Thursday, March 23, 2017

The weather, and other considerations

Doing research from a ship poses a number of logistical challenges that must be taken into consideration along with the science goals of the mission. We are out here to look for and study a particular phenomenon, but this means not only finding it in the first place (as discussed in earlier posts), but also having acceptable conditions in which to operate. In the case of this project, since we are hoping to look at restratification processes (several days of de-mixing) following a strong mixing event (i.e. a storm) at a front (a fairly narrow physical feature), we need to be in the right place at the right time without putting the ship in danger. Ideally, we’d like to time it so that the equipment is already in the water when the storm hits, because if things get too exciting, we either can’t deploy our instruments or we need to vacate the region, neither of which is good for the science. Fortunately, we have a very experienced ship crew on the Sikuliaq that is both very helpful in making sure the science happens but also conscientious about making sure that no unnecessary risks are taken.

Consulting about the optimal measurement spot on the bridge. From left: Chief Scientist James Girton, Captain of the Sikuliaq Diego Mello, Co-PI Eric Kunze, Co-PI John Mickett, and Second Mate John Hamill. (Photo credit: RE)
We are currently surveying the region of our final deployment with SWIMS to determine where exactly we want to place the buoy and the floats for the next round of observations. The first step in selecting this location was looking at the most recent data sent back from Argo[1] floats in the region to see if we could find places with a deeper mixed layer that would also better coincide with the storm track in the northern Pacific Ocean. We also looked at satellite altimetry (ocean height) and sea-surface temperature measurements to confirm that the deeper mixed layers could be found near a front. This allowed us to define a general box of interest, with the intent of doing on-site verification of the required features as we approached.

Ryan Newell, Eric Kunze, and Chris Siani work on reconnecting the winch cable to SWIMS after repairing the electrical connection, which is essential for transmitting data back to the ship as the instrument profiles. (Photo credit: RE)
Because the ship has to go so much slower when we are towing SWIMS, once we arrived at the beginning of our large spatial box, we used a different instrument to get a rough picture of the mixed layer, known as an “expendable bathythermograph” (XBT). This instrument is standard fare in the world of oceanography, and is frequently used on ships of opportunity because they are so simple (and inexpensive) to use. The XBT is a small torpedo shaped instrument with a lead weight at one end and a thermistor that measures temperature. Depth is calculated from a simple speed-of-fall estimation, and the data is transmitted to the ship in real time as a thin copper wire unspools rapidly. All three deployments, spaced roughly one degree of latitude apart, showed a mixed layer closer to 70 or 80 meters, rather than the 30 meters we observed at our last site, which is great news.

Marine Tech Bern explains how the XBT works to volunteer Ethan Brush. The tip of the actual instrument is just visible inside the black plastic cylinder it is housed in until deployment. (Photo credit: RE)
As mentioned earlier, however, picking a site is not as simple as finding a place in the ocean that has the right properties and going to work. Since we are now closer to the storm track, it is also important that we are not putting the ship at risk when doing the science. The box we had initially outlined for this portion of the cruise included some regions that were considerably farther north. After consultation between the chief scientists, the captain, and the mates, it was determined that if we could achieve the same scientific goals without entering that region of the ocean, both the ship and our instruments would probably be better off. As a result, we are about to embark on round three of buoy and float deployment for the home stretch of the project.

[1] The Argo program is a worldwide consortium of researchers using floats very similar to our EM-APEX floats that do a 2000 meter temperature-salinity-depth profile once every 10 days, often for 5 or more years. (Some floats are now equipped with additional sensors, such as dissolved oxygen and nitrogen sensors). One huge asset to this program is that the floats are distributed throughout the world ocean and profile year-round, often in places that are not readily accessible to ships all the time. You can find out more about the program and the data at

Wednesday, March 22, 2017

Rolling around

We’re currently in the middle of a 48-hour transit to what will likely be our final measurement site, which means we’re cruising along at close to 10 knots rather than the 3 or 4 knots we go when we’re towing SWIMS behind us. One of the consequences of this is that the ship is rolling a lot more than it does when we’re going slowly. This makes a number of ordinary tasks quite challenging: drinking coffee, walking across the room, sleeping. Using the treadmill is as much of an arm workout as it is a leg workout if you want to make sure you don’t pitch off the edge. The extra (and often unexpected) rolling also means that it is even more important to make sure all the valuables are strapped down tightly. Our computers and electronic equipment are more or less bolted in place, using a combination of non-slip mats, bungee cords, hooks, and screws. The other day we rolled to a 25-degree angle, which quite effectively woke up anyone who was sleeping and had everyone else grabbing for the nearest handle as their chairs slid across the room. The Sikuliaq tends to roll more than many of the other research vessels because the bottom is rounded to allow it to work effectively in the icy conditions of the Arctic.

If you’re curious what this is like and wish to experience it vicariously, you have several options. Watching the opening scenes to Mary Poppins where the ladies of the house are holding onto furniture and china is a remarkably accurate representation of what it’s like in the lab when we hit a particularly big roll. The dancing scene at the end of Grease, where Sandy and Danny are walking around on the teeter-totter-esque platform is also pretty good (except that scene should really last 48 hours to do justice the ship’s motion). However, if neither of these quite do it for you, you can always abruptly lift a table at one end and see what falls off.

Monday, March 20, 2017

Plastic in the water around us

A couple of days ago an engine strainer – a big metal strainer used to filter the water taken in by the ship’s engine to cool itself – was taken off for a weekly cleanup, and our engineers, knowing that we have an ecologist on board, kindly suggested that I take a look. 
It was strewn with technicolor plastic bits, as well as tiny living beings that had got caught in the strainer during the week of filtering through the ocean water at 6-meter depth.

I should say, this unexpected strainer – frankly, I had no idea than an engine even had one - gave me a much clearer vision of what is really happening in the water here than any of the samples I'd tried to look at before that. 
Well, this part of the ocean appears to be sadly full of small-sized plastic, even though you won’t see it when looking at the gorgeously, impeccably blue water surface. It’s beautiful, by the way, how this principle seems to hold for everything in life: looking just at the surface, more often than not you are in for some very wrong conclusions.

These plastic bits are submerged in the water column, and establishing the layer, or the depth of their predominant concentration is very easy – one has to simply filter through the chosen depth for a while - but not technically available to me on this cruise.

What I will have a chance to do, though, is take a good look at the strainer a couple more times to see how much it accumulates every week while we’re steaming away northwards from the center of the Gyre. 

Volunteers at Work

We have a fantastic group of researchers, engineers, technicians, students, and volunteers out here in the science party, all putting in long hours under often-challenging conditions. Yes, 3 volunteers are working 12-hour watches and participating in the full range of our activities, from assembling and fixing equipment to launching and recovering gear, to watching the mind-numbing screen of the automated SWIMS winch system for days at a time. Here's a tremendous "thank you" to all of them for their contributions to our science!

Volunteer Keaton Snyder and Co-PI Eric Kunze during the pre-cruise loading in Honolulu. (photo credit: James Girton)
Co-PI John Mickett and volunteer Ethan Brush prepare the over-the-side ADCP pole. (photo credit: JG)

Volunteer Keaton Snyder, biologist Kate Kouba, and grad student Hyang Yoon demonstrate their safety gear during a drill the first day of the cruise. (photo credit: JG)

Volunteer Olga Mironenko discovers a treasure-trove of sea life and drifting plastic in the ship's water intake strainer. (photo credit: JG)

Saturday, March 18, 2017

Cast away

With the advent of technology that allows us to measure conductivity, and by association salinity, with great accuracy, the CTD has become a standard oceanographic instrument. They come in all shapes and sizes, depending on the platform to which they are applied (ship, float, towed instrument, etc). Most, if not all, oceanographic research vessels have a ship-board CTD, but other instruments that get deployed from a ship also typically carry some form of a CTD.
The ship-board CTD suspended over the water from its crane. The red spring-loaded disk at the top protects the CTD cage from damage by the crane. The numbered bottles of the rosette are visible in gray, with the sensors mounted below. (Photo credit: Rosalind Echols)
 The value in a CTD, which is short for “conductivity-temperature-depth” sensor, is that it allows oceanographers to measure the three variables that affect the density of the water, and density is a primary driver of circulation in the ocean. Warmer water is less dense than cold water, fresh water is less dense than saltier water, and (even though water is mostly incompressible) water at great depth with a huge column of water stacked on top of it is denser than water at the sea surface. As a result, knowing each of these three values is of great interest in determining the density of the water. On our particular project, we are using CTDs on SWIMS, the floats, the buoy, and the ship. Each of them is a different size and has a different sampling frequency according to the limitations of the platform. Ultimately, the measurements each CTD provides allow us to calculate density and then look at how this changes in time and space, which in turn governs how water can mix and move.
Marine techs Jen and Bern and Bosun John guide the CTD back into its home inside the ship. You know what's awesome? A door in the side of the ship opens when it's time to deploy the CTD. (Photo credit: RE)
 Ship-board CTDs are often accompanied by additional instruments, such as a fluorometer (which enables subsurface chlorophyll measurements) and a dissolved oxygen sensor. This expands the range of the CTD from purely physical properties to those of interest to biologists as well. Many CTDs are also equipped with a “rosette” (seen in the picture here), which is a set of large bottles that can be closed on demand to gather water from various depths. Once the water is on board the ship, the water can be tested for pH (acidity, effectively), nutrients, and various other chemical species (like CFCs, heavy metals, and so on), and samples can be collected for biological analysis. Each of these tests allows oceanographers to say something about the ocean: who lives there, what nutrients it uses, how long since a particular chunk of water last interacted with the atmosphere, how the water is changing over time, how organisms are effected by physical changes to a system, and so on.
Kate preserves samples by freezing them in liquid nitrogen. (Photo credit: RE)
On this trip, our biologist Kate is collecting water samples at depths ranging from 5 to 200 meters, using the density profile shown by the CTD on the way down to decide where to collect bottle samples on the way up. Once the CTD is back on board, she collects samples for two later analyses: flow cytometry (which will be used to look at chlorophyll levels) and DNA analysis. Some research cruises are equipped with more elaborate biological equipment on board, but in this case much of the space is taken up by the physics equipment, so she is preserving the samples for later use. The goal of the project she is working on with Dr. Anne Thompson of Portland State University is to look at the prevalence of different strains of the cyanobacteria Prochlorococcus, and to see how this relates to what is happening in the physical system (particularly how they adjust their chlorophyll levels after mixing events that move them to a new location in the water column). This is a great example of a project where physicists and biologists are collaborating to understand how two different aspects of a system relate, something that is incredibly important in a complex arena like the ocean.

The CTD is visible below the surface in the super clear water. (Photo credit: RE)

(Deploying the CTD off the ship is called a "cast", hence the title of the post). 

Thursday, March 16, 2017

Looking at Data, Episode 2

As mentioned in a previous post, one of the ways we make sure that our instruments are functioning properly is to plot the data in real time and make sure there are no bizarre glitches. This has already allowed us to catch at least one issue, which was fortunately a problem with the data transfer between computers rather than a problem with the sensors on SWIMS (and therefore more easily resolved). Another advantage of looking at the data as we collect it, even if the plotting is fairly rough and not something you would put in a paper, is that it allows us to see interesting features and keep an eye on how things are changing in time and space. One example of an interesting plot we saw during our first survey is shown below. As with many plots of oceanographic data, there’s quite a bit going on.

To orient you to the plot, we’ll start with the basic set up. Each section of the plot captures roughly two hours worth of profiles from SWIMS (the instrument we are towing behind the ship). Time is plotted horizontally (“Yday”), but since the ship is moving, this also represents change in position horizontally along the ship track. Rather than plotting the profiles themselves, as with the plot shown in the previous post about data, here we are gridding the data, which essentially means filling in the blanks between measurements to get a general idea of the three dimensional structure. These plots may not be publishable in a formal setting yet, but they are incredibly valuable for understanding approximately what we are measuring. The top plot shows the temperature from near the surface down to about 100 meters; the middle plot shows the same thing for salinity and the bottom plot shows the same thing for density (which is calculated from the temperature, salinity, and depth since there is no way to measure it directly with a sensor at the moment).
Plot of temperature, salinity, and density from SWIMS data. We look at plots in color scales like these to help make trends in the data be more visually apparent.

The colorbar to the right of each plot shows what each color represents in terms of a number. For temperature, this is degrees Celsius, with red being warmer temperatures and blue being cooler temperatures. Intuitively, looking at this plot makes sense because in some way we expect warmer things to be reddish. For salinity (in “practical salinity units”), saltier is red and fresher is blue, and with density (kilograms per cubic meter, minus 1000), heavier water is red and lighter water is blue. As we expect to see, the densest water is at the bottom, with progressively lighter water above it. We call this “stably stratified”, because there don’t appear to be any situations where heavy water is sitting on top of light water. When this does happen, we expect it to lead to an overturning circulation where the dense water sinks and the light water rises.

The most interesting feature of this plot is the bands of high and low salinity and high and low temperature that we see. In the very first profile, which would be on the left of each plot, we see a fairly typical temperature progression, where it starts out warm and gets progressively cooler. However, as we move farther to the right on the plot, we can see that the temperature goes warm-cool-warm-cool, and the salinity alternates fresh-salty-fresh in a similar way. Put together, this ends up leading to a warm and fresh bit of water at the surface, followed by a cool and fresh chunk of water, then a warm and salty chunk of water, and finally another cool and relatively fresh chunk of water. As we discussed in the last data post, there doesn’t seem to be much of a mixed layer: both temperature and salinity show substantial variations almost all the way up to the surface.

Observing the evolution of structures like this in time and space, and speaking to why they occur, is one of our goals. This could be an example of “interleaving” (or some other comparable restratification process), where two adjacent water masses with different properties and densities slide past each other horizontally, with the lighter water sliding on top and the denser water below. Cool fresh water could also be the result of a rain storm, that then got covered up with another water mass. One of the things that we will be doing once we have finished collecting data is going back to look at features like this to see if we can combine this data with that gathered from our other instruments to get a more complete picture of what’s going on. This will require some effort to separate spatial features associated with the ship moving from temporal features associated with the dynamics of the region, which is not a trivial problem.

Wednesday, March 15, 2017

The challenges of marine technology

If you open up a magazine about marine technology, you will most likely be inundated with advertisements and articles for equipment that can resist corrosion, extreme pressures, and “biofouling”. These are all major threats to the successful deployment of equipment, particularly if it is intended for long-term use. This applies to oceanographic equipment as well: any metal pieces on our equipment must be corrosion resistant, and the sensors will universally work better if organisms don’t take up residence on or near them.
Another view of the recovered rope shown in Olga's post. (Photo credit: Rosalind Echols)

A couple days ago we recovered a length of rope floating in the ocean that we had passed several times while doing a circuit around a region. While rope may seem innocuous, if a ship drives over one and it becomes tangled in the propeller, it can go from a piece of trash to a huge issue, so it made sense to pick it up. When we get it on deck, we discovered that it was covered in gooseneck barnacles. Unfortunately for the barnacles, taking the rope out of the ocean means they won’t be able to survive, but the threat to navigation in this case seemed important.
Close up view of the top of a float. Notice the tiny grain-like creatures clustered around the bottom of the ports. (Photo credit: Rosalind Echols)

When we picked up our floats a few days later, we noticed that there were tiny organisms growing on them, mostly clustered where there are sharp right angles that create some sort of crevice. Upon further inspection at 50x magnification (using a microscope that looks like its heyday was in the 1950s), we pursued some amateur biological classification and decided that they were probably barnacle larvae. In the larval stage, like many other marine organisms (including benthic ones, or those that ultimately live on the bottom of the ocean as adults), they drift freely in the ocean until something comes along that they can attach to. The odds of them finding one of the floats, given the immensity of the ocean, seems staggeringly small, and yet in only 5 days there were hundreds clinging on.
The tiny critter (barnacle larva?) at 50x magnification. Picture taken with a phone through the microscope lens, so please excuse the quality. (Photo credit: Rosalind Echols)

This is just one example of the phenomenon of biofouling, which could also be described in a more positive light as the impressive determination of marine organisms to survive. Any instrument that is going to be in the ocean for a long period of time will likely have to contend with this at some point.

Tuesday, March 14, 2017

Encounters with marine life

A couple of days ago we came across a thick rope that had been adrift in the ocean for a while and pulled it up on board. A nice bonus: while we were at it a whale started breaching right off the ship and slapping its pectoral fins as if in a thanks. 
When we pulled the rope on board we found that it had become home for a whole community of gooseneck barnacles and crabs of all ages, from tiny transparent babies to well-grown sturdy reddish adults. Our team fished out all the crabs, much as they tried to run for it and escape from the big two-legged creatures in colored hard hats, which they did, and released them back into the water. 
The barnacles, being attached to the rope, were less lucky and, to be honest, we all feel really sorry for them. 

Monday, March 13, 2017

Prepping for Round Two

We just concluded a 24-hour transit to our new location with a cast from the ship's CTD and a midnight deployment of SWIMS to start surveying the area. During the transit, even though we weren’t actively gathering new data with most of our instruments, we still had plenty to do. As thoroughly as we tested everything before we left, the ocean is a harsh and unpredictable place, and there are always improvements to be made to insure that we make the most of our time out here, whether it’s cleaning an instrument, opening it up to check the circuits, or fixing glitches in our processing programs.  

One of the projects we undertook was stabilizing the ADCP attached to the bottom of the buoy chain. The design of the cage around the ADCP was such that the battery and instrument weren’t being held in place as tightly as they needed to be, threatening the power cable and reliability of the measurements. The new-and-improved design increases the friction between the clamps and the frame, and secures the power cable more tightly to the instrument.

The ADCP (black) and its battery (blue) in the holding cage. It hangs vertically from the buoy chain, which means preparing for strong vertical motions is important for keeping the instrument working. (Photo credit: Rosalind Echols)

Every time we use the big ship-board CTD with the rosette (a set of 24 bottles used to gather water samples from different depths for biological and chemical tests), we have to empty it, reset all the firing pins that close the bottles, and rinse it thoroughly with fresh water. In fact, every time we take an instrument out of the water we perform this fresh water rinse to minimize the corrosive effects of the salt water. One of the primary challenges oceanographers face when trying to make measurements in the ocean is that many of the interesting characteristics of the ocean (it is deep, turbulent, and salty, for example) are really bad for electronics, metals, and so on. Many of the engineering challenges are comparable to launching something into space.

Our biologist, Kate Kouba (from Portland State University) resets firing pins at the top of the CTD rosette after gathering water samples. (Photo credit: Rosalind Echols)

Before we put everything back in the water, we are also looking at the data we’ve already gathered, both to keep an eye out for interesting physics but also to see if there were any bizarre data standouts that might suggest a malfunctioning instrument. Sometimes, weird, unexpected features of the data are interesting phenomena, but they can also mean that a probe isn’t working correctly, so closely monitoring the data as it comes in is an important step in making sure that the data we come home is meaningful.