data – NOAA Teacher at Sea Blog

May 18, 2018

Jennifer Dean: Data Analysis and Downward Dog, May 17, 2018

NOAA Teacher at Sea

Jennifer Dean

Aboard NOAA Ship Pisces

May 12 – May 24^th, 2018

Mission: Conduct ROV and multibeam sonar surveys inside and outside six marine protected areas (MPAs) and the Oculina Experimental Closed Area (OECA) to assess the efficacy of this management tool to protect species of the snapper grouper complex and Oculina coral

Geographic Area of Cruise: Continental shelf edge of the South Atlantic Bight between Port Canaveral, FL and Cape Hatteras, NC

Date: May 17th, 2018

Weather Data from the Bridge
Latitude: 23° 29.6290’ N
Longitude: 80° 09.6070’ W
Sea Wave Height: 2-3 feet
Wind Speed: 18.2 knots
Wind Direction: 199.3°
Visibility: 8–9 nautical miles
Air Temperature: 25.3°C
Sky: Scattered clouds

Science and Technology Log

Software: ArcGIS and Microsoft Access
Data processing may be seen by some to be a less glamorous role compared to ROV operators and their joysticks. But data management is essential for communicating and validating findings of the ROV dives. Huge data sets are created on each dive. 24,000 records were created on just 2 dives that needed to be inventoried and processed.

Processing Photos — Stephanie Farrington processing the photo grabs taken every 2 minutes from the dive

Stephanie Farrington, Biological Research Specialist with Harbor Branch Oceanographic Institute at Florida Atlantic University, gave me a crash course on data management that may be better explained through some of the pictures and activities I was involved in below. Two types of software seemed of particular significance, ArcGIS and Microsoft Access.

ArcGIS screen — ArcGIS (Geographic Information System) provides layers of information

ArcGIS (Geographic Information System) provides layers of information, anything from land use patterns, topography to local data for an area on water quality or hurricane patterns. The software allows you to stack this information on top of each other geographically to look for patterns or to make graphic and visual displays of complex data sets. On May 16^th the dive gathered footage at two sites where barges were dropped to the ocean floor in 2014, one at approximately 80 meters and the other at 100 meters. After seeing that the structure had undergone considerable changes in its integrity, a question arose about the potential impact a hurricane could have made with these barge structures. The photo above is an example of a layer of information on hurricane travel patterns and how GIS might be used to make predictions on whether this sort of event could have impacted the barge wreck sites integrity.

Access is a Relational Database and is used as an information and storage management tool for larger data sets. It is less prone to errors compared to Excel and better for managing “big data”. One skill Stephanie demonstrated to me was her code writing abilities that, once written, allow the keyboard and the database to communicate with each other. As I typed in the key for “new note,” the image below with the heading on the right saying “Site Number” would pop up ready for me to enter information about the type of bottom substrate, the slope and other features of the sample site. Each of these button choices immediately populated the database and created a running record of the dive’s key features. Microsoft Access is built using SQL and uses VBA script to create macros (repeated, automatic behaviors).

The X-Keyboard was purchased from a company called P.I. Engineering and comes with its own GUI (Graphical User Interface) for programming the individual keys.

In the image below is an example of a portion of one of John Reed’s notes taken during the dive to record times, observations and coral reef communities observed. Notice that Weather, Salinity, Wind Direction and Depth are all added into the notes as well as discrepancies or issues that arise. Notes on this page demonstrate a point early in the dive when it became clear the map features between the ROV operator and Stephanie’s screen were off by many meters, this was because an incorrect Geographic Datum (the screen displaying in WGS 1984 but the ROV feed was being sent to the screen in NAD 1983 causing a false skew in the visualized data stream).

Picture taken during my lesson on where each key was coded to represent a certain feature that would automatically enter the database.

This is a section of the screen I worked within to add notes, such as written description of a metal ladder structure seen in a different location on barge then previous dive.

This is an example of a portion of one of John Reed’s notes taken during the dive to record times, observations and coral reef communities observed. Notice that Weather, Salinity, Wind Direction and Depth are all added into the notes as well as discrepancies or issues that arrive.

The bathymetric data collected by NOAA is available here for anyone to download;
https://maps.ngdc.noaa.gov/viewers/bathymetry/

The following links provides more information on the differences between Excel and Access and the advantages and disadvantages. And additional information on the uses of GIS.
https://www.weather.gov/gis/
https://webgis.wr.usgs.gov/globalgis/tutorials/arcview.htm
https://www.opengatesw.net/ms-access-tutorials/What-Is-Microsoft-Access-Used-For.htm

Personal Log

How many people can say that one of their first yoga experiences happened on the flying bridge on a NOAA ship in an offshore location in the Atlantic? LT Felicia Drummond, a newly certified yoga instructor, introduced us to Ashtanga yoga philosophy and techniques, and I finally know what the pose downward dog should look like. Ashtanga yoga philosophy focuses on breathing and balanced movements to build the strength of your core and muscles.

Classes held on the ship’s deck like this would certainly tone one’s body and improve your focus. There are standing, sitting and finishing poses. I considered myself lucky if I didn’t fall on my face or crash into the pillars with anything but a sitting pose. But it reminded me of the balance needed in life- both in the physical and mental demands we put on ourselves. Even at sea there is a need to search for these moments of time to quiet our mind.

Today I am reminded of the different ways of knowing. I have always been a bit of a bookworm, introverted and learning through textbook study. But learning through experience on this ship is a whole different level in the depth of comprehension. I am immersed in both the history and story-telling of the original discovery of these reefs by watching 1970’s footage of Professor John Reed’s first “Lock-Out” dives within Florida’s Deep-Water Oculina Reefs. At the same time I am witnessing and participating first-hand in the collection of new data in similar locations. Although it is sad to see some of the trawling devastation of the past, the regrowth of these areas and the dedication to their protection brings a positive message for me to share with my students. I am excited to share the video I watched today with them when I return and the story about a Warsaw grouper, Hyporthodus nigritus, that tried to steal calipers during Professor Reed’s coral measurements many years ago. To read more about some of Reed’s work click on the hyperlink.

Did You Know?

Hermodice carunculate, the Bearded Fireworm, bristle out their setae upon touch and those setae act like hypodermic needles to inject a powerful neurotoxin into the offending predator or careless tourist. The injury can give a sensation that feels like a fire burning for hours. It reminded me of a fuzzy underwater centipede. This creature was spotted on an ROV dive near a sunken barge at around 100 meters. Others were clustered along the walls of the barge that were encrusted with oysters and a few purple sea urchins. Seen in this image next to the Fireworm are hermit crabs.
https ://www.scienceandthesea.org/program/201701/fireworm

Fact or Fiction?

NOAA ships never leave port on Fridays. Check the links below for more information about marine operations and for Fisheries superstitions.
https://www.omao.noaa.gov/learn/marine-operations/ships
https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/archive/education/voicesofthebay/pdfs/superstitions.pdf

What’s My Story? Jason White

The following section of the blog is dedicated to explaining the story of one crew member on NOAA ship Pisces.

What is your specific title and job description on this mission? ROV Pilot/Technician. He assists in keeping the ROV running efficiently and safely. His job includes taking turns on this mission with Eric Glidden to pilot the ROV and deploy and recovery of the ROV from the ship.

How long have you worked for University of North Carolina? He has worked for University of North Carolina for almost 5 years.

What is your favorite and least favorite part of your job? Troubleshooting computer problems is his least favorite part of the job. His favorite part of the job is getting to work with different scientists from all around the United States and world on different types of scientific projects.

When did you first become interested in this career (oceanography) and why? He grew up watching the weather channel and surfing in North Carolina. Dr. Steve Lyons on weather channel and predicting surf inspired his original interest in the study of meteorology/oceanography.

What science classes or other opportunities would you recommend to high school students who are interested in preparing for this sort of career? He said if you are a student interested in the technical aspect of the study of oceanography you should look for a marine technology program at a university or community college. He uses a lot of math and physics and recommends at the high school level to take a full course load in both. He also recommends taking any available electronic classes and stay proficient in computers.

What is one of the most interesting places you have visited? His most interesting trip was in the Philippines where he ate white rice for 2 weeks straight and people were on the back deck of the ship fishing for the very same fish he was collecting video footage on. He mentioned that the Philippines had the most beautiful coral he had ever seen.

Questions from my Environmental Science Students in Camas, WA

How heavy is the ROV? With the skid on it, approximately 800 lbs

How tough is it? Moderately –you can run the ROV into things but don’t want to run into a steel ship or you break things.

How expensive is it? If it somehow broke, what would you have to do? Try and repair it on the ship with spare parts? A half-million dollars. Yes. They have spares for most everything except the high definition video camera and digital stills camera, which cost $27,000 and $32,000 respectively.

How many cameras are on the ROV and how easy is it to maneuver? 5. One main video camera to navigate the ROV, digital still camera, 3 lipstick cameras on the skid to collect samples and see with the manipulator. If there is no current then the ROV is fairly easy to maneuver but when conditions decrease by, murkiness, current (more than ½ knot) or terrain is in high relief it becomes more difficult. Ship wrecks with steel debris are also especially difficult to maneuver around.

What is the ROV like to control, does it respond quickly or is there a lag time from when you control it to when it responds? It instantaneously responds.

Do you have to have training to be able to operate it? It is on the job training however there are a few ROV specific training schools around the country.

Labelled image of ROV — A labeled diagram of an ROV

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June 25, 2013August 11, 2021

Robert Ulmer: Build Upon a Strong Foundation, June 19, 2013

NOAA Teacher At Sea

Robert Ulmer

Aboard NOAA Ship Rainier

Underway from June 15 to July 3, 2013

Current coordinates: N 56⁰35.547’, W 134⁰36.925’

(approaching Red Bluff Bay in Chatham Strait)

Mission: Hydrographic survey

Geographical area of cruise: Southeast Alaska, including Chatham Strait and Behm Canal, with a Gulf of Alaska transit westward to Kodiak

Log date: June 19, 2013

Weather conditions: 10.93⁰C, less than 0.5 km visibility in thick fog, 95.42% relative humidity, 1013.38 mb of atmospheric pressure, light variable winds (speed of less than 3 knots with a heading between 24⁰ and 35⁰)

Explorer’s Log: Survey, sample, and tide parties

Scientists are explorers, wandering the wilderness of wonder and curiosity their with eyes and minds wide open to events, ideas, and explanations that no other humans may have previously experienced. And by definition, explorers — including scientists — also are builders, as they construct novel paths of adventure along their journeys, built always upon the strong foundations of their own reliable cognitions and skill sets.

Ensign Rosemary Abbitt making a level sighting measurement

Starting from their own observations of the world around them, prior knowledge, and context, scientists inject creativity and insight to develop hypotheses about how and why things happen. Testing those ideas involves developing a plan and then gathering relevant data (pieces of information) so that they can move down the path of whittling away explanations that aren’t empirically supported by the data and adding to the collective body of knowledge, so that they and others might better fathom the likely explanations that are behind the phenomena in question.

Rainier lowering a launch vessel — NOAA Ship *Rainier* lowers launch vessel RA-5 for a survey excursion.

Because progress along the scientific path of discovery and explanation ultimately depends on the data, those data must be both accurate and precise. Often these terms are confused in regular conversation, but each word has its own definition.

Approaching the shore from the skiff — A view from the skiff of the shoreline where the benchmarks and tide gauge staff already are installed.

Accuracy is a description of the degree of closeness or proximity of measurements of a quantity to the actual value of that quantity. A soccer player who shoots on goal several times and has most of his shots reach the inside of the net is an accurate shooter. Likewise, a set of measurements of the density of a large volume of seawater is more accurate if the sample data all are near the actual density of that seawater; a measurement that is 0.4% higher than the actual density of the water is just as accurate as another measurement of the same water that is 0.4% below the actual density value.

HAST Curran McBride visually examining the condition of the tide staff — Before making more detailed data collections, Hydrographic Assistant Survey Technician (HAST) Curran first conducts a visual inspection of the previously-installed tide staff upon arriving at the shore.

Precision (also called reproducibility or repeatability), on the other hand, is the degree to which repeated measurements under unchanged conditions show the same results. If every shot attempted by the soccer player strikes the left goalpost four feet above the ground, those shots aren’t necessarily accurate – assuming that the player wants to score goals – but they are very precise. So, similarly, a set of measurements of seawater density that repeatedly is 5.3% above the actual density of the water is precise (though not particularly accurate).

HAST Curran McBride collecting data near the tide staff — HAST Curran collects data near the tide staff during the closing level run in Behm Canal.

The NOAA teams that conduct hydrographic surveys, collect seafloor samples, and gather data about tide conditions must be both accurate and precise because the culmination of their work collecting data in the field is the production of nautical charts and tide reports that will be used around the world for commerce, recreation, travel, fisheries management, environmental conservation, and countless other purposes.

Cabin of the launch vessel — Crew of the survey/sample team in the cabin of the launch vessel (and the Coxswain piloting the boat)

Hydrographic surveys of some sort have been conducted for centuries. Ancient Egyptian hieroglyphs show men aboard boats using ropes or poles to fathom the depths of the water. In 1807, President Thomas Jefferson signed a mandate establishing the Survey of the Coast. Since that time, government-based agencies (now NOAA’s Office of Coast Survey) have employed various systems of surveying depths, dangers, and seabed descriptions along the 95,000 miles of navigable U.S. coastlines, which regularly change due to attrition, deposition, glaciation, tectonic shifts, and other outside forces.

Analyzing data aboard the launch — Hydrographic Senior Survey Technician Barry Jackson and Physical Scientist Kurt Brown analyze historic and new data from multi-beam sonar aboard the launch vessel.

For most of that history, data were collected through a systematic dropping of weighted lines (called “lead lines”) from boats moving back and forth across navigable channels at points along an imaginary grid, with calibration from at least two shore points to assure location of the boat. Beyond the geometry, algebra, and other mathematics of measurement and triangulation, the work was painstakingly slow, as ropes had to be lowered, hauled, and measured at every point, and the men ashore often traveled alongside the boat by foot across difficult and dangerous terrain. However, the charts made by those early surveys were rather accurate for most purposes.

The biggest problem with the early charts, though, was that no measurements were made between the grid points, and the seafloor is not always a smooth surface. Uncharted rocks, reefs, or rises on the seabed could be disastrous if ships passed above them.

HSST Barry Jackson collecting sea floor sample — HSST Barry Jackson pulls a line hand over hand to retrieve a scooped sea floor sample from a depth of more than 45 meters in Behm Canal.

HSST Barry Jackson analyzing sea floor sample — … and then analyzes what the scoop captured: mud and gravel in this case.

Starting in the 1990s, single-beam sonar became the primary mechanism for NOAA’s surveys. Still looking straight down, single-beam sonar on large ships and on their small “launch vessels” (for areas that couldn’t be accessed safely by larger craft) provided a much more complete mapping of the seafloor than the ropes used previously. Sonar systems constantly (many times per second) ping while traveling back and forth across and along a channel, using the speed and angle of reflection of the emitted sound waves to locate and measure the depth of bottom features.

Handwritten notes about sea floor samples — Data about sea floor samples first are recorded by hand on a chart aboard the launch vessel before being uploaded to NOAA computers later.

Sound waves travel at different speeds through different materials, based on the temperature, density, and elasticity of each medium. Therefore, NOAA also deploys CTD devices through columns of surveyed waterways to measure electrical conductivity (which indicates salinity because of ionization of salts dissolved in the water, thus affecting solution density), temperature (which usually is colder at greater depths, but not necessarily, especially considering runoff from glaciers, etc.), and depth (which generally has a positive-variation relationship with water pressure, meaning more pressure – and thus, greater density – as depth below the surface increases).

CTD device about to be deployed — This CTD device measures conductivity, temperature, and depth in the water. All three affect the speed of the sound waves in water, and the speed of sound is a necessary bit of data when using sonar (which tracks reflected pings of sound) to determine the distance to the sea floor.

The most modern technology employed by NOAA in its hydrographic surveys uses multi-beam sonar to give even more complete coverage of the seafloor by sending sound waves straight downward and fanned outward in both directions as the boat travels slowly forward. Even though sonar beams sent at angles don’t reflect as much or as directly as those sent straight downward, uneven surfaces on the seabed do reflect some wave energy, thus reducing the occurrence of “holidays” (small areas not well-defined on charts, perhaps named after unpainted bits of canvas in portraits because the painter seemed to have “taken a holiday” from painting there).

Acquiring hydrographic data — FOO Mike Gonsalves and HAST Allix Slagle acquire hydrographic data with the ship’s Kongsberg EM-710 multi-beam sonar.

TAS Rob Ulmer retrieving sea floor sample in Behm Canal — Aboard the small launch vessel, everyone works. This is Teacher At Sea Rob Ulmer hauling in a sea floor sample in Behm Canal.

But that’s not all. To help sailors make decisions about navigation and anchoring – and often giving fishermen and marine biologists useful information about ecology under the waterline – NOAA also performs systematic samples of the types of materials on the sea floor at representative points in the waterways where it conducts surveys. Dropping heavy metallic scoop devices on lines* dozens of meters long through waters at various locations and then hauling them back aboard by winch or hand-over-hand to inspect the mud, sand, silt, gravel, rocks, shells, plants, or animals can be physically demanding labor but is necessary for the gathering of empirical data.

* A note about terminology from XO Holly Jablonski: Aboard the ship, lines have a job. Think of a “rope” as an unemployed line.

Additionally, Earth’s moon and sun (along with several underground factors) affect the horizontal and vertical movement of water on Earth’s surface, especially due to their gravitational pulls as Earth spins on its axis and orbits the sun and as the moon orbits Earth. Therefore, information about tides is extremely important to understanding the geography of nautical navigation, as the points below the waterline are identified on charts relative to the mean low water mark (so sailors know the least amount of clearance they might have beneath their vessels), and points above the waterline are identified relative to the mean high water mark (including notation of whether those object sometimes are fully submerged).

Evidence of tidal changes along the shoreline of Behm Canal — Can you see the evidence of tidal changes along the shoreline of Behm Canal? Color differences form strata along the rocks, and lowest leaves of the trees give further evidence of the highest reach of the water.

Ensign Damian Manda manually levels the sighting rod upon the “turtle” using a carpenter’s bubble-leveling device.

To gather accurate and precise data about tidal influences on local waters, NOAA sends tides-leveling shore parties and dive teams into difficult conditions – commonly climbing up, down, and across rock faces, traversing dense vegetation, and encountering local wildlife (including grizzly bears here in Alaska!) – to drill benchmarks into near-shore foundation rocks, install (and later remove) tidal gauges that measure changing water heights and pressures, and use sophisticated mathematics and mechanics to verify the levels of those devices.

Pondering the next measurement — Ensign Rosemary Abbitt and HST Brandy Geiger ponder the placement of equipment before the next level measurement.

Needless to say, this description is significantly less detailed than the impressively intricate work performed at every level by NOAA’s hydrographic scientists, and in the end, all of the collected data described in the paragraphs above – and more, like the velocity of the sonar-deploying vessel – must be analyzed, discussed, and interpreted by teams of scientists with broad and deep skills before the final nautical charts are published for use by the public.

Portable tools of the trade — A leveling rod is balanced on the highest point of a “turtle,” positioned carefully to be seen from multiple points.

As you choose where and how to proceed in your own journeys, remember that you can be more confident about your decision-making by using information that is both accurate and precise. And keep exploring, my friends.

View from the benchmark — This is the view from the benchmark atop a rocky outcropping (under an 80-foot evergreen) along Behm Canal while righting a measurement rod with the tide gauge leveling party.

Did You Know?

NOAA Ship Rainier in Behm Canal with launch vessels underway — NOAA Ship *Rainier* in Behm Canal with launch vessels underway

Every ship in the NOAA fleet also is a voluntary mobile weather station, and so are many other seagoing vessels around the world. For many years ships have been required to report their locations and identities on a regular basis to agencies like the U.S. Coast Guard and local or regional harbormasters. Those periodic reports were (and still are) vital for local traffic control on the waters and for helping to provide quick response to emergency situations on vessels at sea.

View aft while launch is underway — The view aft through Behm Canal from the launch vessel

Eventually, someone insightful realized that having the ships also provide weather reports from their positions along with those identity-and-location reports would make a much richer and broader network of timely data for the National Weather Service, which is another branch of the National Oceanic and Atmospheric Administration. As NWS adds the weather data from those many boats to the data gathered at land-based NWS stations and from voluntary land-based reporters of conditions, their models and forecasts become stronger.

(For more info about being a volunteer weather observer or volunteering with NOAA in some other capacity related to oceans, fisheries, or research, please visit www.volunteer.noaa.gov.)

Especially because weather conditions are the results of interactions among local phenomena, regional climate, and the global systems, building more accurate and precise forecast models depends on information from everywhere, but the result is that everyone benefits from the better forecasts, too.

Evidence of tectonic activity and rundown — Southeast Alaska is area with frequent tectonic activity, including uplift and earthquakes. Here a scar among the trees on the mountainside shows evidence of tectonic shifts, which also creates a ready path for meltwater to move downhill from the snowy mountaintop to the seawater below, taking trees and soil with it.

NOAA Ship Rainier ready for the returning skiff — NOAA Ship *Rainier* waits offshore, ready to receive the skiff returning with the tide/level shore party.

May 8, 2013August 11, 2021

Rita Salisbury: Winding Down, April 29, 2013

NOAA Teacher at Sea
Rita Salisbury
Aboard NOAA Ship Oscar Elton Sette
April 14–29, 2013

Mission: Hawaii Bottomfish Survey
Geographical Area of Cruise: Hawaiian Islands
Date: April 29, 2013

Weather Data from the Bridge:
Temperature: 79°F / 26°C
Dewpoint: 68°F / 20°C
Humidity: 70%
Pressure: 29.98 in (1015 mb)
Winds: S 10.4 mph (S 17 kph)

Science and Technology Log:
This has been an amazing voyage for me; I have learned about science process and technology in a real world application that I can take back to my classroom and incorporate throughout my curriculum. Real science on this cruise involved using multiple survey methods to determine the population and of Bottomfish species in a prescribed area. Acoustics, video recording by BotCam, AUV, and ROV, fishing by professional fishermen, and fishing from the side of the research vessel were all techniques employed in this study. These different methods will be compared and, eventually, a process will be formulated that will probably combine several of the methods in order to compile data to help regulate the bottom fisheries.

Some of the methodologies, such as the BotCams, have been compiling data for five or more years, so there is a sizable amount of information upon which to base decisions. Adding to the general knowledge base is an important part of scientific research; without data it is impossible to make informed decisions.
After the last deployments of the AUV and ROV yesterday, we all pitched in to help pack equipment to get ready for today’s end of the cruise. We cleaned floor mats, vacuumed, mopped, wiped down counters, and also cleaned our staterooms, heads, and common rooms. Even though this is a scientific research cruise, the scientists are considered guests on the ship and it only makes sense to help clean up. You never know when you’ll be back on the ship for more research and you sure want to be welcomed back!

Personal Log:
My mind is racing like a runaway train, thinking of ways to integrate what I’ve seen and learned on this cruise into my curriculum when I get back to Delaware. I cannot wait to sit down with my co-teachers, Dara Laws and Kenny Cummings, and brainstorm ways to make the science standards I am required to cover more meaningful and engaging to our students. We teach in a project-based, technology-rich environment and the possibilities to “amp up” the lessons and make them more rigorous, as well as captivating, are enormous. In addition to a fresh insight into science process, environments, populations, communities, and the overarching ecosystem, I now have real people I can contact to act as experts and representatives of their fields of study. I cannot thank NOAA, the Teacher at Sea program, Dr. Donald Kobayashi, Chief Scientist, or the Officers and Crew of the Oscar Elton Sette enough. Their openness and willingness to host another Teacher at Sea will make a difference to countless students in the years to come.

Not only did I make new contacts, I made new friends. I’m looking forward to making Clementine’s Chicken Curry for my family and friends and staying in touch with my new friends. I only wish every teacher I know could take advantage of such an amazing opportunity.

July 15, 2012August 11, 2021

Carmen Andrews: Transforming Fish into Data, July 15, 2012

NOAA Teacher at Sea
Carmen Andrews
Aboard R/V Savannah
July 7 – 18, 2012

Mission: SEFIS Reef Fish Survey
Location: Atlantic Ocean, off the coast of Cape Canaveral, Florida
Date: July 15, 2012

Latitude: 28 ° 50.28’ N
Longitude: 80 ° 26.26’ W

Weather Data:
Air Temperature: 28.6° C (83.48°F)
Wind Speed: 18 knots
Wind Direction: from the Southeast
Surface Water Temperature: 27.6 °C (81.68°F)
Weather conditions: Sunny and Fair

Science and Technology Log

How are fish catches transformed into data? How can scientists use data derived from fish to help conserve threatened fish species?

The goal of the Southeast Fishery-Independent Survey or SEFIS is to monitor and research reef fish in southeast continental shelf waters. Marine and fisheries scientists have developed sophisticated protocols and procedures to ensure the best possible sampling of these important natural resources, and to develop fisheries management recommendations for present and future sustainability.

During the cruise, important commercial fish in the snapper and grouper families are caught over as wide an area as possible; they are also taken in large enough numbers that they can be worked up into statistically reliable metrics. In addition to counts and measurements, biological samples are also taken at sea for future analysis in land-based research labs.

Gag grouper ready for its work up — Gag grouper ready for its work-up

Scientists strive to render an informative snapshot of reef fish stocks in a given time interval. Reports that analyze and summarize the data are submitted to policy-makers and legislators to set fisheries rules, restrictions and possible quotas for commercial and sports fishermen.

After fish are caught and put on ice, processing includes several kinds of measurement that occur on deck. This data is referred to as ‘Length Frequency’. Tag information from the trap follows the fish through all processing. Aggregate weight measurements for all the fish of one species caught in a trap are made and recorded in kilograms.

David is weighing the gag grouper, with Adam P. looking on

The length for each fish in the trap is noted, using a metrically scaled fish board. Not all fish are kept for further processing.

David measuring the length of the gag grouper

Species-specific tally sheets randomly assign which fish from the catch are kept and which ones are tossed back into the ocean. These forms, which specify percentages of fish identified as ‘keepers’, are closely consulted by the data recorder and the information is shared with the scientist who is measuring the catch.

Shelly is recording length frequency measurement data

Kept fish are put in a seawater and ice slurry. The others are thrown over the side of the boat.

Age and reproductive sampling are done next in the wet lab.

Small yellow envelopes are prepared before fish work up can begin. Each envelope is labeled with cruise information, catch number, fish number, and the taxonomical name of the fish, using binomial nomenclature of genus and species.

Adam P. and Shelly labeling envelopes and plastic specimen containers

A small color-coded plastic container (the color indicates fish species tissue origin), with the fish’s source information riveted at the top, is also prepared. This container will store fish tissue samples.

The fish trap catch number is documented on another data form, along with boat and science team identification, collection method and other important information about the circumstances surrounding the fish catch. Each species’ data is separately grouped on the data form, as individual fish in a catch are sequentially numbered down the form.

Me, transcribing fish weight & length data

Each fish is weighed, and the weight is noted in grams. The scale is periodically calibrated to be sure the fish is weighed accurately.

Vermilion snappers and scamp, labeled and ready for dissection

Three length measurements that are made: standard length (SL), total length (TL), and if the fish species has a fork tail — fork length (FL). The fish is laid, facing left on a fish board. The board is long wooden plank with a metric measuring scale running down the center.

Standard length does not include the caudal fin or tail. It begins at the tip of the fish’s head; then the fish measurer lifts the tail up slightly to form a crease where the backbone ends. Standard length measurement includes the fish’s head to end of backbone dimension only. Total length is the entire length of the fish, including the caudal fin. In fork-tailed species, the fork length measurement begins at the fish’s snout and ends at the v-notch in the tail.

Source: Australian Government – Department of Environment, Water, Population and Communities

Part of the dissection of every fish (except gray triggerfish) is the extraction of otoliths from the fish’s head. An otolith is a bone-like structure made of calcium carbonate and located in the inner ear of fish. All vertebrates have similar structures that function as gravity, balance, movement, and directional indicators. Otoliths help fish sense changes in horizontal motion and acceleration.

To extract the otoliths, the scientist makes a deep cut behind the fish’s head and pulls it away from the body. The left and right otoliths are found in small slits below the brain. They must be removed carefully, one at a time with forceps. They can easily break or slip into the brain cavity.

Otoliths reveal many things about a fish’s life. Its age and growth throughout the first year of its life can be determined. Otoliths have concentric rings that are deposited over time. The information they show is analogous tree ring growth patterns that record winter and summer cycles. Other otolith measurements can determine when the fish hatched, as well as helping to calculate spawning times in the fish’s life.

The oxygen atoms in calcium carbonate (CaCO3) can be used to assay oxygen isotopes. Scientists can use these markers to reconstruct temperatures of the waters the fish has lived in. Scientists also look for other trace elements and isotopes to determine various environmental factors.

Each pair of otoliths is put into the small labeled yellow envelope.

The otoliths on the gray triggerfish are too small to be studied, so the spine from its back is collected for age and growth analysis.

The last step standard data collection is determining the sex and maturity of the fish. The fish is cut open at the belly, similar to preparing the fish as a filet to eat it.

If the fish is big, the air bladder must be deflated. The intestines are moved or cut out of the way. The gonads (ovaries and testes) are found, and the fish can be identified as a male or female. (Groupers can be hermaphroditic.) The fish’s stage of maturity can also be determined this way. Maturational stages can be classified with a series of codes:

U = undetermined

1 = immature virgin (gonads are barely visible)

2 = resting (empty gonads – in between reproductive events)

3 = enlarging/developing (eggs/sperm are beginning to be produced)

4 = running ripe (gonads are full of eggs/sperm and are ready to spawn)

5 = spent (spawning has already occurred)

Dissected gonad specimens are removed from the fish and placed in a plastic containers, snapped shut and stored in a formalin jar to preserve them. These preserved samples will be analyzed later by histology scientists. Histology is the science of organ tissue analysis.

Red snappers have their fins clipped to provide a DNA sample. They may also have their stomachs removed and the contents studied to better understand their diets.

Video data from the underwater cameras is downloaded in the dry lab. This data will be analyzed once scientists return to their labs on land.

Personal Log

Many different kinds of echinoderms and other invertebrates have been pulled up in the fish traps. Several are species that I’ve never seen before:

Basket Star — I am holding a basket star. It is a type of brittle star in the echinoderm phylum.

Small crab, covered in seaweed, shell and sand

We also catch many unusual large and small fish in the traps and on hooks. Several of these have been tropical species that I’ve only seen in salt water aquariums.

July 2, 2012August 11, 2021

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

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.

This is a male fish. Notice the arrow pointing to the testes.

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

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.

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.

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.

TAS 2012 (162) — 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!

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!

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.

How about some jelly soup?
(there are about 500 jellies in there!)

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!