Dawn White: Sampling the Pacific, June 24, 2017

NOAA Teacher at Sea

 Dawn White

Aboard NOAA Ship Reuben Lasker

June 19 – July 1, 2017


Mission: West Coast Sardine Survey

Geographic Area of Cruise: Pacific Ocean; U.S. West Coast

Date: June 25, 2017


Weather Data from the Bridge


Date: June 25, 2017                                                         Wind Speed: 22 kts

Time: 4:00 p.m.                                                                 Latitude: 5026.55N

Temperature: 14.3oC                                                      Longitude: 12808.11W


Science and Technology Log


Although the scientists have not performed any fishing trawls since departing San Diego, there is a survey crew on board that has continuously been monitoring the water column for a variety of factors using acoustics and an instrument called a Conductivity/Temp/Depth (CTD) probe.

Last night I was able to observe the launch and retrieval of a small, handheld CTD probe.  It looks very much like a 2 ft torpedo. The electronics and sensors built into the probe measure such factors as salinity, sound speed, depth, and water temperature.  This smaller probe is launched off the tail of the boat and let out on a line of filament from a reel that appears very similar to a typical fishing reel.  It does not take more than a couple of minutes for the probe to sink to a depth of about 300 meters.  Data is collected from the probe at various depths on the way down.  Once the probe has reached its target depth, it is simple reeled back in using a winch to retrieve it.  This requires quite a bit of energy as the probe is deployed with enough line for it to end up about 3 miles behind the ship.  The data from this probe is then blue-toothed to the program used by those monitoring the water column acoustically.  It help the techs make corrections in their acoustical readings.


White_scientists deploying probe_R

Surveyor Jian Liu and scientist Juan Zwolinski deploy the smaller CTD probe off the stern of NOAA Ship Reuben Lasker


The Reuben Lasker also carries a larger version of the CTD probe with the additional capabilities such as water collection at various depths.  However, this version requires the ship to be stationary.  Taking measurements with the unit slows down the work of the day as each stop takes about 30 minutes from launch until retrieval.  The launch of the larger CTD can be seen below.


White_CTD probe in basket

CTD Probe in steel protected basket


The data from the CDT probe is recorded real-time on the survey team’s computers.  Below you can see how this data presents itself on their video screens.


On the left video display you can see that there are several variables that are plotted against a depth vs. temperature. The green line tracks fluorescence (a measure of the chlorophyll concentration); the light blue line tracks dissolved oxygen; the red line represents temperature; the blue line is for salinity.


Extension question for my students reading this:  What correlations or relationships do you see happening as you observe the change in variables relative to changes in depth?


White_Lasker route

Route of NOAA Ship Reuben Lasker

Here is the route taken by the Reuben Lasker during the past 24 hours or so.  As you can see from the chart, the ship has now reached the northern-most end of Vancouver Island.  This is where the CDT recordings, marine mammal watching, deployment of two sets of plankton nets (to be explained later) and fish trawling will begin along the predetermined transect lines.

Note at the base of the screen the other parameters that are continuously recorded as the ship moves from place to place.



Personal Log

The action on-board is increasing dramatically today.  We have arrived at our outermost destination today, along the northernmost coast of Vancouver Island.  The sights from the bridge are amazing…all this blue water and rugged, pine covered coastline.  I am still waiting for that orca whale sighting!

The waves are up today but I’m holding my own.  Yeay!  Especially as the night fishing will begin in a few hours.

Unique activity of the day – I just finished a load of laundry!  The ship possesses 3 small washer/dryer units so we can redo our towels and whatever else we have used up during the course of this first week.  How serviceable can you get! I’ll retrieve mine as soon as dinner is over.  We have set meal hours and if you miss…it’s leftovers for you!  Best part of this is I am actually ready to eat a normal meal, even with the ship rocking the way it is today.

I have now been assigned deck boots and a heavy duty set of rain gear to cover up with when the fish sorting begins.  I can’t wait to see what all we pull up from these nutrient rich waters!


Did You Know?

Much of the data collected by the CTD and acoustic equipment from the Reuben Lasker is entered into a large data set managed by CalCOFI (California Cooperative Oceanic Fisheries Investigation).  Anyone interested in utilizing and analyzing this data can access it via the organization’s website located here.  There is an incredible amount of information regarding the work and research completed by this group found on this site. Check it out!

Spencer Cody: What Remains Unseen, June 17, 2016

NOAA Teacher at Sea

Spencer Cody

Onboard the NOAA Ship Fairweather

May 29 – June 17, 2016

Mission:  Hydrographic Survey

Geographical Area of the Cruise:  along the coast of Alaska

Date: June 17, 2016

Weather Data from the Bridge: 

Observational Data:

Latitude: 55˚ 10.643′ N

Longitude: 132˚ 54.305′ W

Air Temp: 16˚C (60˚F)

Water Temp: 12˚C (54˚F)

Ocean Depth: 30 m (100 ft.)

Relative Humidity: 81%

Wind Speed: 10 kts (12 mph)

Barometer: 1,013 hPa (1,013 mbar)

Science and Technology Log:

106_0507 (2)

Hydrographic Senior Survey Technician Clint Marcus is cataloguing all of the discreet hazards and objects by location and by photographic evidence that will be available for the new nautical charts once the survey is complete.

Uncovering potential dangers to navigation often requires more that acoustic equipment to adequately document the hazard.  Many hazards are in water that is shallow enough to potentially damage equipment if a boat were to be operating in that area and may also require special description to provide guidance for those trying to interpret the hazard through nautical charts and changing tides.  This is one of the key reasons so much planning must be placed into assigning survey areas determining the size and extent of polygons for mapping.  Depending on the complexity of the area’s structures, the polygon assignment will be adjusted to reasonably reflect what can be accomplished in one day by a single launch.  Near-shore objects may require a smaller boat to adequately access the shallow water to move in among multiple hazards.  This is where a smaller boat like the Fairweather’s skiff can play a role.  The skiff can be sent out to map where these near-shore hazards are using equipment that that will mark the object with a GPS coordinate to provide its location.  Additionally, a photograph of the hazard is taken in order to provide a greater reference to the extent of the object and what it looks like above or below the water.  This information is collected and catalogued; so, the resulting nautical chart will have detailed resources and references to existing nautical hazards.

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Ensign Pat Debroisse covers nautical hazards such as rocks and kelp indicated throughout a very shallow and hazardous inlet.

Nautical hazards are not the only feature found on charts.  Nautical charts also have a description of the ocean bottom at various points throughout the charts.  These points may indicate a rocky bottom or a bottom consisting of silt, sand, or mud.  This information can be important for local traffic in terms of boating and anchoring and other issues. In order to collect samples from the bottom, a launch boat drops a diving probe that consists of a steel trap door that collects and holds a specimen in a canister that can be brought up to the boat.  Once the sample is brought up to the boat, it is analyzed for rock size and texture along with other components such as shell material in order to assign a designation.  This information is collected and catalogued so that the resulting nautical chart update will include all of the detailed information for all nautical hazards within the survey area.

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Bottom samples are taken with a heavy steel torpedo-shaped probe that is designed to sink quickly, dive into the ocean bottom, clamp shut, and return a sample to the boat.  Credit Ensign Joseph Brinkley for the photo.

Personal Log:

Dear Mr. Cody,

The food on the cruise ship is great. They have all of our meals ready and waiting.  There are many people who prepare and serve the food to us to make our trip enjoyable.  (Dillion is one of my science students who went on an Alaska cruise with his family in May and will be corresponding with me about his experiences as I blog about my experiences on the Fairweather.)

Dear Dillion,

The food onboard the Fairweather is also very good.  Much of the work that they do happens so early in the morning that most never see it take place.  Our stewards take very good care of us by providing three meals a day, snacks, and grab bag lunches for all of our launches each day.  They need to start early in morning in order to get all of the bagged lunches for the launches prepared for leaving later that morning and breakfast. They start preparing sandwiches and soup for the launches at 5 AM and need to have breakfast ready by 7 AM; so, mornings are very busy for them.  A morning snack is often prepared shortly after breakfast for those on break followed by lunch and then an afternoon snack and finally dinner.  That is a lot of preparation, tear down, and clean up, and it all starts over the next day.  The steward department has a lot of experience in food preparation aiding them in meeting the daily demands of their careers while preparing delicious and nutritious food that the crew will enjoy.

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What are you doing at 5:15 in the morning?  Mornings are very busy for the steward department preparing lunches for the day’s hydrographic launches and breakfast for the entire crew.  From left to right, Chief Steward Frank Ford, Chief Cook Ace Burke, Second Cook Arlene Beahm, and Chief Cook Tyrone Baker.

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Chief Steward Frank Ford is preparing a delicious mid-morning snack for the crew.

Frank Ford is the chief steward. He has been in NOAA for six years.  Before joining NOAA he had attended culinary school and worked in food service for 30 years in the restaurant and hotel industry.  “I try to make meals that can remind everyone of a positive memory…comfort food,” Frank goes on to say, “Having good meals is part of having good morale on a ship.”  Frank and the others in the steward department must be flexible in the menu depending on produce availability onboard and available food stores as the mission progresses.


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Chief Cook Tyrone Baker helps prepare breakfast.

Tyrone Baker is the chief cook onboard. He has been in NOAA for 10 years and has 20 years of food service experience in the Navy.  Ace Burke has been with NOAA since 1991 and has served in many positions in deck and engineering and has been a steward for the last 15 years.  He came over from the NOAA ship Thomas Jefferson to help the steward department as a chief cook. Arlene Beahm attended chefs school in New Orleans.  She has been with NOAA for 1 ½ years and started out as a general vessel assistant onboard the Fairweather and is now a second cook.


Did You Know?

Relying on GPS to know where a point is in the survey area is not accurate enough.  It can be off by as much as 1/10 of a meter.  In order to increase the accuracy of where all the points charted on the new map, the Fairweather carries horizontal control base stations onboard.  These base stations are set up on a fixed known location and are used to compare to the GPS coordinate points.  Utilizing such stations improves the accuracy of all points with the survey from 1/10 of a meter of uncertainty to 1/100 of a meter or a centimeter.

Can You Guess What This Is?109_0609 (2)

A. an alidade  B. a sextant  C. an azimuth circle  D. a telescope

The answer will be provided in the next post!

(The answer to the question in the last post was D. a CTD.  A CTD or Conductivity, Temperature, and Depth sensor is needed for hydrographic surveys since the temperature and density of ocean water can alter how sound waves move through the water column. These properties must be accounted for when using acoustic technology to yield a very precise measurement of the ocean bottom.  The sensor is able to record depth by measuring the increase of pressure, the deeper the CTD sensor goes, the higher the pressure.  Using a combination of the Chen-Millero equation to relate pressure to depth and Snell’s Law to ray trace sound waves to the farthest extent of an acoustic swath, a vertical point below the water’s surface can be accurately measured.  Density is determined by conductivity, the greater the conductivity of the water sample running through the CTD, the greater the concentration of dissolved salt yielding a higher density.)

Leah Johnson: Physical and Chemical Properties of Ocean Water (There’s More Here Than Just Fish!) , July 26, 2015

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

Mission: Southeast Fishery – Independent Survey
Geographical Area of Cruise: Atlantic Ocean, Southeastern U.S. Coast
Date: Sunday, July 26, 2015

Weather Data from the Bridge:
Time 12:38 PM
Latitude 34.24389
Longitude -76.6625
Water Temperature 23.75 °C
Salinity –No Data-
Air Temperature 28.6 °C
Relative Humidity 68 %
Wind Speed 12.6 knots
Wind Direction 67.01 degrees
Air Pressure 1014.8 mbar

Science and Technology Log:
The primary purpose of this cruise is to survey reef fish. Our main task is to collect data pertaining to presence and number of fish species, species length frequency, and sample materials for fish age and growth. However, other types of measurements are being made as well. For example, the CTD is an instrument that measures different properties of ocean water with depth. It is deployed every time the fish traps are dropped.

CTD instrument

The CTD sits on the starboard side of the deck of NOAA Ship Pisces.

The acronym “CTD” stand for conductivity, temperature, and depth. The instruments that measure these properties are affixed to a metal cylinder called a rosette. A range of sensors can be attached depending on what needs to be measured. Additionally, containers can be attached to the frame in order to collect sea water samples at different depths. When the ship reaches the designated coordinates, the survey technician calls to the deckhands and instructs them to use the winch to lower the CTD to a designated depth, and then haul it back up.

Deckhands assist with lowering the CTD

Deckhands assist with lowering the CTD.

Below you can see a graph of the data collected earlier in the week:

CTD Data

CTD Data

The y-axis represents depth in meters. The CTD actually measures water pressure, which is then converted to depth. Pressure and depth are directly related: as depth increases, pressure increases.

There are several different properties represented on the x-axes, shown in different colors:

light green = oxygen (mg/l)
orange = conductivity (S/m)
dark green = temperature (°C)
purple = salinity (PSU, or ppt)

What do these measurements mean? As depth increases, temperature decreases. Sunlight warms the sea surface, and wind and ocean currents distribute this heat energy throughout the upper waters. Beneath this mixed layer, temperature decreases steadily with depth. In deeper water (not at this location), this rate of change decreases and the temperature of deep ocean water is nearly a constant 3 °C. Salinity refers to the concentration of dissolved salts in the water. Average ocean salinity is 35 ppt (parts per thousand), though this varies by a few parts per thousand near the surface. Increased precipitation, runoff, or melting of sea ice can decrease salinity, and evaporation and ice formation can increase salinity. Conductivity (measured in Siemens per meter) is a measure of how much current can travel through the water, and this is affected by both salinity and temperature. Finally, fish and other marine organisms require dissolved oxygen to breathe. By measuring the amount of oxygen at different levels in the water column, we can determine how much sea life can be supported in a given area. Dissolved oxygen in the ocean comes from mixing at the surface, and is also produced by photosynthetic organisms. As temperature and salinity increase, dissolved oxygen levels decrease. Additionally, temperature and salinity data can be used to determine the water density, or the mass of water per unit volume. Different fish can tolerate certain ranges of all of these chemical and physical parameters.

With respect to the fish survey, this information is important because we can monitor the conditions of the water near the ocean floor where the traps are located. For scientists who are interested in characterizing reef fish habitat, this data is a critical component of their research.

There are other ways in which this data can be used. The depth profiles of each of the chemical and physical properties at a given site can be compared to other local sites in order to identify any spatial anomalies. This is of great interest for seafloor mapping and ocean exploration cruises. For example, a change in conductivity and temperature at a site in the middle of the ocean could indicate the presence of a hydrothermal vent. Or, a decrease in salinity in a region along a coastline could indicate freshwater runoff.

Additionally, as measurements are made at similar locations over a period of time, temporal changes may be observed. This could reveal seasonal changes, or a long-term trend. Because we are observing an increase in average global temperatures and experiencing global climate change, it is critical to collect data that can be used to assess changing ocean conditions.

Personal Log:
“Will you be eating a lot of fish on the ship?” I heard this question a lot before I left for this cruise. I wondered myself. It seemed reasonable that fish would be prepared for meals because, well, we will be living at sea! On the other hand, I wondered if everyone on board would be sick to death of fish because we would be looking at them all day. As it turns out, fish is prepared for nearly every meal; however, there is often another meat option, as well as a variety of other non-meat dishes. Now we know!

ship mess

Ship mess

Did You Know?
There are many fish that make a grunting sound. When we have tubs full of tomtates in the wet lab, it sounds like a bunch of miniature pigs making snorting noises!

tomtates and nurse shark

Still from video of tomtates near a trap. A nurse shark can be seen in the background.

Daniel Rivera, Day 2, First Day Out At Sea, Jul7 17, 2014

NOAA Teacher at Sea

Daniel Rivera

Aboard the Ship R/V Fulmar

July 16-24, 2014 


Mission: Water conductivity, temperature, and depth (CTD) readings; marine bird and mammal counts

Geographical Area: Gulf of the Farallones and Cordell Bank National Marine Sanctuaries; Sonoma County Coast, Pacific Ocean

Dates: July 17, 2014


Weather Data from the bridge: Wind speed variable, less than 10 knots; wind waves less than 2 feet; visibility about 3 km, temperature range from 57-66 F


Science and Technology Log: During our week long cruise we take CTD readings with the CTD device and record marine bird and mammal sightings from the Gulf of the Farallones and Cordell Bank Marine Sanctuaries, marine protected areas (MPA) off the northern coast of California. CTD readings tell us the levels of salinity of the water and the temperature of the water, and the depth at which these two conditions exists, along with the number of marine birds and mammals in the area, can tell scientists a lot about the health of the ocean. The scientist aboard the R/V Fulmar are looking for correlations between the number of birds and mammals along the transects and the CTD readings. Are conditions changing, staying the same? Has any kind of natural or manmade disaster affected the numbers?

Today’s mission was extra special because these two MPAs are currently undergoing a proposed expansion, and for the first time the science team took samples from this proposed expansion area. The transect lines covered today were 14, 13, and N13.

An expansion of these two MPAs would increase the area allotted to the protection and preservation of our coastal waters and, by extension, marine life within those waters. The reason behind the expansion of the MPAs is due to the upwelling that starts north of the current MPA, at a spot along the coast called Point Arena. The large amount of upwelling that begins at Point Arena eventually moves down the coast with the California Current, creating the spectacular assortment of rich life that exists in the Gulf of the Farrallones and the Cordell Bank Sanctuaries. By protecting the starting point of the massive upwelling, we are ensuring the protection of the explosion of life that continues along California Current. 


Personal Log: Todays begins with my alarm clock going off at 5:30 am. Why so early? Because we leave port no later than 7am, and with 11 people on board one ship, I don’t want to be the last one in line for the bathroom. Plus I like to have coffee in the morning. And I’m a little nervous because it’s my first day at sea. Any one of these excuses work. 

Once everybody’s is up and ready to go, my first task is go over emergency procedures with Dave Benet, the mate of the ship. We go through the safety protocols and when done I don the immersion suit, which looks like a giant red gumby suit and leaves you with as much dexterity as do ski mittens. I’m told it will keep you warm in the water if you manage to zip it up before you hit the water; I do not want to test out this theory, so I take Dave’s word.

This gumby-looking outfit, called an immersion suit, will keep you afloat and warm if you happen to abandon ship.

This gumby-looking outfit, called an immersion suit, will keep you afloat and warm if you happen to abandon ship.

As we head out to sea and towards out first transect, everybody is excited that the water and weather are calm; very little to no wind, glass-like water, no waves. This is a treat for all on board because during the last cruise the waves were so bad that the boat had to return to shore because it was too dangerous to be out at sea.

The first task of the day is on the top deck, where scientists monitor the marine birds and mammals within the transect line. As birds and mammals are spotted along the transect, data is collected about each organism. Among this data is type of organism, the direction of travel, the sex (if known), age (if known), the behavior, and location of the organism. There is one spotter for birds and two spotters for mammals, and as each organism is spotted, a series of numbers and names is called out to the recorder, the scientist who inputs the data into a log on a laptop. Today is mild, weather-wise, so the crew calls out the information and logs it in as the boat gently sways back and forth along the transect; last month I would’ve seen the same crew holding on for dear life, trying to keep in their meals, while still recording the data. 

Because I’m not trained on how to spot birds and mammals, my task while on board is to assist with CTD and plankton net deployment. Along predetermined spots along the transect the boat stops and we drop the CTD to about 5 meters above the seafloor. Our first CTD reading had us at 200 meters to the bottom, so we sent the CTD down to 195 meters below. Once it hits 195 meters we immediately bring it back up and secure the device back to the boat. After that we then launch the hoop net, which is a big plankton net that is dragged behind the boat till a depth of 50 meters. Once it’s down to 50 meters, we then bring the net back up to the boat, empty the contents into a jar, and add preserving agent to bring the samples back to the lab. Once at the lab the plankton samples are counted and recorded, giving us a picture of the biological activity in that particular area of the transect.

The CTD is deployed down to a depth that is 5 meters above the surface and collects conductivity, temperature, and depth data.

The CTD is deployed down to a depth that is 5 meters above the surface and collects conductivity, temperature, and depth data.

The handling of the hoop net and CTD take practice to properly deploy, and the parameters of the deployment have to be very exact or else we risk losing the very costly tools. If the measurements for depth are not accurate, the CTD could hit the bottom of the ocean, causing damage to the CTD. We could also risk snagging and losing the hoop net if it is dragged along the bottom, so these measurements are doubled- and triple-checked by the captain and the scientists to avoid costly mistakes. 

Did you know? Just as there are hotspots of magma flow on land, there are hot spots of life at sea. The transect lines monitored aboard the R/V Fulmar help to pinpoint these hotspots of sea-life activity. 

Question of the Day? What does the acronym MPA stand for? Provide 2 examples of MPAs.

New Term/Phrase/Word: CTD; hoop net.

Something to Think About: The more you eat while on a cruise, the less seasick you will become, which is counterintuitive.

Challenge Yourself: How might wind waves affect the efficiency of a cruise?

Kainoa Higgins: Mantas and Megalopae, June 28, 2014

NOAA Teacher at Sea
Kainoa Higgins
Aboard R/V Ocean Starr
June 18 – July 3, 2014

Mission: Juvenile Rockfish Survey
Geographical Area of Cruise: Northern California Current
Date: Saturday, June 28, 2014

Weather Data from the Bridge: Current Latitude: 45° 59.5’ N Current Longitude: 125° 02.1’ W Air Temperature:  12.7° Celsius Wind Speed: 15 knots Wind Direction: WSW Surface Water Temperature: 15.5 Celsius Weather conditions: Partly cloudy

Find our location in real time HERE!

Science and Technology Log:

Neuston Net and Manta Tow Today, the weather is pleasant but the sea seems more than restless. The show must go on! I step onto the open deck behind the wet lab just as Dr. Curtis Roegner, a fisheries biologist with NOAA, is placing a GoPro onto the end of an extensive net system.

Dungeness Crab – A Pacific Northwest Delight Photo Credit: http://www.smokeybay.com

While Curtis specializes in the biological aspects of oceanography, he is especially interested in the synthesis of the ocean system and how bio aspects relate to other physical and chemical parameters. He joins this cruise on the Ocean Starr as he continues a long-term study of distribution patterns of larval crabs. The species of focus: Cancer magister, the Dungeness crab; a table favorite throughout the Pacific Northwest.

While I have been known to eat my weight in “Dungies”, I realize that I know very little about their complex life cycle. We begin with “baby crabs”, or crab larvae. Once they hatch from their eggs, they quickly join the planktonic community and spend much of their 3-4 month developmental process adrift – at the mercy of the environmental forces that dictate the movement of the water and therefore, govern the journey of these young crustaceans. It has been generally assumed that all planktonic participants float wherever the waters take them. In that context, it makes sense that we have been finding large numbers of larvae miles offshore during our nighttime trawl sorting. Still, not all are swept out to sea. Every year millions make their way back into the shallows as they take their more familiar, benthic form which eventually grows large enough to find its way to a supermarket near you. The question is: How? How do these tiny critters avoid being carried beyond the point of no return? Is it luck? Or is there something in the evolutionary history of the Dungeness crab that has allowed it to adapt to such trying conditions?

Dungeness Crab Megalopae

“Dungie” babies

Curtis tells me about recent research that suggests that seeming “passive” plankton may actually have a lot more control of their fate than previously supposed.  By maneuvering vertically throughout the column they can quite dynamically affect their dispersal.  Behavioral adaptation may trigger vertical migration events that keep them within a particular region, playing the varied movement of the water to their advantage.  Curtis believes the answer to what determines Dungie abundance lies with with the Megalops, the final stage of the larva just prior to true “crab-hood”. By the end of this stage they will have made their way out of the planktonic community and into estuaries of the near shore zone.

Kainoa and Curtis

Dr. Curtis Roegner explains the importance of his study

This continued study is important in predictably marking the success or failure of a year’s class of crab recruitment. That is to say, the more Megalopae that return to a region, the better the promise of a strong catches for the crabbing industry – and a better chance for you and me to harvest a crab or two for our own table!

As Curtis and I discuss his research, he continues preparing his sampling equipment. The instrument looks similar to the plankton nets we use in marine science at SAMI only it’s about ten times longer and its “mouth” is entirely rectangular, unlike the circular nets I am used to using. I’ve heard the terms “manta”, “bongo” and “neuston” being tossed around lab and yet I am unable to discern one from the other. It’s time I got some answers!

Curtis explains that the Megalopae he wants to catch are members of the neuston, the collective term given to the community of organisms that inhabit the most surface layer of the water column. The Neuston net is named simply for its target. It occurs to me that a “plankton net” is a very general term and that they can come in all shapes and sizes. In addition, the mesh of the net can vary drastically in size; the mesh on our nets at school is roughly 80µm, while the mesh of this net is upwards of 300μm (1 µm or micrometre is equivalent to one millionth of a metre).

Manta tow & Neuston net

The manta body design for neuston sampling. A specialized plankton tow.

I’m still confused because I am fairly certain I have heard others refer to the tool by another name. Curtis explains that while any net intended to sample the surface layer of the water column may be referred to as a neuston net, this particular net had a modified body design which deserved a name of its own. The “manta” is a twin winged continuous flow surface tow used to sample the neuston while minimizing the wake disturbance associated with other models. The net does seem to eerily resemble the gaping mouth of a manta ray. These enormous rays glide effortlessly through the water filtering massive volumes of water and ingesting anything substantial found within. On calm days, our metallic imposter mimics such gracefulness. Today however, it rides awkwardly in the chop, jaggedly slicing and funneling the surface layer into its gut. It’s all starting to make sense. Not only is this a plankton net designed to sample plankton, it is also a plankton net designed to sample only the neuston layer of the planktonic community.   The modified body sitting on buoyed wings designed to cover a wider yet shallower layer at the top of the water column further specified the instrument; a neuston net towed via manta body design for optimized sampling. Got it.

Collected Plankton Sample

A filtered sample of various crustaceans collected from the neuston

After the tow is complete, Curtis dumps the cod end of the net into a sieve, showing me an array of critters including more than a dozen Megalopae! Two samples are frozen to ensure analysis back at the Hammond Lab in Astoria. There, Curtis will examine the developmental progress of the Megalopae in relation to the suite of data provided by the CTD at each testing site. This information, along with various other chemical and physical data will be cross-examined in hopes of finding correlation – and perhaps even causation – that make sense of the Dungeness crabs’ biological and developmental process.

Analysing CTD Data

Dr. Curtis Roegner looks for patterns relating crab Megalopae and CTD data

The CTD 


The CTD measures conductivity, temperature and depth among other auxiliary measurements

Fundamentally, a CTD is an oceanographic instrument intended to provide data on the conductivity, temperature and depth of a given body of water. The CTD is one of the most common and essential tools on board a research ship. Whether it’s Jason exploring benthic communities, Sam hunting jellies, or Curtis collecting crab larvae, all can benefit from the information the CTD kit and its ensemble of auxiliary components can provide about the quality of the water at a given test site. In general, the more information we collect with the CTD the better our ability to map various chemical and physical parameters throughout the ocean. Check out the TAScast below as I give a basic overview of and take a dive with the CTD and its accessories.  



Personal Log:

Just when I thought I was beginning to get the hang of it…. Hold on, I have to lie down. As I mentioned above, the seas have been a bit rougher and I’ve been going through a phase of not-feeling-so-hot for the first time this trip. It’s odd because we hit some rougher ocean right out of Eureka and it didn’t seem to faze me much. I stopped taking my motion sickness medicine a few days in, and though I’ve picked it back up just in case, I’m not entirely convinced it’s the only contributing factor. I think it has more to do with my transition onto the night shift and all the plankton sorting which requires lots of focus on tiny animals. The night before last was particularly challenging. In the lab, all of the papers, books and anything else not anchored down slid back and forth and my body felt as if it were on a giant swing set and seesaw all at once. In addition, each time I looked out the back door all I could see was water sloshing onto the deck through the very drainage holes through which it was intended to escape. I remember wondering why there were so many rolls of duct tape strapped to the table and why chairs were left on their side when not in use. Well, now I know. Earlier today we made a quick pit stop in Newport, Oregon – home of the Hatfield Marine Science Center as well as NOAA’s Marine Operations Center of the Pacific. In short, this is where NOAA’s Pacific fleet of vessels is housed and the home base to several members of my science team, including Chief Scientist, Ric Brodeur.

The NOAA Pacific Fleet

The NOAA Pacific fleet at rest in Newport, OR.

I remember the anticipation of seeing the R/V Ocean Starr, a former NOAA vessel, for the first time. Growing up in Hawai’i, I remember these enormous ships making cameo appearances offshore, complete with a satellite dome over the bridge, only imagining the importance of the work done aboard. Now here I was, walking amongst the giants I idolized as a kid – the difference being that my view was up close and personal from behind the guard gate, a member of their team. I’m totally psyched even though I attempt to pretend like I’ve been there before. As much as I could have spent all afternoon admiring, I needed to make the most of our two hour layover in the library uploading blog material. Unfortunately the satellite-based internet is incredibly finicky out at sea. It’s a first world problem and understandably a part of life at sea, I realize, but all the same, I apologize to all those anticipating regular updates. I continue to do the best I can. I can say, however, that the Hatfield Marine Science Center boasts a fantastic library. I look forward to exploring the rest of the facility upon my final return in a little over a week. ‘Till then, BACK TO SEA!

Bhavna Rawal: Conductivity, Temperature, Depth (CTD) and Water Testing, August 7, 2012

NOAA Teacher at Sea
Bhavna Rawal
Aboard the R/V Walton Smith
August 6 – 10, 2012

Mission: Bimonthly Regional Survey, South Florida
Geographic area: Gulf of Mexico
Date: Aug 7, 2012

Weather Data from the Bridge:
Station: 6.5
Time: 21.36 GMT
Longitude: 080 17’ 184
Latitude: 250 3’ 088
Water temp: 29.930 oC
Wind direction: East
Wind speed: 8 knots
Sea wave height: 3 ft

Science and Technology log:

Hello students! We know how to do water testing in our lab class using the testing kit. Today, I am going to explain to you the way ocean water is sampled and tested in the South Florida coastline.

Our 5 day cruise consists of over 80 stations along the Atlantic and Gulf coast of Florida.  At each station we take water samples, and at about 20 of the stations we tow nets to catch fish, seaweed or plankton and sometimes scuba dive to recover the instruments mounted on the seafloor.

Our journey begins at station #2 at Dixie shoal, which is near Miami; you can see this on the South Florida bimonthly Hydrographic survey map below (see fig).

South Florida Bimothly Hydrographic Survey map

South Florida Bimothly Hydrographic Survey map

At each station we performed CTD (conductivity, temperature and depth) operations. The CTD is a special instrument to measure salinity, temperature, light, chlorophyll and the depth of water in the ocean. It is an electronic instrument mounted on a large metal cage that also contains bottles to collect samples.  These bottles are called niskin bottles and every oceanographer uses them.  They are made of PVC and are specially designed to close instantaneously by activation from the computer inside the ship. Collecting water samples at various depths of the ocean is important in order to verify in the lab that the instruments are working properly. Each bottle has an opening valve at the bottom and top to take in the seawater. The top and bottom covers are operated by a control system. Once a certain depth is reached, the person sitting at the control system triggers and it closes the bottles. You can control each bottles through this system to get a pure water sample from different depths. For example, when the ocean floor is 100 meters deep, water is sampled from the surface, at 50 meters deep, the very bottom.

Hard hat and life vest on and ready for CTD

Hard hat and life vest on and ready for CTD

The CTD instrument is very large, and is operated by a hydraulic system to raise it, to place it and lower down into the ocean. Rachel (another fellow member) and I were the chemistry team; we wore hard hats and life vests while we guided the CTD in and out of the water. This is always a job for at least two people.

Guiding CTD in and out of water

Guiding CTD in and out of water

The team usually closes several bottles at the bottom of the ocean, in the middle layer and surface of the ocean. We closed the bottles in the middle layer because the characteristics of the water are different from at the bottom and the surface.  Remember, the ocean water is not all the same throughout, at different depths and locations it has different chemical characteristics. We closed two bottles per layer, just in case something happened with one bottle (it is not opened properly, for example) then the other bottle can be used.

Taking water sample out of CTD bottles

Taking water sample out of CTD bottles

Rachel and I took water samples from the CTD bottles and used them in the lab to conduct experiments. Before I explain the analysis, I want to explain to you the importance of it, and how a “dead zone” can happen. Remember phytoplankton need water, CO2, light and nutrients to live and survive. The more nutrients, the more phytoplankton can live in water. As you all know, phytoplankton are at the base of the food chain. They convert the sun’s energy into food. Too many nutrients mean too much phytoplankton.

  1. If certain species of phytoplankton increase, it increases the chance of a harmful algal bloom. Too much of one kind of plankton called the dinoflagellates can release toxins into the water which harms the fish and other ocean life and it can even cause people to feel like they have a cold if they swim in the water that has those plankton.
  2. Large amounts of plankton die and fall to the sea floor, where bacteria decompose the phytoplankton. Bacteria use available oxygen in water. The lack of oxygen causes fishes and other animals die. The zone becomes ‘the dead zone’.
    We prepare the sample for nutrient analysis to measure nutrients such as nitrate, nitrite, phosphate, ammonium and silicate in the water.
    We also prepare the sample for chlorophyll analysis. In the lab, we filter the phytoplankton out of the water. Phytoplankton contains special cells that photosynthesize (chloroplasts) which are made of chlorophyll. If we know the amount of chlorophyll, we can estimate the amount of phytoplankton in a given area of the ocean.
filtering the phytoplankton out of the water

Filtering the phytoplankton out of the water

Preparing the sample for nutrient analysis

Preparing the sample for nutrient analysis

Phytoplankton needs carbon dioxide to grow. Carbon dioxide analysis is useful because it provides an estimate of total carbon dioxide in the ocean.  It is also important in understanding the effects of climate change on the ocean.  If you increase the amount of CO2 in the atmosphere (like when you drive cars), it enters into the ocean.  If you think about a can of soda it has a lot of CO2 dissolved into it to make it fizzy, and it also tastes kind of acidic.  This is similar to when CO2 dissolves into seawater.  When the ocean becomes more acidic, the shells of animals become weaker or the animals cannot produce the shells at all.

Colored dissolved organic matter (CDOM) analysis informs us where this water comes from.  The dissolved organic matter comes from decomposing plants, and some of these dead plants entered the water through rivers.  You can tell for example that water came from the Mississippi River because of the CDOM signal.  You can then follow its circulation through the ocean all the way to the Atlantic.

From the CTD instrument, we measured temperature, light, salinity, oxygen etc. and graphed it on a computer (see figure) to analyze it.

Measured temperature, light, salinity, oxygen etc. and graphed it

Measured temperature, light, salinity, oxygen etc. and graphed it

Generally, I see that ocean surface water has high temperature but low salinity, low chlorophyll, and low oxygen. As we go deeper into the sea (middle layer), temperatures decrease, dissolved oxygen increases, chlorophyll and salinity increases. At the bottom layer, chlorophyll, oxygen, temp and salinity decrease.

Personal Log:

I arrived on the ship Sunday evening and met with other people on the team, tried to find out what we are going to do, how to set up, etc. Asked so many questions… I explored my room, the kitchen, the laundry, the science lab, the equipment, etc. Nelson (the chief scientist) gave me a really informative tour about the ship, its instruments and operations. He showed the CTD m/c, the drifter, the wet lab etc. He also gave me a tour of a very important instrument called the “flow-through station” which is attached to the bottom of the ship. This instrument measures temp, salinity, chlorophyll, CDOM, when the boat drives straight through a station without stopping. I was really stunned by how precise, the measurements taken by this instrument are.

flow-through station

Flow-through station

The next morning, Nelson explained that if we have enough tide the ship would leave. We had to wait a bit. As soon as we got the perfect tide and weather, R/V Walton Smith took off and I said ‘bye bye’ to Miami downtown.

‘bye bye’ to Miami downtown

‘Bye bye’ to Miami downtown

I learn so much every day in this scientific expedition. I saw not only real life science going on, but efficient communication among crew members. There are many types of crew members on the ship: navigation, technology, engineering, and scientific. Chief scientists make plans on each station and the types of testing. This plan is very well communicated with the navigation crew who is responsible for driving the ship and taking it to that station safely. The technology crew is responsible for efficient inner working of each scientific instrument. 10 minutes before we arrive on a station, the ship captain (from navigation crew) announces and informs the scientific team and technology team in the middle level via radio. So, the scientific team prepares and gets their instruments ready when the station arrives. I saw efficient communication and collaboration between all teams. Without this, this expedition would not be completed successfully.
I have also seen that safety is the first priority on this oceanic ship. When any crew member works in a middle deck such as CTD, Net Tow etc, they have to wear a hard hat and life jacket. People are always in closed toe shoes. It is required for any first timer on the boat to watch a safety video outlining safe science and emergency protocol. People in this ship are very friendly. They are very understanding about my first time at sea, as I was seasick during my first day. I am very fortunate to be a part of this team.

The food on the ship is delicious. Melissa, the chef prepares hot served breakfast, lunch and dinner for us. Her deserts are very delicious, and I think I am going to have to exercise more once I come back to reduce the extra weight gained from eating her delicious creations!

Watch TV, play cards and have dinner together

Watch TV, play cards and have dinner together

My shift is from 5 a.m. to 5 p.m. and I work with Rachel and Grant. After working long hours, we watch TV, play cards and have dinner together. I am learning and enjoying this expedition on the ship Research Vessel Walton Smith.

Question of the Day:

Why we do water testing in different areas of river and ocean?

New word:

Colored dissolved organic matter (CDOM)

Something to think about:

How to prevent dead zone in an ocean?

Animals Seen Today:
Two trigger fishes
Three Moon Jelly fishes
Five Crabs

Did You Know?
In ship, ropes called lines, kitchen called galley, the place where you drive your ship is called bridge or wheel house.

Amanda Peretich: CTD and XBT – More Acronyms? July 8, 2012

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

Mission: Pollock Survey
Geographical area of cruise:
Bering Sea
July 8, 2012

Location Data
Latitude: 57ºN
Longitude: 172ºW
Ship speed: 11.2 knots (12.9 mph)

Weather Data from the Bridge
Air temperature: 6ºC (42.8ºF)
Surface water temperature: 7ºC (44.6ºF)
Wind speed: 2.5 knots (2.9 mph)
Wind direction: 156ºT
Barometric pressure: 1020 millibar (1.0 atm, 765 mmHg)

Science and Technology Log
Today’s post is going to be about two of the water profiling devices used on board the Oscar Dyson: the CTD and XBT.

CTD stands for Conductivity, Temperature, and Depth. It’s actually a device that is “dropped” over the starboard side of the ship at various points along the transect lines to take measurements of conductivity and temperature at various depths in the ocean. On this leg of the pollock survey, we will complete about 25-30 CTD drops by the end. The data can also be used to calculate salinity. Water samples are collected to measure dissolved oxygen (these samples are analyzed all together at the end of the cruise). Determining the amount of oxygen available in the water column can help provide information about not only the fish but also other phytoplankton and more. Although we are not doing it on this leg, fluorescence can also be measured to monitor chlorophyll levels.


From left to right: getting the CTD ready to deploy, the winch is used to put the CTD into the water, the CTD is lowered into the water – notice that the people are strapped in to the ship so they don’t fall overboard during deployment

DYK? (Did You Know?): What exactly are transect lines? Basically this is the path the ship is taking so they know what areas the ship has covered. Using NOAA’s Shiptracker, you can see in the photo where the Oscar Dyson has traveled on this pollock survey (both Leg 1 and Leg 2) up to this point in time.

Transect Lines

Using NOAA’s Shiptracker, you can see the transect lines that the Oscar Dyson has followed during the pollock cruise until July 8. The ship started in Dutch Harbor (DH), traveled to the point marked “Leg 1 start” and along the transect lines until “Leg 1 end” before returning to DH to exchange people. The ship then returned to the point marked “Leg 2 start” and followed transect lines to the current location. The Oscar Dyson will return to DH to exchange people before beginning Leg 3 of this survey and completing the transect lines.

Deploying the CTD

I was lucky enough to be able to operate the winch during a CTD deploy. The winch is basically what pulls in or lets out the cable attached to the CTD to raise and lower it in the water. Special thanks to the chief boatswain Willie for letting me do this!

The CTD can only be deployed when the ship is not moving, so if weather is nice, we should just stay mostly in one place. The officers on the bridge can also manually hold the ship steady. Or they can use DP, which is dynamic positioning. This computer system controls the rudder and propeller on the stern and the bowthruster at the front to maintain position.

Here is a video from a previous Teacher at Sea (TAS) about the CTD and showing its “drop” into the water: Story Miller – 2010. Another TAS also has a video on her blog showing the data being collected during a CTD drop: Kathleen Harrison – 2011.



The thermocline is the area where the upper isothermal (mixed) layer meets the deep water layer and there is a decline in temperature with increasing depth.

XBT is the acronym for the eXpendable Bathymetric Thermograph. It is used to quickly collect temperature data from the surface to the sea floor. A graph of depth (in meters) versus temperature (in ºC) is used to find the thermocline and determine the temperature on the sea floor.

DYK? Normally, temperature decreases as you go farther down in the sea because colder water is denser than warmer water so it sinks below. But this is not the case in polar regions such as the Bering Sea. Just below the surface is an isothermal layer caused by wind mixing and convective overturning where the temperature is approximately the same as on the surface. Below this layer is the thermocline where the temperature then rapidly decreases.

The MK-21IISA is a bathythermograph data acquisition system. This is a portable (moveable) system used to collect data including ocean temperature, conductivity, and sound velocity and various depths using expendable probes (ones you can lose overboard and not get back) that are launched from surface ships. The depth is determined using elapsed time from surface contact and a known sink rate.

There are three different probes that can be used with this data acquisition system:
1. XBT probe – this is the probe that is used on OD, which only measures water temperature at various depths
2. XSV probe – this probe can measure sound velocity versus depth
3. XCTD probe – this probe measures both temperature and conductivity versus depth

On the XBT probe, there is a thermistor (something used to measure temperature) that is connected to an insulated wire wound on two spools (one inside the probe and one outside the probe but inside the canister). The front, or nose, of the probe is a seawater electrode that is used to sense when the probe enters the water to begin data collection. There are different types of XBT probes depending on the maximum depth and vessel speed of the ship.

XBT Canister and Probe

This shows a sideview (left) and topview (middle) of the canister that houses the probe (right) released into the water during an XBT.

There are really four steps to launch the XBT probe using the LM-3A handheld launcher on board:
1. Raise contact lever.
2. Lay probe-containing canister into cradle (make sure to hold it upwards so the probe doesn’t fall out of the canister!).
3. Swing contact level down to lock in canister.
4. Pull release pin out of canister, aim into ocean, and drop probe.
Important: the wire should not come in contact with the ship!

Launching an XBT

“Launching” an XBT probe from starboard side on the Oscar Dyson. There is no actual trigger – you just make a little forward motion with the launcher to allow the probe to drop into the water.

Be sure to check out the video below, which shows what the data profile looks like as the probe is being dropped into the water. An XBT drop requires a minimum of two people, one at the computer inside and one outside launching the probe. I’ve been working with Scientist Bill and ENS Kevin to help out with the XBT launches, which also includes using the radios on board to mark the ship’s position when the probe hits the water.

Personal Log

Quickest Route?

We’ve been taught in school that the quickest way from point A to point B is a straight line, so you’d think that the red voyage would be the fastest way to get from Seattle, Washington across the Pacific Ocean to Japan. But it’s actually a path up through Alaska!

It’s been a little slow on the trawling during my shift recently, so I’ve had some extra time to wander around the ship and talk to various people amidst researching and writing more blog posts. I think one of my favorite parts so far has been all of the great information I’ve been learning up on the bridge from the field operations officer, LT Matt Davis.

DYK? When looking at the map, you’d think the quickest route from Seattle, Washington to Japan would be a straight line across the Pacific Ocean. But it’s not! Actually, ships will travel by way of Alaska and it is a shorter distance (and thus faster).

View from the Bow

View from the bow of the Oscar Dyson.

Vessels  use gnomonic ocean tracking charts to determine the shortest path. Basically a straight line drawn on the gnomonic projection corresponds to a great circle, or geodesic curve, that shows the minimum path from any two points on the surface of the Earth as a straight line. So on the way to Japan from Seattle, you would travel up through Alaskan waters, using computer software to help determine the proper pathway.

I’ve also had some time to explore a few other areas of the ship I hadn’t been to before. I’ve learned some new lingo (look for this in an upcoming post) and plenty of random facts. One of the places I checked out is the true bow of the ship where, if I was standing a bit higher (and wearing a PFD, or personal flotation device), I’d look like I was Rose Dawson in one of the scenes from Titanic.

Animal Love
All of the time I spend on the bridge also allows for those random mammal sightings and I was able to see a few whales from afar on July 7!

Whale Sighting

Whale sighting from the bridge! You have to look really closely to see their blow spouts in the middle of the photo.