Denise Harrington: Post Processing — Final Days, May 2, 2014

NOAA Teacher at Sea
Denise Harrington
Aboard NOAA Ship Rainier
April 20 – May 3, 2014

Geographical Area of Cruise: North Kodiak Island

Date: May 2, 2014, 23:18

Location: 57 43.041’ N  127o 152.32.388’ W

Weather from the Bridge: 13.09C (dry bulb), Wind 1 knots @ 95o, clear, 0′ swell, balmy “crazy nice weather”  say Able Seaman Jeff Mays

Our current location and weather can also be seen at NOAA Shiptracker: http://shiptracker.noaa.gov/Home/Map

Science and Technology Log

Today’s blog is all about post processing, or “cleaning up” the data and being on night shift.  It is a balmy, sliver moon night at port here, in Kodiak.  We have come a long way in the last two weeks, during which survey crews have been working hard to finalize a Cold Bay report from last season before they devote themselves entirely to North Kodiak Island. I am in the plot room with Lieutenant Junior Grade Dan Smith who is on Bridge Duty from midnight until 4 a.m. with Anthony Wright, Able Seaman.

Able Seaman Anthony Wright consults with Ensign Steven Wall about conditions on the bridge and other things.
Able Seaman Anthony Wright consults with Ensign Steven Wall about conditions on the bridge and reports “all conditions normal.”

People work around the clock on Rainier whether it be bridge watch, processing data, or in the engine room.  One thing that makes the night shift a little easier is that there is no shortage of daylight hours in Alaska: within two months, there will be less than an hour of complete darkness at night.

After watching Commander Brennan guide us north, and seeing all the work it entails,  it is a great sight to see him enjoy a 10 p.m. sunset.
After watching Commander Brennan guide us north, with all the work it entails, it is a great sight to see him enjoy a 10 p.m. sunset with his wife (by phone).

In previous blogs, I described how the team plans a survey, collects and processes data.  In this blog, I will explain what we do with the data once it has been processed in the field. Tonight, Lieutenant Dan Smith is reviewing data collected in Sheet 5, of the Cold Bay region on the South Alaskan Peninsula.  In September, 2013, the team surveyed this large, shallow and therefore difficult to survey area.  The weather also made surveying difficult.  Despite the challenges, the team finished collecting data for Sheet 5 and are now processing all the data they collected.

Cold Bay Sheet Map
Cold Bay Sheet Map.  Recall the shallow areas are shaded light blue, and as you can see much of the north end of Sheet 5 is blue.

While I find editing to be one of the most challenging steps in the writing process, it is also the most rewarding.  Through the editing process, particularly if you have a team, work becomes polished, reliable and usable.  The Rainier crew reviews their work for accuracy as a team and while Sheet 5 belongs to Brandy Geiger, every crew member has played a part in making the Sheet 5 Final Report a reality, almost.  On the left screen, Lieutenant Smith is looking at one line of data.  Each color represents a boat, and each dot represents the data from one boat, and each dot represents a depth measurement  computed by the sonar. The right screen shows which areas of the map he has already reviewed in green and the areas he still needs to review in magenta.

Dan looks for noise after midnight.
Lieutenant Smith looks for noise after midnight.

While the plot room is calm today in Kodiak, there have been times when work conditions are challenging, at best.

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The crew continues on, despite the weather, so long as work conditions are safe.

Several days ago, Lieutenant Smith taught me the difference between a sonar ping that truly measured depth, and other dots that were not true representations of the ocean floor.  Once you get an eye for it, you kill the noise quickly.  In addition, when Lieutenant Smith finds a notable rise in the ocean floor he will “designate as a sounding.”  Soundings are those black numbers on a nautical chart that tell you how deep the water is.

This line shows three colors, meaning three boats sent pings down to the ocean floor in this area.
This line shows three colors, meaning three boats sent pings down to the ocean floor in this area.

If the line has dots that rise up in a natural way, the computer program recognizes that these pings didn’t go as far down as the others and makes a rise in the ocean floor indicated with the blue line.  It is the hydrographer’s job to review the computer processed data.  One of the differences between a map and a nautical chart is the high level of precision and review to ensure that a nautical chart is accurate.

This nautical chart went through many layers of analysis, processing and review before becoming published as a  nautical chart that can be used as a legal document.
This nautical chart of Cold Bay went through many layers of analysis, processing and review before becoming published as a nautical chart that can be used as a legal document. It may be updated after Brandy Geiger and NOAA’s hydrography work in the area is completed.
This is a topographical map of the same area, Cold Bay, that provides some information about landmarks but not necessarily the same legal standing or authority.
This is a topographical map of the same area, Cold Bay, that provides some information about landmarks but not necessarily the same legal standing or authority.

NOAA has several interesting online resources with more information about the differences between charts and maps: http://oceanservice.noaa.gov/facts/chart_map.html .

Now let’s kill some noise on this calm May evening.

In this image of a shipwreck on the ocean floor most sonar pings reached the ocean floor or the shipwreck and bounced soundings back to the survey boat.  Look carefully, however, and you see white dots, representing pings that did not make it down to the ocean floor.  Many things can cause these false soundings.  In this case, I predict that the pings bounced back off of a school of fish.  Here, the surveyor kills the “noise” or white pings by circling them with the mouse on his computer. It wouldn’t be natural for the ocean floor or other feature to float unconnected to the ocean floor, and thus, we know those dots are “noise” and not measurements of the ocean floor.

Lieutenant Smith estimates that at least half of his survey time is spent in the plot room planning or processing data.  The window of time the team has in the field to collect data is limited by weather and other conditions, so they must work fast.  Afterward, they spend long, but rewarding hours analyzing the data they have collected to ensure its accuracy and to provide synthesized information to put into a nautical chart that is easy to use and dependable. Lieutenant Smith believes that in many scientific careers, as much time or more time is spent planning, processing and analyzing data than is spent collecting data.

 

Personal Log

As we post process our data, I too, begin post processing this amazing adventure.  I am hesitant to leave: I have learned so much in these two short weeks, I want to stay and keep learning.  But at NOAA we all have many duties, and my collateral, wait–my primary duty is to my students and so, I must return to the classroom.  I will leave many fond memories and a camera, floating somewhere in Driver Bay, behind me.  I will take with me all that I have learned about the complexity of the ocean planet we live on and share my thirst to know more back to the classroom where we can continue our work. I will miss the places I’ve seen and the people I met but look forward to the road or channel of discovery that awaits me and my students.

I am also taking with me a NOAA flag, full of memories from the North Kodiak Island crew and my new friends.
I am also taking with me a NOAA souvenir flag, full of memories from the North Kodiak Island crew — my new friends.

Did You Know? The Sunflower Sea Star is the largest and fastest moving sea star travelling up to one meter per minute.

Here we taking a quick break during a tide gauge set up to look at sea stars and anemones.
Here we taking a quick break during a tide gauge set up to look at sea stars and anemones.

Below are a few photo favorites of my time at sea.

Suzanne Acord: Preparing to Embark! March 12, 2014

NOAA Teacher at Sea
Suzanne Acord
(Almost) On board NOAA Ship Oscar Elton Sette
March 17 – 28, 2014

Mission: Kona Area Integrated Ecosystems Assessment Project
Geographical area of cruise: Hawaiian Islands
Date: March 12, 2014

Personal Log

Aloha, from Honolulu, Hawaii! My name is Suzanne Acord. I teach high school social studies with Mid-Pacific Institute in Honolulu, Hawaii. More specifically, I teach Asian Studies, World History, and IB History. I also teach one Pacific Island History course with Chaminade University. In addition to teaching, I advise our Model United Nations delegation and coordinate our school’s History Day efforts.

Prior to teaching in Hawaii, I served as a Peace Corps volunteer in Yap, Micronesia. Two years of living a subsistence lifestyle in Yap helped me to understand our intimate and reciprocal relationship with our earth. Yap State Legislator, Henry Falan, sums up this relationship by stating, “In Micronesia, land is life.” Both man-made and naturally occurring disasters can be felt throughout the Pacific. World War II, El Nino, tsunamis, and nuclear testing are just a few world events that have left their mark on the Pacific Ocean. Their impacts on the reefs, the fish supplies, and the water quality are apparent daily.

Peace Corps hut
My first hut in Yap, Micronesia. I lived here while serving in the Peace Corps.

I applied for the NOAA Teacher at Sea program to gain a better understanding of the human relationship with our oceans. My history students frequently determine how our relationship with the ocean changes as a result of environmental change, political change, economic change, and cultural change. My experiences during this cruise will allow my educational community to consider real world solutions for the environmental challenges we face and will face in the future.

I couldn’t be happier to set sail on NOAA Ship Oscar Elton Sette on March 17, 2014. We will travel from Ford Island (a WWII place of interest) to the Big Island of Hawaii, which is also known as Hawaii Island. The Big Island is the largest of the Hawaiian Islands and is the home of Volcanoes National Park. Most of our time will be spent on the Kona coast of the island.  One of the many goals of the Kona Area Integrated Ecosystems Assessment Project is to gain “a complete understanding of the Kona ecosystem, from the land to the ocean…to provide scientific advice used in making informed decisions in the Kona area.”

Suzanne at desk
Anticipating the adventure in my classroom.
Photo credit: Scot Allen

The thorough NOAA Teacher at Sea training has given me peace of mind. I feel much better prepared for the TAS journey now that I have read the official requirements and the tips from past Teachers at Sea. The videos helped me to visualize the experience. Don Kobayashi, our Chief Scientist, has kept all members of the scientific expedition in the loop throughout the planning process. I was excited to see my name listed on the “science party” document and amused when I learned that my daily shift would span from 3 am to noon daily. I will surely experience amazing sunrises over the Pacific. This will definitely be an intellectually stimulating adventure!

My next blog will be written aboard the Sette. Aloha for now.

Andrea Schmuttermair: Collecting Data, June 30, 2012

NOAA Teacher at Sea
Andrea Schmuttermair
Aboard NOAA Ship Oregon II
June 22 – July 3

Mission: Groundfish Survey
Geographical area of cruise: Gulf of Mexico
Date: June 30, 2012

Ship  Data from the Bridge
Latitude: 2830.05N
Longitude: 8955.4W
Speed: 10 knots
Wind Speed: 7.11
Wind Direction: S/SW
Surface Water Salinity: 29.3
Air Temperature: 28.4C
Relative Humidity: 63%
Barometric Pressure: 1012 mb
Water Depth: 257.19m

Don’t forget to follow the Oregon II at: www.shiptracker.noaa.gov

Science and Technology Log

fish board
This is the fish board we use for measuring each critter in our sample.

Now that we’ve talked about how we collect, sort, and measure our catch, let’s take a closer look at the way we measure, weigh and sex our critters.

When measuring the critters, we use a fish board that is activated by a magnetic wand to measure the animal to the nearest millimeter.

When the fish is placed on the measuring line, we touch the magnetic wand to the board and the length is recorded into our computer program, FSCS (Fisheries Scientific Computer System).

Depending on the type of fish we catch, there are different ways to measure it.

scorpion fish total legnth
Here is Alex measuring the total length of our scorpion fish.
total length measurement
This is how we would measure a fish for its standard length, which is just before the tail fin starts.
fork length measure
This is how we would measure a fish for its fork length.
Cutlass measuring
For fish such as this cutlassfish, we measure the length from the head down to the anus, as seen here on the board.

When we are done measuring, the fish is placed on a scale to determine its weight to the nearest gram. When we confirm the weight of the fish, that weight is automatically put in the computer for us- no need to enter it manually.

Our last task is to determine the sex of the fish. For many fish, this is done by making an incision in the belly of the fish from their anus to their pelvic fins. It’s easiest to determine the sex when it is a female with eggs. In the males, you can see milt, or sperm, which is a milky white color.

male fish
This is a male fish. Notice the arrow pointing to the testes.
female fish
Here we have a female fish.

For the flatfish, you can see the female’s ovaries when you hold the fish up to the light. Males lack this feature.

male flat fish
This is a male flat fish.
female flat fish
Here we have a female flat fish- notice her gonads.

Because we were catching quite a few shrimp earlier in the leg, I got pretty good at sexing the shrimp. Remember, we take samples of 200 for each type of shrimp, and we often had more than one type of shrimp in each trawl. Male shrimp have a pestama on their first pleura to attach onto the females. The females are lacking this part. Although it’s not necessarily an indication of sex, on average the female shrimp tend to be larger than the males.

male shrimp
Here is a male shrimp.
female shrimp
Here we have a female shrimp, which is lacking a pestama.

You  know from my previous post what we do with the data we gather from the shrimp, but what about the other fish? With the other fish and critters we catch, we use the data to compare the distribution across the Gulf and to compare it to the historical data we’ve collected in the past to look for trends and changes.

Sometimes scientists also have special requests for samples of a certain species. Some scientists are doing diet studies to learn more about what certain types of fish eat.  Other studies include: species verification, geographic range extensions, age and growth, and distribution. Through our program, we have the ability to create tags for the scientists requesting the samples, allowing us to bag and freeze them to send to labs when we return to land.

showers
There are 2 communal showers for our use on the bottom deck.

Personal Log

I’ve had a few people ask me what the living quarters and the food is like on the ship, so I wandered around the ship with my camera the other day to snap some shots of the inside of the Oregon II. There are 17 staterooms on board. Most of the staterooms are doubles, such as mine, and are equipped with bunk beds to sleep on. It makes me reminisce of my days at camp, as it’s been a while since I’ve slept on a bunk bed! We have a sink and some cabinets to store our belongings. Once a week they do room inspections to ensure our rooms are neat and orderly. Most importantly, they want to make sure that our belongings are put away. If we hit rough waters, something such as a water bottle could become a dangerous projectile.

Walter, doing what he loves

My stateroom is on the bottom deck, where there are also communal showers and toilets for us to use. We can do our laundry down here, providing the seas aren’t too rough. Most of the staterooms are on this bottom deck, as the upper 2 levels are the “living areas” of the ship. On the main deck is the galley, where we eat all our meals, or where we head to when we are trying to make it through the shift to grab a snack or a cup of coffee. This tends to be right around 4:30/5:00am for me, especially when we aren’t too busy. I’ve gotten used to the night shift now, but it still can be tiring, especially when we have a long wait in between stations. Our stewards take very good care of us, and there is always something to snack on. Meals have been pretty tasty too, with plenty of fresh seafood. My favorite!

chart room
Junie, one of the NOAA Corps officers, working in the chart room on the navigational charts

On the top deck we have the lounge, a place where we hang out in between shifts. We have quite a good movie selection on board, but to be honest we haven’t had the time to take advantage of it. They’ve kept us very busy on our shifts so far, and today is one of the first days we’ve had a lot of downtime. Outside we also have some workout equipment- a bike and a rowing machine- to use on our off time. When you set the rowing machine out on deck, it’s almost like you are rowing right on the ocean!

dive
LT Harris, LT Miller, and Chris getting ready for the dive. Jeff and Reggie help them prepare.

The other day, 2 of the NOAA Corps officers, LT Harris and LT Miller (who is also the XO for the Oregon II) and 2 of the deck crew, Chris and Tim, got ready to go out on a dive. NOAA Corps officers need to do a dive once a month to keep up their certification. Sometimes they may need to fix something that is wrong with the boat, and other dives are to practice certain dive skills. They dove in the Flower Gardens, which is a national marine sanctuary with a wide diversity of sea life. I was hoping they’d see a whale shark, but no such luck. We stopped all operations for the duration of their dive.

Favorite Catch of the Day: Here are a few cool critters we pulled up today. In addition to these critters, we also started seeing some sea stars, lots of scallops, and a variety of shells.

angel shark
An angel shark
jelly soup
How about some jelly soup?
(there are about 500 jellies in there!)
large flounder
Southern Flounder
roundel skate
A roundel skate

Critter Query: This isn’t a critter question today, but rather a little bit of NOAA trivia. 

What is the oldest ship in the NOAA fleet and where is its home port?

Don’t forget to leave your answers in the comments below!