Caitlin Thompson: Zooplankton, Ocean Currents, and Wave Gliders, August 7, 2011

NOAA Teacher at Sea
Caitlin Thompson
Aboard NOAA Ship Bell M. Shimada
August 1 — 14, 2011

Mission: Pacific Hake Survey
Geographical Area: Pacific Ocean off the Oregon and Washington Coasts
Date: August 7, 2011

Weather Data from the Bridge
Lat. 47 degrees, 00.8N
Long. 124 degrees, 29.8W
Present weather: Cldy 8/8
Visibility: 10 n.m.
Wind direction: 323
Wind speed: 08 kts
Sea wave height: 1 feet
Swell waves – direction: —
Swell waves – height: —
Sea water temperature: 13.7 degrees C
Sea level pressure: 1018.8 mb
Temperature – dry bulb: 15.8 degrees C
Temperature – wet bulb:  14.7 degrees C

Science and Technology Log

On the fish deck in my work clothes

On the fish deck in my work clothes

The Shimada conducts research around the clock, with crew members working twelve-hour shifts. So far, I have worked with the acoustics team studying hake during the day, when the hake school together and are easy to fish. Last night I branched out, staying up with Steve Pierce, the oceanographer studying ocean currents, Jennifer Fisher, a faculty assistant at Oregon State University (OSU) who is studying zooplankton, and her intern, Angie Johnson, a graduate student at OSU. All the different research on this trip complements each other, and I learned more about the acoustic team’s work from the night people.

Gray's Harbor Transects

Gray's Harbor Transects

The map at right shows the transects we follow and the stations that the night team takes samples, which Steve chooses. Just like the acoustics team, he only chooses sites on the east-west transects. The night team usually works one transect ahead of the day team, and must have the ship back where they started by sun-up. Steve is mapping small currents because, he says, surprisingly little is known about ocean currents, even though they have a tremendous impact on ocean life.

He is especially interested in the polar undercurrent that brings nutrient-rich water from the south up along the west coast. A small current, it is nonetheless important because of the nutrients it carries, which come to the surface through upwelling. He uses an acoustic device, the Acoustic Doppler Current Profile (ADCP), to find the velocity of the water at various depths. The data from the ADCP is skewed by many factors, especially the velocity of the ship. Later, Steve will use trigonometry to calculate the true velocity. He also uses the Conductivity, Temperature, Depth (CTD) meter, lowered into the water at every station during the night. The CTD gives much more information than its name would suggest, including salinity, density, and oxygen. It is deployed with a high-speed camera and holds bottles to capture water samples. I was impressed by the amount of work – and math! – that Steve does in between cruises. When he has down time on this cruise, he told me, he is calculating work from two years ago.

Jennifer divides a sample in the Folsom plankton splitter

Jennifer divides a sample in the Folsom plankton splitter

Jennifer and Angie are studying plankton, the organisms at the very bottom of the food web. Immediately, I recognized euphausiids, or krill, from the contents of hake stomachs. Actually I recognized their small black eyes, which always reminded me of poppy seeds when I saw them in hake stomachs. Jennifer is conducting this work through her group Northwest Fisheries Science Center, which, as she describes it, gives her a wonderful freedom to research different projects related to ocean conditions, especially salmon returns. In this project, they measuring phytoplankton, tiny, photosynthetic organisms, by measuring chlorophyll and nutrients. They are also looking at zooplankton, like euphausiids, salps, and crab larvae, which we examined other the microscope. To help the acoustics team refine their ability to use sonar to identify zooplankton, Jennifer and Angie record certain species. The acoustics team will match up the acoustics data that is continuously generated on this ship with the samples.


Angie takes water samples from the CTD.

Today, the second catch of the day was aborted because of whales too close to the ship. However, the NOAA’s Pacific Marine Environmental Laboratory (PMEL), had asked the Shimada to investigate its waveglider. A waveglider is type of robot called an autonomous underwater vehicle (AUV). Programmed to travel and record data, it does not need an operator. The PMEL folks were concerned, however, that its AUV might have a problem.The bridge set the course for the AUV, described as a yellow surfboard, and I headed up to the flying deck, the highest deck and an ideal spot for observation, to watch for it. Immediately we saw a humpback whale, just starboard of the ship, spout and roll through the water, its tail raised in the air. Soon the AUV appeared. We saw nothing wrong with it but communicated our observations, photographs, and video tape of it to PMEL. The PMEL’s system of wavegliders monitor carbon dioxide levels and use the kinetic energy of ocean waves to recharge the batteries. The acoustics team hopes to get their own waveglider next year to collect acoustic data in between transects. As I was peering  over the edge of the boat, examining the surfboard-like robot below, I heard a loud splash. A bout ten  Dall’s porpoises were playing around the bow of our boat, rippling in and out of the water. Dall’s porpoises are tremendously playful creatures, and will often play around ships. But our ship was barely moving, and the porpoises soon lost interest and swam away.

Wave Glider

Wave Glider, seen from above

Personal Log

I’m getting a little of everything on this cruise. I would have stayed up two nights ago for the deploymentof the CTD and zooplankton samples, but the propeller developed a loud enough whamming sound to suspend all operations indefinitely. I woke up at 4:00 AM yesterday because the boat was swaying back and forth violently. (Violently by my standards, that is; more experienced mariners insist the swell is nothing.) Since our bunks go port to starboard, I could feel my weight sliding from hip to head to hip to head as I was rocked back and forth in bed. Meanwhile a discarded lightbulb in a metal shelf was rolling back and forth steadily – rattle-rattle-WACK! rattle-rattle-WACK! – until Shelby Herber, a student at Western University and my roommate, got up, found the culprit, and wrapped it in a shirt. When I woke again, it was eleven hours after the discovery of the problem with the prop and well past breakfast, and I started to get up until Shelby told me we were off transect, headed to shore because of the propeller.

Wave Glider

Wave Glider from beneath the water, taken from PMEL's website

So we took our time getting up. But when I finally arrived in the acoustics lab, Rebecca was running up the hall, saying, “Caitlin, I was looking for you! There’s a great big shark outside, and we’re pulling up the ROV!” The ROV is the remotely controlled vehicle, a robot like the AUV, but one that requires an operator to make it move. Unfortunately, out on the fish deck, the ROV was being put away and the shark gone off on his fishy business. To console me, John had the videotaped footage from the ROV and the dorsal fin of the shark, and showed me both. The ROV revealed no damage and I was invited down to the winch room, where the bang-bang-bang coming from the propeller was unnerving.


Puzzled birds approach the ROV

Everyone was in an uproar trying to decide what to do, an uproar made all the more dramatic by the steady lurching and swaying of the ship, which throughout the day has sent most of the scientists to their room for at least a few hours and most of the deck hands to tell stories of unhappy tourists who couldn’t find their sea legs. Finally, the engine guys decided the warped propeller would not prevent us from getting to Port Angeles, and Rebecca decided it would not interfere with the acoustics, and we got back on transect.



I’m getting a little bit of everything on this cruise. I’ve seen sharks and marines mammals, calm seas and rockier seas, an impressively well-functioning ship and a number of technological problems. I’ve interviewed scientists, NOAA Corps officers who command the ship, and crew members who recount endless adventures at sea. I’m even signed up for the cribbage tournament, which I’m not entirely thrilled about since I don’t know how to play bridge. I’ve been impressed by how much time and information everyone seems to have for me. I am constantly thinking how I can bring this experience back to my students. Some ideas are to have a science and math career day, collect weather data like the data the bridge collects, dissect hake, and examine zooplankton under a microscope. Various people on board have volunteered to help with all my ideas.

Heather Diaz, July 15, 2006

NOAA Teacher at Sea
Heather Diaz
Onboard NOAA Ship David Starr Jordan
July 6 – 15, 2006

Mission: Juvenile Shark Abundance Survey
Geographical Area: U.S. West Coast
Date: July 15, 2006

Science and Technology Log 

They did a swordfish set last night around midnight.  We hauled in the set around 5:30am. We caught 4 blues and 2 makos.  We also caught one pelagic ray.  They set a shark line out around 7:45. We were hoping to be able to finish one last set before going into port. We were scheduled to be in port around 3.

Teacher at Sea, Heather Diaz, holds up a Blue shark.

Teacher at Sea, Heather Diaz, holds up a Blue shark.

Dr. Russ Vetter explained what the different computers are used for in the aft lab.  There is one called at EK500/EQ50 which uses a split beam transponder to create a “map” of the ocean floor, so the scientists can use the data to find high spots, which sometimes are better for fishing. It also works as a sort of “fish finder” and the different things in the water show up in scale and color, so that you can see the approximate size of the animal/plant in the water.  He also explained the Navigation computer, which digitally shows the charts (with soundings), topographical features (like islands and coastline), and our course. It also provides information on other vessels that are nearby, and when available, that vessel’s name and number…the same navigation computer they also use on the Bridge. The Nav. Comp. also provides information like our latitude and longitude and our speed.

There is another computer which monitors wind speed and direction, temperature of the water (under the boat), barometric pressure, and salinity of the water.  All of these are real-time, and provide important information to the scientists.  There is also an ADCP (Acoustic Doppler Current Profiler) computer which displays a constantly changing graph of current velocity relative to the ref layer.

The very last set of this leg was a bit slower than most, which may have been a good thing, since most people were starting to get a bit tired.  We had 2 blues and 2 makos. We were very pleased to find out that we had, during the entire leg, managed to capture 80 blue sharks (78 were measured, sexed, and released), 63 mako sharks (61 were tagged and released), 23 pelagic rays (23 were released, none were tagged), 3 molas (3 were tagged and released), and 1 lancetfish (which was released but not tagged).  Everyone seemed very pleased with the results, and now Dr. Suzy Kohin (Chief Scientist) and Dr. Heidi Dewar will head back to their lab at Southwest Fisheries to analyze the data.

Personal Log 

Last night the sky was very clear, so we were able to see a lot of stars, including the Milky Way, which was very easy to see last night.  The view from the Flying Bridge (the very top of the ship) is amazing, and we felt like we could see every star in the universe, even though we know we couldn’t. We could also see the far away glow of Los Angeles, a reminder that we will soon be back in port and that our trip is nearly over.  Nearby, there was a large tanker and a container ship, which also looked neat in the dark.  The container ship was still nearby this morning when we woke up.

The sunset this morning was amazing.  There were a few wispy Cirrus clouds in the sky, which reflected the glow of the sun long before the sun made its first appearance in the sky. It was truly a beautiful sunrise, and a great way to start off our last day!  This morning after the set, everyone was a bit disappointed that we have not caught a swordfish this trip.  But, Dr. Heidi Dewar said she would consider doing another swordfish study in the future.

Everyone is busy packing and getting their gear ready to go home.  Everyone, including me, is excited to be going home to see family and friends, but I think most people will be a little sad, too. For me, this has been an absolutely amazing experience!  I have learned so much, and I have seen more in the past week than I ever could have from reading books or watching documentaries.  There is just something so special about being able to feed a sea lion, touch a shark, or come within inches of a mola to feel the power of nature and the beauty of the ocean. I am awe struck in so many ways.  The people aboard the DAVID STARR JORDAN could not have been kinder, and everyone has gone far out of their way to make me feel like part of the DSJ family.  Everyone from the captain and the officers, the boatswains, the stewards, and everyone in engineering has been friendly and helpful. I will surely miss everyone on board.  As for the scientists, they did an outstanding job of helping me to learn things and to make me feel like I was a real part of their crew. I will miss the lapping of the waves, the rolling of the ship, the camaraderie, the food, the animals, the scenery, the sunsets, and the sunsets.  And, although I cannot take any of them with me, I will have the memories of them all forever.

I want to sincerely thank Lieutenant Commander Von Saunder, the amazing crew of the DAVID STARR JORDAN, Dr. Suzy Kohin, and her wonderful team of scientists for a fantastic experience!  I never imagined it would be this incredible!  I will be grateful to you all for a long, long, long time!  Thank you for allowing me to share these past 10 days with you, and I wish you all safe travels and many more beautiful sunsets at sea to come!

Geoff Goodenow, May 7, 2004

NOAA Teacher at Sea
Geoff Goodenow
Onboard NOAA Ship Oscar Elton Sette

May 2 – 25, 2004

Mission: Swordfish Assessment Survey
Geographical Area:
Hawaiian Islands
May 7, 2004

Time: 1615
Lat: 18 41N
Long: 158 34W
Sky: scattered cumulus clouds; bright and sunny
Air temp: 26.6 C
Barometer: 1012.04
Wind: 87 degrees at knots 6.7 knots
Relative humidity: 50%
Sea temp: 26 C
Depth: 4558 m

Scientific and Technical Log

We left the shelter of the Kona coast and steamed all night toward Cross seamount arriving there between 0900 and 1000 hours. We trolled a couple lines across it for several hours but pulled in no fish. This is where we wanted to lay the line tonight, but in communicating with a fishing vessel in the area, that crew indicated they have 30 miles of line in the water now. Protocol, I presume, says it’s their place for now so we will respect that and go elsewhere.

Elsewhere is another seamount about 45 miles west and slightly north of Cross. But why are we hanging out at these things called seamounts? Rich (remember, chief scientist) explained to me that above seamounts are local currents called Taylor Columns that sort of swirl around above these features. Small fish tend to concentrate within these and, of course, that attracts the big boys. Cross is well known for that effect due to its shallowness (182 fathoms). The one we are going to is much deeper and consequently does not have as dramatic an impact as Cross.

Here is a bit about a couple tools that we are not using on this ship for this mission. One is called the Acoustic Doppler Current Profiler. It sends out a high frequency signal and allows determination of current direction and speed under the ship. Another is the CTD (conductivity, temperature and depth). This circular array of water sampling bottles is lowered into the water. Temperature and conductivity are monitored and recorded continuously as it moves through the water. On ascent, bottles can be triggered to close at specific depths thereby bringing water samples from different levels in the water column for further testing on board.

Personal Log

More about life on the ship:

There will be no shore time during this trip, but there are several forms of entertainment aboard. Just listening to crew members speak of other places and projects around the globe they have participated in on NOAA vessels is fascinating. There is a small work out room and a couple rooms where we can view videos/cds or watch TV. There is quite a library of viewing materials and books available. Some crew members have their own TVs and stereo equipment in their cabins. On the more mundane side, there is a laundry to do personal items and once a week stewards give us a change of linens and towels.

Communication with home:

We download and upload email three times per day: 0700, 1300, and 1900 hours. Phone calls can be made but they are expensive and generally reserved for emergencies. The ship’s total communications bill can run up to $10,000 per month. So far, a typical day for me has been something like this after breakfast (0700-0800): collect samples from longline catch, assist cleanup, cleanup self, lunch (1100-1200). Check emails, enter some notes to log until tiring of that, R&R (reading, snoozing on shaded deck, interview someone or observe their work) and help with any fish coming in on troll lines. Dinner (1630-1730), R&R, input to log, help set longline (2000 -2130), finish the day’s log and send to Washington (that makes me sound pretty important doesn’t it?), R&R, and to bed 2300-2400 hours.

Since we did not set a line last night and no fish came on by trolling today was kind of slow. I used the time to have a tour of the bridge by executive officer Sarah and electrical technician, John. It was very interesting to learn more about the ship’s scientific monitoring abilities (as briefly and incompletely described above), navigation and safety features for times of distress.

Crew assisted me to string my swordfish bills so to drag along behind us. This is done to get some of the flesh and oils out of them. I am told that this will take a week or more to accomplish.


Estimate the distance in miles between yesterday’s and today’s position (today at 2018 hours we are at Lat 18 53 N and Long 158.59 W).

What is a seamount?

Looking at the nautical chart on the bridge I can see the top of Cross seamount is at (a shallow) 182 fathoms. We are headed to one that is 406 fathoms. Between the two the chart shows a maximum depth of 2585 fathoms. What is the depth of the water over the seamounts and the deepest point between them in feet?