Mark Van Arsdale: Waking up Copepods, September 23, 2018

NOAA Teacher at Sea

Mark Van Arsdale

Aboard R/V Tiglax

September 11 – 26, 2018


Mission: Long Term Ecological Monitoring

Geographic Area of Cruise: North Gulf of Alaska

Date: September 23, 2018

Weather Data from the Bridge

Variable winds, partially cloudy, calm seas

60.20 N, 147.57 W (Prince William Sound)


Science Log

Waking Up Copepods

One of the scientists on board is interested in the life cycles of a particular species of Neocalanus copepod. Neocalanus is a remarkable looking copepod.  They have long antennae with feathered forks at the ends. They have striking red-orange stripes on their bodies and antennae that reminds you a bit of a candy cane. Neocalanus is an important copepod in the Gulf of Alaska ecosystem, and it typically makes up the largest portion of zooplankton biomass in the spring.

Neocalanus cristatus, photo credit Russ Hopcroft, UAF
Neocalanus cristatus, photo credit Russ Hopcroft, UAF

Its life cycle is interesting.  If zooplankton were cars, the Neocalanus might be a Toyota Prius.  It’s not fast or fancy, but it’s efficient.  Neocalanus copepods feast in the spring and early summer and then settle down several hundred meters below the surface to enter into a diapause state.  Diapause is a kind of dormancy that involves slowing basic metabolic functions to near zero.  It is a strategy used by other Alaskan arthropods, most notably mosquitos, to survive long winters.  As for why they travel deep into the water column, the answer seems to be that they use less energy in the dark, cold, high pressure waters at depth.  Inside the Neocalanus there is an unmistakable large, sausage shaped sack of oil that should provide the energy reserves needed to survive prolonged diapause.

When the Neocalanus females wake up, they have to restart their metabolism and begin meiotic development of their oocytes (egg cells.) They have previously mated and they store the male’s sperm within their bodies during diapause.  Each of these biological events involves turning on several dozen genes.  What our scientist wants to know is what genes get turned on, in what order, and what environmental clues tell the initial genes to start making RNA. To study all of this, she needs living copepods in diapause.  Our collection process inevitably wakes them up, but it gives her a time zero for observing this transformation.  For the next twelve hours, she separated and preserved copepods every hour for later genetic analysis that may give her insight into when genes turn on and in what order as the copepods wake up.

In order to get her copepods, the night team did a vertical Multi-net tow at four AM.  We dropped the Multi-net down to a depth of 740 meters. The work we were doing was sensitive, as she needed the copepods alive and undamaged.  I was glad to have slept a few hours as we were moving between sampling stations, because what came up in the tow was pretty amazing.  Along with the Neocalanus, there were many other types of zooplankton including the copepod MetridiaMetridia produce an intense bioluminescence when disturbed. When we brought the nets to the surface, the cod ends were glowing electric blue and individual copepods could be seen producing pinpricks of light that were remarkably bright.

Bioluminescence is ubiquitous amongst deep sea species.  Deep sea fishes, jellies, and plankton use it to attract prey, to camouflage their silhouette, to surprise and distract predators, and likely to communicate with members of the opposite sex.  The deep oceans make up 95% of biological habitat on Earth.  If you consider bioluminescence communication a kind of language, it may be the most commonly spoken language on the planet.

Luciferin production and luciferase transcription in the bioluminescent copepod Metridia lucens. Michael Tessler et al (2018)

Personal Log

Protected Waters

Knight Island Passage, Prince William Sound
Knight Island Passage, Prince William Sound

Waking up in Prince William Sound today felt good.  I was closer to home this morning than at any time since leaving Seward.  The Sound feels comfortable and protected.  Should bad weather come up, and it sounds like it will tomorrow, there are hundreds of sheltered bays to hide in.

Chenega Glacier, Icy Bay, Prince William Sound.
Chenega Glacier, Icy Bay, Prince William Sound.

Prince William Sound’s beauties are hard to describe without sounding cliché.  Most striking of all are the large tidewater glaciers.  In the evening, we made our way to Chenga Glacier, to do CTD cast.  It was a quite a sight, as were the three hundred harbor seals hauled out on the floating ice in front of the glacier.

These glaciers directly shape the ecosystem of the Sound.  They provide a large freshwater input that is high in trace minerals, while creating pockets of cold water, which serve as micro-climates within the larger area.  These glaciers are melting at incredible rates, and freshwater inputs are greater than they have been at any time since the last ice age.  Sampling stations that were once near the face of the Chenga and Columbia Glaciers are now miles away from their quickly receding faces. Click here to watch the satellite images of Columbia’s retreat.  This ecosystem is changing, and only through long term ecological monitoring will we know exactly how or what it means.

The completion of the road to the town of Whittier has also changed the Sound.  It’s late September, and most pleasure boaters have stowed their boats for the winter, but the number of boats and people coming into the sound to fish, hunt, and sight see has increased dramatically.  Many Alaskans have come to recognize the coastal gem that lays just seventy miles and one long tunnel through the mountain from Anchorage.

Columbia Glacier 1986 (left) 2011 (right). Image from
Columbia Glacier 1986 (left) 2011 (right). Image from


Animals seen today

  • Lots of harbor seals near Chenega Glacier
  • Sea otters
  • Fewer birds today, mergansers, Kittlitz’s murlets, mew gulls, goldeneyes,



Heather O’Connell: Shore Party, Sumdum and Sawyer Glaciers, June 15, 2018

NOAA Teacher at Sea

Heather O’Connell

NOAA Ship Rainier

June 7 – 21, 2018

Mission: Hydrographic Survey

Geographic Area of Cruise: Seattle, Washington to Southeast, Alaska

Date: 6/15/18

Weather Data from the Bridge

Latitude and Longitude: 57°43.2’ N, 133 °35.7’ W, Sky Condition: Overcast , Visibility: 10+ nautical miles, Wind Speed: 2 knots, Sea Level Pressure: 1024.34 millibars, Sea Water Temperature: 7.2°C, Air Temperature: Dry bulb: 11.78°C, Wet bulb: 10.78°C

Science and Technology Log

Yesterday was my first small vessel operation where we took down a base station and set up a new system on an islet next to Harbor Island. We took RA-7, a skiff that used a crane to lift it off the flying bridge of the ship and into the water. This local satellite receiver allows for a reference point for data acquisition that occurs in Alaska, where the GPS system is not as dependable as the lower forty eight states. The positioning given from this high accuracy base station, called GNSS, will assist with nautical charts developed from the Tracy Arm project once time sonar data has been collected. Since the lower forty eight states have permanent base stations with this highly accurate positioning, there is no need to set up these stations.

GPS base station
Setting up a high-accuracy GPS base station

The base stations work by comparing the satellite positioning to a theoretical ellipsoid that was generated in Canada to standardize positioning. Before this, different areas would utilize various landmarks as the reference point and this inconsistency proved challenging when comparing data internationally or even across the states. So, geodesists, scientists who study geometric shape, positioning in space and gravitational field, generated a theoretical ellipsoid. This was created by rotating the shorter axis of an ellipse to mimic the shape of the Earth. Since the poles of the Earth are flat and the equator bulges, this ellipsoid is an accurate representation. This system gives all points on Earth a unique coordinate, similar to an address, and is extremely helpful in developing nautical charts. However, the limitations of this theoretical ellipsoid include its inability to take into account the actual shape of the Earth.

Setting up Base Station on Harbor Island
Setting up Base Station on Harbor Island

While being on the skiff and learning about theoretical positioning ellipsoids, I heard a lot of talk about RA-2, one of the shoreline launches on Rainier.  I learned that in addition to a single beam sonar, this vessel also has LIDAR. LIDAR, Light Detection and Ranging, can be used in bathymetric data acquisition and is currently used for shoreline data on Rainier. This remote sensing technology can survey up to seventy meters of depth in coastal waters by sending out a laser. LIDAR sends out light pulses and senses the time it takes for these lasers to return to the sensor, to gather data on different land structures. LIDAR gets cloud point data and dots make up the image of the ocean floor. From this, three dimensional maps can be generated. Since the light can penetrate a canopy just like the sun, this technology is used in South America to find hidden cities under tree lines. This technology can also be mounted on planes and is most likely the future direction of shoreline data acquisition. Lasers survey the land and they get the height of different landmasses and can be used for bathymetric data or topographic data.

Sources –

Personal Log

Tracy and Endicott Arms are part of two alpine, or tundra, ecosystem areas that ship Rainier will survey. Twenty percent of these areas are covered in glaciers and snow fields and are too cold to support trees. The coastal areas of Tracy and Endicott Arms are part of the Terror Wilderness, which is part of Tongas National Forest, the largest national coastal temperate rainforest. Observing my first glacier, Sumdum Glacier, off the coast of Harbor Island while we were at the inlet of Tracy and Endicott Arms, reminded me of a time much before humans existed.

Sumdum Glacier
Sumdum Glacier

Here, out of Holkham Bay, I experienced my first expedition in a skiff, RA-7, to remove a horizontal control base and help set up a new one.  Stepping foot on an actual landmass with all of the different living parts of an ecosystem was a treasure and it most certainly felt like a shore party, as the name suggests. I observed several calcium carbonate shells of urchins, amongst kelp, mussels, and barnacles. The shells transitioned into a forest with Devil’s Club, the only member of the ginseng family present in Alaska, with woody, prickly stems.  This shrub was growing under a Sitka Spruce forest with cone-bearing trees present among the steep rocks of granite. These trees can grow up to one hundred and seventy feet tall and can be as old as seven hundred and fifty years old in Southeast Alaska. After an exciting afternoon of a shore party, we safely returned to the ship and headed into Tracy’s Arm.

Proceeding into the Southern arm of Tracy’s Arm, I saw calves of the tidal glacier that we would soon see. The refrozen and pressurized snow became glacial ice and carved the valleys to form the deep inlets with massive granite slabs on either side of us. South Sawyer glacier was off to the East and the air seemed to get colder as we approached it. Even in the rain and weather, I couldn’t pull myself away from the incredible beauty of this inlet. After endless waterfalls, we approached Sawyer Glacier which was once big enough to cover all of Tracy’s Arm. This acted as a reminder of the Ice Age and its effect on geology.

Sawyer Glacier
Sawyer Glacier

During this journey through Tracy’s Arm, I saw two eagles perched on an iceberg and shortly afterwards three orca whales showing their dorsal fins and playing in the water. As XO informed me, orca whales are actually the largest species of dolphins and these carnivorous mammals can weigh up to six tons. These creatures use echolocation to communicate to their pods, and I wonder how the multi-beam sonar affects this form of communication.

Eagles on Iceberg
Eagles on Iceberg. Photo Credit: Jonathan Witmer



Studebaker, Stacy. Wildflowers and Other Plant Life of the Kodiak Archipelago.

National Geographic Orcas

Did You Know?

When glacier ice melts, it is filled with air bubbles. As new layers of ice form on top of the old ice, the ice gets denser and the air bubbles get smaller. As the human eye detects the yellow and red light reflected from glacial ice, it appears a spectacular blue. Since snow is full or air bubbles, it reflects the entire spectrum of light and appears white.

Jessie Soder: Geology on Georges, August 17, 2011

NOAA Teacher at Sea
Jessie Soder
Aboard NOAA Ship Delaware II
August 8 – 19, 2011 

Mission: Atlantic Surfclam and Ocean Quahog Survey
Geographical Area of Cruise:  Northern Atlantic
Date: Wednesday, August 17, 2011

Weather Data
Time: 12:00
Location:  41°19.095 N, 71°03.261
Air Temp:  22°C (°F)
Water Temp:  21°C (°F)
Wind Direction: South
Wind Speed: 7 knots
Sea Wave height:  0
Sea Swell:  0

Science and Technology Log

Gulf of Maine: Including Georges Bank

So far, we have spent this entire trip on Georges Bank.  This famous geographical location off the east coast of the United States is something that I had only heard about before this trip.  After several tows over the past week I have been able to see a variety of materials brought up from the ocean floor of Georges Bank.  I have seen loads of clams, empty shells, sand, mud and clay, and smooth polished rocks.  We have even pulled up a few boulders that must have weighed a couple of hundred pounds.  It was the smooth polished rocks that caught my attention. How would a rock from the bottom of the ocean become smooth and rounded?  It probably meant that Georges Bank must not have always been the bottom of the ocean.

During the Wisconsin Glaciation the ice reached its maximum around 18,000 years ago.  The Laurentide ice sheet paused in the area of Georges Bank and Cape Cod and left behind a recessional moraine that created these landforms.  This ice also had several meltwater streams flowing from it and these streams were responsible for the polishing the rocks and cutting some of the canyons found on the seafloor today.  The Northeast Channel off the northeast side of Georges Bank was the principle water gap for most of the meltwater.

Smooth Polished Rocks From the Ocean Floor

Georges Bank is a huge oval-shaped shoal bigger than Massachusetts that starts about 62 miles offshore.  It is part of the continental shelf and its shallowest areas are approximately 13 feet deep and its deepest areas 200 feet.  In fact, thousands of years ago Georges Bank used to be above water and an extension of Cape Cod.  About 14,000 years ago the sea rose enough to isolate this area and it was home to many prehistoric animals such as mastodons and giant sloths.  Today, traces of these animals are sometimes found in fishing nets!  These animals died out about 11,500 years ago when the sea level rose further and submerged the area.

Georges Bank is a very productive fishing area in the North Atlantic.  (The Grand Banks is more productive, but not as geographically accessible as Georges Banks.)  Why is Georges Bank a prime feeding and breeding area for cod, haddock, herring, flounder, lobsters, and clams?  It has to do with ocean currents.  Cold, nutrient rich water from the Labrador Current sweeps over the bank and mixes with warmer water from the Gulf Stream on the eastern edges of Georges Bank.  The mingling of these two currents, plus sunlight, creates an ideal environment for phytoplankton, which is food for the zooplankton.  In fact, the phytoplankton grow three times faster here than on any other continental shelf.  All of this plankton feeds the ecosystem of fish, birds, marine mammals, and shellfish that flourish on Georges Banks.

Personal Log

Yesterday we left Georges Bank for stations off the coast of Rhode Island.  After dark, I stepped out on the back deck and Jimmy pointed out the lights of Nantucket and Martha’s Vineyard.  We were in sight of land for the first time in a week.  It wasn’t long before people had their cell phones out and were making calls.

A few times during this trip I have thought about sailors in the past and how they would leave for months, and even years, at a time and not have contact with their families and loved ones until they returned.  I have had email contact this entire time, yet I am really excited to go home to see those that I miss.  I can hardly imagine what it would be like to be gone for a year with no contact at all.

Throughout this trip I have been getting to know others on this cruise.  I have learned that several of them have families and young children at home.  Many of them are at sea for many weeks, or months, a year.  After being on this cruise, I have gained a lot of respect for people who choose to work on the ocean for a living.  It takes a certain type of person who can work hard, maintain a positive attitude, and live away from their home and loved ones for extended periods of time.  It has been an honor to work with these people.