Scott Donnelly, April 27, 2008

Posted on April 27, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 27, 2008

CTD getting a much needed rest

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10-15 kts
Seas: 2-3 ft
Light rain showers, dense fog, in port.

Science and Technology Log

Coordinates for today’s measurements (two sampling stations) are 43^O30’N, 124^O23’W and 125^O40’W, six and twenty miles from the coast at depths of 100m (330ft) and 400m (1,315ft) respectively in addition to measurements (three sampling stations) for coordinates 43^O40’N, 124^O16’W to 125^O25’W, three to ten miles from the coast at depths of 80m (265ft) to 120m (395ft). Bob and I have become efficient pros at deploying and retrieving the four biological sampling nets. It takes us no more than 35 minutes to complete all the biological sampling and that includes the ten minute tow required for the Manta net to sample the surface.

Personal Log

Today is the last day of the cruise. My final 4-hour early morning shift of the cruise went well. The last sampling station for the cruise was completed at ~0930. I spent the morning downloading data, adding information to my NOAA TAS logs, packing my personal gear, cleaning my sleeping area, and enjoying the last few hours on the open ocean from atop the flying bridge philosophically pondering its future and perhaps humanity’s future. In the meantime the NOAA crew was busy making preparations for docking in Coos Bay. For the last leg of the cruise into Coos Bay the science team assembled on the McARTHUR II flying bridge to enjoy the Oregon coastal scenery, relax, and take photos. Lots and lots of photos! I overheard one science team member say that he took 1.7 gigabits of photos during the cruise! Another took over 200 photos in one day alone. Wow! Thank goodness for digital cameras or else that would have been quite expensive to process if film had been used.

Entering the channel to Coos Bay, OR

The cruise’s end was bittersweet. For ten days I had been away from my wife and two young children. I missed them even though I emailed them everyday from the ship. I can’t wait to see them. At the same time though the cruise was so enjoyable in so many ways it’s hard to pinpoint one or two that stand out head and shoulders above the rest. It was hard work no doubt about it and at times I thought I’d never get a decent sleep. But the science team assembled by Chief Scientist Steve Rumrill was from the beginning and to the end a well-oiled machine that understood the mission’s objectives and dealt with problems that came to light in a timely and professional manner. I’m not aware of any issues that arose during the cruise between the science team members themselves or between the science team and NOAA crew. If they existed, then they must have been dealt with and worked out immediately. To me it’s a testament to the professionalism shown by all- science team and NOAA crew- on the cruise and the leadership of those chosen to lead.

The Lorax

Over time I’ll likely forget most of the names of those I met on this cruise. Time and age tend to do that as I’ve already experienced even in my relatively young age. But it’s less likely that I’ll forget the faces, the natural scenes observed, and the conversations had. How could I forget the graceful albatross gliding without effort and with such skill inches above the water without ever flapping its wings? Or the bioluminescence of krill? Or the first time while on the bridge the bow of the ship sunk low in the trough of a wave, the horizon and sky disappearing.

And what’s to become of the world’s oceans? What’s for sure is that for the next twenty years humanity will continue to exert more pressure on the world’s oceans to feed its relentless population growth, satisfy its rapacious appetite for resources, and serve as the transportation conduit to keep the world’s consumer economies afloat (no pun intended). Throughout human history the marine world has always delivered but there are signs that it may be in trouble, too tired to keep up with the maddening pace that the modern world has set, too exhausted to give freely as its finite resources are an ever alarming rate. I’m reminded of two small, unassuming but prophetic (and hence controversial) children’s books written by Dr. Seuss and Shel Silverstein almost forty years ago, The Lorax and The Giving Tree respectively. I’ve read them to my two children numerous times. After this cruise they make even more sense.

The Giving Tree

Without complaint the oceans have given much to humanity. In many ways the oceans are liquid gold. The history of human achievement is defined in large measure by our historical relationship with the marine world. It’s teeming with an abundance of life struggling to survive in the oceans’ harsh salt water environment. The current plight of the marine world represents a defining challenge humans must confront when planning for the future of our troubled planet. The historical narrative of the oceans is written in its sediments, water, and the genetic database of the million of organisms that call the ocean home. The future narrative is being written right now. What is its fate?

In conclusion, this cruise has given me a rarefied, first-hand look at the ocean world in which I live. To be sure our planet is misnamed. Rather than Earth, instead it should be named Oceanus, for our world is a water world that gives so much pleasure and asks for so little in return. What is its fate?

OCEANUS….what is its fate?

Scott Donnelly, April 26, 2008

Posted on April 26, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 26, 2008

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10-15 kts
Seas: 2 ft
Light rain showers, reduced visibility

NOAA TAS Scott Donnelly ready to deploy a bongo net

Science and Technology Log

Both the morning and afternoon shifts went off without any problems. Coordinates of the seven sites for the longitudinal sampling along the Coquille Estuary Line are 43^O07’N, 124^O29’W to 125^O15’W extending 2 to 40 miles from shore and from depths of 44m (145ft) to 2,300m (7,550ft). My tenth 4-hour shift was spent traveling north to the first sampling site along the Umpqua Estuary Line. Coordinates for the longitudinal measurements are 43^O40’N, 124^O16’W to 125^O02’W extending 3 to 40 miles from shore and from depths of 80m (265ft) to 1,300m (4,265ft). See map below.

Personal Log

Coordinates for the longitudinal measurements of the first sampling site of my shift

In preparing for Saturday’s early morning shift, I noticed when I walked onto the ship’s fantail that the night sky was clear and stars dotted the dark night heavens. I made my way to the flying bridge to observe the cloudless night sky lit up with millions of stars. All the major constellations visible in the northern hemisphere at this time of year just after midnight were easily seen in all their brilliance and mystery. The cool, crisp salty air added to the beauty of the moment. It made for a peaceful, philosophical moment. But as I have found in my brief stay in Oregon such celestial opportunities do not present themselves often and when they do it’s not for long. Clouds soon appeared, blocking the view and ending any chance to identify and name all the major constellations. After finishing the early morning shift I stayed up until after sunrise to take advantage again of photographing the sun rising above the eastern horizon through a thin layer of clouds.

Such meteorological conditions created a sky painted with various shades and hues of red, orange, and yellow. It was if a giant painter had a brush and painted the sky- his canvas- a riot of colors pleasing to the eye and emotions. The science of immaterial light from the sun interacting with the material gaseous atmosphere and clouds and the timing made for a time of quiet reflection and contemplation of the vastness of the universe and the relative insignificance of the Milky Way galaxy and our blue ocean planet. Tomorrow is the last day of the cruise. I have one more early morning shift. We are scheduled to dock in Coos Bay sometime in the early afternoon.

Sunrise off the southern Oregon coast as seen from NOAA ship McARTHUR II

Scott Donnelly, April 25, 2008

Posted on April 25, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 25, 2008

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 5-10 kts
Seas: 2 ft
Rain likely

A nautical chart of the Coos Bay area

Science and Technology Log

Longitudinal sampling continues along the Coos Bay Line. Coordinates for all measurements (twelve sampling stations total) along Coos Bay are 43^O20’N, 124^O27’W to 125^O27’ extending 3 to 55 miles from shore and from depths of 50m (165ft) to 2,800m (9,200ft). Today was my seventh (morning) and (afternoon) eighth 4-hour shift. All went well.

Personal Log

After the morning shift I asked my shift mate and veteran sailboat skipper Bob Sleeth to give me some pointers on how to set a nautical heading using parallel rulers. I know all about latitude and longitude but have never sat down with a nautical chart and looked at all the interesting information found on them. As a kid I watched a lot of old World War II naval films like Midway and Iwo Jima and I remember the scenes where the captain and senior officers are studying a nautical chart of the western Pacific with obvious intensity in order to plot a heading to cut off supplies for the Japanese navy or whatever. I always thought those scenes cool.

NOAA TAS Scott Donnelly charting a marine navigational heading

So here I am thirty years or so later, a happily married father of two and professor of chemistry, in my mind pretending the role of ship’s navigator on the famous WWII battleship USS Missouri as I consult with Capt. Stuart Murray in setting a heading to Tokyo Harbor with General of the Army Douglas MacArthur on board, making last-minute preparations for the surrender of the Empire of Japan ending World War II. I guess I can blame all the fresh ocean air I’ve taken in the past week for such a fantasy.

About mid-morning after a deep sleep I went to the flying bridge (observation deck) located above the ship’s operations bridge to watch the true masters of the sky- the albatross- glide effortlessly just inches above the glassy, mirrored ocean surface. The albatross rarely flaps its wings when flying. Rather, the albatross conserves its energy for its long distance oceanic travels by using the uplift from the wind deflected off ocean waves. Their long, slender, aerodynamically efficient wing structure allows the albatross to stay aloft for hours at a time. They soar in long looping arcs. They indeed are a grand spectacle to observe.

View from the McARTHUR II flying bridge

Scott Donnelly, April 24, 2008

Posted on April 24, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 24, 2008

Water collection from Niskin bottles

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10 kts
Seas: 2 ft
Light rain showers possible

Science and Technology Log

As forecasted for Wednesday night the turbulent seas have calmed and the howling winds coming from all directions have subsided. On occasion a large wave smashes into the ship broadside. But, for the most part, it seems like the storm has moved onto land. Sampling operations restarted around 2000 (8pm) last night. This morning from 0100 to 0500 is my sixth 4-hour shift. Today nearshore and offshore CTD and biological sampling continues at different longitudes 124^O29’W to 125^O15’W but constant latitude 43^O07’N. This is called a longitudinal sampling survey. The latitude and longitude coordinates align with the westward flow of water from Coos Bay estuary in Coos Bay, OR. Along these coordinates CTD deployment will reach depths as shallow as 50m (164ft) to as deep as ~2,800m (~9,200ft)! Round-trip CTD measurements will take more time due to progressively greater depths with increasing distance from the OR coast. On my morning shift we collected samples at two stations. At the second station 30 miles from the coast the CTD was deployed to a depth of 600m (1,970 feet).

Monitoring CTD data

During Thursday’s afternoon shift (my seventh 4-hour shift) the CTD was lowered to a depth of ~2,700m (~8,860 feet) located 50 miles from the coast. At this distance out at sea, the coastal landmass drops below the horizon due to the curvature of the earth and the up and down wave action. The round-trip CTD deployment and retrieval to such great depths take about two hours to complete. The dissolved oxygen (DO) probe measurements indicate a secondary DO layer in deep water. So how are the continuous data measured by the CTD organized? What are the trends in data? In science graphs are used to organize numerical data into a visual representation that’s easier to analyze and to see trends. Below is a representative drawing of how CTD and wet lab data are organized and presented in the same visual space. Note the generous use of colors to focus the eyes and show the differences in data trends.

What are some trends that can be inferred from the graph above? First, with increasing depth, seawater becomes colder (maroon line) until below a certain depth the water temperature is more or less at a constant or uniformly cold temperature (compared to the surface). Second, the amount of dissolved oxygen (DO) in seawater (green line) is greatest near the surface and decreases, at first slightly then abruptly, with increasing depth below the surface. Third, salinity (red line), which is directly related to conductivity, increases with increasing depth. Furthermore, in general seawater pH (blue line) becomes more acidic (and conversely, less basic) with increasing depth. Last, marine photosynthetic activity as measured by chlorophyll a in phytoplankton (purple line) is limited to the ocean’s upper water column called the photic zone. Below this depth, sunlight’s penetrating ability in seawater is significantly reduced below levels for photosynthesis to be carried out efficiently and without a great expense of energy.

The consistently low (acidic) pH measurements of deep water collected by the Niskin bottles and analyzed on deck in the wet lab are a concern since calcium carbonate (CaCO3) solubility is pH dependent. On this cruise the pH measurements between surface and deep waters show a difference of two orders of magnitude or a 100 fold difference. Roughly, pH = 8 for surface water versus pH = 6 for deep water offshore. This difference in two pH units (ΔpH = 2) is considerable as it indicates that the deep water samples are 100 times more acidic than the surface water. pH is a logarithmic base ten relationship, i.e. pH = -log [acid] where the brackets indicate the concentration of acid present in a seawater sample. A mathematical difference in two pH units (ΔpH = 2) translates into a 100 fold (10^ΔpH = 10²) difference in acid concentration. Refer to the Saturday, April 19 log for a discussion concerning the importance of CaCO3 in the marine environment and the net acidification of seawater.

Personal Log

After the morning shift but before a hearty breakfast of eggs, hashed browns, sausage, bacon, and juice, I hung out on the ship’s port side to watch the sunrise, a memorable mix of red, yellow, and orange painting the sky. It was one of the best sunrises I remember and that’s saying a lot since I live in southern Arizona, where the sunrises and sunsets are the stuff of legends. With the low pressure system having moved over land, the sea was calm and the temperature considerably warmer with no clouds positioned between it and the ocean. Perhaps surprisingly, I haven’t sighted a whale or a whale spout, even in shallower, more nutrient-rich coastal waters. It’s not that I haven’t looked as each day I’ve visited the flying bridge (observation deck) above the operations bridge enjoying the immensity of the vast Pacific.

A flock of albatross have begun following the ship I suspect in hopes of getting a fish meal, mistakenly thinking that the McARTHUR II is a trawler. I saw trash, which I couldn’t identify without binoculars, floating on the surface. Sadly, even the vast, deep oceans and its inhabitants are not immune from humanity’s detritus. The history of humanity and its civilizations are intimately linked to the world’s oceans. This will not change. Humanity’s future as well is linked to its maritime heritage. The oceans have fed us well and have unselfishly given its resources without complaint. Perhaps it’s time we return the compliment and lessen our impact.

Scott Donnelly, April 23, 2008

Posted on April 23, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 23, 2008

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10 kts, 30 kt gusts
Seas: 4-7 ft
Light rain showers

Low resolution radar image of the storm system that postponed cruise operations

Science and Technology Log

My fourth (0100 to 0500, 1am to 5am) and fifth (1300 to 1700, 1pm to 5pm) 4-hour shifts are postponed due to the continued inclement weather. Seas are turbulent (combined seas 16 feet) and the winds blow non-stop (30 knots with gusts near 40 knots) from all directions it seems. Standing on deck both port and starboard, the howling wind throws sharp sea spray darts at my unprotected face. For a seasoned mariner these conditions are probably routine, if not prosaic. But for a newbie like me, with a little more than 48 hours of sea time experience, they are impressive and awe-inspiring, especially so given that I’m watching

it all from in the midst of the storm and not from the relative safety of the shore as I’ve done at times in San Diego. I climb the stairs to the ship’s bridge to watch and videotape this grand spectacle. The captain is calm and seems unimpressed with the temperamental, chaotic happenings outside. As I make my way to the bridge’s front viewing window he says to me, “Crummy weather isn’t it.” Without thinking, I nod my head in agreement. Also, a gale warning remains in effect until 1400 (2pm) this afternoon. A gale force wind has sustained surface speeds greater than 34 knots (39mph).

CTD deployment and biological sampling with the nets are postponed until the weather subsides and is more conducive to on deck activity. If the weather cooperates and the night forecast is accurate, the plan is to resume water sampling with the CTD and collection of marine organisms around 2000 (8pm) tonight. In the meantime the CTD has been securely fastened to the fantail deck. The coordinates for today’s postponed longitudinal sampling (constant latitude, changes in longitude) are 43^O07’N, 124^O29’W to 125^O15’W.

With the postponement in work activity in today’s log I’ll discuss a number of topics. In the following paragraphs I’ll discuss some of the nautical terms used in marine weather conditions as found in today’s forecast (see beginning of log, top) and what a low pressure system is. In yesterday’s log I described what a bongo net is and how it works. Today I’ll talk about the marine organisms that a bongo net collects and also describe the other three zooplankton nets used on this cruise- the Manta, ring, and HAB nets. Let’s begin with nautical terms used in marine weather forecasts.

Winds are identified with respect to the direction from which the wind originates. Surface water currents on the other hand are identified with respect to the direction they are flowing. So for example, today’s morning forecasted southeast (SE) winds originate from the southeast and blow toward the northwest (NW) since in general winds travel in a straight line path when not disrupted. Conversely, today’s forecasted morning southwest (SW) swells are traveling in the southwest direction. Marine wind and ship speeds are measured in terms of knots (kts). One knot (one nautical mile per hour, nm/hr) equals 1.15 statuary (or land) miles per hour, mph. Today’s forecasted morning wind speed of 25kts then equals 29mph, with morning gusts (G) forecasted at 30kts or 35mph and subsiding by mid-afternoon.

A change in winds from the SE to the E and then NW as forecasted from AM to PM indicates that the storm system is moving in a northeast direction onto land.

What is a swell? A swell is a mature wind wave of a given wavelength (distance between successive wave crests, i.e. the highest point of a wave) that forms orderly undulations seen on the ocean surface. Swells are described with respect to their height and period. Wave height is self-explanatory. What about wave period? Notice in the weather forecast that a wave period is defined in terms of time (typically seconds). Let’s use a hypothetical situation to explain a wave period. Suppose you are standing on deck, looking out across the vast sea, and a wave passes across your line of sight. Seven seconds later another wave crosses your line of sight, which remains unchanged. Seven seconds later another wave passes; your line of sight is still unchanged. The wave period then is the time elapsed for successive waves to pass a fixed point. In general, the longer the period, the calmer the sea.

Dense krill “soup”

Since my arrival in Oregon on Friday, April 18 a low pressure system has been positioned off the Oregon coast bringing clouds and precipitation. Today’s stormy seas are a result of a low pressure system. The winds and clouds in a low pressure system rotate in a counter-clockwise direction when viewed from satellites above. So if the winds blow from the southeast (SE) and are sustained, this indicates that the northern region of the low pressure system is south of the observer. In yesterday’s log I wrote briefly about how a bongo net is deployed and its function. So what marine organisms are collected in a bongo net? On this cruise at the depths the bongo net is deployed, it’s mostly a thumb-sized, shrimplike crustacean called krill. Krill are an important and central component of the oceans’ food chains and webs. In the northeastern Pacific the predominant species of krill is Euphausia pacifica. They are prolific consumers of microscopic marine organisms too small to see with the naked eye. But they too are consumed in enormous quantities by seabirds, squid, fishes, whales, and more recently, humans.

As seen in the upper right photo Euphausia pacifica krill have red “spots” along the entire length of their transparent, tubular bodies. These “spots” are photophores (light emitting organs) that emit blue light when a krill is agitated. During the 0100 to 0500 shift when it’s relatively dark on deck, one can see the blue emitted light from individual krill (but not all simultaneously) when the detached cod end of the bongo net is shaken. The emission of light from living organisms is called bioluminescence. Remember the scene in the 2003 Academy Award winning, computer-animated family film Finding Nemo when Nemo’s iconic clownfish father, Marlin, and his absent-minded blue tang friend Dory descend into the pitch-black deep water to find the scuba mask dropped when Marlin’s colorful, curious son Nemo was captured by the scuba diver. Dory is mesmerized by a glowing light that suddenly appears. Both eventually escape becoming a meal for a deep water fish that uses bioluminescence to attract and then eat unsuspecting prey.

Euphausia pacifica

A sub-category of bioluminescence is chemiluminescence, which refers to the emission of visible light on account of a chemical reaction. In the krill’s photophores is a creatively named molecule called luciferin, which combines with its complementary enzyme called luciferase, to emit blue light. Of all the known bioluminescence in the natural, biological world, an overwhelming majority is found in marine organisms, especially those found in deep water where light from the sun does not penetrate.

In yesterday’s log I wrote briefly about the function of a bongo net in collecting marine organisms (zooplankton) in a horizontal water column below the ocean’s surface. How are the nearly weightless, free-floating zooplankton found at the ocean’s surface and a few inches below collected? In the following paragraphs I’ll answer this question and also describe the nets used to collect marine organisms in a water column vertical (or perpendicular) to the surface.

Manta net in action

A Manta net (also called a Neuston net) collects zooplankton at and a few inches below the ocean’s surface. Like a bongo net it too collects marine organisms found in a horizontal column of seawater. This requires the ship to be moving forward. Since a Manta net collects marine organisms at the surface and a few inches below, weights are not attached to the Manta net’s metal rectangular frame which also serves as its mouth. Floats are permanently attached to the right and left of the net’s mouth. A rotary flowmeter is suspended in the net’s mouth so the water volume can be determined. Like a bongo net the biomass density (number of organisms per volume water) then can be estimated. For our cruise the Manta net was deployed starboard once every shift for a total of ten minutes for each cast.

Scott Donnelly (green helmet) retrieving a Manta net

Two other nets used on this cruise are a ring net and a HAB (Harmful Algal Bloom) net, both of which are used to collect samples in a column of water vertical or perpendicular to the ocean surface. Consequently, the ship must not be moving and the net weighted for vertical sampling of a water column to occur since the nets themselves are not dense enough to sink. Deployment and retrieval of both nets are simple enough. Basically, the net is attached to a winch cable and a weight, is slowly lowered into the water to the desired depth and kept there for the desired time before it’s slowly lifted upward through the water, brought alongside the ship and suspended, washed with seawater, lifted onto the ship’s deck, and the collected sample removed from the cod end. The organisms collected represent those found in the vertical column of water through which the net ascended. On account of their small, compact size and weight, both the ring and HAB nets can be managed with one person, thereby freeing the other to take care of other sampling tasks.

Manta net skimming the surface for zooplankton

What is Harmful Algal Bloom (HAB)? HAB is caused by the elevated levels of toxins produced by certain marine algae that proliferate when seawater conditions are favorable for increased rates of reproduction. The microscopic algae are consumed by the ocean’s voracious eaters called phytoplankton. One of the toxins released by these certain marine algae is domoic acid, which accumulates in the phytoplankton that consume the algae. The phytoplankton are eaten by shellfish and fish such as anchovies and sardines. Domoic acid is poisonous to the shellfish and other fish thereby increasing mortality rates. If the toxin levels are elevated, massive die-offs occur, beaches are closed, and the sale and human consumption of shellfish, etc. are prohibited. The biological, social, and economic impacts are painful.

Personal Log

In spite of the ship’s constant pitching and rolling in these unsettled, stormy seas, I slept well Tuesday night, taking two hour catnaps, waking for ten minutes or so, and then falling back to sleep for another two hours or so before waking after midnight to get ready for the 1am shift. About mid-morning I made a visit to the bridge where ship operations are carried out. According to ship’s radar the low pressure system and local squalls causing the inclement weather shows signs of letting up.

HAB net deployment as seen from above

Almost three full days on the ship and I have shown no indications or symptoms of sea sickness in spite of the constantly changing seas. According to the NOAA crew I’ve earned my sea legs and it’s not likely that I’ll get sea sick. So much for all the tablets of Dramamine I brought. I took some memorable video from the bridge (both inside and outside) of the ship’s bow rising and falling between waves, some of them smashing violently into the McARTHUR’s bow on both the port (left) and starboard (right) sides, sending seawater spray up to the bridge window and all about the bow’s deck. I felt like a true mariner. Still no sightings of whales, orca, or the Black Pearl of Pirates of the Caribbean film fame.

Scott Donnelly, April 22, 2008

Posted on April 22, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 22, 2008

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10 kts, 25 kts gusts
Seas: 4-7 ft
Rain showers possible

Open Niskin bottles on CTD platform

Science and Technology Log

What’s the significance of the NH Line (Newport Hydrographic, 44^O39’N)? Water and biotic data acquisition at the NH Line began over 40 years ago. The NH Line then is significant on account of the long-term historical sample collection and data sets that it provides. Consequently, temporal (time) comparisons involving water and biotic data can be made over decades as opposed to shorter lengths of time such as years or months. It’s my understanding that nearshore and offshore sampling along the Oregon Continental Shelf (OCS) always includes the NH Line. My second 4-hour shift began at 0100 and ended shortly after 0500. Regardless of time of day each shift sets up and collects water samples from each of the twelve Niskin bottles on the CTD rosette. Typically, three water samples are collected at a particular depth. How does remote sub-surface water sampling work? When the CTD is deployed from the ship’s fantail, initially the top and bottom lids on all twelve Niskin bottles are open as shown in the photo below.

The CTD is lowered into the water and once the desired depth is reached the requisite number of Niskin bottles are closed electronically from the ship by whoever is in the control room. For my shift it’s team leader Ali Helms. After that is done, the CTD then is lowered or raised to another depth where another “firing” takes place and more water samples at a different depth are collected. When sampling is complete, the CTD is raised to the surface and onto the ship where it is secured to the fantail deck. The water in each Niskin bottle is collected and taken to the ship’s wet lab where each water sample collected at a particular depth is analyzed for other water quality parameters not measured by the CTD.

YSI datalogger

Other water parameters measured on this cruise in the wet lab include: total dissolved solids (TDS), pH, and turbidity (how transparent, or conversely cloudy, is the water). A YSI 6600 datalogger interfaced with a multi-sensor water quality probe (sonde) is used to measure the aforementioned water parameters. See photos below. The CTD and Niskin bottles then are hosed down with freshwater and reset for the next sampling site. After the CTD is reset for the next sampling site, then it’s time to collect biotic samples from the surface and at different depths. Biological sampling always follows a CTD cast. On this cruise biological sampling is carried out on the ship’s starboard side just fore of the fantail. Collection of marine invertebrate (boneless) organisms uses nets that vary in size, shape, density of net mesh (number of threads per inch), and volume of detachable sample collection container (called a cod end). Sampling nets are conical in shape and typically are made from Dacron or nylon threads that are woven in a consistent, interlocking pattern. Each specifically designed net is attached to a wire cable and deployed from the starboard side. If collection/sampling is done below the water’s surface (also called sub-surface), a weight is attached to the net’s metal frame. A bongo net is an example of a net used for the collection of invertebrate marine organisms at some defined depth below the surface (see photos below).

Multi-sensor water sonde

A bongo net collects organisms by water flowing into the net, which is parallel or horizontal to the water surface at some depth below the surface. Consequently, use of a bongo net requires that the ship moves forward. Deployment of a bongo net requires the use of trigonometry, a favorite math course of mine in high school a long time ago. The length of cable let out by the NOAA deckhand operating the winch with cable does not equal the depth that the bongo net is lowered below the surface. (This would be true if the net was simply dropped straight down over the side of the ship.) Let’s use the drawing below to illustrate this.

Suppose sample collection is to be done at 100m (328 feet) below the water’s surface. More than 100m of cable needs to be let out in order to lower the bongo net to 100m below the water’s surface. How much cable beyond 100m is let out (x) depends on the angle (θ) of the net (and hence cable) to the water’s surface. The angle θ is measured by a protractor attached to the cable and pulley at the position identified with the blue star in the drawing. The angle θ in turn depends on the ship’s forward speed. To calculate the length of cable that needs to be let out, the following trigonometric formula involving right triangles is used: sin θ = cos^-1θ = 100mx. The calculated value x is communicated to the NOAA deckhand, who controls the winch that lets out the desired length of cable. When this cable length is reached, retrieval of the bongo net begins.

Duel sampling bongo nets ready for retrieval

The volume of water that contains the marine organisms and that flows through the bongo net is recorded by a torpedo-shaped rotary flowmeter (left photo below), which is suspended by wires or thick fishing line in the middle of the net’s mouth. As water moves past the meter’s end, it smacks into and transfers its momentum to the flowmeter’s propeller, which rotates or spins. The propeller’s shaft in turn is linked to a mechanical counter inside the meter’s body (right photo below). A complete revolution of the propeller equates to a certain number of counts and that is related to a certain volume of water that has flowed past the meter. The mathematical difference between the two numbers recorded before the net’s deployment and after the net’s retrieval is plugged into a mathematical formula to obtain the estimated total volume of water that flowed through the net’s mouth during the time of collection. Consequently, the weight or number of biomass collected by the net can be related to the volume of water in which the biomass was found. This gives an idea about the density of biomass (weight or number of biomass units per volume seawater, g/m³) in a horizontal column of seawater at a given depth and site. In tomorrow’s log I’ll talk about what marine organisms a bongo net collects (including photos) and also discuss and describe the three other nets used on this cruise to collect marine invertebrates.

Mechanical counter in flowmeter

Personal Log

So far after one full day at sea, I haven’t experienced any indications of sea sickness in spite of rough seas (see weather forecast at beginning of log). Four other science team members haven’t been as fortunate. I didn’t witness any visible bioluminescent surface events on the early morning shift (0100 to 0500). I walked to the ship’s bow since this would likely be the best place to witness bioluminescence given all the agitation of seawater there. I left a bit disappointed but there are still five days remaining. The CTD and both the DO and chlorophyll probes (sensors) operated without any problems.

Bob and I communicate well and have similar personalities and intellectual interests. Before carrying out a task we discuss how it’s to be done and then agree to do it as discussed and in the order discussed. Communication is critical because when sampling for biological organisms for example, the nets have large, heavy weights attached so once the net is lifted from the ship’s deck for deployment the weight is airborne so to speak and free to move without resistance. Getting clobbered in the head or chest obviously would not be pleasant. The bongo net uses a 75 pound weight and the net’s solid metal frame must weigh another 25 pounds. Caution and paying attention are paramount once 100 pounds are lifted from the deck, suspended from a cable free to move about with the rolling and pitching of the ship with only air providing any sort of resistance against its movement.

Rotary flowmeter

Bob and I have delegated certain tasks between us. We agreed that when a net is deployed, he will always control the net’s upper halve where the net’s “mouth” and weight are located; I in turn will control the net’s bottom halve where the netting and sample containers or cod ends are located. When the net is ready to be lifted from the sea and returned to the ship’s deck, the tasks for retrieval are the same as for deployment, though in reverse order from deployment. Before the net is lifted shipboard, it’s washed or rinsed top to bottom with seawater from a garden hose that gets seawater pumped directly from the Pacific. Washing is necessary because the collected marine organisms adhere to the net’s mesh so in order to get them into the sample container (cod end) at net’s end they must be “forced” down into the cod end. Once the net is shipboard, the cod end and collected organisms are emptied into a sample jar, sample preservative is added, and the container is labeled appropriately.

Scott Donnelly, April 21, 2008

Posted on April 21, 2008 by Teacher at Sea

NOAA Teacher at Sea
Scott Donnelly
Onboard NOAA Ship McArthur II
April 20-27, 2008

Mission: Assembly of Science Team and Movement of Science Gear/Equipment
Geographical Area: Coos Bay to Astoria, Oregon
Date: April 21, 2008

Weather Data from the Bridge
Sunrise: 0620 Sunset: 2010
Wind: 10 kts
Seas: 4-7 ft
Rain showers

Cape Disappointment Lighthouse where the mighty Columbia River collides with the Pacific Ocean

Science and Technology Log

With childlike anticipation and excitement I waited for the McARTHUR II to be freed from its berth and be given the freedom to sail towards the ocean world ruled by Neptune, the god of water and sea in Roman mythology. The time had finally arrived and with the captain’s decision we pulled away from the dock, turned 180^O, and set “sail” due west to where the water worlds of the Columbia River and Pacific Ocean collide. After exiting the Columbia and entering the Pacific, the McARTHUR II would turn south and set a heading toward the first sampling station located about nine miles offshore due west of Cape Falcon. ETA (Estimated Time of Arrival) is early afternoon. In the meantime I enjoyed the rugged, coastal scenery of the far southwestern tip of the state of Washington on the northern shore of the Columbia River. Before long I was officially an ocean mariner. An important question was soon to be answered: How long would it take for me to obtain my sea legs?

It was time to get to work. Before reaching the first sampling site the science team met in the lounge to try on thermal survival suits to determine if they fit properly. It was cumbersome putting on the heavy red suit; I looked liked the cartoon character Gumby (but red rather than green) but it gave me a bit of peace of mind. Hopefully, that’s the last I’ll see of that suit. Next, we met on the ship’s fantail (back lower working deck of the ship). The Chief Bos’n discussed shipboard operations that are carried out on and safety issues associated with the fantail, the working section of the ship. Hardhats and a working vest are mandatory. We then learned how to operate the “A” frame that aids in deployment and retrieval of the heavy, bulky CTD platform, how to properly attach the Niskin bottles’ cables to the triggering latch at the top of the CTD, and lastly how to correctly deliver the water collected inside the Niskin bottles to a sample container for analysis in the ship’s wet lab.

From the fantail we moved to the main deck on the starboard side aft of the ship’s middle section to learn how to deploy, retrieve, and collect samples from the four types of zooplankton nets, each of which also requires recording certain kinds of data about the cast. I’ll discuss biological sampling in more detail later. Admittedly, when it was all done I was a bit overwhelmed but figured that after a station or two when I developed a rhythm and familiarity with the equipment and time scale for collecting samples, I would get the hang of it.

It was 1500 (3pm) and the McARTHUR II had rendezvoused with the first nearshore sampling site about 10 miles west of Cape Falcon (45^O46’N, 124^O10’W). Preparations were complete and now it was time to begin 24 hour non-stop operations. I put on rain gear and rubber boots, found some dry gloves, and adjusted my hardhat and workvest. With that, Bob Sleeth and I made our way to the “A” frame to prepare for the first CTD deployment.

Personal Log

Winch (foreground left) and “A” frame (background) used to deploy and retrieve the CTD platform

My first full day at sea. We departed early morning on schedule from the Astoria dock. As expected we met rough waters where the Columbia River and Pacific Ocean meet. The day was overcast as is typical for this region of the U.S. this time of year, and cold. It snowed during the trip out to sea. Along the Columbia I was treated to the gorgeous coastal cliffs of Cape Disappointment to the north and the snow capped mountains south of Astoria. The swells subsided once the McARTHUR II reached water depths >200 feet. I’ve been out to sea for over twelve hours now and I’ve experienced no signs of sea sickness though the waters have been relatively calm. I am still earning my “sea legs” but I suppose by cruise’s end I won’t run into the hallway walls, the hallway water fountain, or my bed as often.

The overcast, gray skies ruined any chance in witnessing a marine sunset. I was still energized and excited like a kid on a “candy high” when I crawled into my lower bunk bed at 1900 (7pm). With my first shift complete I looked forward to my second shift at 0100 (1am). I figured though that I wouldn’t sleep with it being a new environment, new sounds, new smells, and the ship pitching and rolling. For the next five hours I went back and forth between sleep and semi-sleep where you’re relaxed but at the same time fully aware of the surroundings. Half past midnight I rolled out of bed, got dressed, and went to the dry lab to prepare for the 0100 to 0500 shift.

NOAA Teacher at Sea Blog

Tag Archives: noaa ship mcarthur II

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