Sherie Gee: Male or Female? June 29, 2013

NOAA Teacher At Sea
Sherie Gee
Aboard the R/V Hugh R. Sharp
June 27 — July 7, 2013

Mission:  Sea Scallop Survey
Geographical Area of Cruise:  Northwest Atlantic Ocean
Date:  June 29, 2013 

Science and Technology Log:

Most of the shifts consisted of sorting out the animals from the dredges and carrying out the process of weighing, measuring and counting.  One other component to the process is that on every dredge, five of the scallops are scrubbed, weighed and dissected.  Once this is done, gender can be determined since this species of sea scallops have separate sexes.  Then each scallop is numbered, labeled, tagged, and bagged.  These five sea scallops will be brought back to the lab on land to be analyzed and aged.  This is done by counting growth rings on the shell.   The part of the scallop that is used as food is not the actual animal but the adductor muscle that is located in the middle of the shell.  This is the muscle that can open and close the scallop’s shell.  This is the only bivalve to be motile.  Often times other organisms find a nice little resting spot inside of the shells of the scallops.  This is a form of commensalism where the organism benefits while not harming the host.  We saw a small red hake living inside the shell of a dissected sea scallop.

The Atlantic Sea Scallop

The Atlantic Sea Scallop

After every other dredge, the crew brings out the CTD which is an apparatus that collects conductivity, temperature, and depth.  This data enters the database and is used in the labs on shore.  We could always tell when they were lowering the CTD because the ship had to come to a complete stop while collecting data.  Then they would bring the CTD back in and the ship would resume forward.

The CTD - Conductivity, Temperature and Depth

The CTD – Conductivity, Temperature and Depth

Did you Know:

The male sea scallop’s gonad is white and the female’s gonad is red.  Gonads are reproductive organs.

Personal Log:

I learned the secret to gearing up efficiently with the boots and foul weather overalls from Larry.  When you are ready to take them off, pull the overall part down toward the boots and leave about an inch of the boots exposed. Then just step out of the boots into regular shoes.  I’m glad I brought some slip-on shoes which made things a lot easier.  Then when it is time to gear up again, all I had to do was slip back into the boots and pull up the pants and suspenders.  We also had to wear rubber work gloves that kept us from cutting ourselves during the dredges.

Boots and Foul Weather Gear

Boots and Foul Weather Gear

I interviewed our steward, Lee, for one of my requirements by NOAA. I found her to be a very interesting and social person.  She is also the cook so she takes on two responsibilities at one time. She has to plan the meals, cook the meals and clean up after the meals. In addition to taking care of all kitchen duties, she also has to clean the heads (bathrooms), vacuum the carpets, clean the staterooms and do the laundry. She had to take some extensive courses on basic safety training for commercial vessels. Her satisfaction to the job is making food that people like and keeping up morale on the ship.  She has a designated drawer which serves as a treasure chest of gold only the gold is actually tons of candy. All kinds of candy.  She also keeps one big freezer full of ice cream and a refrigerator full of most types of can sodas.

Lee's Shrimp Jambalaya

Lee’s Shrimp Jambalaya

The Ship's Treasure

The Ship’s Treasure

Lee- The Ship's Cook and Steward

Lee- The Ship’s Cook and Steward

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.

Lizardfish

Lizardfish

Sargassumfish

Sargassumfish

Hooked blacktip shark

Hooked blacktip shark

Scrawld Filefish

Scrawld Filefish

Spotted butterflyfish

Spotted butterflyfish

Jack knife fish

Jack knife fish

Marian Wagner: From Fishing to Dissecting in the Wet Lab, August 22, 2011

NOAA Teacher at Sea
Marian Wagner
Aboard R/V Savannah
August 16 — 26, 2011

Mission: Reef Fish Survey
Geographical Area: Atlantic Ocean (Off the Georgia and Florida Coasts)
Date: Monday, August 22, 2011

Science Team on R/V Savannah Aug 16-26, 2011: Back row: Chief Scientist Warren Mitchell, Christina Schobernd, Katie Rowe, Mike Burton. Front row: Shelly Falk, Stephen Long, Sarah Goldman, Marian Wagner, David Berrane.

Weather Data from the Bridge (the wheelhouse, where the controls of the ship are)
S-SW Wind at 15 knots
(This means wind is travelling 15 nautical miles per hour, 1.15 statute miles = 1 nautical mile)
Sea depth today ranged from 45 meters to 74 meters
Seas 3-4 feet in the morning, 2-3 feet in the evening (measure of the height of the back of the waves, lower the number = calmer seas and steadier boat)

Science and Technology Log

In my last blog, I explained what I am doing on the  first half of my shift (noon to around 6:00pm/dinnertime) and how we conduct our research on the aft deck of the boat: we drop chevron traps to the ocean floor with cameras attached and then pick up the traps with fish sample collections.  The fish we trap and the cameras recording the activity around the traps help us estimate the fish populations.  We finish up this segment of our work on the deck of the boat by recording this data in a systematic data collection sheet called “Length Frequency”.  If we didn’t record the data the same way every time, it would be impossible to compare the thousands of samples in the past and into the future and understand what is happening to the populations of fish over time.

Length Frequency Data Recording

Here is a picture of us recording the weight and length of the fish and the frequency (how many we caught) in a systematic way,  always keeping track of where the fish were caught as well.  Because we catch large numbers of certain fish species (such as Vermillion Snapper, Red Porgy, Gray  triggerfish, and Black Sea Bass), we do not keep all of them for further research.  When recording/reporting “toss” or keep” got monotonous, I found ways to communicate creatively—how many words can you think of that rhyme with “toss” and “keep”? I got 11 for toss and 16 for keep.  David, Katie, and Stephen were such sports for going along with my silly games!

After this point in the day, the fish are in bags and put on ice, and we wash up for dinner.

After dinner, our work moves into the wet lab, where we prepare biological samples for further research.  For the rest of this log section I describe more about how and why we
use the biological samples.

Dissecting vermillion snapper in wet lab, in search of otoliths and gonads.

We use the biological samples to obtain and report important biological measures such as age, length, weight, feeding habits, and genetics.  In order to know specific ages of the fish, we take out a small bone in the fish called the OTOLITH, which is located in the inner ear. An otolith is a reliable source to obtain the age of a fish. They show age in rings similar to how trees show their age in their growth rings.  We also take the GONADS from the fish to give important information about reproductive development.  Here is a picture of me dissecting a vermillion snapper and taking out the otolith (right hand) and gonads (left hand) to send to the lab back in Beaufort, North Carolina, where scientists work.

Here I just reeled in a gray triggerfish, one of our target species for hook and line catch.

Sometimes after dinner we had time to fish with hook and line in the stunning sunset.  This method of catching fish provided us with fish samples to study that did not have stomachs full of bait like the rest of our fish samples caught in traps. We did this so we could study their stomach contents and learn about what they are eating and get information about the ecosystem they are dependent upon. We were targeting vermillion snapper and gray triggerfish, fish that are known to really gorge on bait in the traps.  Sarah was dissecting the stomach of scamp grouper and found an octopus beak!

Sarah dissecting stomach of scamp grouper and finds octopus beak!

When Sarah was dissecting the stomach of a scamp grouper, she found an octopus beak, the last part of the octopus to be digested. Exciting find!!

When fishing becomes chaotic, teamwork is key.

Here is one of my favorite pictures of all, captured during one of our hook and line battles, and a testament to the incredible teamwork of the scientists and crewmen. How many people does it take to catch a fish? Here, 5 of us were working on the same task.  Lines from 4 reels were tied up from a strong fish swimming in circles, and it took an intense team effort to unravel them in a critical moment. Success was sweetly earned.

Click here for more info on the fish we are studying for stock assessments.

Personal Log

I’m on a boat!  This phrase has been repeated many times and it captures my enthusiastic awe (with a touch of humor) that I have had many privileges, and the fortune to be around some remarkable people, day in and day out. I took the opportunity to interview a few of them so I could share it here.  (Next blog: Interview with Captain Raymond Sweatte)

Richard's showing me how to tie the speed bowline knot, see http://survival.atactv.com/?mediaId=743 to learn this knot.

Interview with Richard Huguley, engineer

Marian: When you were a kid, would you have imagined yourself here now?
Richard: Yes. In Mobile, Alabama, where I grew up, I played with wooden boats, making them go up and down the creek, and spent time catching crawfish. I could see this as where I’d be.
M: How often did you play outside?
Richard: From sun-up to sun-down.  I skipped out to the woods all day some days.  I was never afraid to be in the woods. I played with snakes, frogs, had a baby pet squirrel I kept in my pocket.  It poked its head out to eat, and then crawled back into my pocket.
M: How did you become prepared for work as an engineer on a boat?
Richard: I have worked in all different fields required of an engineer: electrical, metal manufacturing-welding, automotive, building race cars and motor cycles, etc.  I always had the interest to take a challenge someone else wouldn’t take—not a challenge that just required physical strength, but more of intellectual puzzle.  It takes lots of time.  I took the time to figure the challenges out.  I can visualize math.  My dyslexia is a strength I use to my advantage.  I see people struggling with something, and it’s like I see it from the opposite end.  I do it without thinking about it.  Jigsaw puzzles are good for this kind of challenge.  It would be good for your students to try doing a jigsaw puzzle with the pieces upside down so they build the puzzle from the angles of the edges.
Thank you, Richard, for taking the time to talk and share your stories and the many skills you taught me. You are one-of-a-kind and I hope you can come visit my classroom someday!

Katie Rowe on the deck of the aft.

Interview with Katie Rowe, scientist and scuba diver/instructor

Marian: What do you like about working in a lab?

Katie: Lab work is about exploration, you don’t know entirely what you’ll find. We’re looking for otoliths, etc, but there is a possibility to find anything!

M: What makes the best partnerships in the lab?

Katie: I like working with people who are organized and efficient, people who can interpret and know what needs to be done next.  It takes an organized system for people to work like this, like we work here.  The system works well here so everyone knows what they are doing, and what happens next so we can all step in and do what needs to be done.

M: What’s your favorite animal?

Katie: Bull shark, Carcharhinus leucas, because they are adaptable.  They can survive in fresh water.  In Nicaragua, one was found in fresh water going after fish to eat, and they thought it was a new species, but then realized it was the bull shark.  They have the highest testosterone of any animal in the world, so they are bad-tempered, but I still love them.  I named my cat Leucas after the bull shark’s Latin name.

Thanks Katie!  It was great to work with you day in and day out!  You are a tough gal and make an excellent partner, very organized and efficient!

Tossing grappling hook to "catch" buoys attached to fish traps.

Fun extra:  How do we retrieve the buoys and pull up the fish traps?  I got to try my hand at this new sport, the grapple hook toss.  I am so grateful to have had the chance to try my hand at so many different roles.  Thanks for the opportunity!

John Taylor-Lehman, June 29, 2011

NOAA Teacher at Sea 
John Taylor-Lehman 
Onboard R/V Savannah 
June 24 – July 1, 2011 
NOAA Teacher at Sea: John Taylor-Lehman 
Ship: R/V Savannah 
Mission: Fisheries Survey
Geographical area of the cruise: Continental Shelf off of Florida
Date: Wednesday, 29 June 2011

Weather Data from the Bridge 
Longitude. 80.15
Latitude 29.08
Salinity 36.343
Temperature 27.25
Barometric pressure 32.00
Depth 47.7 m
Winds S,SW 26 knots

Science and Technology Log 

We continue to bait and deploy traps during the daylight hours. Three sets of 6 traps are typically deployed at one location. On Tuesday, 4 sets were deployed because of the low number of fish caught on the previous 3 sets.

There is an art to selecting sites and retrieving traps. Some traps can get hung-up on the ledges they were meant to be resting upon. Our Chief Scientist, Nate Bacheler, must communicate with the winch operator and captain with gestures to subtly move the tether in the hopes of freeing the trap. In rare events, a trap can be lost.

Here I am getting ready to deploy a fish trap.  On the right is the camera that goes on the front of the trap.

Camera on top of the fish trap.

Here I am getting ready to deploy a fish trap. On the right is the camera that goes on the front of the trap

Here I am getting ready to deploy a fish trap. On the right is the camera that goes on the front of the trap

Mounted on each trap are 2 video cameras. They record the habitat and activity in the vicinity of the trap. The resolution on the videos is remarkable! During the winter months the films will be viewed and the fish species identified and counted.

What Happens to the Data? 

Eric taking measurements on a Red Snapper

Eric taking measurements on a Red Snapper

The data collected on these cruises allows scientists to create an “index of abundance” for each species of interest. This information is combined with information from other sources and in-put to an existing assessment (population) model. The South Atlantic Fisheries Management Council then looks at the output from the model to decide on management regulations. They’ll decide on loosening or strengthening harvesting rules for each species.

So What Happens Once the Fish Are Caught? 

There is a great deal of information collected on each fish caught. For example: site location, weight, species, total length, length to fork in tail, and length before the tail. Select fish are later dissected to collect their otoliths (a bone in the head that can be used to determine age) and gonads (for maturity and sex determination). All fish are kept on ice in a large cooler until they are processed. Some of the fish are filleted, wrapped and frozen to ultimately be given away to charity.

Personal Log 

I no longer see the placid Atlantic under the ship. Strong winds (40 knots) have been blowing and stirring up the surface, creating 3-4 ft. waves and at times 4-5 ft. My stomach has noticed the change in conditions so I have been trying to keep busy and my mind distracted. Tried chewing some ginger, a remedy many people have suggested. Later, as the seas calmed and/or the ginger took effect, my stomach settled.

The weather conditions have stimulated much discussion among the science staff and crew. It was decided that conditions were ok to deploy the traps but too “sketchy” to retrieve them safely.

Zeb , David and Nate, members of the science crew

Zeb , David and Nate, members of the science crew

The chief scientist seems to have many contingency plans for when the weather does not cooperate. Decisions can be made at a moment’s notice to head to another site or cancel the trap drops. The fall back plans maximize the productivity of the research with the limited time at sea. The “down” time has given me some extra time to interview the science staff and crew. They are all very interesting people.

Zeb , David and Nate, members of the science crew

New animal sightings: (birds) brown boobies, yellow-throated warbler, Wilson’s storm-petrel, royal terns, (fish) reticulated moray eel, purplemouth moray, and red porgy.

Here I am holding a Red Snapper

Here I am holding a Red Snapper