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

NOAA Teacher at Sea

Jennifer Dean

Aboard NOAA Ship Pisces

May 12 – May 24th, 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: 89 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 16th 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).

Keyboard programmed to automatically communicate information into a database for quick counts and standard methods of habitat classifications

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).

The bathymetric data collected by NOAA is available here for anyone to download; 

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.

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.

Forward fold = Uttanansana

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, Bearded Fireworm

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.

Fact or Fiction?

NOAA ships never leave port on Fridays.   Check the links below for more information  about marine operations and for Fisheries superstitions.

What’s My Story?     Jason White

Jason White at the ROV controls.
Jason White at the ROV controls.

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 bothHe 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







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
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.

Starboard of launch vessel RA-4
Starboard of launch vessel RA-4

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
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

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.

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.

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
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
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
Shelly is recording length frequency measurement data
Length frequency data entries
Length frequency data entries
Red Porgy keep/toss percentage sheet
Red Porgy keep/toss percentage sheet

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
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
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
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.

Fish length measurements
Fish length measurements

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.

Red snapper with removed otolith
Red snapper with removed otolith

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.

Spine removed from a gray triggerfish
Spine removed from a gray triggerfish

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.

Making a cut into a vermilion snapper
Making a cut into a vermilion snapper

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.

Dissected fish gonads
Dissected fish gonads

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.
A red sea star
A red sea star
Spikey sea star
Spikey sea star
Small crab, covered in seaweed, shell and sand
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.

Hooked blacktip shark
Hooked blacktip shark
Scrawld Filefish
Scrawld Filefish
Spotted butterflyfish
Spotted butterflyfish
Jack knife fish
Jack knife fish

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:

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.

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!

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!

Kaci Heins: Surveying and Processing, September 30 – October 3, 2011

NOAA Teacher at Sea
Kaci Heins
Aboard NOAA Ship Rainier
September 17 — October 7, 2011

Mrs. Heins Taking a CTD Cast

Mission: Hydrographic Survey
Geographical Area: Alaskan Coastline, the Inside Passage
Date: Tuesday, October 4, 2011

Weather Data from the Bridge

Clouds: Overcast 7/8
Visibility: 8 Nautical Miles
Wind: 21 knots
Dry Bulb: 12.0 degrees Celsius
Barometer: 997.0 millibars
Latitude: 55.23 degrees North
Longitude: -133.22 degrees West

Science and Technology Log

Watching The Sonar

I was able to go out on another launch boat Sunday to collect survey data.  It was a beautiful day with amazing scenery to make it by far the best office I have ever been too.  Despite the fact that the ship is usually “off the grid” in many ways, the location of their work environment, or office, in Alaska is visually stunning no matter where you turn.  Keeping your eyes off the cedar trees and focused on the sonar in a launch can be challenging at times!  However, when there is a specific job to be done that involves time and money, then the scenery can wait until the job is finished.  During Sunday’s launch survey we had to clean up some “Holidays” and acquire some cross line data.

View Of the Data Acquired For the Ship On The Bridge

The word “Holiday” might lead to some confusion about what you might think we are doing when you read that word.  Holiday =vacation right?  In this case it is when there is a gap, or missing information, in the survey data that is acquired.  This poses a problem for the survey technicians because this leaves holes in the data that they must use for their final charts.  Holidays can be caused by the boat or ship being off the planned line, unexpected shoaling (or where the water gets shallow) so the swath width decreases, or a slope angling away from the transducer so that a return path for the sound wave is not possible.  The speed, direction, weather, swells, rocking of the boat, and the launches making wider turns than anticipated. It is easy to see where holidays occur as we are surveying because amidst the rainbow of color there will be a white pixel or square showing that data is missing.  When we are finished surveying or “painting” an area, we communicate with the coxswain where we need to go back and survey over the missing data or holidays.  If there are holidays or data is missing from the survey, then the survey technicians must explain why the data is missing in their final Descriptive Report.  This document covers everything that was done during the project from how the area was chosen to survey, what data was collected, what data wasn’t collected and why.  This is where holidays are explained, which could be due to lack of time or safety concerns.

Ship Hydrographic Survey

This launch was a little different because we were cleaning up holidays from the Rainiers’ multibeam.  Not only do the smaller survey boats collect sea floor surface data, but the Rainier has its own expensive multibeam sonar as well.  The ships sonar is called a Kongsberg EM 710 and was made in Norway.  Having the Rainier fitted with a multibeam sonar allows the ship to acquire data in deeper water and allows for a wider swath coverage.  The lines that are surveyed on the ocean floor are also much longer than those in a launch.  This means that instead of taking around 5-10 minutes to acquire a line of data, it can take around 30 minutes or more with the ship.  This is great data because again, the ship can cover more area and in deeper water. We also took the ships previous data and ran cross lines over it.  The importance of running a cross line over previous survey data helps to confirm or deny that the data acquired is good data.  However, there is a catch to running a cross line.  To confirm the data they have to use a different system than what was used before, the cross line has to be conducted on a different day, and it has to be during a different tide.  All of this is done to know for sure that the data is acquired has as few errors as possible before the projects are finished.

Rainier Multibeam Sonar

Personal Log

Each day when the scientists go out and survey the ocean floor they acquire tens of gigabytes of information!  The big question is what is next after they have acquired it all?  When they are on the launch they have a small external hard drive that holds 500 gigabytes to a terabyte of information plugged into their computer.  At the end of the day all their information and files are downloaded to this hard drive and placed in a water tight container in case it happens to get dropped.  Keeping the newly acquired data safe and secure is of the utmost importance.  Losing data and having to re-survey areas due to a human error costs tens of thousands of dollars, so everything must get backed up and saved constantly.  This is where I have noticed that computer skills and file management are so important in this area of research.

Once we get off of the boats the data is brought upstairs to what is called the plot room.  This is where all the survey technicians computers are set up for them to work on their projects.  The technicians that are in charge of downloading all the data and compiling all the files together is called night processing.  There are numerous software programs (tides, CTD casts, POS, TPU, Hypack,) and data from these programs that all have to be combined so that the technicians can produce a finished product for the Pacific Hydrographic Branch (part of Hydrographic Surveys Division), who then process the data some more before submitting to Marine Charting Division to make the final chart. The main software program that combines all the different data is called Caris and comes out of Canada.  Once all of the data has been merged together it allows the technicians start cleaning up their data and produce a graphic plan for the launches to follow the next day.  Every movement on the keyboard or with the mouse is very important with surveying because everything is done digitally.  Numerous new files are created each day in a special way so that anyone that reads the name will know which ship it came from, the day, and the year.  File management and computer skills are key to keeping the flow of work consistent and correct each day.

Hydrographic Survey Data In Caris

We have also had numerous fire drills while on the ship.  This is very important so that everyone knows where to go and what to do in case of an emergency.  They had me help out with the fire fighters and the hose this time.  I learned how to brace the fire fighter so that the force from the hose doesn’t knock them over.  I never knew that would be an issue with fire fighting until this drill.  I learn so many new things on this ship every day!

Fire Drill Practice

Student Questions Answered


Animals Spotted


Sea Otters

Question of the Day

Kevin Sullivan: Zooplankton, September 1-5, 2011

NOAA Teacher at Sea
Kevin C. Sullivan
Aboard NOAA Ship Oscar Dyson
August 17 — September 2, 2011

Mission: Bering-Aleutian Salmon International Survey (BASIS)
Geographical Area:  Bering Sea
Date:  September 1-5, 2011

Weather Data from the Bridge 

Leg 1 has concluded.  Oscar Dyson is currently at port in Dutch Harbor.  Please use link (NOAA Ship locator) to follow ship in future research cruises and current location/conditions.

Science and Technology Log

I am back home and my expedition aboard the Oscar Dyson has come to a conclusion.  My travels home had me leaving Dutch Harbor at 7:30 PM and arriving into Newark, NJ the following day at 2:30 pm EST, an incredibly long, red-eye flight back home.  Although my involvement aboard the ship has come and gone, the ship is currently in port at Dutch Harbor taking on more fuel and supplies and readying to do a “turnaround trip”.  For Leg II they will be heading back out into the Bering Sea to obtain further data.  The following is a map that depicts the stations for Leg 1 and 2.  For Leg 1, all of the green stations (40#) represents the areas where we conducted our research.  For Leg II, they will be focusing on the black circle stations.  When all of this field work is complete, and the numbers are “crunched” they can be extrapolated out to get a better idea of the overall health of the Bering Sea ecosystem as detailed in prior blogs.

BASIS 2011 Station Grids
BASIS 2011 Station Grid

So, before I left Alaska, I was discussing a bloom and readying the blog platform for a discussion of zooplankton and other higher-ordered interactions of the Bering.  Ok, so moving on…the next feeding level in the marine world would be the primary consumers….the zooplankton.  Zooplankton, although a very simplified explanation, are essentially animals that drift (planktonic) while consuming phytoplankton (for the most part).  These zooplankton in turn, are a resource for consumers on higher trophic levels such as the Pacific Cod, salmon,  and Walleye Pollock (which are a primary focus on this survey).  Zooplankton are typically small and in order to obtain samples from the sea, we have been utilizing specialized nets (information and pictures to follow) to extract, analyze and collect them for further investigations back at the lab.

The following picture is a good visual to represent this flow of energy that we have been discussing since the first Blog Entry.  An important observation is that the sun is the “engine” that initiates all of these interactions.  The exchange of carbon dioxide compliments of Photosynthesis and respiration, the abundance of phytoplankton in the photic zone (see last blog entry), which are food for the zooplankton, which in turn, become food for higher-order carnivores.

Marine Food Chain
Marine Food Chain

One of the more important zooplankton species out in the Bering are the euphasiids.  These are small invertebrates found in all of worlds oceans.  The common name is Krill.  These species are considered a huge part of the trophic level connection, feeding on the phytoplankton and converting this energy into a form suitable for the larger animals.  In the last blog, I put in some pictures of euphasiids that we caught.  These euphasiids have a very high lipid content (fat) and in turn, are what is responsible for getting salmon their richness in oily flesh, the Omega Fatty acids, and there natural, pink-fleshed color.  I have read before about the differences between farm-raised vs. wild salmon from a nutritional standpoint.  Farm-raised salmon often lack the abundant Omega oils that are found in the wild species.  Also, it is true that in order for the farm-raised salmon to get their pinkish color to the flesh, they are fed a nutritional supplement to give the color….essentially, like adding a food dye.  So, in class this year, we will have to be very careful when analyzing the pros and cons of aquaculture/fish-farming.

Personal Log

Although my official involvement with the Oscar Dyson has come to an end, I will take with me the experiences and knowledge for a lifetime.  It was everything I was hoping it would be and then so much more.  These blogs, the pictures, the video…… all do the expedition no justice.  However, I have pledged to make every effort possible to spread the word about NOAA and its mission and this is exactly what I will do.  I have several more decades of career in front of me and I know that between now and that date, I will use this recent expedition countless times and will hopefully convince the general public about the overall importance of government agencies like NOAA and how common resources must be valued and protected to ensure the health of all of Earth’s inhabitants.

There are so many people who I would like to thank for providing and delivering such an extraordinary experience.  All of the crew aboard the Oscar Dyson, from the engineers, to the chef,  and captain……Thank You.  Your professionalism and ability were truly inspiring.

To the Scientists, You were really the “teachers at sea”.  May you always continue your motivated path to revealing the beautiful secrets this planet has to offer.  Also, my hope that it continues to be done in a fashion that I saw while during my time on the water…..In a professional, unbiased, non-political fashion.  You have reassured my passion for the sciences and have given me fuel to disprove any “non-believers” who claim that the sciences have become corrupted.  In the end, you have shown me the most universal and balanced approach at reaching the truth.

Thanks for reading.

Jessie Soder: Drag It Along, Dump It Out, Count ‘Em Up, August 14, 2011

NOAA Teacher at Sea
Jessie Soder
Aboard NOAA Ship Delaware II
August 8 – 19, 2011 

Mission: Atlantic Surfclam and Ocean Quahog Survey
Geographical Area of Cruise:  Northern Atlantic
Date: Wednesday, August 14, 2011 

Weather Data
Time:  16:00
Location:  41°47N, 67°47W
Air Temp:  18°C  (64°F)
Water Temp:  16.5°C  (62°F)
Wind Direction:  SE
Wind Speed:  6 knots
Sea Wave height:  0
Sea Swell:  0

Science and Technology Log

A fellow volunteer, Rebecca, and myself measuring clams

When I found out that the Teacher at Sea trip that I would be on was a clam survey, I thought, “Oh, clams.  I see those on the beach all the time.  No problem.”  I learned that the clams are collected using a hydraulic dredge.  I knew  that a dredge was something that you dragged along the bottom of the ocean.  That seemed simple enough.  Drag it along, dump it out, count ‘em up, and you’re done.

Quickly, I learned that this project is not that simple!  A few questions came to mind after we had done a couple of tows:  How many people are needed to conduct one tow for clams and quahogs? (operate the machinery, the ship, sort through a tow, collect the data, etc.)  How many different jobs are there during one tow?

Sorting through contents of a dredge

Those questions are hard to answer, and I don’t have a precise answer.  What I have learned is that it takes a lot of people and everyone that is involved has a job that is important.  I asked the Chief Scientist, Victor Nordahl, how many people he preferred to have on a science team per watch.   He told me that it is ideal to have six people dedicated to working on sorting the contents of the dredge, processing the catch, and collecting data per watch.  Additionally, he likes to have one “floater,” who can be available to help during each watch.  This seems like a lot of people, but, when there is a big catch this number of people makes the work much more manageable.  There are six people, including myself, on my watch.  Four of us are volunteers.

Each time the dredge is lowered, pulled along the ocean floor, and then brought back onto the ship it is called an “event.”  In my last post I included a video of the dredge being hauled up onto the deck of the ship after it had been pulled along the bottom.  An entire tow, or “event,” is no small feat!  During my watch Rick operates the machinery that raises and lowers the dredge.  (Don’t forget the dredge weighs 2500 pounds!)

There are also two people working on deck that assist him.  (You can see them in the video from my last post.  They are wearing hard hats and life vests.)  Additionally, an officer on the bridge needs to be operating and navigating the ship during the entire event.  There are specific times where they must speed up, slow down, and stop the ship during a tow.  They also have to make sure that the ship is in the correct location because there are planned locations for each tow.  Throughout the entire event the science team, deck crew, and the bridge crew communicate by radio.

Rick, in front of the controls he uses to lower and raise the dredge

As I said, this project is not simple!  To make it more complicated, equipment often breaks, or is damaged, which means that the deck crew and the science team have to stop and fix it. On this trip we have stopped to fix equipment several times.  Various parts of the dredge get bent and broken from rocks on the ocean floor.  Before the dredge is lowered, the bottom is scouted with a depth sounder to try to avoid really rough terrain.  On the screen of the depth sounder different substrates are shown in different colors.  For example sand is shown in green and rocks are shown in red.  We try to avoid a lot of rocks.  However, all the rocks cannot be avoided and sometimes we hit them!

Personal Log

Vic getting a hair cut

Before coming on this trip I was told that the work can be strenuous and, sure enough, it is.  Sometimes a tow brings up hundreds of pounds of rocks (with some clams mixed in!) that we need to sort through and, as you know, rocks are heavy!  The work is also a bit, well, gross.  We have to measure all the clams, whole and broken and we also have to collect weights of “clam meat.”  That means that we have to open the shells and scrape the meat out.  I have a pretty high tolerance for gross things, but I am starting to grow weary of clam guts!

In between tows there is a little bit of down time to catch your breath, drink coffee and eat cookies, watch the ocean, and read a book.  During one of these breaks, the Chief Scientist Victor Nordahl, took the moment and had his hair cut!

Nathan Pierantoni, Tuesday 4.5.11

NOAA Teacher at Sea: Nathan Pierantoni

University of Miami Ship R/V Walton Smith

South Florida Bimonthly Hydrographic Survey

Florida Bay

Tuesday, April 5 2011

Weather Data from the Bridge

1400 hrs Local Time

Barometric pressure = 1014 Millibars

80 F

94% Humidity

Visibility = good

Wind S 14 knots

Science and Technology Log

Its Tuesday evening and I am finally taking the opportunity to organize my thoughts. The ship has been a whirlwind of activity since Sunday evening when scientists and crew began arriving and preparing for this 5-day research cruise to the Florida Keys and the Florida Bay. I have done my best to learn as much as I can in my time aboard the Walton Smith. The science that is being conducted on this cruise falls into three different areas of oceanography: physical oceanography, ocean chemistry, and marine biology. At all times there are scientists doing the fieldwork necessary to answer questions in these areas of science. In this log I will discuss the physical oceanography that is being conducted by Nelson Melo, a physical oceanographer, and our mission’s chief scientist.

Nelson is the leader when it comes to the organization and coordination of all of the work aboard the ship. Nelson is thoughtful and helpful, and has provided me with all of the information I need to make sense of the myriad of activities going on aboard our ship. Nelson Works for NOAA, and has multiple degrees in areas of physics ranging from nuclear physics to solid state transistors. He holds a PhD in Oceanography and is passionate about protecting and preserving the ocean. Originally from Cuba, he came to the United States 8 years ago.

Nelson’s work involves the synthesis of remote sensing data that is being shot from space via satellite with corollary data that he is working to collect from our ship as we pass through waters of the Florida Bay. For example, as the ship moves from one location to the next, the water might appear green or deep blue. These color changes are also visible from space and are being collected via satellite. The satellites used to collect this data are scanning the sea and creating multispectral images which, when processed and combined, appear like a color photograph of the ocean. These colors change as the conditions in the ocean change, and can be used to tell scientists about the health of the ocean. From the ship, we are moving throughout the Florida bay in order to sample many different parameters of water quality. One of them is chlorophyll. Nelson is most interested in the amount of chlorophyll in the water, because it serves as an indicator for the autotrophic life in the water column. Put simply, the presence or absence of chlorophyll in the water is valuable scientific information as it relates to many areas of study for ecologists, marine biologists and nearly every scientist who studies the ocean. As we collect water samples from different locations throughout the cruise, Nelson is using a sensor to measure the light as it appears at different depths of water. Today we were in about 7 m of water, and while the chemistry team sampled chlorophyll levels at different depths of water, Nelson put a photosensitive device over the side of the ship and slowly lowered it to the bottom. This device captured the intensity of light as it moved from the surface to the bottom, and all of the data was recorded on his computer. Then, he graphed his results. With the chlorophyll levels that the chemistry department has collected and the information from his submersible, as well as other parameters such as water current, salinity, and temperature he and many other scientists from the University of South Florida will work toward building an algorithm that will allow scientists in the future to use remote sensing from satellites to measure water parameters from space.

In fact, this work is already being done and oceanographers already have the tools to do this very accurately for offshore waters where there is less distortion from the reflection of the bottom or noise from particles in suspension due to shore currents or dissolved organic materials. Nelson is part of a team of scientists that is fine -tuning the algorithms used to measure water parameters from space that is more accurate for inshore waters.

Personal Log

Wow! Its been a busy couple of days!!! There is so much going on its kind of hard to know where to begin. The thing that I think I most appreciate right now is just how hard everyone is working. There hasn’t been much time to ‘mingle’, because everyone on the ship has a job to do, and it’s a full time operation. I think this is mostly due to the fact that this cruise it in relatively shallow waters, with many stops in close proximity to one another. And the ‘stops’ aren’t even really stops; they are simply the places where we slow down enough to do a CTD (which I’ll explain in a chemistry log tomorrow) or to do a net tow or to run the submersible photometer. Other than that, there is recording, chemistry, data analysis, and preparation for the next station to be done during transit times. The ship just keeps on following our prescribed cruise plan, from station to station, and if there is work to do during mealtime then everyone finishes their work before they get to eat. And the boat is divided into day shifts and night shifts for the science crew, and 6 hour on and off shifts for the ships crew. I appreciate that Nelson is packing in as much science as he can into this operation, because its obvious that great amounts of resources are going into these studies. I feel very lucky to get the opportunity to participate in this operation!

It is too bad that there are some other members of this cruise who I will not get to know as well, simply because they are asleep while I am awake. The ship is the most lively during the shift changes, when everyone is up for a meal of to catch each other up on the progress we had made during the day.

A special note to my classes:

Keep writing on the blog with questions, and I will keep catching opportunities to answer them, to upload pictures, and to go into more depth tomorrow about the chemistry and biology that are going on on the ship!

Here is the machine that Dr. Nelson uses to take his measurements, the PRR 2600.

PRR 2600
PRR 2600

Here is a shot off of Dr. Melo’s computer, it is recently acquired satellite data measuring the light specra from the earth. Notice the curvature at the left hand side of the screen, that is how the satellite sees the earth.

Dr Melo's computer
Dr Melo's computer

Here is the PRR 2600 at the surface of the water.

PRR 2600 in the water
PRR 2600 in the water

This is data from the ship. Notice duplicate measurements for parameters such as temp and salinity, and notice four sig figs. Those are real measurements, to a 10,000th of a degree!

data from the ship
Data from the Ship

Here is a shot of Dr Melo and with his submersible. He is slowly lowering the machine to the bottom while it takes accurate measurements of the light from the sun. At different depths the spectra of light change, and the amount that they change is related to the amounts of chlorophyll and other water parameters. This type of information from near-shore locations is what scientists will use to build accurate algorithms for interpreting future remote sensing data.

Dr. Melo lowering his Submersible
Dr. Melo lowering his Submersible

Caroline Singler, August 29-31, 2010

NOAA Teacher at Sea: Caroline Singler
Ship: USCGC Healy

Mission: Extended Continental Shelf Survey
Geographical area of cruise: Arctic Ocean
Date of Post: 31 August 2010

Under the Seafloor

Location and Weather Data from the Bridge
Date: 29 August 2010
Time of Day: 23:15 (11:15 p.m. local time); 06:15 UTC
Latitude: 79º 40.2’ N Longitude: 130º 26.2’ W
Ship Speed: 9.4 knots Heading: 254º (SW)
Air Temperature: 0.6ºC / 33.0ºF
Barometric Pressure: 1008.2 mb Humidity: 92.8 %
Winds: 10.1 knots SSW Wind Chill: -6.3ºC/20.8ºF
Sea Temperature: -1.4ºC Salinity: 27.78 PSU
Water Depth: 3505.8 m
Date: 30 August 2010 Time of Day: 22:00 (10:00 p.m. local time); 05:00 UTC
Latitude: 76º 52.8’ N Longitude: 137º 35.8’ W
Ship Speed: 9.8 knots Heading: 200.9º (SW)
Air Temperature: -0.3ºC
Barometric Pressure: 1008.5 mb Humidity: 99%
Winds: 3.2 knots W
Sea Temperature: -0.5ºC Salinity: 25.8 PSU
Water Depth:3675 mDate: 31 August 2010 Time of Day: 22:25 (10:25 p.m. local time); 05:25 UTC
Latitude: 74º 43.9’ N Longitude: 137º 26.1’ W
Ship Speed: 8.5 knots Heading: 124.8º (SE)
Air Temperature: 1.35ºC / 34.42ºF
Barometric Pressure: 1009.2 mb Humidity: 91.7%
Winds: 10.8 knots NNW Wind Chill: -4.1ºC/25.1ºF
Sea Temperature: -0.5ºC Salinity: 24.33 PSU
Water Depth:3418.4 m
Me on the deck
Me on the deck

Science and Technology Log
Most of the geology on this cruise is geophysics – we employ remote sensing techniques to generate computer images of the seafloor without direct observation. Bathymetric tools like the multibeam sonar system are valuable for oceanographers because it removes the veneer of the ocean water and reveals the shape of the underlying seafloor. It also makes a seafloor map look like a game of Candy Land – except when we are mapping in ice and it looks more like Pick Up Sticks. (One night on watch, my partner and I talked about how after a while you start to think of the seafloor as if it were colored like a rainbow!) Subbottom seismic profiles go even deeper and provide clues about the sediment and rock below the seafloor, and a trained geophysicist can read the signature reflections of different materials and make strong inferences about the subsurface. But for geologists like me, the highlight is sampling — bringing pieces of the seafloor above sea level and directly observing what is there. One reason that I was excited to join this cruise was because I visited the core library at Woods Hole Oceanographic Institution (WHOI) with the Lincoln-Sudbury NOSB team two years ago. The realization of how important such samples are to our understanding of the geological and climatological history of the earth made me eager to be present when a core was taken from the seafloor.

On a bathymetric survey expedition like this, opportunities to stop the ship for an extended period of time are few and far between, but we have had a few windows of opportunity for seafloor sampling. USGS geologists Brian Edwards and Andy Stevenson, armed with bathymetric maps and subbottom profiles from previous surveys, came on the cruise with several potential sampling targets in mind. USGS engineering technicians Jenny White and Pete dal Ferro are ready at a moment’s notice to get to work assisted by Healy’s team of marine science technicians (MSTs).

Coring the seafloor is a lot different from coring on land. The work site is the fantail (stern) of ship in the Arctic Ocean. The target is a point on the seafloor thousands of meters below, guided only by bathymetry and the ship’s navigation system. It takes more than an hour on average to lower the coring equipment on cables to the seafloor, and the water around us is moving with the current, requiring great skill on the part of the Coast Guard crew to hold station – keep the ship in a steady position – for many hours during sampling operations. Add in some wind, cold temperatures, and sometimes ice floes moving around the ship, and it’s easy to see why everyone’s energy level is cranked up a notch when coring operations are the plan of the day.

Coring Equipment
Coring Equipment

So far, we have collected core samples at three locations. A core is a long cylindrical section of seafloor. A core provides a relatively undisturbed sample of a vertical section of seafloor, preserving sediments in their natural layers with internal structures more or less intact. This provides a vertical timeline of deposition on the seafloor – the sediment at the bottom of the core represents the oldest material and the sediment at the top is the youngest. Core samples provide “ground truth” that supports the findings of remote sensing techniques like subbottom profiling. They allow scientists to “read” the history of the area. Geologists analyze the size and composition of sediment and infer depositional processes and possible sediment sources. Oceanographers and climatologists use information from the sediment and the microfossils they may contain to learn how the ocean and atmosphere has changed over time with respect to physical parameters such as water temperature and salinity.

Gravity Core on the deck
Gravity Core on the deck

We have employed two coring techniques on this core – gravity coring and piston coring. A gravity core uses a 2,000 pound weight attached to a 10-foot section of pipe. The pipe is lowered by cables and winches to the seafloor and uses the force of gravity pulling on the weight to drive it into the subsurface. A piston core is a variation on the gravity core that allows for deeper sampling by stringing together multiple sections of pipe. The main core barrel is fitted with a retractable piston in the top of the tube and the same 2,000 pound weight attached. A separate smaller coring apparatus is connected to the top of the piston core barrel by cables and a trigger arm. It hangs beside the piston core barrel, and the entireapparatus is lowered together to the seafloor. The trigger core reaches the bottom first and penetrates the surface sediments. As it falls, it triggers the mechanism at the top of the piston core which freefalls into the sediment. As the piston retracts inside the core barrel, it creates suction inside the barrel that helps pull the sediment into the core barrel and allows for collection of a longer, deeper, and potentially less disturbed sample than a gravity core.

Piston Core Apparatus
Piston Core Apparatus
Attaching Trigger Core
Attaching Trigger Core
The steel pipes used for coring are lined with plastic liners. At the end of the core barrel is a core cutter and a core catcher with metal teeth that fits into the bottom of the core barrel and holds the core in the barrel. When the core is retrieved, grab samples are collected from the core cutter and core catcher. (In the photo on the right, USGS scientists Brian Edwards and Andy Stevenson collect samples from a gravity core.) The outside of the core barrel is scraped to provide a sample that can be examined for microfauna (remains of microscopic organisms) in the sediment. The plastic liner is removed from the core barrel, starting at the bottom of the core, and is cut into sections. In this case, the preferred section length is 150 centimeters because that is the size of the containers in which the core will be stored back in the laboratory. Each section is measured, capped, sealed, and carefully labeled to indicate the top of the section and the core location. (In the photo on the bottom right, USGS scientists Brian Edwards, Andy Stevenson, and Helen Gibbons measure and cut the core sleeve from a piston core.) All information is recorded on a log in the field. The core sections are then stored horizontally in a specially built box that is kept in a refrigerator on the ship. The cores will be transported back to the USGS laboratory in California after the cruise where they will be cut, examined and logged, and then carefully stored for future reference.
Gravity Core Sample
Core Catcher and Cutter
Core Catcher and Cutter
Measuring cutting core
Measuring cutting core

Sometimes a core contains a real surprise. When the piston core from our first locationcame up on deck, we saw a white crystalline substance in the core cutter and catcher. It was gas hydrate. (Photo courtesy of Helen Gibbons, USGS Scientist.) Water molecules under high pressure may start to solidify at temperatures above the normal freezing point of water, crystallizing into a solid form of water with an internal structure that contains larger open spaces than typical ice crystals. Normally, these crystals are very unstable and will continue to cool and form the more stable molecule we know as ice. However, gases present in the environment may become incorporated into the open spaces within the solid water molecules and form a gas hydrate. This is a physical combination – there is no chemical bonding between the two – but it allows the solid to remain stable as long as it remains in a high pressure and low temperature environment. Seafloor sediments on deep continental margins and buried continental sediments in polar regions (i.e. permafrost regions) are common places where these compounds form. They contain abundant organic matter. Over time, biogenic processes (bacterial action) or thermogenic processes (high pressure and temperature) act on the organic material and produce gases, most commonly methane. These may become trapped in the solid water and form gas hydrates.

Core in reefer
Core in reefer
Methane Hydrate
Methane Hydrate

There is a lot of scientific interest in gas hydrates. Some estimates suggest that methane hydrates in permafrost and marine sediments contain more organic carbon than all other known naturally occurring fossil fuel deposits combined. Thus, gas hydrates are considered to be a potential energy source. However, one concern is that hydrates are very unstable at conditions other than those under which they form – the solid water crystals dissociate (i.e. melt) and the gases escape. We saw this with the sample we brought up in the core which began fizzing and off-gassing as soon as it was exposed at the surface. Potential environmental changes that might destabilize naturally occurring hydrates could potentially result in the release of large quantities of methane, a greenhouse gas, to the atmosphere.

We have sampled at four locations to date, shown on the map below. One location was near the top of a small seamount that was first mapped during last year’s expedition. Another sample was from a submarine fan complex. All locations were selected based on some prior data followed by good inferences, a little luck and a lot of skill.

Coring Locations on map
Coring Locations on map

All coring attempts have been successful, with good core recovery each time. It is difficult to predict what we will get when aiming for a target that is so far beneath us. There is only so much that the monitors on the ship that track wire depth and tension can tell us. Given time constraints, there are no “do overs”, so we are happy whenever the core barrel comes up with something inside – it represents more information than we had before we sent it to the bottom. The moments before the barrel is back on deck are full of tense expectation, and one can tell from the look of satisfaction on a scientist’s face when there is a good sample inside. One person’s mud is another person’s treasure! Although I will not get to examine the cores myself, I look forward to hearing what they find when they cut and log the cores back in California. And I have a little bit of ocean floor mud of my own to take home as a souvenir.

Core Sample
Core Sample

National Energy Technology Laboratory: The National Methane Hydrates R&D Program – All about Hydrates
TDI-Brooks International: Piston Coring for Surface Geochemical Exploration.
USGS Fact Sheet: Gas (Methane) Hydrates – A New Frontier. 1992.
USGS Woods Hole Science Center
Woods Hole Ocean Instruments

Personal Log
This is the last week of the trip. After all the preparation that it took to get here, the time has passed rather quickly – even while I did not have a very clear perception of the passage of time. If I were home, I would have met my classes for the first time yesterday and today. I am sorry to miss school, but I am grateful to be among a relatively small group of people who have the opportunity to experience this part of the world. I am fortunate to have a strong support network of colleagues at Lincoln-Sudbury Regional High School who encouraged me to take advantage of this opportunity and did their best to assuage my feelings of guilt about not being at work. I am fortunate to have such caring friends and colleagues. Thank you, everyone who helped me prepare for the trip and to all those who are keeping things going for me while I am away. You gave me the peace of mind to do this.

The Arctic is a wilderness unlike any other. Whether in the icy desert at latitudes above 80ºN; in thin, patchy ice in the southern and western part of the basin; or in the open waters off the coast of Alaska, each day is something special. I look forward to my first trip out on deck each morning to enjoy the day’s views, and I have not been disappointed. And here in the last week of the trip, as the amount of darkness increases while the latitude decreases, it is actually snowing – enough to make a little snowman on the bow.

Midnight on the ship
Midnight on the ship


Karen Matsumoto, April 22, 2010

NOAA Teacher at Sea: Karen Matsumoto
Onboard NOAA Ship Oscar Elton Sette
April 19 – May 4, 2010

NOAA Ship: Oscar Elton Sette
Mission: Transit/Acoustic Cetacean Survey
Geographical Area: North Pacific Ocean; transit from Guam to Oahu, Hawaii, including Wake Is.
Date: April 22, 2010

Science and Technology Log

Acoustic monitoring for cetaceans is a major part of this research effort. A hydrophone array is towed 24 hours each day, except when it needs to be pulled up on deck to allow for other operations, or required by weather or other maneuvers. The hydrophone array is hooked up to a ship-powered hydraulic winch system that brings up or lowers the hydrophone into the water. A team of two acoustic scientists listen to the hydrophone array during daylight hours and collect and record data by recording the sounds made by cetaceans, and locating their positions.

Sonobuoys, as described in the previous log entry are also used to collect acoustic data. Sonobuoys transmit data to a VHF radio receiver on the ship. Scientists monitor these buoys for an hour each recording session, and often communicate with the other group monitoring the hydrophone array about what they are hearing or seeing on the computer screen. They often don’t hear or see the same things!

Launching the hydrophone array
Monitoring the array.

A standard set of information is recorded each time a sonobuoy is launched. This includes the date, time (measured in Greenwich Mean Time!), Latitude and Longitude, approximate depth of the ocean where the buoy was launched, as well as specific information on the buoys. This is just like the information you would record in your field journals when conducting your own field investigations.

Setting the buoy instructions.
Launching the buoy into the water.
Success! When the buoy is deployed, the orange flag pops up.

One of my duties as Teacher at Sea is to conduct acoustic monitoring. This means checking the buoy and setting it to the correct settings so information can be received by VHF radio, and data collected by computer on any cetacean vocalizations we may observe. Many of the cetacean calls

can’t be heard, only seen on the computer screen! The computer must be visually monitored, and it takes a keen eye to be able to pick out the vocalizations from other “noise” such as the ship’s engine, sounds of the water hitting the buoy, and even the ship’s radar!

The person monitoring the buoy also wears headphones to hear some of the vocalizations. Clicks and “boings” made by some cetaceans can be heard by humans. Other sounds made by cetaceans, especially the large baleen whales are very low frequency, and can’t be heard by the human ear.

Karen listening in and visually monitoring the Sonobuoy. I can actually hear minke whales “BOINGING”!
Data is collected and recorded on the computer on a program called “Ishmael”.
All observations are also hand written in a “Sonobuoy Log Book” to help analyze the computer data and as back up information.

Personal Log

There is so much to learn, and I am anxious to get up to speed with the research team (which could take many years!). I have always been fascinated by cetaceans, and have had a keen interest in gray whales since whale-watching on the coast of California since I was a child. Grey whales have also been an integral part of the culture of First Peoples living on the Washington Coast, and so I have been interested in learning more about them.

I am an avid birder, and it is always an exciting challenge to go to a new place, learn about other ecosystems and see birds I am not familiar with. I have always loved pouring through and collecting field guides, which are like wish lists of animals I want to see someday. Out here in the western Pacific ocean, I have a whole new array of whales for me to learn about, and learn how to identify by sight and sound! I have been reading my new field guide to whales and dolphins, reviewing PowerPoint presentations about them, and trying to learn all I can, as fast as I can! I have been drawing whales in my journal and taking notes, which helps me to remember their shape, form, and field identification features. At the top of my wish list is to see a sperm whale! I’ll be happy just to hear one, knowing they are here!

Karen sketching whales in her journal to learn their profiles and field marks.

Question of the Day: Did you know that many baleen whale vocalizations are at such a low frequency, that they can’t easily be heard by the human ear? We need computers to help us “visually hear” calls of fin, sei, blue, and right whales.

New Term/Phrase/Word of the Day: mysticetes = baleen whales. Mysticeti comes from the Greek word for “moustache”.

Something to Think About:

“Call me Ishmael,” is one of the most recognizable opening lines in American literature and comes from the novel, Moby Dick by Herman Melville, published in 1851. The story was based on Herman Melville’s experiences as a whaler. Melville was inspired by stories of a white sperm whale called “Mocha Dick” who allegedly battled whalers by attacking ships off the coast of Chile in the early 1800s! Melville’s story was also an inspiration to the founders of Starbucks and also influenced the maker of the acoustic software we are using to track cetaceans on our research trip! (Can you tell me how?)

Animals Seen Today:

  • Sooty shearwater
  • Wedge-tailed shearwater

Did you know?
The earth has one big ocean with many features. The part of the ocean we are studying is called the
North Pacific Ocean and divided into three very general regions east to west: The western Pacific,
eastern Pacific, and the central Pacific. We are traveling along a transit from Guam, northeast to
Wake Island, then almost due east to O‘ahu, Hawai‘i. Can you trace our route on a map of the