Scientific spaghetti

by Neill MacKay

It’s been a busy few days for this blogger as 4 out of 5 of the NOC moorings have been recovered and redeployed, and I’ve also had the chance to see what’s involved for the first time. Compared with the NIOZ (the Royal Netherlands Institute for Sea Research) moorings also being serviced on this cruise, the NOC moorings present some additional challenges when it comes to recovery. Rather than just the big buoyant smartie on the top, the NOC moorings are designed with smaller packages of buoyancy – glass spheres surrounded by orange plastic – at various points along their length. The additional buoyancy means that if the top part of the mooring breaks away due to some violent weather or some other event during the year, the rest of the instruments below remain supported and so will continue gathering data until the mooring is recovered. The downside of this design becomes apparent when we come to recover the moorings, as they have a tendency to become tangled! So rather than coming on board in an orderly fashion, the instruments arrive in a number of tangled spaghetti-like bundles, and not necessarily in the order you expected! In the worst cases the cable has to be cut to sort out the mess, and great care is taken not to drop any loose end, as this would mean any instruments attached and still in the water would be lost forever!

Once we have recovered all the instruments, we download the data onto a computer and do some initial processing to make sure everything has worked OK. In one or two cases we may not have a full year’s worth of data from an instrument – this can happen for example because of a faulty battery, but from almost all the instruments recovered from the first 4 moorings there are no obvious deficiencies which is good news! The next step is to carry out a ‘cal dip’ – attaching mooring instruments to the CTD and ‘dipping’ them into the water (actually sending them to the bottom!) to check how well they are working. In the case of the microcats, we compare their measurements of temperature, salinity and pressure with those on the CTD and with each other for consistency. The information from the cal dips is used when deciding which instruments to deploy on the subsequent moorings, and which ones to swap out.

The final preparations are then made for redeployment of the mooring, including putting shiny new chains on the buoyancy packages to hold them together in groups of between 2 and 7 spheres. Then it’s time to put it all back in the water! This job is rather easier than the recovery because we can stream the wire onto which all the mooring instruments will be attached out behind the ship, maintaining a steady 1-2 knots to make sure that things do not get tangled. The instruments are then attached to the wire one by one and checked off as they go; these moorings contain microcats and current meters like the NIOZ moorings, but also have an Acoustic Doppler Current Profiler, or ADCP, near the bottom. The ADCP gives a vertical profile of the current speed and direction over a range of depths, obtaining its measurement by firing sound waves into the water and detecting a change in frequency – or ‘doppler shift’ of the waves as they return to the sensor having been reflected off of particles moving with the water. Finally the anchor is attached – and rather than the solid blocks used on the NIOZ moorings, these have giant chains weighing 900kg which are hoisted onto the deck with the crane and then lowered over the water before being dropped in.

The anchor having been dropped, we then take the acoustic transducer which we use to communicate with the mooring acoustic release mechanism and monitor its progress as it sinks to the bottom at a rate of around 100m per minute. When it reaches the bottom, the ship then moves about a mile away from the anchor drop location to begin triangulating the mooring’s final position. At 3 points surrounding the drop location we range to the acoustic release, and use the 3 ranges to do the triangulation. So we know where to look when we come back to retrieve the data next year!

Talking to the acoustic release


Buoyancy spheres caught up in a tangle

Trying to untangle the spaghetti

Big anchor chain!

Float on

by Ryan Peabody

Imagine that you were inclined to make an observation about the ocean. As someone reading an oceanography blog, there is a very good chance that you are exactly the kind of person who would be. In this hypothetical situation, you would walk down to your hypothetical dock, and record some property of the water – let’s say current speed. If you were to repeat this activity over time, we could then build a time series, a record of these speeds over time at a fixed location. This is what an oceanographic mooring does, with multiple types of information. It records data continuously at one location, giving a very good sense of what is going on at that spot over time.
Our record of observations would only tell us what was going on at that one point. We might be able to guess what was happening elsewhere, but we would not be able to verify our guesses. We can overcome these limitations by deploying more moorings and instruments, but each is still fixed in location. Our ability to guess at what is happening elsewhere improves, but we still only know what is happening where we choose to look. When tracking the pathways that ocean currents take throughout the ocean, we run into an issue: if we do not know the pathways that these currents take, how can we decide where to look in the first place?
Besides in situ observations, there are other ways to examine oceanographic currents. We can use satellite altimeters to examine ocean height and derive surface currents, or we can physically put objects in the water and watch where they go. However, what do we do when these currents are far beneath the surface of the water? We can place instruments at those depths on moorings, or observe how sound waves change as they bounce back from depth, but we run into the issue discussed earlier: we limit ourselves to observations constrained in space. It is in our interest to know where and how these water masses move, not simply what the speed is at a handful of points.
The ocean is layered, with denser waters filling the deep ocean basins, and “lighter”, less dense water masses floating on top of one another subsequently to the surface. An oceanographic instrument with a certain density would then float on top of a dense water mass, but sink through the one overlying, riding the interface as a surface float would between the ocean and atmosphere. RAFOS floats are 2 m-long glass tubes that do exactly that. Each has a specially made steel weight that allows it to sit at a certain height above the bottom of the ocean. In this way, we can follow the pathways that deep ocean currents take.
2000 m below the surface of the ocean, it is pitch black. Light does not transmit very far through water, attenuating in the surface waters high above. Similarly, signals from GPS satellites, radio waves, and most of the mediums we use for communication do not propagate well. It is one thing to deploy a RAFOS float beneath the surface, but knowing where it goes and then recovering that information require additional processes. Sound sources deployed throughout the North Atlantic emit a pulse of sound every 24 hours. Unlike light, sound can travel for great distances underwater. By calculating the difference in time between emission and reception from these sound sources, the position of the float can be calculated as it moves underwater.
Each float looks like a long, glass thermometer, sitting atop a metal weight. The weight connects on the bottom, screwing into a plastic socket, connected to the main tube with a thin wire, next to a hydrophone and a temperature and pressure sensor. Above the sensors lies a battery pack, satellite transmitter, microprocessor, and a connecting rod that runs through the middle of the glass tube to the antenna, located in the top of the glass tube. Once they are turned on, they are lowered (dropped) off the stern of the ship, where they sink underwater, and record their positions for two years. After two years, a current is passed through the connection point for the wire, heating it to the point that the wire shears, dropping the weight to the bottom of the ocean and allowing the float to truly float, up through the water column until it reaches the surface where it can upload its data to a satellite.
Of the thirty-four floats we started with, fourteen have been deployed, on a transect perpendicular to the Reykjanes Ridge south of Iceland. Two will surface after eight and eighty days, to verify that the sound sources are working as expected. Twelve will stay under for the full two-year deployment. The remaining twenty will be deployed on a transect further west, perpendicular to the coast of Greenland. The data gathered from the deployments at different depths and different locations will provide insight into the movement of deep water in this part of the North Atlantic.
It was initially intimidating to plan out the timing of my deployments in the context of the larger cruise mission. Our course can be simply visualized at two east to west transects: one off Greenland and the other off Iceland. Each transect is performed three times, to recover permanent moorings, perform CTD casts and deploy the RAFOS floats, and to redeploy the moorings (with fresh batteries and instruments, stripped of data from the previous deployment). If I had my way, all the RAFOS deployments would occur over the course of a couple days, between 11:00 AM and 3:00 PM, and then everyone else could figure out their stuff while I relaxed with a cup of coffee. Unfortunately, my scientific plan has been rejected in favor of one more “economically efficient” and that “actually makes sense,” so I deploy floats when we arrive at my stations, regardless of the hour.
Fortunately, there is plenty of coffee and just-shy-of-unbearably salty Dutch licorice on board. With night a barely perceptible dimming of the sun behind clouds, and my ability to avoid an eight-hour CTD shifts, it is sometimes hard to keep track of what time it is. Maybe a structured work schedule makes it easier, but I exist in a gray limbo, punctuated by meals and float deployments. At eye level, the horizon is approximately 5 km away. Raising or lowering the viewpoint changes the distance accordingly. We will be able to see Greenland soon, giving at least one boundary to the horizon that is not more water, tucked away from view by the curvature of the earth. Until then, we will all just keep looking out at the horizon.

Rafos 1

Rafos 2

Up CTD, down CTD

by Neill Mackay

For the last couple of days we have been on CTD watches which means that we work in 3 teams covering 8 hours each of a round-the-clock operation (which for this blogger means starting at 4am, and my first experience of darkness since leaving the UK as we have nearly 24 hours of daylight at this latitude!). Once we have arrived at the location of the first station, we make the CTD ready for deployment and then it is lowered into the water on a winch. We then issue instructions to the winch driver over the radio, telling them how far to lower the CTD on the way down, and giving them fair warning so that it does not hit the bottom! An early warning system in the form of a weight dangling down from the CTD hits the bottom first and sounds an alarm, making sure that we do not end up with a CTD covered in mud! On our shift the winch drivers coped particularly well with regular switches between instructions in English and Dutch, depending on which of us was on radio duty! On the way back up the CTD is stopped at intervals and the Niskin bottles closed one by one to collect the water samples. Finally the CTD is brought on deck and we take the samples for oxygen and salinity from the Niskin bottles, before making the CTD ready for the next station. And repeat!

Having completed the CTD stations, we now find ourselves back at the point where we recovered our first mooring, ready for redeployment. The mooring instruments are attached to the cable from the top down, starting with the smartie-shaped buoy we saw in the previous blog post. Then each sensor is added one by one, with the cable being paid out on a winch in between – a mixture of ‘microcats’ which measure temperature, salinity and pressure (a sort of mini-CTD), current meters, and thermistors which provide a backup for the temperature measurement. Finally the anchor – a large metal weight – is attached to the end of the cable and lifted over the back of the boat using a crane. A pin attached to a rope is used to release the anchor and *splash*, into the water it goes!

We have had a filmmaker on board during this cruise taking footage of our work. There is now a YouTube channel where you can find some clips he’s been making:


The CTD being lowered over the side


Disappearing into the depths!


Attaching some buoyancy to the mooring


 Mooring anchor about to be dropped into the water

Spot the orange smartie

by Neill Mackay

So after a quick turnaround in Reykjavik, leg 2 of the OSNAP cruise is now underway. A new science crew are on board – except for Loic and Colin who are in the unenviable position of knowing what’s going on, so have been answering all of our questions! After 2 days of transit in near-perfect weather we arrived this morning at the site of our first mooring. First the acoustic signal is sent to the release mechanism at the bottom of the mooring (see ‘How to catch a mooring’ earlier in this blog), and then the group exercise of staring into the distance looking for a small round orange object in a large expanse of blue ensues – the smartie-shaped buoy which floats at the top of the mooring. The spotting game took longer than usual as some rougher weather had arrived in time for the mooring recovery, which means that the buoy has to be spotted in the intervals when it reaches the crest of a wave before diving back out of sight. Eventually however it was spied from the bridge and we headed towards it to pick it up.

Alongside the recovery, servicing and redeployment of the moorings in the western half of the OSNAP east array on this cruise, we will be making CTD casts to gather some extra data (the CTD is explained in ‘Check check and triple check’ earlier in this blog, and you can see another picture below). For those of us new to the procedures, we had a run-down on how to make the CTD ready for deployment, how to monitor its progress as it goes down to the sea floor and comes back up again, and how to take samples once it is back on deck. On this leg of the cruise we will be taking samples of water from the Niskin bottles to measure nutrients and oxygen as well as the usual salinity used to cross-check the CTD sensor itself. Oxygen can be used as a tracer to learn about the history of the water at a particular depth – if the water sampled is high in oxygen this indicates that it originated at the surface where it absorbed oxygen from the atmosphere. Sampling the water for oxygen has to be done carefully using special sample bottles so that the samples are not contaminated with oxygen from the surrounding air.

Gathered around the CTD for our briefing on procedures

Abandon ship drill on the transit (Maarten the camera man is on board making a short film about our work)

Hooking the mooring for recovery

Smartie on deck!

Whale sighting during the transit

Home Sweet Home

by Clare Johnson

Sorry for not writing for a few days. I got back home yesterday but am still feeling very tired and a little woozy – unfortunately I’ve always had problems with land-sickness when getting off a ship – the equivalent of sea-sickness as your body re-adjusts to being on a none-moving environment again!

We managed to finish the last couple of mooring recoveries and deployments before some forecast bad weather forced us to head for Iceland where we docked. It was a very successful trip with 12 out of 13 moorings being brought up from the deep, serviced and re-deployed to make measurements for the next year. Unfortunately it looks as if the thirteenth mooring is lost. This mooring was in fairly shallow water within a known fishing area. We had used a special trawl-proof frame to minimise the risk of the mooring being damaged by trawling, but it looks as if this wasn’t sufficient. Although we are disappointed, all marine scientists know that if you put things in the inhospitable ocean for a year there is a chance that it won’t come back… However, sometimes ‘lost’ instruments wash up on a remote beach or are found by a fisherman years later so you never know!

The last few days of a trip are always hectic: any remaining data has to be processed, checked and have calibrations applied. Instruments and computers need to be packed away and lab spaces emptied and cleaned. Additionally every trip has to produce a ‘cruise report’. This is a document which details everything a person who later uses the data may need to know. During the last few days the ship is full of scientists typing away – we all know from experience that it is much harder to finish this report once you leave this ship and the pressures of everyday work and life creep back in.

As you get closer to land a sort of excitement begins to fill the ship, particularly for crew members who have been at sea for 6 weeks and are due leave. The ladder for the pilot to come aboard and the docking ropes were ready when Iceland was still a small blob on the horizon! However, no-one is allowed to leave the ship until it has been cleared by customs and immigration. Once given the all clear though we were free to stretch our legs, sample the local beer or ice creams (a big thing in Iceland) and eat anything we had been craving which was salad for quite a few people! The next two days however involved a massive re-arrangement of the ship. Nearly all the equipment was unloaded via a crane and placed on the dockside. Some of this was packed into a container for shipping home to the US whilst other bits were packed into a separate container to be placed in the ships hold out of the way. Simultaneously all the instruments for the next leg of the cruise were unpacked out of a container and placed in accessible areas of the ship. Finally, with the ship re-packed, the scientists and crew who were leaving ashore, and the new scientists and crew on board, the Pelagia set sail for her next trip: servicing more moorings between Iceland and the southern tip of Greenland.

Pic 1: an instrument that measures current speed and direction in a trawl-proof frame waiting for deployment on board Pelagia.

Pic 2: one of the landmark buildings in Reykjavik (Icelands capital) near the docks.

Wildlife ahoy

by Clare Johnson

Yesterday I (finally) saw my first whale / dolphin of the trip. There had been various sightings before but I was either too slow getting on deck, asleep, or on watch and unable to leave the lab. However, yesterday when I heard ‘pilot whales port side’ I was able to go out and see them. They were a group of Pilot Whales, a whale that I’ve seen quite often in the eastern North Atlantic. From what I’ve seen, Pilot Whales travel in groups (10-30 animals) and seem to be pretty inquisitive. They tend to turn up whilst the ship is stationary (at a CTD station or mooring recovery) and often hang around until we move slowly off. Unlike for larger whales that often just take a few breathes before diving deep again, Pilot Whales dip in and out of the waves and seem to enjoy being at the surface and playing around us. They remind me more of otters, dolphins or seals because of their interest and playfulness than larger whales.
We have also seen a number of seabirds on our trip. I am reliable informed we have seen Terns, Black-back Gulls, Skuas and kittiwakes – bird identification is not a strong point of mine! By far the most common bird once away from land (and Rockall) is the Fulmar. Even I can identify these white and grey birds. Fulmars spend nearly their entire life out at sea only returning to land to breed, and like Pilot Whales they often hang around a ship in groups as well. [I guess because they are hoping that we are a trawler and will be discarding fish, but also because the ship can provide some shelter from the wind.] Fulmars are wonderfully adapted to their life at sea with the black blob at the top of their beak converting seawater into fresh water for them to drink. In hot dry countries seawater is transformed into drinking water in huge energy-demanding desalination plants, I love the fact that Fulmars have their own little built-in desalination plant! Fulmars can often be the only wildlife I see during a trip to sea and I enjoy watching them bob about on the waves and squabble if a neighbouring bird comes to close. I also think about how unpleasant it must be for them in winter when the wind whips up the sea into spray and I am (hopefully!) all nice and toasty inside somewhere. As we get closer to Iceland we will probably see some other seabirds, and if we are lucky some more whales.


A pod of Pilot Whales taken by Karen Wilson.

Check, check and triple check

by Clare Johnson

The excitement yesterday was that it was one of the scientists birthday. To celebrate the crew put up bunting in the bar, the cook made a very large and very yummy cake, and the birthday girl got a home-made card from us all. Other than that we are plodding through our mooring recoveries and deployments. We are currently steaming towards mooring number nine (I think!).

Before we put any instrument in the ocean, especially one that we are going to leave for a year collecting data, we do everything we can to check that it is working as well as it can be. Firstly the instruments are checked in the lab: do they look ok, are there any known problems from previous trips, can we connect to it ok – all the instruments are programmed using a computer. Then the instruments are checked again, this time by testing them in the ocean at the maximum pressure they will have to work at during their years deployment.

To do this we attach them to a CTD rosette. This is a large metal frame around 6 foot tall and 5 foot in diameter with various instruments and water bottles attached. It is a mainstay of marine science and a different CTD rosette was used continuously to make measurements on the Discovery cruise. To check instruments that will be used on the moorings we attach these to the rosette frame and lower it from the sea surface to just above the seabed before winching it back. This allows us to check that the mooring instruments have recorded data ok and not let in any water under the pressure the ocean exerts. It also allows a comparison of the values the mooring instrument is measuring relative to the instruments on the CTD rosette. Is there a very small (and allowable) offset or is the mooring instrument measuring incorrect values? [As an aside, we check the CTD rosette instruments are accurate in their measurement of temperature and salinity using a second reference thermometer and water samples to measure the salinity on another very accurate laboratory instrument. The CTD rosette instruments are also sent back to the manufacturer for calibration at regular intervals.] We also check that we can ‘talk’ to the hooks that tether the mooring to the weight on the seabed and are vital for the recovery of the mooring.

Finally, just before deployment of the mooring in the ocean for a year we do our final checks on the instruments, programme them how we’d like them to sample and press ‘start data recorder’. Although we do everything we can to ensure that we will get the mooring and instruments back, and collect good quality data, there is just bad luck and things we cannot control. So keep your fingers crossed for us that things are going well for our instruments down there in the cold, dark, deep North Atlantic!


CTD rosette with some instruments that will be deployed on a mooring attached (LHS) so they can be checked against the rosette instruments values. The grey bottles are closed at chosen depths in order to collect water. The yellow instrument measures current direction and speed.


The CTD rosette and attached mooring instruments going over the side. It is lowered to the seabed and then raised again on a wire which transmits real-time data to the ship.


The lab instrument that we use to very accurately determine salinity in water samples collected from the bottles on the CTD rosette. This enables us to check that the CTD sensors are working as well as possible. Running water samples through this machine is mind-numbingly dull and is referred to as ‘working in the salt mine’!