EXPRESS – NOAA Teacher at Sea Blog

September 10, 2024September 10, 2024

Lisa Werner: eDNA Studies, September 6, 2024

NOAA Teacher at Sea

Lisa Werner

Aboard NOAA Ship Bell M. Shimada

August 29-September 13, 2024

Mission: EXPRESS Project

Geographic Area of Cruise: Pacific Coast, near Northern California

Date: September 6, 2024

Weather Data from the Bridge (Mendocino Ridge Essential Fish Habitat Conservation Area):

Latitude: 40º18.178’ N

Longitude: 124º48.470’W

Wind Speed: 5.87 knots

Air Temperature: 14.3ºC/57.74ºF

Conditions: Foggy

Science and Technology Log

There are many methods of studying the ecosystem of the ocean on the mission that I am on, and another method we are utilizing is that of Environmental DNA (referred to as eDNA). Every living organism in the ocean leaves behind traces of its existence. Much like humans shed skin cells and hair, and cats and dogs shed fur, ocean organisms leave behind skin, scales, and waste products. These artifacts contain DNA, and can last in the water for anywhere from 7 to 21 days. Scientists have ways of collecting eDNA using the CTD (Conductivity, Temperature, and Depth) rosette.

view up the starboard deck of the ship as a large apparatus - a circle of gray cylinders contained in a metal frame - is hoisted above the ocean surface by a davit arm. four crewmembers wearing hard hats and life vests stand on deck watching. the sky is gray clouds, and the ocean is calm. — *Deploying the CTD*

top down view of the CTD rosette as it is lowered into the water — *CTD off the side of the ship.*

A CTD rosette is a device that is routinely lowered off of the ship to monitor the temperature and conductivity of the water at measured depths in the water column. NOAA Ship Bell M. Shimada’s rosette has 12 containers, called Niskin bottles, that are opened before deployment, and then triggered at different depths one at a time as the rosette ascends, trapping the water from that depth inside. Separate from these collections, sensors analyze the temperature, salinity (salt levels), pressure, dissolved oxygen, turbidity (cloudiness), and other useful information. The data collected from the CTD shows up instantaneously on a computer screen aboard the ship.

photo of a computer screen showing two side by side graphs. we can see different colored lines on the graphs - which have depth as the y axis - but it is hard to make out details on the graphs. — *Data coming in from the CTD dive*

To collect eDNA, the scientists look at where the biggest temperature changes happen (called the thermocline). Once the CTD is back aboard the ship’s deck, the scientists pump the water collected in the Niskin bottles triggered at the depths surrounding the thermocline through a filter. The eDNA material is collected and strained into this filter, where it is preserved to be sent to a lab for further analysis. Once the eDNA gets to the lab, scientists look at the DNA “fingerprints” left behind by organisms and match them to a database of known DNA. The scientists then have knowledge of what organisms were present in that location in the ocean at the depths those samples were collected from.

fairly close-up view of a woman wearing an orange hard hat, a purple jacket, and purple latex gloves, crouching near the CTD rosette and the net-covered rail of the ship's deck. she grasps a sort of hose in her left hand and uses her right to point to a small filter attached to the hose. — *Scientist Alice Kojima-Clarke pointing out the eDNA filter*

This goes hand in hand with the work I blogged about last on the MultiNet. The identification of the plankton that Jenn is doing is part of the work that goes into the database helping scientists identify DNA from the eDNA samples.

Personal Log

I’ve gotten a lot of questions about what the food is like on the ship, and anyone who knows me knows that food is a big part of my life! The ship’s cook, Ronnie, is amazing. He cooks the food from scratch, and it is not uncommon to see meatballs being rolled out for the next meal, or other prep taking place. The meals are served buffet-style, and there is no shortage of food. Even the pickiest eater would be happily satisfied here.

view of a computer screen reading: MENU SEPT 4, and listing the food options available at breakfast, lunch, and dinner. dinner options include chicken schnitzel, pork chops, vegetable couscous. — *The menu from a few days ago*

top down view of a metal food service bar, with labels pointing out roasted lamb, fried rockfish, garlic potatoes, etc. — *Dinner from tonight*

For Labor Day, we got to have a cookout on the ship’s back deck. It was quite the feast, featuring all of the grilled meat and fixings you could want.

a man stands at a grill flipping chicken patties as the fire leaps up from the coals. — *Grilling steaks for Labor Day*

Also, if at any meal you ‘forget’ to take dessert, Ed, the steward, will remind you. He’s always looking out for your best interest! He also always has the best jazz music playing in the kitchen.

view into the galley of a man standing at a metal sink washing dishes; in the background another man carries metal trays to a counter. — *Ed always has the biggest smile on his face – you can tell he takes great pride in his job! Ronnie is in the background, and his food is spoiling us!*

Finally, I have to take a minute to wish my Dad a happy birthday! I had some cake to celebrate you today, Dad!!!

close-up view of a large piece of red velvet cake on a serving plate; the cake is iced with white frosting and topped with chocolate curls. — *I saved you a piece of Red Velvet Cake!*

Music Connections

In looking at how the eDNA analysis works, I’m going to compare it to listening to an audio recording of a high school band. When a person listens to a recording of the band, they can tell what instruments are represented in the recording. For example, you may notice that there are flutes, oboes, clarinets, and saxophones, but perhaps the band is missing a bassoonist. If the group does a really good job of section playing, you would have a very tough time picking out HOW MANY flutists are in the recording. You may be able to hear that there are a lot of them, based on the depth of sound you hear throughout the dynamics being played, but you could not say with any confidence whether there are 7, 8, or 9 flutists. You also would not know whether one of the high school students was absent that day, or whether a guest was playing on the recording as well. The process of eDNA analysis is the same way – scientists can tell what was present in that one snapshot of time, based on the DNA present in the sample. They cannot tell you how many of each organism is present, or whether those organisms live there or were merely just migrating through the area.

For today’s audio clip, I recorded the ship’s horn being blown as a result of the reduced visibility from the fog. I learned that there are several different patterns for the horn to blow, and the example I have for you here is the long fog horn blast followed by two short blasts, signaling that we are unable to change course (in this case, due to the fact that we are acoustically tethered to the AUV that was in the water at the time)

The ship’s fog horn

Student Questions

Students asked me to be on the lookout for dolphins. On our third day at sea, we saw a whole pod of dolphins right next to the ship! Here’s a very short video to watch them all, and I am not zoomed in at all with my phone!

Pod of dolphins swimming past NOAA Ship Bell M. Shimada

September 2, 2024September 2, 2024

Lisa Werner: Popoki Goes to Sea, August 30, 2024

NOAA Teacher at Sea

Lisa Werner

Aboard NOAA Ship Bell M. Shimada

August 29-September 13, 2024

Mission: EXPRESS Project

Geographic Area of Cruise: Pacific Coast, near Oregon

Date: August 30, 2024

Weather Data from the Bridge (Daisy Bank)

Latitude: 44.37 º N

Longitude: 124.44º W

Wind Speed: NW at 3.17 knots

Air Temperature: 15.7° Celsius (60.26° F)

Conditions: Foggy

Science and Technology Log

Today was the first deployment of the autonomous underwater vehicle (or AUV) for this sailing. The AUV’s name is Popoki ‘Eiwa (which is Hawaiian for ‘Cat Nine,’ and refers to Popoki’s catlike stealth, and the fact that this is the ninth one of this class of AUVs). There was a lot of prep work done yesterday to make sure Popoki was ready for her first outing for this trip (though she has had close to 300 deployments, according to Chief Scientist Dr. Elizabeth Clarke).

Crewmembers on the deck of the ship surrounded a large piece of scientific equipment suspended above the deck's surface by a cable. It is made of two yellow cylinders, each tapered on one end, mounted one above the other by metal beams. There is propeller mounted vertically midway across the front metal beam. There is another propeller mounted horizontally atop the lower cylinder. We can also see instrumentation, a red flag sticking up out of the bag, the NOAA symbol and the name Popoki. Crewmembers wear hard hats and float vests or life vests. — *Preparing to deploy Popoki*

An autonomous underwater vehicle (AUV) is unique because it is not tethered to NOAA Ship Bell M. Shimada in any way. The AUV must be programmed to do what the scientists want. The advantage of Popoki over other submersibles is that Popoki hovers a few meters over the ocean floor, so it can handle rocky terrains better. While underwater, Popoki takes pictures of the ocean floor every few seconds, allowing scientists to see fish, coral, and the marine habitat of the location.

Images from Popoki

underwater image of what must be corals - a few small fish swim nearby — Small fish swim among the deep-sea corals

underwater image of a skate swimming across sandy bottom — A skate swims along the ocean bottom

underwater view of an orange sea star with as many as 22 arms, on sandy bottom — An orange sunflower sea star

underwater view of a striking orange and pink fish, probably a rockfish of some sort, above ocean floor with some rocks and corals — A rockfish

underwater view of a mottled brown fish resting on a rocky bottom, near a white coral — Fish spotted near the ocean bottom

The first thing necessary for Popoki’s deployment today was to have a Green-Amber-Red (GAR) Daily Risk Assessment Meeting. This took place on the bridge, and Chief Scientist Dr. Clarke and her science team met with Commanding Officer Gibson and her ship crew. Both parties looked at current conditions and the necessary actions of the deployment, mission, and recovery of the AUV. They assessed categories such as resources, weather, and mission complexity to determine whether conditions were acceptable for a deployment today. Everyone communicated questions and concerns about the mission objectives. In the end, it was decided the mission was an Amber level – meaning to use extra caution. This is normal for the first deployment of a sailing, as there are new crew involved who have never dealt with Popoki before. Also, during the dive, the ship needs to be able to stay in a position to communicate with the AUV. The risk assessment served as a reminder to everyone to pay very close attention to everything that was going on and to communicate effectively and efficiently to get the job done.

After some deck testing, it was time to get Popoki to sea. She was hoisted off of the deck using the ship’s winch and side a-frame, and then gently lowered to the water. It takes many crew members to make sure that the 600-lb. Popoki does not get hurt or that she does not rub along the side of the ship.

Popoki was deployed a little before 10 am, and recovery started around 2:30 pm. She has a very busy work day (the subsequent dives for our trip will be around 7 hours), and Jeff Anderson, AUV pilot and scientist, will have a busy evening of analyzing the pictures she is bringing back. The recovery process is fascinating to watch, as it is an intricate dance of ship control by the highly skilled bridge of the ship, and the scientists and deck crew with impressive skill trying to wrangle the AUV with lines, hooks, and the winch. No easy feat for sure, though they certainly made it look less difficult than it was! Popoki will be deployed every day of this sailing, weather permitting.

view over the ship's railing of the autonomous underwater vehicle in the water on its return. from the surface, we can only see one of the two yellow cylinders that make up the instrument's body. We also see the red flag mounted on the back. Crewmembers farther down the deck extend hooks on poles, connected to winch cables, toward the swimming AUV. The ocean is fairly calm, and gray, reflecting a foggy gray sky. — *Hooking the Popoki to bring her back*

view down the ship's railing as crewmembers wearing hard hats and life vests use hooks on poles, and cables, to hoist the autonomous underwater vehicle out of the water; in this view it is suspended just above the ocean surface, dripping water. The ocean is calm and gray, reflecting a gray foggy sky. — *Hoisting Popoki back onboard to the ship*

Popoki does not just bring back pictures – she has a sophisticated collection of sensors that will graph the salinity, dissolved oxygen, and temperature, along with graphs that monitor the use of her propellors, battery usage, buoyancy, etc. It is really impressive to see all that she has encountered during the entirety of her dive.

photo of a computer screen displaying a graph labeled "Depth vs Time," with Mission Time as the x-axis and Depth as the y-axis. There is a dark purple line and a green line displaying the data. — Data showing Popoki’s different depths over the time of her dive – notice how many peaks and valleys occur – that’s a lot of shifts for ocean floor terrain, telling us it is very rocky and a lot of terrain changes below Popoki

Personal Log

I really enjoyed being a part of the risk assessment meeting and noticing how important it was that every person involved in the deployment, operation, and return of Popoki had all of the information of the day’s agenda. Every aspect of the day’s goal was planned, with every person aware of which portion he/she was responsible for. Although I don’t necessarily need to assess the risks involved with holding a music concert, the coordination of communication reminded me a lot of how big music events run at our school. Every person in our school – teachers, students, custodians, parent volunteers – all have a very important role to play in the success of the concert. The risk assessment for Popoki gave me a new perspective on how to best address all of the moving pieces necessary to communicate the needs for the concert, and the involvement of everyone in the success of the event!

Additionally, the pictures that came back from Popoki were so impressive to see, even while unedited (the computer runs a color-correction program). It is truly remarkable how the majority of people can be floating above 300 meters of water and never know what is directly below us! It was like looking at pictures from an oceanography documentary, except knowing that I was right above what was being shown on the screen. Seeing something that so few people get to see while being in the location the pictures were taken is an incredible experience! I am just in awe!

view over a man's shoulder of the laptop that he is working on. The laptop displays a black-and-white image of coral. The man sits at a metal desk or bench and uses an attached computer mouse with his right hand. In front of him is a cloudy window through which we can see an exterior ship railing. — *AUV Pilot and Scientist Jeff Anderson looking at initial images from the AUV.*

Music Connection

I did not talk about this up above, because I really wanted to discuss this here in the Music Connection: How do you think scientists on NOAA Ship Bell M. Shimada communicate with Popoki?

If you guessed through the use of sound, you are correct! The technology is similar to that of a fax machine – a computer translates the programming from the scientist into a series of audio tones that are sent to Popoki. Popoki communicates back with a set of digital signals. It is a complicated oscillation of pitches in a variety of rhythms from the scientist doing the programming, a handoff period (because you do not want both the ship and Popoki transmitting at the same time), and then tones of different durations from Popoki responding with what actions she is doing (confirming the commands being followed, documenting images being recorded, recording position, etc.).

This is a sample of the audio coming from Popoki during her testing on the deck of the ship before deployment.

Student Questions

The students I teach made up a list of questions for me to get answers for them, which I called “Homework for your Teacher.” One of the questions they asked was if there were any jellyfish in the area I was going to be. After my visit to the aquarium, I learned that Moon Jellyfish were in the area. Today, while I was on the bridge, Ops Officer Lt. Jaime Hendrix showed me a jellyfish that we could see in the water, as it was near the surface. It was incredible to see a jellyfish outside of an aquarium, and I was impressed I could see the Moon Jellyfish all the way up on the bridge!

August 31, 2024August 31, 2024

Lisa Werner: Introduction to OREGON (Not Alaska!) – August 29, 2024

NOAA Teacher at Sea

Lisa Werner

Aboard NOAA Ship Bell M. Shimada

August 29 – September 13, 2024

Mission: Expanding Pacific Research and Exploration of Submerged Systems (EXPRESS) Project

Geographic Area of Cruise: Pacific Coast, near Southern Oregon and Northern California

Date: August 29, 2024

Weather Data (Newport, OR)

Date: 08/29/2024
Time: 0730
Latitude: 44.6°N
Longitude: 124.05°W

Science and Technology Log

Originally I was scheduled to be a part of NOAA Ship Fairweather‘s hydrography mission, but ship repairs have changed my assignment. I am now going to be on NOAA Ship Bell M. Shimada, working on the EXPRESS mission. EXPRESS stands for Expanding Pacific Research and Exploitation of Submerged Systems.

This project has three main goals:

To guide wise use of living and non-living marine resources,
To inform potential offshore energy decisions, and
To improve offshore earthquake, landslide, tsunami, and nautical hazard assessments.

One of the main aspects of this larger project that I will be experiencing will be the use of an autonomous underwater vehicle (AUV) named Popoki. I am incredibly excited to see the variety of experiments being done for this project!

Before we get going on the project, I had the great fortune of getting a tour of the NOAA Fisheries Lab (part of the Northwest Fisheries Science Center) and the Hatfield Marine Science Center with Alicia Billings, a Fishery Research Biologist. Alicia showed me where her office and work spaces are, taught me about how fish ages are figured out by counting the growth bands of the otoliths (“Ear stones”), and taught me a lot about the nets used for her studies on Pacific Hake. She had just gotten back from being at sea aboard NOAA Ship Bell M. Shimada, so she had a lot of insights as to how the time at sea works and how much the scientists look forward to being able to work in the ocean environment.

close-up photo of a printed poster or bookpage. This section is titled Pacific Hake: Maximum age: 25 years. There is a photo of a hake resting on the seafloor, and two magnified images of otolith crossections. — Pacific Hake otolith example – note the rings to count!

I also had the opportunity to visit the Oregon Coast Aquarium, which had some incredible touch tanks and viewing tunnels showing the marine life of Oregon. I was able to find answers to many of the homework questions the students I teach gave me before I left (mainly about the octopus, crab, and jellyfish populations!)

view of a Pacific Giant Octopus hanging out near the window of an aquarium tank — Pacific Giant Octopus

a zookeeper wearing latex gloves kneels to offer a piece of squid to a sea otter floating on its back near the edge of the water of its enclosure — Pacific Giant Octopus

Oregon Coast Aquarium images:
(1) The students I teach really wanted to see how an octopus moves, so they will love the videos I took of this very large octopus! (2) I arrived at the aquarium just in time to see the sea otters being fed. (3) One of the 3 tunnels that immerses visitors in the sea life of Oregon.

We leave port later today, and I cannot wait to see the incredible work being done!

Personal Log

I am very excited to be sailing aboard NOAA Ship Bell M. Shimada. I am so grateful to Emily Susko for arranging this quick change (while on her week off of work) so that I could still be a part of the Teacher at Sea program, despite the delays with NOAA Ship Fairweather.

Lisa, wearing her Teacher at Sea hat and t-shirt, poses for a photo by pointing excitedly at her nameplate on a wooden door. There are three other nameplates on this door, as well as smaller papers with muster station assignments — My name is on my stateroom door!

The EXPRESS program will be an excellent example of interdepartmental work, as it will feature scientists from NOAA, University of Alaska, and the Bureau of Ocean Energy Management. Combined with the beautiful partnership between the NOAA Officer Corps (the people who run the ships) and the NOAA science team (the people working on the specific project that sails aboard the ships), it will be great to see how all of these groups of people contribute to the greater project – definitely some great lessons and examples to bring back to the students in our school!

Music Connection

Since it is my belief that music connects to everything, the last section of each blog post will feature connections to music. While I was getting a tour of the beautiful Gladys Valley Marine Studies Building from Alicia, I saw an exhibit on a musical instrument that has been made from hollow bull kelp. There was a listening station where you could hear a hollowed bull kelp being played. The beauty of this instrument is that it is environmentally responsible – the bull kelp wash ashore regularly, so they do not need to be harvested. Kelp decays quickly, so the horn must be played within a week of it washing ashore. The projects displayed were showing the collaboration between music and ecology.

photo of a printed photo and caption displayed on a wall. the image shows a single piece of bull kelp lying in the sand. Mounted beneath, the caption reads: "Bull kelp, Nereocystis leutkeana, meaning "mermaid's bladder" is an annual macroalgae. It has a lovely natural history that weaves the story of our narrative. By providing structure to the rocky subtidal, it gives life to many organisms, past and present, small and large. From tiny juvenile rockfish to massive grey whales, extinct sea cows to urchin divers, many call kelp forests home." — Picture of bull kelp. Alicia Billings mentioned that sea lions and seals sometimes hold onto the kelp while feeding.

a man wearing long orange gloves holds a stalk of bull kelp, with his right hand grasping one end as if it were a garden hose, and his left hand holding the other end of the kelp to his lips. His cheeks are puffed out from blowing into the horn. He stands on a beach with muted colors. — Picture of bull kelp. Alicia Billings mentioned that sea lions and seals sometimes hold onto the kelp while feeding.