Longitude to 95 deg W Longitude
Date: Monday, 19 July 2010

Weather Data from the Bridge
Cloud Cover: 5/8, Cloud Type” Cumulus,
Visibility: 10 Nautical miles,
Wind bearing: 150 degrees,
Wind speed: 20 knots,
Wave height: 2 – 3 feet,
Swell height: 6 -7 feet,
Atmospheric pressure: 1015.5 mb,
Temperature: 24.5 degrees C (76.1 degrees F)
Current Position: 2 degrees North Latitude, 110 degrees West Longitude

Science and Technology Log

I recently had the opportunity to spend some time talking with Senior Survey Technician (SST), Tonya Watson. Tonya was a Cold War Ocean Systems Technician for four and half years in the US Navy, worked for six years at the California State Dept of Water Resources in the benthic macro invertebrate lab and water quality lab, and has been a civilian Wage Mariner in NOAA for six and a half years both on the Hydrographic vessel Rainier and on the Ka’imimoana (KA). She has an Associates of Science degree from Shasta College and triumphs people who have to rely on work experience without the benefit of four year degrees. Her primary responsibility is running the CTD (Conductivity, Temperature, and Density/Depth) sensor array.

Senior Survey Tech, Tonya Watson

Collecting data from the CTD involves lowering a large cylindrical aluminum frame (about 5 feet high and 5 feet in diameter) to a predetermined depth, typically 1000 or 3000 meters (0.6 miles or 1.9 miles), into the sea and slowly retrieving it to the surface, thus creating a classic temperature salinity profile on the way down and collecting water samples for salinity processing on the way up. A typical 3000 meter run takes about 4 hours from start to finish and the CTD is generally deployed at each buoy station and at a number of intermediate latitude coordinates.

Above: The CTD; Right: An open Niskin bottle

The platform has numerous points onto which a variety of sensors and ballast may be secured, such as other current profiling sensors like an ADCP (Acoustic Doppler Current Profiler), or varied optics. The SST monitors the operation of the sensors (when the sensors are actually operating and collecting data) and handles tag lines (lines that control the horizontal position of the CTD) during the deployment and retrieval of the CTD package and communicates via radio with a winch operator who operates a “J” Frame winch from a control station located directly above the Survey Operations room. While the CTD is being deployed, a NOAA Corps conning officer is navigating the ship from a remote helm called the Bridge Wing. This location permits the officer to observe the deployment and attempt to hold the ship as stable as possible using only rudder maneuvering by watching the angle of the CTD cable entering the water. The conning officer has to be paying close attention to the wind direction and local ocean currents – anything that will affect the position and motion of the vessel, in order to avoid having the package get fouled under the boat or in the screws. The whole operation can be likened to a musical trio – each playing a different instrument but working to play in harmony to complement one another and complete the piece of music: The conning officer stabilizing the ship, the hoist operator raising and lowering the CTD, and the SST monitoring and operating the sensors, while all three continuously communicate back and forth. It is a fine example of effective team work.

Crewmember, Francine Grains, operating the J-hooist during the CTD deployment
NOAA Corps Officer, Sarah Slaughter, at the starboard bridge wing during the CTD deployment

The CTD also has the ability to collect water samples during the retrieval phase of operation. The sensors send back a continuous stream of data during the entire round trip measuring the conductivity, the temperature, and the density (depth) of the sea water. In addition, there are a number of 5L water sampling bottles (called Niskin Bottles) secured to the CTD platform that can be remotely triggered to close bringing water samples back from specific depths (they are left open on the way down to avoid being crushed by the immense pressure). These water samples are analyzed in the KA’s wet lab for salinity (concentration of salt) in an Autosal.

The results from the lab work are then compared to the CTD conductivity data log for the same depth. Because there is a direct mathematical relationship between electrical conductivity and salt concentration, this procedure compares the two outcomes looking for a high level of precision (an effective way to verifying the accuracy of the electronic data). Also, an important historical database can be created for an area of the ocean not often accessible to many scientists, which can show trends in temperature and salinity.

Lowering the CTD

Once the data is collected the SST uses various software to put the file into a more readable and easier to use format, and distributed via DVD and ftp upload to the various organizations referred to as “”customers. These customers are other government institutions (both US and foreign), universities, or even other research organizations. In addition, much of this data is available online to the general public for those that are interested. Besides the typical CTD measurements that are made during a standard run other instruments can be mounted on the CTD platform. For example, sensors that measure water clarity (transmissometer), dissolved carbon dioxide concentration, dissolved oxygen concentration, and more can be added to the frame.

Personal Log

The first buoy we reached was at 8 deg N, 110 deg W Longitude. There were no problems with this buoy so this visit was simply for a visual inspection and this we accomplished by making several passes circling around it. Since this buoy is moored in French territorial waters (it is not far from the Clipperton Islands, which is owned by France) we had to obtain permission from the French government to be able to do more than cruise straight by the buoy. We did not receive that permission until the morning of the day we were scheduled to reach the buoy. During this time a number of the crew members put fishing lines out off the fantail (the extreme stern) of the ship. The buoys appear to attract various small fish which of course attract bigger fish and so on up the food chain. In a short time they had caught four nice size (3 – 4 feet long) Mahi mahi (also known as the Dolphin Fish). I assume we will be having a fish dinner sometime very soon. After the inspection we ran a CTD to 3000 meters that did not finish until quite late at night.

The 8 deg North, 110 deg West, TAO Buoy
Crew member Dana Mancinelli with her Mahi mahi

Animals Seen

I already mentioned that we caught a number of Mahi mahi during the day but during the evening CTD run we had a real treat. Normally a large powerful spotlight is pointed at the water’s surface where the CTD is placed into and removed from the water. During this evening run I joined several of the science members of the crew on deck at the ship’s railing watching squid drawn to the bright spotlight in the water. At times we saw 6 or 7 squid at a time near the surface. They appeared a pinkish red color and were up to approximately a foot long or so. After a while we spied a shadowy figure swimming around and when it came close to the surface we realized it was a small shark no doubt drawn by either the light or the prospects of an evening meal.

Justin Czarka, August 9-10, 2009

NOAA Teacher at Sea
Justin Czarka
Onboard NOAA Ship McArthur II 
August 10 – 19, 2009 

Mission: Hydrographic and Plankton Survey
Geographical area of cruise: North Pacific Ocean from San Francisco, CA to Seattle, WA
Dates: August 9-10, 2009

Weather data from the Bridge

Sunrise: 6:26 a.m.
Sunset: 20:03 (8:03 p.m)
Weather: fog Sky: partly to mostly cloudy
Wind speed: 15 knots
Wind direction: North
Visibility: less than 1 nautical mile (nm)
Waves: 9 feet

Science and Technology Log 

August 9 was a day for getting all the science gear aboard.  In order to conduct a research cruise at sea, you have to plan and pack all the materials you envision needing beforehand.  Once out at sea, there is nowhere to stop and pick up additional supplies.  Bill Peterson, the chief scientist from NOAA/ Northwest Fisheries Science Center (NWFSC), and another member of the science team,

The McArthur II at port in San Francisco prior to the cruise. She is 224 feet long with a breadth (width) of 43 feet.
The McArthur II at port in San Francisco prior to the cruise. She is 224 feet long with a breadth (width) of 43 feet.

Toby Auth out of Oregon State University, Hatfield Marine Science Center (HMSC), up all the science equipment onto the deck of the McArthur. Some of the equipment we hauled onto the ship included bongo frames and bongo nets (used to collect specimen samples in the ocean), Niskin bottles (to collect water samples in the water column at various depths), dissecting microscopes, a fluorometer (to measure the amount of phytoplankton in the water), and crate after crate of sample jars.

In order to transfer all of the science equipment onto the McArthur II we laid out a cargo net flat on the pier that the crane dropped to us.  Then we hauled the equipment from the truck and placed it on the cargo net.  Next the cargo net holds were attached to the crane, which lifted the materials onto the deck of the ship. We unpacked the cargo net, conducted additional cargo lifts, and then stored all the equipment in the labs.  Using the crane sure beat hauling up all the equipment by hand!  The scientists have to get all the equipment placed in the labs, which is a lot of work.  I helped one of the scientists, Tracy Shaw, who studies zooplankton, set up the dissection microscope by securing it to the table.  On dry land, tables will not move around, but we had to tie it down to prepare for any possible rough seas.

This is me working to prepare the CTD for a practice launch in San Francisco Bay. We made sure that the Niskin bottle seals were in working condition.
This is me working to prepare the CTD for a practice launch in San Francisco Bay. We made sure that the Niskin bottle seals were in working condition.

August 10 we were to set sail in the morning. That has been changed until this afternoon, which gives the science team time to prepare some of the equipment before heading out to sea, along with conducting emergency drills and briefings. This morning the science team and NOAA crew worked together to prepare the Conductivity, Temperature, and Depth (CTD) probe. This involved cleaning the Niskin bottles and replacing cracked O-rings to ensure a secure seal around the bottle openings. If the bottles are not sealed properly, water and air (upon reaching the surface) can enter the bottle from the water column at an undesired location.  We also ensured that the lids close tightly, providing a vacuum seal.

Personal Log 

Living and working on a boat will be a new experience for me.  There are many unknowns in the process, but it is exciting to be learning something new nearly every minute.  I took a walk around the ship’s interior this afternoon, amazed by how much space is contained inside the McArthur II. The staterooms (where one sleeps) are large, containing a desk and a lounge chair.  They also have a sink, with a bathroom that is shared by the adjoining stateroom. The McArthur also has a fitness room for staying fit at sea, along with a lounge to for relaxing with movies, books, and even espresso!  The McArthur II surely will be home for the next nine or ten days.

I have been most impressed with the welcome I have received from both the NOAA crew and the scientists from NOAA, Oregon State University, the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) and the U.S. Coast Guard.  Everyone is friendly, helpful, and full of cooperation. It is encouraging to observe the teamwork between people.  I appreciate having the opportunity to learn alongside the scientists and crew.  Being a teacher, I am used to being the one with the knowledge to impart or the activity to do.  It is exciting being aboard because now I am the student, eager to take notes, ask questions, and learn from those alongside me.  I have to say, each person has been an effective teacher!  So we are off to Bodega Bay for our first sampling and there’s a rumor going around that a Wii Fit competition might be getting under way!

Today’s Vocabulary 

Transect line- when conducting research at a predetermined latitude or longitude and continue to collect data samples along that line Niskin bottles- these containers have openings on both the top and bottom.  As it drops through the water column it fills with water.  At a predetermined depth both ends close, capturing water from that specific depth inside the bottle that can be brought back to the surface and analyzed. Water Column- a vertical section of water where sampling occurs

Scott Donnelly, April 24, 2008

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 24, 2008

Water collection from Niskin bottles
Water collection from Niskin bottles

Weather Data from the Bridge 
Sunrise: 0620 Sunset: 2010
Wind: 10 kts
Seas: 2 ft
Light rain showers possible

Science and Technology Log 

As forecasted for Wednesday night the turbulent seas have calmed and the howling winds coming from all directions have subsided. On occasion a large wave smashes into the ship broadside. But, for the most part, it seems like the storm has moved onto land. Sampling operations restarted around 2000 (8pm) last night. This morning from 0100 to 0500 is my sixth 4-hour shift. Today nearshore and offshore CTD and biological sampling continues at different longitudes 124O29’W to 125O15’W but constant latitude 43O07’N. This is called a longitudinal sampling survey. The latitude and longitude coordinates align with the westward flow of water from Coos Bay estuary in Coos Bay, OR. Along these coordinates CTD deployment will reach depths as shallow as 50m (164ft) to as deep as ~2,800m (~9,200ft)! Round-trip CTD measurements will take more time due to progressively greater depths with increasing distance from the OR coast. On my morning shift we collected samples at two stations. At the second station 30 miles from the coast the CTD was deployed to a depth of 600m (1,970 feet).

Monitoring CTD data
Monitoring CTD data

During Thursday’s afternoon shift (my seventh 4-hour shift) the CTD was lowered to a  depth of ~2,700m (~8,860 feet) located 50 miles from the coast. At this distance out at  sea, the coastal landmass drops below the horizon due to the curvature of the earth and the up and down wave action. The round-trip CTD deployment and retrieval to such great depths take about two hours to complete. The dissolved oxygen (DO) probe measurements indicate a secondary DO layer in deep water.  So how are the continuous data measured by the CTD organized? What are the trends in data? In science graphs are used to organize numerical data into a visual representation that’s easier to analyze and to see trends. Below is a representative drawing of how CTD and wet lab data are organized and presented in the same visual space. Note the generous use of colors to focus the eyes and show the differences in data trends.

Screen shot 2013-04-20 at 4.55.48 AMWhat are some trends that can be inferred from the graph above? First, with increasing depth, seawater becomes colder (maroon line) until below a certain depth the water temperature is more or less at a constant or uniformly cold temperature (compared to the surface). Second, the amount of dissolved oxygen (DO) in seawater (green line) is greatest near the surface and decreases, at first slightly then abruptly, with increasing depth below the surface. Third, salinity (red line), which is directly related to conductivity, increases with increasing depth. Furthermore, in general seawater pH (blue line) becomes more acidic (and conversely, less basic) with increasing depth. Last, marine photosynthetic activity as measured by chlorophyll a in phytoplankton (purple line) is limited to the ocean’s upper water column called the photic zone. Below this depth, sunlight’s penetrating ability in seawater is significantly reduced below levels for photosynthesis to be carried out efficiently and without a great expense of energy.

The consistently low (acidic) pH measurements of deep water collected by the Niskin bottles and analyzed on deck in the wet lab are a concern since calcium carbonate (CaCO3) solubility is pH dependent. On this cruise the pH measurements between surface and deep waters show a difference of two orders of magnitude or a 100 fold difference. Roughly, pH = 8 for surface water versus pH = 6 for deep water offshore. This difference in two pH units (ΔpH = 2) is considerable as it indicates that the deep water samples are 100 times more acidic than the surface water. pH is a logarithmic base ten relationship, i.e. pH  = -log [acid] where the brackets indicate the concentration of acid present in a seawater sample. A mathematical difference in two pH units (ΔpH = 2) translates into a 100 fold (10ΔpH = 102) difference in acid concentration. Refer to the Saturday, April 19 log for a discussion concerning the importance of CaCO3 in the marine environment and the net acidification of seawater.

Personal Log 

Screen shot 2013-04-20 at 4.56.10 AMAfter the morning shift but before a hearty breakfast of eggs, hashed browns, sausage, bacon, and juice, I hung out on the ship’s port side to watch the sunrise, a memorable mix of red, yellow, and orange painting the sky. It was one of the best sunrises I remember and that’s saying a lot since I live in southern Arizona, where the sunrises and sunsets are the stuff of legends. With the low pressure system having moved over land, the sea was calm and the temperature considerably warmer with no clouds positioned between it and the ocean.  Perhaps surprisingly, I haven’t sighted a whale or a whale spout, even in shallower, more nutrient-rich coastal waters. It’s not that I haven’t looked as each day I’ve visited the flying bridge (observation deck) above the operations bridge enjoying the immensity of the vast Pacific.

A flock of albatross have begun following the ship I suspect in hopes of getting a fish meal, mistakenly thinking that the McARTHUR II is a trawler.  I saw trash, which I couldn’t identify without binoculars, floating on the surface. Sadly, even the vast, deep oceans and its inhabitants are not immune from humanity’s detritus. The history of humanity and its civilizations are intimately linked to the world’s oceans. This will not change. Humanity’s future as well is linked to its maritime heritage. The oceans have fed us well and have unselfishly given its resources without complaint.  Perhaps it’s time we return the compliment and lessen our impact.


Scott Donnelly, April 22, 2008

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 22, 2008

Weather Data from the Bridge 
Sunrise: 0620 Sunset: 2010
Wind: 10 kts, 25 kts gusts
Seas: 4-7 ft
Rain showers possible

Open Niskin bottles on CTD platform
Open Niskin bottles on CTD platform

Science and Technology Log 

What’s the significance of the NH Line (Newport Hydrographic, 44O39’N)? Water and biotic data acquisition at the NH Line began over 40 years ago. The NH Line then is significant on account of the long-term historical sample collection and data sets that it provides. Consequently, temporal (time) comparisons involving water and biotic data can be made over decades as opposed to shorter lengths of time such as years or months. It’s my understanding that nearshore and offshore sampling along the Oregon Continental Shelf (OCS) always includes the NH Line. My second 4-hour shift began at 0100 and ended shortly after 0500. Regardless of time of day each shift sets up and collects water samples from each of the twelve Niskin bottles on the CTD rosette. Typically, three water samples are collected at a particular depth. How does remote sub-surface water sampling work? When the CTD is deployed from the ship’s fantail, initially the top and bottom lids on all twelve Niskin bottles are open as shown in the photo below.

The CTD is lowered into the water and once the desired depth is reached the requisite number of Niskin bottles are closed electronically from the ship by whoever is in the control room. For my shift it’s team leader Ali Helms. After that is done, the CTD then is lowered or raised to another depth where another “firing” takes place and more water samples at a different depth are collected. When sampling is complete, the CTD is raised to the surface and onto the ship where it is secured to the fantail deck. The water in each Niskin bottle is collected and taken to the ship’s wet lab where each water sample collected at a particular depth is analyzed for other water quality parameters not measured by the CTD.

YSI datalogger
YSI datalogger

Other water parameters measured on this cruise in the wet lab include: total dissolved solids (TDS), pH, and turbidity (how transparent, or conversely cloudy, is the water). A YSI 6600 datalogger interfaced with a multi-sensor water quality probe (sonde) is used to measure the aforementioned water parameters. See photos below. The CTD and Niskin bottles then are hosed down with freshwater and reset for the next sampling site.  After the CTD is reset for the next sampling site, then it’s time to collect biotic samples from the surface and at different depths. Biological sampling always follows a CTD cast. On this cruise biological sampling is carried out on the ship’s starboard side just fore of the fantail. Collection of marine invertebrate (boneless) organisms uses nets that vary in size, shape, density of net mesh (number of threads per inch), and volume of detachable sample collection container (called a cod end). Sampling nets are conical in shape and typically are made from Dacron or nylon threads that are woven in a consistent, interlocking pattern. Each specifically designed net is attached to a wire cable and deployed from the starboard side. If collection/sampling is done below the water’s surface (also called sub-surface), a weight is attached to the net’s metal frame.  A bongo net is an example of a net used for the collection of invertebrate marine organisms at some defined depth below the surface (see photos below).

Multi-sensor water sonde
Multi-sensor water sonde

A bongo net collects organisms by water flowing into the net, which is parallel or horizontal to the water surface at some depth below the surface. Consequently, use of a bongo net requires that the ship moves forward. Deployment of a bongo net requires the use of trigonometry, a favorite math course of mine in high school a long time ago. The length of cable let out by the NOAA deckhand operating the winch with cable does not equal the depth that the bongo net is lowered below the surface. (This would be true if the net was simply dropped straight down over the side of the ship.) Let’s use the drawing below to illustrate this.

Suppose sample collection is to be done at 100m (328 feet) below the water’s surface. More than 100m of cable needs to be let out in order to lower the bongo net to 100m below the water’s surface. How much cable beyond 100m is let out (x) depends on the angle (θ) of the net (and hence cable) to the water’s surface. The angle θ is measured by a protractor attached to the cable and pulley at the position identified with the blue star in the drawing. The angle θ in turn depends on the ship’s forward speed. To calculate the length of cable that needs to be let out, the following trigonometric formula involving right triangles is used: sin θ = cos-1θ = 100mx. The calculated value x is communicated to the NOAA deckhand, who controls the winch that lets out the desired length of cable. When this cable length is reached, retrieval of the bongo net begins.

Duel sampling bongo nets ready for retrieval
Duel sampling bongo nets ready for retrieval

The volume of water that contains the marine organisms and that flows through the bongo net is recorded by a torpedo-shaped rotary flowmeter (left photo below), which is suspended by wires or thick fishing line in the middle of the net’s mouth. As water moves past the meter’s end, it smacks into and transfers its momentum to the flowmeter’s propeller, which rotates or spins. The propeller’s shaft in turn is linked to a mechanical counter inside the meter’s body (right photo below). A complete revolution of the propeller equates to a certain number of counts and that is related to a certain volume of water that has flowed past the meter.  The mathematical difference between the two numbers recorded before the net’s deployment and after the net’s retrieval is plugged into a mathematical formula to obtain the estimated total volume of water that flowed through the net’s mouth during the time of collection. Consequently, the weight or number of biomass collected by the net can be related to the volume of water in which the biomass was found. This gives an idea about the density of biomass (weight or number of biomass units per volume seawater, g/m3) in a horizontal column of seawater at a given depth and site. In tomorrow’s log I’ll talk about what marine organisms a bongo net collects (including photos) and also discuss and describe the three other nets used on this cruise to collect marine invertebrates.

Mechanical counter in flowmeter
Mechanical counter in flowmeter

Personal Log 

So far after one full day at sea, I haven’t experienced any indications of sea sickness in spite of rough seas (see weather forecast at beginning of log). Four other science team members haven’t been as fortunate. I didn’t witness any visible bioluminescent surface events on the early morning shift (0100 to 0500). I walked to the ship’s bow since this would likely be the best place to witness bioluminescence given all the agitation of seawater there. I left a bit disappointed but there are still five days remaining. The CTD and both the DO and chlorophyll probes (sensors) operated without any problems.

Bob and I communicate well and have similar personalities and intellectual interests. Before carrying out a task we discuss how it’s to be done and then agree to do it as discussed and in the order discussed. Communication is critical because when sampling for biological organisms for example, the nets have large, heavy weights attached so once the net is lifted from the ship’s deck for deployment the weight is airborne so to speak and free to move without resistance. Getting clobbered in the head or chest obviously would not be pleasant. The bongo net uses a 75 pound weight and the net’s solid metal frame must weigh another 25 pounds. Caution and paying attention are paramount once 100 pounds are lifted from the deck, suspended from a cable free to move about with the rolling and pitching of the ship with only air providing any sort of resistance against its movement.

 Rotary flowmeter
Rotary flowmeter

Bob and I have delegated certain tasks between us. We agreed that when a net is deployed, he will always control the net’s upper halve where the net’s “mouth” and weight are located; I in turn will control the net’s bottom halve where the netting and sample containers or cod ends are located. When the net is ready to be lifted from the sea and returned to the ship’s deck, the tasks for retrieval are the same as for deployment, though in reverse order from deployment. Before the net is lifted shipboard, it’s washed or rinsed top to bottom with seawater from a garden hose that gets seawater pumped directly from the Pacific. Washing is necessary because the collected marine organisms adhere to the net’s mesh so in order to get them into the sample container (cod end) at net’s end they must be “forced” down into the cod end. Once the net is shipboard, the cod end and collected organisms are emptied into a sample jar, sample preservative is added, and the container is labeled appropriately.

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