Julia West: Science Is About the Details, March 29, 2015

NOAA Teacher at Sea
Julia West
Aboard NOAA ship Gordon Gunter
March 17 – April 2, 2015

Mission: Winter Plankton Survey
Geographic area of cruise: Gulf of Mexico
Date: March 29, 2015

Weather Data from the Bridge

Time 1600; clouds 35%, cumulus; wind 170 (S), 18 knots; waves 5-6 ft; sea temp 24°C; air temp 23°C

Science and Technology Log

We have completed our stations in the western Gulf! Now we are steaming back to the east to pick up some stations they had to skip in the last leg of the research cruise, because of bad weather. It’s going to be a rough couple of days back, with a strong south wind, hence the odd course we’re taking (dotted line). Here’s the updated map:

sampling stations 3/29/15

Here’s where we are as of the afternoon of 3/29 (the end of the solid red line. We’ve connected all the dots!


I had a question come up: How many types of plankton are there? Well, that depends what you call a “type.” This brings up a discussion on taxonomy and Latin (scientific) names. The scientists on board, especially the invertebrate scientists, often don’t even know the common name for an organism. Scientific names are a common language used everywhere in the world. A brief look into taxonomic categories will help explain. When we are talking about numbers, are we talking the number of families? Genera? Species? Sometimes all that is of interest are the family names, and we don’t need to get more detailed for the purposes of this research. Sometimes specific species are of interest; this is true for fish and invertebrates (shrimp and crabs) that we eat. Suffice it to say, there are many, many types of plankton!

Another question asks what the plankton do at night, without sunlight. Phytoplankton (algae, diatoms, dinoflagellates – think of them like the plants of the sea) are the organisms that need sunlight to grow, and they don’t migrate much. The larval fish are visual feeders. In a previous post I explained that they haven’t developed their lateral line system yet, so they need to see to eat. They will stay where they can see their food. Many zooplankton migrate vertically to feed during the night when it is safer, to avoid predators. There are other reasons for vertical migration, such as metabolic reasons, potential UV light damage, etc.

Vertical migration plays a really important role in nutrient cycling. Zooplankton come up and eat large amounts of food at night, and return to the depths during the day, where they defecate “fecal pellets.” These fecal pellets wouldn’t get to the deep ocean nearly as fast if they weren’t transported by migrating zooplankton. Thus, migration is a very important process in the transport of nutrients to the deep ocean. In fact, one of the most voracious plankton feeders are salps, and we just happened to catch one! Salps will sink 800 meters after feeding at night!


Salp caught in the neuston sample. Salps are a colony of tunicates (invertebrate chordates for you biology students – more closely related to humans than shrimp are!)

Now it’s time to go back into the dry lab and talk about what happens in there. I’ll start with the chlorophyll analysis. In the last post I described fluorescence as being an indicator of chlorophyll content. What exactly is fluorescence? It is the absorption and subsequent emission of light (usually of a different wavelength) by living or nonliving things. You may have heard the term phosphorescence, or better yet, seen the waves light up with a beautiful mysterious light at night. Fluorescence and phosphorescence are similar, but fluorescence happens simultaneously with the light absorption. If it happens after there is no light input (like at night), it’s called phosphorescence.


An example of phosphorescence. We haven’t seen it yet, but I hope to! (From eco-adventureholidays.co.uk)

Well, it is not just phytoplankton that fluoresce – other things do also, so to get a more accurate assessment of the amount of phytoplankton, we measure the chlorophyll-a in our niskin bottle samples. Chlorophyll-a is the most abundant type of chlorophyll.

We put the samples in dark bottles. Light allows photosynthesis, and when phytoplankton (or plants) can photosynthesize, they can grow. We don’t want our samples to change after we collect them. For this same reason, we also process the samples in a dark room. I won’t be able to get pictures of the work in action, but here are some photos of where we do this.

chlorophyll lab

This is the room where we do the chlorophyll readings.

We filter the chlorophyll out of the samples using this vacuum filter:

chlorophyll filter

Each of these funnels filters the sea water through a very fine filter paper to capture the chlorophyll.

The filter papers are placed in test tubes with methanol, and refrigerated for 24 hours or so. Then the test tubes are put in a centrifuge to separate the chlorophyll from the filter paper.

filter paper for chlorophyll

Some of the test tubes for chlorophyll readings, and the filter paper. This box costs about $100!

The chlorophyll values are read in this fancy machine. Hopefully the values will be similar to those values obtained during the CTD scan. I’ll describe that next.


This fluorometer reads chlorophyll levels.

While the nets and CTD are being deployed and recovered, one person in the team is monitoring and controlling the whole event on the computer. I got to be this person a few times, and while you are learning, it is stressful! You don’t want to forget a step. Telling the winch operator to stop the bongos or CTD just above the bottom (and not hit bottom) is challenging, as is capturing the “chlorophyll max” by stopping the CTD at just the right place in the water column.

Bongo graph

This is the graph that comes back from the SeaCAT on the bongo. We are interested in the green line, which shows depth as it goes down and comes back up.

The dry lab

Here I am trying my hand at the computers. The monitor on the left is the live video of what is happening on deck (see the neuston net?). Photo by A.L. VanCampen


CTD scan

This is the CTD graph after it has been completed. The left (magenta) line is the chlorophyll, and the horizontal red lines are where we have fired a bottle and collected a sample. Notice the little spike partway down. That is the chlorophyll max, and we try to capture that when bringing it back up. The colored chart shows columns of continuous data coming in.

Here’s another micrograph of larval fish. Notice the tongue fish, the big one on the right. It is a flatfish, related to flounder. See the two eyes on one side of its head? Flatfish lie on the bottom, and have no need for an eye facing the bottom. When they are juveniles, they have an eye on each side, and one of the eyes migrates to the other side, so they have two eyes on one side! Be sure to take the challenge in the caption!

Larval fish 2

There is a cutlass fish just right of center. Can you find the other one? How about the lizard fish? Hint – look back at the picture in the last post. Photo credit Pamela Bond/NOAA

Personal Log

It’s time to introduce our intrepid leader, Commanding Officer Donn Pratt, known as CO around here. CO lives (when not aboard the Gunter) in Bellingham, WA. He got his start in boats as a kid, starting early working on crab boats. He spent 9 years with the US Coast Guard, where he had a variety of assignments. In 2001, CO transferred to NOAA, while simultaneously serving in the US Navy Reserve. CO is not a commissioned NOAA officer; he went about his training in a different way, and is one of two US Merchant Marine Officers in the NOAA fleet. He worked as XO for about seven years on various ships, and last year he became CO of the Gordon Gunter.

CO is well known on the Gunter for having strong opinions, especially about food and music. He loves being captain for fish research, but will not eat fish (nor sweet potatoes for that matter). A common theme of meal conversations is music; CO plays drums and guitar and is a self-described “music snob.” We have fun talking about various bands, new and old.

CO Donn Pratt

CO Don Pratt on the bridge.

One of the most experienced and highly respected of our crew is Jerome Taylor, our Chief Boatswain (pronounced “bosun”). Jerome is the leader of the deck crew. He keeps things running smoothly. As I watch Jerome walk around in his cheerful and hardworking manner, he is always looking, always checking every little thing. Each nut and bolt, each patch of rust that needs attention – Jerome doesn’t miss a thing. He knows this ship inside and out. He is a master of safety. As he teaches the newer guys how to run the winch, his mannerism is one of mutual respect, fun and serious at the same time.

Jerome has been with NOAA for 30 years now, and on the Gunter since NOAA acquired the ship in 1998. He lives right in Pascagoula, MS. I’ve only been here less than two weeks, but I can see what a great leader he is. When I grow up, I want to be like Jerome!

Jerome Taylor

Chief Bosun Jerome Taylor, refusing to look at the camera. No, he’s not grilling steaks; he’s operating the winch!


Challenge Yourself!

OK, y’all (yes, I’m in the south), I have a math problem for you! Remember, in the post where I described the bongos, I showed the flowmeter, and described how the volume of water filtered can be calculated? Let’s practice. The volume of water filtered is the area of the opening x the “length” of the stream of water flowing through the bongo.

V = area x length.

Remember how to calculate the area of a circle? I’ll let you review that on your own. The diameter (not radius) of a bongo net is 60 cm. We need the area in square meters, not cm. Can you make the conversion? (Hint: convert the radius to meters before you calculate.)

Now, that flow meter is just a counter that ticks off numbers as it spins. In order to make that a usable number, we need to know how much distance each “click” is. So we have R, the rotor constant. It is .02687m.

R = .02687m

Here’s the formula:

Volume(m3) = Area(m2) x R(Fe – Fs) m

Fe = Ending flowmeter value; Fs = Starting flowmeter value

The right bongo net on one of the stations this morning had a starting flowmeter value of 031002. The ending flowmeter value was 068242.

You take it from here! What is the volume of water that went through the right bongo net this morning? If you get it right, I’ll buy you an ice cream cone next time I see you!🙂


Sunset from the Gordon Gunter as we are heading east.


6 responses to “Julia West: Science Is About the Details, March 29, 2015

  1. I love the phosphorescence picture! I hope you get to see some phosphorescence up close before returning home. Does the government make fishing policy based on the results of the plankton surveys? How long before some of the fish in your photographs become adults?

  2. Hi Zoë – Check the next post to find an answer about the adult age of fish. And yet, this research is used for fishing policy. I’ll also discuss that a little bit, but research is done on different stages of fish development, and it’s all put together to help form the policies. Also, the take by fishermen is well documented, and that becomes part of the big picture.

  3. How much work do you usually end up doing on the computers and/or technical machinery every day? Or are the different jobs you do more of a general helping and working everywhere type of experience? I love the angle of the picture of Chief Bosun Jerome Taylor. It most certainly makes it look like he is grilling something! : )

    P.S. I’m going to email you what I think the answer is to your challenge math question!

  4. Wow! This is very interesting. I am learning a lot from the posts you put up on the blog. The phosphorescence picture is amazing. The pictures are really helpful.

  5. Hi Caroline – I got your email first and didn’t realize you had commented here! When I was on the computers, I was being closely watched and coached. There are so many little steps that they weren’t going to let me have it on my own yet. Yes, I am sort of a general helper, helping out with both shifts. I do a lot of hosing of nets, and putting sample in jars.

  6. The first time I saw phosphorescence, Emalie, I was off the coast of Maine. It happens all over – I don’t know why you see it sometimes and not others. The next post is loaded with pics – I wish I had a higher quality camera! It’s a mix of pictures from my iPad and my waterproof Canon, which is getting old.

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