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).

X-Keyboard

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;
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.

yoga

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?

fireworm

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.
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

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

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Jennifer Dean: Scientists and Surveys, May 16, 2018

NOAA Teacher at Sea

Jennifer Dean

Aboard NOAA Ship Pisces

May 12 – May 24, 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 16th, 2018

Weather Data from the Bridge
Latitude: 32° 05.2647’ N
Longitude: 79°13.2777’ W
Sea Wave Height: 1-3 feet
Wind Speed:  9.2 knots
Wind Direction: 166.61°
Visibility: 7-8 nautical miles
Air Temperature: 21.7 °C
Sky:  Overcast, rainy and lightning

Science and Technology Log
Scientists- A Team of Diverse Skills:

Swiftia exerta

Swiftia exerta identified and photographed prior to collection by the ROV

After the ocean floor has been mapped with multibeam sonar, ROV (Remotely Operated Vehicle) dives are made to ground truth the maps and to describe the benthic habitat and fauna and flora.  In order to identify the taxonomy of what we see in the video and photos, we often need to sample the macrobiota.  Many species of sponges, gorgonians and black corals are very difficult to identify from photos alone, and some are even new species.  Taxonomist, specializing in deep-coral ecology, Professor John Reed, works in this field of science that involves an understanding of organisms by using a variety of features both on the macroscopic and microscopic level for identification.   The red arrow in the picture is pointing to one of the target species in these dives, the gorgonian coral, Swiftia exerta.  Gorgonian octocorals are often called by their common names of sea fans and sea whips.  They are characterized generally by being sessile (attached to the bottom), colonial (composed of hundreds of individual animals called polyps) and belonging to the phylum Cnidaria. For more information about corals see the link below.
https://oceanservice.noaa.gov/education/kits/corals/coral01_intro.html

ROV collects coral

Manipulator used to sample the Swiftia before depositing into a sampling bottle or drawer.

Once the coral is identified through visual inspection with the ROV’s high-definition video, Andrew David uses the robotic arm (called the “manipulator”) to get the sample into a collection bin. The ROV brings the sample to the surface to be processed by the scientists.  And yes — this picture with the red arrow pointing at a book below the monitor screen is for my students — they still use field guides!

Field guides help in confirming identification and to confirm key features on those species that may be spotted that are less common- or for science teachers who are trying to do a quick cram study.

Field Guide

Scientists still use field guides!

 

The calyces contain many calcareous sclerites that can interfere with the PCR reaction.  PCR selectively can amplify codes of DNA that then can be sequenced and its DNA compared in a nucleotide database program like BLAST (Basic Local Alignment Search Tool).  These samples will serve as an outgroup for phylogenetic analysis of Swiftia in the Gulf of Mexico. The captions of the pictures explain the actions of each of the scientific team members seen in the images and a listing below gives their names, titles, associated organization and a very brief description of a portion of their skill sets brought for this expedition at sea.

Stephanie Farrington, biological research specialist from Harbor Branch Oceanographic Institute at Florida Atlantic University. She not only has ability to identify the marine biota but also manages, analyzes and tracks the enormous amounts of data collected during the trip.

Elizabeth Gugliotti, graduate student at the University of Charleston.
She collects and processes the coral samples for future phylogenetic analysis. Her thesis advisor is Dr. Peter Etnoyer, a marine biologist and lead scientist for NOAA’s Deep Sea Coral Ecology Lab. In addition, on this adventure, she is my state room bunk mate.

Jason White, ROV technician, to be featured in the next blog.  University of North Carolina Wilmington Undersea Vehicles Program.  Piloting the ROV underwater to capture photo/video images and samples, bringing the ROV on and off the ship using a winch and pulleys.

Eric Glidden, ROV technician, University of North Carolina Wilmington Undersea Vehicles Program.  Piloting the ROV underwater to capture photo/video images and samples, bringing the ROV on and off the ship using a winch and pulleys.

Stacey Harter, research ecologist, NOAA National Marine Fishery Service, Panama City Laboratory.  See her featured in earlier blog under What’s My Story.

Andrew David, research fisheries biologist at Panama City Lab in Panama City, Florida.
He makes a running commentary on habitat and species recording with the live video footage, as well as operating the robotic arm to collect samples.

John Reed, Research Professor at Harbor Branch Oceanographic Institute, featured below.  He specializes in taxonomy of invertebrate and deep-sea coral ecology.  Featured below in What’s My Story.

LT Felicia Drummond, research scientist and NOAA corps member.  She assists in fish identification and brought the additional bonus skill set as a yoga instructor and volunteered to lead us in yoga on the Skybridge on breaks.

Personal Log

I am enjoying my crash course in fish and invertebrate identification.  LT Drummond in this image offered to identify species out loud for my benefit, filling the background noise of habitat readings and descriptions with shout-outs about Spotted Goatfish and Graysby.  My favorite, so far, has to be the Sharpnose Puffer.

Sharpnose Puffer

Sharpnose Puffer

Everyone on board Pisces is extremely helpful and friendly.  I can’t overstate this point enough, I continue to feel welcome and included in all aspects of the operations of this expedition.

Learning common names

LT Drummond teaching me the common names of a variety of fish species during live video stream during ROV dive

It is interesting to watch how many mini-lessons occur between the crew to help each other. From the database tutorial between a graduate student and the data manager to explanations by the ROV operator to the fisheries biologist on how to operate the joystick and other control buttons on the video equipment.

I could not have possibly anticipated moments like today, May 15th, when Prof. John Reed shared a video made about a deep dive in a manned submersible.  Witnessing the creatures of the deep from people who captured this footage themselves and are making novel discoveries in both the past and present continues to amaze me.

Morning view

Morning view from the porthole of my stateroom on Pisces

 I’m also surprised at the ease to which I am able to sleep on a bunkbed on the Pisces rocking in the Atlantic Ocean.  There is something calming at night about the motion or maybe it is my exhaustion after a full day of activity.  Whichever it might be, my basic needs have been met and exceeded for shelter, food and sleep.  I do miss my family and friends–and even my nonbiological kids (aka my students). I am thankful for my oldest daughter sending me emails that keep me in touch with the happenings at home.   There is so much to tell and words/photos don’t do justice to the experiences I am having.

Did You Know?
Certain species of Scamp or Mycteroperca phenax, have a coloration differential that distinguishes the dominant male in the group from lesser males and females.  And if the dominant male dies or is fished from the group, the most dominant female within 2 months can change sex and become the new leader for the school of females.  For the extra curious read about the research on this phenomenon, authored by R. Grant Gilmore and Robert S. Jones, Color Variation and Associated Behavior in the Epinepheline Groupers, Mycteroperca microlepis (Goode and Bean) and M. Phenax Jordan and Swain in the Bulletin of Marine Science  51(1): 83-103,1992.

Fact or Fiction?
A majority of corals reproduce by asexual reproduction and are considered r-strategist.
To learn more about their reproductive habits of sending out a larval form called a planula (after egg and sperm combine) visit NOAA’s link below.
https://oceanservice.noaa.gov/education/kits/corals/coral06_reproduction.html

What’s My Story? Professor John Reed
The following section of the blog is dedicated to explaining the story of one crew member on Pisces.

What is your specific title and job description on this mission?  Research Professor, Deep Sea Coral Program at Harbor Branch Oceanographic Institute

How long have you worked for Harbor Branch Oceanographic Institute and in this field?  42 years

What is your favorite and least favorite part of your job? Favorite part is going to sea and all parts of fieldwork, whether it is on land or sea.  His least favorite is the administrative paperwork and bureaucratic forms and processes that go along with the job.

When did you first become interested in this career and why?  He always knew he wanted to do something outside, and in middle school was interested in careers of such as a forest ranger or archaeologist.  In high school he started watching The Undersea World of Jacques Cousteau TV series and began following the travels of this family in the documentary type series as they visited underwater coral reefs and original marine habitat never explored and shared with the public before.  After that he was hooked.

What science classes or other opportunities would you recommend to high school students who are interested in preparing for this sort of career? He commented that students should take their basic STEM curriculum, but emphasized it is equally important to have a broad background of the arts, civics and humanities and studies outside the STEM focus.  In high school and undergraduate school students will need to develop their basic foundations of essential understandings of biology, chemistry, genetics, and mathematics including statistics, , and in his field to learn some basic anatomy/physiology of organisms.

What is one of the most interesting places you have visited?  He is by far a world traveler with 60 expeditions around the world, visiting 50 different countries and he considers himself extremely fortunate to have the opportunities to go down to 3000 feet deep in a submersible to see things that have never been seen before. He mentioned Papua New Guinea as one of his favorites, and that during one submersible dive off Granada, they accidentally dropped down into a volcano and then subsequently got blown out by the hot water plume.  In another exciting submersible dive in the Florida Keys, they were the first to dive into giant sink holes, 1000 ft deep and some ½ mile in diameter. On one of the sink hole dives, they got attacked by an eight foot swordfish which hit the plexiglass sphere in which they were sitting in the Johnson-Sea-Link submersible, which was rather unnerving. So in a pitch black environment, except for the lights provided by the sub he said it feels a bit like being in a fish bowl with a 380 degree field of view.

Do you have a typical day or skills and tasks you perform? A typical year involves 2-3 months at sea or in the field and then a return to the lab or office, where his work involves primarily computer work.  Following a typical 2 week cruise an additional 2-3 months is required to analyze the ROV photos and videos, to proof all the notes and data that has been recorded, and then write up the cruise report.  After that, then trying to publish manuscripts and write grants to do the fieldwork takes up the remainder of a typical year.  100% “soft” money is used to support this sort of research. “Soft” money means that they must get grants to support all aspects of the study, paying the principle investigator salary and his/her team, and 48% or more overhead is typically paid to the investigators home institution.

What are some other careers or divisions of study at the Harbor Branch Oceanographic Institute? The engineering division is developing AUVs (Automated Underwater Vehicles), and wave gliders, equipment used on submersibles, acoustics, and software the is used for tracking on the ROV.  Another division is their biomedical unit where chemists are looking at bioactive products from the sponges and other creatures found in the marine environment.  Their aquaculture program is developing a closed circulation system, trying to address the pollution created by some aquaculture programs.. And the division that Prof. Reed works for is the Deep Coral Biology Program that studies corals and fishes, and is  also studying  the genetics and bioinformatics of marine systems.

Why does your research matter?  He views his primary mission in the realm of basic science, discovering and researching new reefs and then trying to protect them.  His research and discoveries resulted in the first deep-water coral Marine Protected Area (MPA) in the world, the Oculina Coral Habitat Area of Particular Concern (HAPC) in 1984; and in 2010, a 16,000 sq. mile Deep-water Coral HAPC which extends from Florida to North Carolina. He is asking scientific questions such as, what kind of fish community do you see on a high relief vs. low relief bottom? How well are the MPAs working–are they providing spawning and breeding grounds, protecting from destructive fishing procedures?  How does the dive footage compare outside and inside the MPA area for human impacts?  In the long run he views his research helping the fishing community and providing protections for sustaining these habitats and food webs for future generations.

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