Alex Miller: Smooth Sailing So Far, May 31, 2015

NOAA Teacher at Sea
Alexandra (Alex) Miller, Chicago, IL
Onboard NOAA Ship Bell M. Shimada
May 27 – June 10, 2015

View of the Hatfield Marine Science Center and NOAA dock as the Shimada pulled away.



Mission: Rockfish Recruitment and Ecosystem Assessment
Geographical area of cruise: Pacific Coast
Date: Sunday, May 31, 2015

Weather Data: 

  • Air Temperature: 11.1°C
  • Water Temperature: 11.8°C
  • Overcast skies
  • Wind Speed (kts) and Direction: 15, SSE

Science and Technology Log

Last of the bridge we'll see for some time.

Last of the bridge we’ll see for some time.

We finally weighed anchor and set sail at 1032 Friday morning. Fog blanketed the shores of Newport as we passed below the Yaquina Bay Bridge and out into the channel created by the North and South Jetties. One of our last sights from shore was Chief Scientist Ric Brodeur’s wife, who had come to see us off. The fog was so thick that before we had even reached the end of the jetty her lime green jacket was hidden from view.

Emily and I and several of the other scientists watched our departure from the flying bridge, the highest observational deck on board the ship. It provides an almost unobstructed 360-degree view of the surroundings—making it perfect for Amanda’s surveys—but it’s also right next to the foghorn, which had to be blown every two minutes until we reached greater visibility. Needless to say, we all found somewhere else to watch the waves.


Visibility was low as we left Newport.

Once the ship had moved farther offshore, some of the fog cleared but the moisture in the air was still enough to cause concern for the computers so Amanda went to the bridge, an enclosed deck that houses the navigational instruments that the captain and other officers use to drive the ship. Here she began setting up her survey equipment.

Up to this point, I’d been getting a lot of great advice about handling the first few hours on board the moving ship. Some people suggested I lay down, but the go-getter in me wanted to work. Using a program that is linked to the ship’s GPS, Amanda taught me how to code the observations she was making of the seabirds and marine mammals. As she kept her eyes glued on the 90-degree quadrant made by making a quarter port (while facing the front of the ship, counter clockwise or left, for you digital folks) turn from the bow (front of the ship) (in the image at the top of this post, you can see a panoramic view of quadrant I, the port bow of the ship), she would call out codes for the species, distance from the ship and behavior of the bird she observed. If she were to spot any marine mammals–pinnipeds (pin-eh-peds) (seal and sea lions) or cetaceans (ceh-tay-shins) (dolphins and whales)–that gets entered in a separate database.

Amanda surveying from the flying bridge.

Amanda surveying from the flying bridge.

Amanda has to be prepared to work alone as she is the only ornithologist on the ship, but with a Teacher at Sea and other volunteers on board willing to learn and help out, she’s able to rely on us to share some of the work. She and I were working as quite the well-oiled machine for a solid 20 minutes before I made peace with the fact that I did not have my sea legs. To my great relief, it’s something you can sleep off.


While at sea, the most important thing to remember is to be safe, so once we had been underway for a few hours, the ship’s crew and team of scientists went through drills to practice safety protocols for two of the three significant events that could happen at sea. A 10-second blast on the horn sounded the alarm for the fire drill, and all crew and scientists mustered (gathered) in their assigned locations. Next, 7-short, and 1-long blast signaled the start of the abandon ship drill. The need to abandon ship is highly unlikely, but out at sea you need to be prepared for anything. Most importantly, you need to know how to get into your survival suit, and fast.

Emily and I decided to practice since we were both first-timers to these impressive red neoprene onesies. Since they’re designed to be large enough to fit over your shoes and warm clothes, they can be awkward to put on, especially when you get to the zipping part. And who cares how they look when the water is 8-10° Celsius, a temperature that could cause hypothermia or fatal loss of body temperature.

Emily and I managed to get the survival suits on!

Emily and I managed to get the survival suits on!


Saturday was spent sampling a little bit of everything. Of course I paid a visit to Amanda up on the flying bridge to hear about how the birding (and marine mammal-ing) was going. Often, I find Emily there assisting with data entry. Since Amanda can only survey when the ship is traveling faster than 7 knots, traveling from station to station gives her time to look, but sometimes these distances are short and our time at the stations, releasing the various equipment needed for different scientists’ data collection, can be long. This is when Amanda goes off effort (not collecting data) for longer periods of time and during these times, Emily and I have taken to teaming up to check out what’s going on in the wet lab.


Jaclyn releases the neuston tow into the water.

Home to most of the science crew, the wet lab is wet. Initially, I thought foul weather gear was meant for, well, foul weather, but between the hauling in, spraying down and rinsing of the samples caught in the nets, everyone in the wet lab is wearing theirs full-time. Also, everyone must wear hard hats and PFDs (personal flotation devices, also known as life jackets) when out on deck as the equipment is being released or hauled in. Safety first, as always!

My cabin mate, Jaclyn Mazzella, and Phil White, are the two survey technicians on the Shimada. They help release and monitor the nets and equipment that are being used on this research cruise. More on these two interesting cats later.

Emily and I working hard to haul in the CTD.

Emily and I working hard to haul in the CTD.

While in the wet lab, Emily and I witnessed the CTD being hauled in. CTD stands for conductivity, temperature and depth. Conductivity is a measurement of salinity, or how salty the ocean water is. The way it works is by passing an electric current through the water and measuring how fast it travels. This is connected to how salty the water is because when salt is dissolved in water, it separates into ions, these particles carry a charge and allow electric current to pass through. More conductive water will be salty, less conductive water will be less salty or fresh. 

We know that temperature provides a measurement of how hot or cold something is. In this case, we’re measuring the temperature of the water. It is mostly cold off the Oregon coast, though the scientists on board have been discussing a recent unexplained area of warmer water, dubbed the “warm blob.” Biologists aim to discover if the warm blob is going to have an impact on the fisheries.

As the CTD is lowered and raised, it can take measurements of these and other factors which allow biologists to compare the diversity and number of species they collect in their nets to the data collected. One of those nets is the neuston tow, a net that skims the surface of the water. It is one of several nets that are being used to collect samples from different layers of the ocean. The scientists on board expect to find jellies and larvae of different species in this net.

Curtis filters the cod-end of the neuston and finds a whole bunch of Vallela vallela.

Curtis filters the cod-end of the neuston and finds a whole bunch of Vellela vellela.

I got a chance to see the neuston being released. After it was hauled in, Dr. Curtis Roegner, a fisheries biologist with NOAA, detached the cod-end–a small container at the bottom of the net that collects everything the net caught–and filtered out the contents. Inside were a bunch of beautiful blue jellies! These guys are commonly known as by-the-wind sailors thanks to their interesting sail adaptation that allows them to harness the power of the wind to aid in their dispersal (scattering) throughout the ocean. I helped Sam Zeman, a biologist with the University of Oregon, Tyler and Curtis measure the diameter–the length at the widest point–of the bodies of the jellies.

Vallela vallela, by the wind sailors.

Vellela vellela, by the wind sailors.

Curtis, Tyler and I working to measure and record the lengths of the sails on the Vallela vallela. (Thanks to Sam for taking this picture!)

Curtis, Tyler and I working to measure and record the lengths of the sails on the Vellela vellela. (Thanks to Sam for taking this picture!)

Personal Log

The more time I spend on the Shimada, the more determined I am to figure out how time travel works so I can go back and thank my September 2014 self for putting in the Teacher At Sea application. I’ve been on the ship for three days now and I love being able to go anywhere, day or night, and be able to observe and assist in research and data collection, but also just sit and talk with people who have all followed many different paths that led them to this ship, for these two weeks.

You might think my biggest struggles right now would be seasickness (which I’m not!) or missing my friends and family, but honestly, the hardest part is keeping the blog down to a readable length. There’s an enormous amount more happening here than I have the room to tell you but I will try and cover everything before our time is up.

Lastly, it’s true, I miss my friends and family, a lot, but there are certain creature comforts here that help ease the transition from land to sea. NOAA certainly knows how to keep morale and productivity up, with a well-stocked kitchen open 24 hours, meals prepared on site by talented cooks, and a TV lounge for socializing with a selection of over 500 movies, it’s easy to feel at home. And when finding a work-life balance is not possible, it’s necessary, all of this helps.

Well, that’s all for now, catch the next installment coming soon to a computer screen or mobile device near you!


Special thanks to Prof. Mary-Beth Decker consulting on the spelling of Vellela vellela and Brittney Honisch for teaching me a good way to remember port vs. starboard. When facing the front of the ship, port is left and both words have four letters.

Christina Peters: Finding Plankton on Oregon II, July 13, 2013

NOAA Teacher at Sea
Chris Peters
Onboard NOAA Ship Oregon II
July 10 – 19, 2013

Mission: SEAMAP Summer Groundfish Survey
Geographic Area of Cruise: Gulf of Mexico, leaving from Pascagoula, MS
Date: July 13, 2013 

Weather and Location:
Time: 23:24 Greenwich Mean Time (7:24 p.m. in Rockville, MD)
Latitude:  25.5340
Longitude:  -82.0215
Speed (knots):  9.30
Water temperature:  28.90 degrees Celsius
Salinity (PSU = Practical Salinity Units): 35.38
Air temperature:  31.20 degrees Celsius
Relative Humidity:  65%
Wind Speed (knots):  8.92
Barometric Pressure (mb): 1013.34
Depth (m) = 19.20

Science and Technology Log

Our Mission

In my introduction I explained that SEAMAP is a state, federal, and university program.  In fact, there is a managing unit called the SEAMAP– Gulf Subcommittee of the Gulf States Marine Fisheries Commission’s Technical Coordinating Committee who manages the activities and operations, including collecting samples and interpreting data, of the Gulf participants, including the Mississippi Laboratory of NOAA and the states of Louisiana, Mississippi,Texas, Alabama, and Florida, as well as certain universities.  Parts of the program include bottom trawls, CTD deployment, and Bongo and Neuston tows.  The bottom trawls involve towing nets at randomly selected spots for ten to thirty minutes. The sea life caught in the nets, normally shrimp and other animals that live at the bottom of the Gulf, are sorted, identified and measured.  All of the data is recorded and helps to determine where the fish and shrimp are, and how much exists in the Gulf.  Because the NOAA Laboratory and the states have worked so well together on this project, most of the trawls were completed on earlier legs of the trip and on the state boats.  We have had opportunities, though, to observe and identify some of the fish from an earlier leg that had been put on ice.  We’ll come back to that process a bit later.

The first twenty-four hours underway were spent heading to our first station, off the southwest coast of Florida.  We have spent much of our time on this leg of the trip completing plankton collections.  My students should remember that plankton includes small and microscopic (too small to see with only your eyes) organisms. The organisms may be animals, plants and plant-like organisms, or bacteria.  The plankton found in the water can tell what the animal population looks like, or will look like if the conditions of the water do not change too much.  Plankton is also a source of food for certain animals, so looking at plankton can give us information about whether enough of a food source is present for those animals.  The purpose of the Bongo and Neuston tows is to collect plankton.  Before we do those tows at each station, however, we deploy the CTD to collect some important information.

Bringing in the CTD

A scientist and deckhand help bring in the CTD

Taking water samples from the CTD

The chief scientist, Kim Johnson, takes water samples from the CTD to verify it’s dissolved oxygen readings.

CTD stands for Conductivity, Temperature, and Depth.  The machine collects data in those areas, as well as other data.  The conductivity data tells how much salt (salinity) is in the water because the amount of salt affects how well the water will conduct (allow to pass through) electricity.  The CTD also measures the oxygen content of the water.  Remember learning about algae bloom in the Chesapeake Bay, and how the algae sucks up all of the oxygen, leaving the plants and animals in the area to die?  When a body of water has an unhealthy level of oxygen, it is called hypoxic.  Scientists are worried about the same kind of thing happening in the Gulf of Mexico, so determining the oxygen content in the water provides important information.  In the stations we have tested so far, the oxygen content has been healthy.  However, we have been far from land and much closer to where the Atlantic Ocean meets the Gulf.  To learn more about hypoxia in the Gulf of Mexico, visit NOAA’s hypoxia page.  Don’t forget to click on the links at the bottom that will take you to descriptions of the problems and causes of hypoxia in the Gulf.

After bringing the CTD back onto the deck, it is time to start a Neuston tow.  The Neuston net is very fine, and attaches to a one meter by two meter frame at the top.  The net gets narrower, and attaches to a “cod end”, a plastic cylinder with screened openings, at the bottom.  This is hoisted out of the boat and into the water by a crane.  It takes several people to launch the Neuston, as the frame is heavy, and it can be hard to manage in the wind.

Neuston net before deployment

The Neuston net is tied down to the boat until it is ready to be deployed.

The Neuston is pulled through the water, with about a foot above the surface, and the rest below.  The purpose is to collect plankton on or near the surface of the water.  Since sargassum, or seaweed, often floats on the surface of the water, sometimes the Neuston collects a lot of that.  We continue to tow the net for ten minutes, and then retrieve it into the boat, again using the crane.  While we did not do trawls and pull in large fish, we did see different kinds of baby fish at almost every station.

Neuston net

The Neuston net is dragged at the top of the water for five to ten minutes

The Bongo contains two 61 centimeter, circular, sturdy plastic frames, to which fine nets are attached.  These nets also narrow to a small area, to which cod ends are attached.  The Bongos are lowered off the port side by using the J frame. The bongos are towed from the surface to the bottom, but no deeper than 200 meters.  The bongo also has the flowmeters on it to calculate how much water passes through the net. The sample is used to estimate the populations, number, and location of animals in parts of the Gulf.  The Bongo also has instruments attached to it that measure temperature, salinity (salt), and depth.  In addition, the bongos have flowmeters attached to calculate how much water passes through the nets.

Bongo nets

The Bongo nets must be rinsed down before being brought into to boat to make sure no plankton is stuck at the top of the nets.

These are complicated tools, and some of the instruments are electronic.  If the instruments are not working correctly, the scientists and engineers must have a back-up plan.  In fact, at one station, the Bongo instruments were not giving accurate readings when the head of the watch (the scientist in charge) looked at the readings from inside.  The back-up plan was for the deckhands to use less accurate depth finding instruments when lowering the Bongo.  This can sometimes present a problem because if the instruments are off, and the Bongo drags on the bottom, a lot of mud can end up in the sample.  Fortunately, a little troubleshooting, in the form of tightening some connections, solved the problem.  Sometimes it’s easy to forget to check the obvious!

Once the Neuston and Bongo are up, we can detach the cod ends, and get to work preserving the plankton samples.  The plankton from the Neuston, and from each of the Bongo cod ends, are preserved and stored separately.  The Neuston and right Bongo plankton are rinsed through a very fine sieve with a chemical solution that is mostly ethanol, and then poured through a funnel into a jar, which is finally filled with the ethanol solution.  The left Bongo plankton is handled similarly, but instead of being stored in ethanol, it is stored in salt water from the Gulf, and a small amount of formalin.  Formalin contains a small amount of formaldehyde, and is used to preserve tissues.  It is a toxic chemical that is harmful to humans, and must be handled very carefully, always using gloves.  The samples are later sent to various laboratories to be sorted and counted.  In addition to providing information about amount and location of different species, scientists can also use the preserved plankton to determine the age, as specific as the number of days old, and genetics of the baby sea animal. The formalin helps preserve the otoliths a LOT better, where the ethanol helps preserve the tissue and/or DNA better.  The otolith is part of the inner ear of the animal and is the part that is used to determine age.

Work station at the stern of the boat

The work station at the stern of Oregon II is where we rinse the plankton and add the chemicals for preservation.

Rinsing the plankton

Sometimes we have to remove jellyfish from our samples. The plankton must be rinsed off the jellyfish before counting and discarding them.

With stations normally being about three hours apart, it would seem like we should have a lot of down time.  However, when there is a lot of sargassum in the Neuston, it must be rinsed to try to get the plankton out of it.  This can take quite a long time.  In addition, sometimes we do get small fish or other animals that need to be sorted, counted, measured and weighed.


There were over 300 of these file fish in one plankton sample. The color made them difficult to find in the sargassum.

A pipe fish from one of the Neuston samples.  What does it remind you of?


Plankton sample

This is a plankton sample from a Neuston tow after it has been preserved in ethanol.

Don’t forget to track our progress by visiting and choosing Oregon II.  While you are there, don’t forget to check out the different types of maps available for tracking Oregon II.  Look in the upper left-hand corner (Streets, Topo, Imagery, NOAA Nautical Charts, and Weather).

Personal Log

Settling in and enjoying the ride

The first three days of the trip had us motoring through incredibly calm waters and sunny days.  Some of the veteran crew members commented that they had never seen the Gulf so calm.  As we traveled further from Pascagoula, the water started getting bluer and bluer.  It is hard to describe the deep blue that we sailed through and the camera just doesn’t seem to capture it.  As we left the waters around Pascagoula, we saw many large ships, possible oil tankers, and quite a few oil rigs.  However, once we passed them, we’ve barely seen another boat.  It is something to look out from the bow of the boat and see nothing but water in every direction.

A calm day in the Gulf of Mexico

A calm day in the Gulf of Mexico

As promised, the food on board is delicious. The cooks take great pride in the food they serve, and there are always choices at every meal.  We’ve had beef tenderloin, veal parmesan, omelets, fresh fruit, fresh vegetables, pasta, Mexican, chocolate custard pie, cookies, pecan pie – all homemade!  The galley is also well-stocked with snacks.  Meals are served on a strict schedule – about an hour and a half for each meal.  However, if you know you will miss a meal, the cooks are happy to set some food aside for you, nicely wrapped in the refrigerator.  Luckily for me, I have the day shift, and if I miss a meal, it is normally breakfast.

Everyone on the ship has been very encouraging and helpful.  Some of the guys did a dive and brought me back some interesting shells to share with my students.  The other scientists have been incredibly patient and helpful.  Kim, the chief scientist, is a great teacher and is always looking for opportunities for me to learn something new, or practice something I just learned!

Did you know?

The starboard side of the ship is the right side, and the port side is the left side.  Starboard comes from the old Anglo-Saxon word, “steorbord” because the steering oar was on the right side of the boat.  Because of this, the ship would pull up to the dock, or port, on the left side. This would avoid damaging the steering oar.

Questions for my students:

What unit of measurement do you think we use to measure the small fish found in the Neuston and Bongo tows?

Can you think of any sea animals that use plankton as their main source of food?  It is okay to research this before you answer!

Thank you for visiting my blog.  I hope you will check back in a few days for an update!