One of the enjoyable things about writing these updates is sitting in my cabin, which is the highest on the ship just aft of the Navigation Bridge, and watching the sky change colour as the sun slowly sets whilst listing to the sea on the hull. It is a very peaceful way to end the day and relaxes me just enough to sit and type.

In an earlier update I mentioned that the ship was carrying out trials of the swath bathymetry equipment and it seems that the results from the trials were excellent and the scientist involved, Rob Larter, has kindly provided me with some images.

The first image is of the seabed as seen by our swath bathymetry system. The detail is excellent, and in the high resolution images the definition is very impressive. As you can see from the colours the area covered water depths down to over 4000m. Picture Rob Larter, BAS.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

The second image supplied is an excellent representation of just how it works, and I feel is a much better example than the one I used the other day. This was produced by Jamie Oliver at BAS.

Image courtesy of Jamie Oliver at BAS

Image courtesy of Jamie Oliver at BAS

Whilst covering old ground, I had an e-mail from John Davies, a radio ham I work from time to time, who passed on the picture of our little bird to the Cornwall County Bird Recorder and had a reply from Tony Mills who advised that it was a Northern Wheatsheat, also known as a Wheatsheaf, possibly from the Greenland race. So, a good result and a big thanks to John for getting the answer. Penguins tend to be easier to identify!

A question: What do you do on a ship if there is an emergency? The answer, initially at any rate, is to deal with it yourself. There are no emergency services that we can call who will turn up in a fire engine of ambulance in the space of five minutes and we have to perform these tasks ourselves. In the case of medical issues we are fortunate that for most of the time the ship is at sea a doctor is carried, although there are periods when we are left to our own devices. Fire fighting is carried out by the ship’s company and we practice on a regular basis to ensure that our skills are at a good level should they be required. This is backed up with courses held ashore during our leave period. Today we had our first exercise, with the scene being set in the Forecastle. The fire alarm sounded and once it was determined that there was, albeit for exercise purposes, a fire, the General Alarm (seven or more short followed by one long blast on the ship’s whistle and internal alarm system) was sounded and then everyone musters at their designated position and prepares to tackle the emergency. The exercise this morning went very well and there will be more as we continue on our passage south.

Science can be very hard work! When there is the chance to lean against the bulwark and enjoy the view and sunshine, it is taken. Here the optical equipment is deployed and the scientists are waiting for it to return on board to then gather the data from all the instruments.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

Meanwhile at the other end of the ship Alice is playing with a hose! The net has just arrived back on board and the samples collected (which I think are of some very very tiny beasties) in the bucket to then be analysed. I think the hose may have something to do with getting the samples from the net, but as I did not want to get a soaking a beat a hasty retreat.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

Working hard is one of the sailors, Fransisco. One of the great joys about this stage of the cruise is that it is nice and warm outside and so our polar clothing is not required. Doing this sort of work in the freezing cold of Antarctica is not as pleasant.

Image courtesy of Richard Turner

Image courtesy of Richard Turner

Back to the emergency services, or lack of, the Doctor has started to run some medical courses and her she is explaining to Pugsy Jnr Jnr how to carry out CPR. I am told that Pugsy Jnr Jnr even has a FaceBook page!

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

The sun has now set and the view from my cabin is one of pith blackness, so that strikes me as being a good point to finish for this evening.

With the swath bathymetry trials now complete, the ship is now settling down in a steady routine of science and steaming. With two science stations daily, accounting for five hours of time per day, the ship will be travelling 209 nautical miles per day for the remainder of the cruise. Our arrival/departure at the Azores has changed and we should now be arriving on the morning of October 2nd. Our visit will be brief, with the pax movements being done by boat and once completed we will then continue with the cruise south.

Our at sea routines are now firmly in place and should remain so until our arrival in the Falkland Islands. Sunday has a routine with the weekly scrub-out of the ship, where everywhere gets a thorough clean and this is followed by an inspection my the Captain. No white gloves are used, but a torch is carried for looking into all the nooks and crannies. Aside from making sure that the ship is clean and tidy, this also serves as a means to pick up any defects, for example lights out in cabins and work spaces that may not have been reported, thus allowing for everything to be kept in a good working order.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

I mentioned earlier in the week that we had a few small birds on board, one in the Combined Office yesterday morning. This is what they look like! It seems that another one got into the accommodation and was found hiding in the Chief Engineers cabin. I still have no idea what it is and welcome any suggestions as to what species it is.

The ship has been rolling to a long low swell today and almost going to about ten degrees from upright. It is not at all uncomfortable but it is a reminder, especially to those who have not been away to sea before, of the importance of keeping things secure and tied down when not in use.

Philippa, the Second Officer (or Navigator) seen ‘shooting the sun’. In the modern age of computers, electronic charts and global position fixing services, the Deck Officers don’t just rely on technology in their navigation. Star sights are used, amongst other things, to check that the compasses are accurate. The compasses on the Bridge-wings will also be used for taking bearings of land in order to double check the position of the ship on the chart.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

A picture for the radio enthusiasts. This shows the 10m vertical antenna that I use with the Kenwood TS-480 HF transceiver. The RF is fed from the transmitter up through the deck and then to the base of the antenna. Typically I operate using 100W, but this is reduced to 20W when using PSK31. It seems I was heard in Australia on the mode recently, so hopefully I will get a contact before too long from there.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

One of the pleasures of the passage between the UK and Antarctica is that the weather tends to be warm and dry for a good portion of it. Whilst we have not made it very far south, being at 45°N, it is very nice out with the temperature being around 20°C and for those not on watch there is a chance to sit out and catch a bit of sunshine and fresh air.

Image courtesy of Mike Gloistein

Image courtesy of Mike Gloistein

This evening there has been a lovely sunset, which I have been able to catch from my cabin window as I write this update. With the weather being so nice I also have both my ports (windows) open and can hear the sound of the waves as the James Clark Ross steams through the Atlantic Ocean.

…….and finally, a Happy Birthday to Emma, the James Clark Ross Doctor.

Thursday was our second full day at sea, after our very short visit to Portsmouth on Wednesday, and this morning we passed Plymouth and are now heading out into the Atlantic in excellent conditions.

The James Clark Ross departing Portsmouth

The James Clark Ross departing Portsmouth

The James Clark Ross departing Portsmouth on Wednesday evening, watched by several readers of this page. My thanks to Shelagh Phelps for taking the picture and sorry that we were not fast enough to keep the light!

Magnetic Compass Binnacle

Magnetic Compass Binnacle

A section of the Magnetic Compass Binnacle. The compass, which is not very large sits just above here, and inside this section (and on a similar one on the other side) are a series of magnets and depending on their placement affects the reading of the magnet. By rotating the ship through 360° the Compass Adjuster will see how far out the Magnetic Compass is in comparison to the gyro compass, and will correct it accordingly. This adjustment is carried out each year and it helps allow for any changes in the metal structure of the ship in the past year. It does not take long, and last night I was on the Monkey Island with the Adjuster and even allowing for the background light the sky was clear and the stars shining brightly.

 Sun shining through the vent fan trunking

Sun shining through the vent fan trunking

Just before we departed Portsmouth the sun was low on the horizon, heading for Australia I think, when I noticed that it was shining through the vent fan trunking, which is normally a very uninteresting grill with some very large, powerful and noisy fans (used to force air into the Engine Room), and the result was it almost looked like the space was on fire.

Sunrise

Sunrise

Sunrise this morning (something that I don’t always get to see….given the chance) was rather lovely and the day continued as it had started, with lovely weather throughout.

This morning saw the first test station take place at about ten thirty. The first test was of the Garrett Screen (I have no idea what this is or does, but will investigate once the science is fully underway). This was followed by a CTD cast to a depth of 70m and finally the optical equipment was deployed. All this was completed by early afternoon. The test station is important as some of the scientists will not have been to sea before or may not be familiar with the equipment and procedures. During the course of the cruise some methods of working may well be modified to make life easier for those doing the sampling.

Once the science starts fully, the intention will be to do a station in the early hours of the morning, before the sun is up. The CTD casts will be to 500m. A second station will then be carried out at around mid-day, to see what is happening in the water column when it is daylight.

For this science cruise, JR303, I will be archiving the pages so if you happen to miss a day or two, you should be able to catch up with them and I will provide a link later in the week to the index of previous pages.

This evening it was evident that we have cleared land and are now heading deep sea, with the James Clark Ross rolling easily to a slight sea. Whilst it is not too bad, I will be securing everything in my cabin and the Radio Room tonight, just in case the weather should change – although this is not anticipated but one can never be too careful when it comes to the weather.

With us being back at sea life on board will now slowly settle into a routine, one that always look forward to. Port visits are always enjoyable, but they do break the routine and it can take a day or two to get back to the way life should be.

On the wildlife front there have been a few birds, mainly boobies and seagulls. I have no idea what we may encounter on the passage south, but hopefully it will be interesting and exciting for all on board.

Another long day for the Officers and Crew on the James Clark Ross with a very brief visit to Portsmouth to load bulk aviation fuel for Rothera base.

The Admiralty Pilot came out to the ship on-board the pilot cutter Solent Racer at about 0645 to take the ship alongside the historic dockyard. As dawn broke and we passed the wonderful sights of the very modern Spinnaker Tower and then the older, far more historical sights of HMS Warrior, HMS Victory, HMS Illustrious, HMS Dragon and, from memory, HMS Richmond.

Once all fast alongside the Middleslip Jetty, the bunker barge made the short journey from the fuelling berth, just across the water, and bunkering commenced.

Alas due to the high security level on the Naval Base it was not possible for everyone to be allowed ashore, however I did manage to hitch a short boat ride early this afternoon out of the base and this meant that I could stock up on some new films for the coming season. Time for a quick cup of coffee and also to meet the Bosuns father, a real sailor who worked on the British Antarctic Survey ships many years ago. Visiting the ship today was the first Captain that I sailed with at BAS, back in 1990, who came down for a social visit. Fortunately he has a dockyard pass and so can come and go at leisure.

Paddle steamer Waverley is down here just now and as we returned to the ship on our little boat (a small ferry used within the dockyard to get personnel around and across the river), it steamed past us. There was a lovely smell of burning coal and the sound of the paddles in the water was lovely to hear. It was a beautiful day for those lucky enough to be on-board, with the sun shining brightly at the time. An improvement on the rain of this morning.

With a Pilot back on board at 1900 this evening the ship slipped the berth and departed Portsmouth at 1915. As well as the Pilot we had embarked a compass adjuster, who was on the ship to check that the magnetic compass, located on the Monkey Island, was reading correctly. In order to do this the compass is swung, which actually means that the ship rotates through 360 and the adjuster makes changes to a set of magnets that are located beneath it. By doing this it is possible to correct the compass for the effects of all the steelwork on the ship, which will change from year to year with additions or removals of various parts as well as something as simple as shot blasting, of which there has been a lot this summer during the refit period.

The ship is now on passage, continuing to head down the English Channel for the Atlantic Ocean, which is where all the real science work will begin. We will be conducting some trials of the swath bathymetry equipment on the way to the Azores, and stopping somewhere off Plymouth to run a test science station.

I think that everyone is delighted and possibly a little bit excited to be at sea at long last, starting a long oceanic passage. Ahead of us will be King Neptune, fine weather, flying fish and some wonderful nights of star gazing without any ground light to interfere with the stunning views of the night sky.

The James Clark Ross alongside the Middleslip Jetty,  Portsmouth

The James Clark Ross alongside the Middleslip Jetty, Portsmouth

The 24th Atlantic Meridional Transect (AMT) research cruise will be leaving Immingham at the end of this week with PML scientists on-board, spending 6 weeks sailing the Atlantic to arrive in the Falklands in early November.

AMT is an inter-disciplinary scientific programme that undertakes biological, chemical and physical oceanographic research during an annual voyage between the UK and destinations in the South Atlantic. This journey crosses a range of marine ecosystems from sub-polar to tropical and from shelf seas and upwelling systems to mid-ocean gyres. The AMT crew perform on-going measurements of the oceanic conditions such as chlorophyll, sea surface temperature, nutrients, optical properties, dissolved gases (including carbon dioxide and nitrogen) and plankton community structure. This year, the crew will also be deploying five bio-argo floats to measure characteristics of the ocean, for example, salinity and temperature. The new data collected by the bio-argo floats, combined with ship-borne observations and satellite data, will revolutionise our understanding of biological, chemical and physical processes and interactions of the marine environment.

This year’s cruise has seven scientists from PML. Also joining them will be Rafael Jose Rasse Boada from the Instituto Venezolano de Investigaciones Cientiicas, Venezuela who will be funded by the Partnership for Observation of the Global Oceans (POGO). POGO has funded a berth for a scientist from a developing country to join the expedition for the last seven years, to learn monitoring techniques aboard a large research vessel.

The scientists on-board AMT continue to provide the Earth science discipline with the knowledge base it needs to understand how this ocean is changing and what it might mean for the ecosystem, as well as the wider implications on climate and society. AMT provides one of the few datasets that will be able to highlight significant shifts in the Atlantic’s processes and functions as a result of climate change and other environmental stressors.

Image: PML scientist Giorgio Dall'Olmo (left) and POGO fellow Rafael Rasse (right) preparing a bio-argo instrument for the AMT cruise. Image courtesy of V.Cheung POGO.

Image: PML scientist Giorgio Dall'Olmo (left) and POGO fellow Rafael Rasse (right) preparing a bio-argo instrument for the AMT cruise. Image courtesy of V.Cheung POGO.

We are roughly 40 degrees south and 45 degrees west and heading for the Falkland Islands where we are due to arrive on Saturday. We have two more days of sampling left and I am very much looking forward to (for the first time in two weeks) not having to get up at 4:30am on Thursday!

We are now in very productive waters. The picture below shows two 25mm GFF filters which have had 1 litre of surface water (~5m depth) filtered through them. The colour in the filter is primarily caused by the concentration of phytoplankton in the water. A few days back, when we were in the very blue waters (see last post), it would probably have taken 6-8 litres of surface water (maybe more) to get anywhere near this colouration.  The yellow colour of the filter is indicative of a phytoplankton community dominated by diatoms and in the right filter you can even spot a red copepod (zooplankton) antenna. 

Phytoplankton filters

Phytoplankton filters

In a space of a day the Secchi depth (the depth at which a 30cm white disk disappears from view) changed from 35m to 19m. The Secchi disk is a white disk that is lowered into the water until the point at which it disappears. The depth of disappearance is known as the Secchi depth. The Secchi disk is one of the oldest bio-optical instruments and has been in use since the late 19th century.  In additional to the high-tech bio-optical instrumentation we have on our optics rig (see below) we also attached a Secchi disk, that way we can continue this decadal long time-series of observations. The Secchi depth can be related to the concentration of phytoplankton in the water (see figure below).  We have compared our Secchi depth measurements taken on this cruise with the average chlorophyll concentration estimated from satellite at the same location in an October climatology (we will use the concurrent chlorophyll concentrations once they are processed after the cruise). Demonstrated in the figure below, as the chlorophyll concentration decreases (a pigment indicative of phytoplankton biomass) the Secchi depth typically increases. The black line shows the typical relationship between chlorophyll and Secchi depth observed elsewhere in the global ocean. These Secchi depth measurements can also be used to validate algorithms designed to estimate the Secchi depth using satellite ocean-colour data, as demonstrated using the October monthly satellite climatology (bottom right figure below).

Optics rig, Secci disk, Secci depth against satellite chlorophyll observations

Optics rig, Secci disk, Secci depth against satellite chlorophyll observations

As we approached 40 degrees south, we have entered the region of the ocean known as the “Roaring forties” and have been blasted by 51 knot (Beaufort 10) winds and the ship has been rocking from side-to-side (see image below). Hopefully the wind is dying down tomorrow, though I am not sure the swell is?

Rough going onboard the JCR with wind speeds approaching 60mph

Rough going onboard the JCR with wind speeds approaching 60mph

Chlorophyll in the South

30th Oct, 2013

Since passing the equator and surviving the “crossing the line ceremony” we have been sampling constantly for over week. Since the start of the cruise I have now filtered nearly 1500 litres of water through 25mm 0.7 micron filter-pads.

We have now crossed the South Atlantic Gyre one of the least productive regions of the ocean (often referred to as an “oceanic desert”). In the South Atlantic Gyre, the water is as blue as it can get (see photo below).

Clear blue of the South Atlantic Gyre

Clear blue of the South Atlantic Gyre

The plot shows the AMT23 transect overlaid onto a satellite chlorophyll climatology of October. The pink dot (roughly -20 latitude and -25 longitude) highlights where this photo was taken. It is in a region of the Atlantic Ocean with the lowest total surface chlorophyll concentration (chlorophyll being a photosynthetic pigment in phytoplankton, indicative of its biomass). Alongside the map shows a remote-sensing reflectance spectra (after an initial processing) captured using our hypersepctral radiometer (Satlantic  HyperSAS) at the same location the photo was taken. The remote-sensing reflectance is essentially a ratio of upwelling radiance to downwelling irradiance (in simple terms the ratio of light coming out of the ocean to that of light going into the ocean), and it is plotted on a linear and a logarithmic scale (y-axis) as a function of wavelength (x-axis) in the UV to visible portion of the electromagnetic spectrum. As can be observed in the plot, at UV and blue wavelengths (300-500nm) the reflectance is very high, whereas as green and red wavelengths (500-700nm) the reflectance is much lower.

South Atlantic Gyre satellite chlorophyll climatology of October alongside the remotely sensed reflectance spectra

South Atlantic Gyre satellite chlorophyll climatology of October alongside the remotely sensed reflectance spectra

Part of the reason these waters are so blue is that the phytoplankton concentrations at the surface are very low (the chlorophyll pigment in phytoplankton absorbs blue light), such that the optical properties of pure sea-water dominate the reflectance signal (pure sea-water absorbs light at red and green wavelengths with a higher intensity than at blue wavelengths, and also scatters blue wavelengths with a higher intensity than red and green wavelengths).

Rough seas of the South Atlantic

Rough seas of the South Atlantic

We are now heading for the Falkland’s where we are due to arrive in a week and a half.   The sea is already getting rough (see image below taken this evening). However, we are heading for greener waters which means two very importance things: i) we are lightly to see more marine life (e.g. whales ect…)  and ii) I will be filtering less water!

Dawn at sea

Dawn at sea

You are walking through a sunny street in a village back home, you hear the birds chirping in the morning, and the people´s funny voices and the laughters from the windows of the surrounding houses. Everything seems so quiet and peaceful. The ground is solid and still. Suddenly, a sharp alarm calls and you wake up within a dark cabin. You realise that your bed is moving slightly from one side to the other, and you hear the cracks and weird noises of the wooden walls around your bed. For a second you feel like if you are within the stomach of a huge beast. You just have discovered that it is 5 o’clock in the morning and that you are in a ship. But somehow you are not surprised, so you stand up quickly.

Minutes later, and still sleepy, you walk through a corridor that goes up and down, from one side to the other, it seems like a joke, but it is not, and you are still able to walk and keep the equilibrium by placing your hands on the walls or wherever is needed. You are going straightforward to your space in the labs where all the material is ready from the day before, the sampling from the morning CTD is coming, though you may go first to the canteen to have a light breakfast. There in the labs, little by little, more and more people, scientists, seamen and technicians, appear silently from every door around… The deep sound of the sea and the murmur of the waves is all the time present. People say good morning, walking carefully on their steel toe rubber boots while they put a helmet on their heads, carrying their dark plastic bottles, tubes, little notebooks, pencils and whatever they need for their sampling.

If you are lucky, you may see , right before the rossette with the niskin bottles is taken from the black depths, a flying fish jumping over the dark surface of the sea, a gleaming red squid trying to catch some food before the sun rises, or may be the elegant shadow of an albatros planing around the ship.

A range of wildlife to see at sea; a masked booby

A range of wildlife to see at sea; a masked booby

The heavy rosette with the CTDs and the 24 niskin bottles is rising from the surface like a wet ghost, hanging from a very solid brown cable. The technicians need to coordinate and to communicate with each other at this moment, so all the precious water from different depths is kept in the niskin bottles and no device is damaged.  Everybody expects it to land on a metal frame on the deck, and tied by thick salty ropes.

Within the scientist, it is very appreciated when somebody trys to cheer you up, and you feel well when you produce the smile of somebody. There is always someone in the same situation than you, and you may be surprised to feel it everyday, through the hours of hard and tiring work, an empathy that you may not experience on land.

This could be the begining of a normal day in a cruise on board of a oceanographic ship, an experience totally extraordinary for most of the people (at least for me). You may not live it again, so you have to enjoy it every moment.

The past week has flown by. The figure below (courtesy of Arwen Bargery) shows the ocean temperature, salinity, fluorescence (an index of phytoplankton biomass), oxygen and beam transmission, derived from the vertical profiles at each station so far sampled. As we moved south through the North Atlantic, we have observed a general increase in ocean temperature (especially at the surface) and salinity. The fluorescence data indicate that at the start of the cruise we were in high chlorophyll waters (relatively speaking), the fluorescence signal then weakened as we moved towards 30 degrees North and the maximum concentration (often referred to the deep-chlorophyll maximum, DCM) deepened, after which we have observed a shallowing of the DCM and a slight increase in the fluorescence signal as we moved toward the equator, likely related to upwelling of nutrient rich waters associated with this region.

Samples so far

Samples so far

My daily routine, described in the previous blog post, has not deviated too much. However, a few days back I helped Giorgio Dall’Olmo deploy two Bio-Argo floats. These devices are at the cutting edge of bio-optical oceanography. Argo floats essentially consist of a floating device that support a number of oceanographic instruments, including temperature, conductivity (from which we can derive salinity) and pressure (from which we can derive depth) sensors. In addition to these instruments, the Bio-Argo floats contain a suite of bio-optical instruments including light sensors, fluorometers and devices that measure optical backscattering. The floats sink to around 1000m and, once every 5 or so days, the device floats journeys to the surface while measuring these oceanographic variables. This information is then transmitted to a satellite and which relays it to the Argo network, where scientists can access the data in near-real time.

Whereas ocean-colour satellite data can only observe the surface of the ocean (40m at maximum) these Bio-Argo floats extend the synoptic capabilities of satellite remote-sensing down into and through the photic zone (the region of the surface ocean where light penetrates). The synergistic use of Bio-Argo floats and satellite ocean-colour data are lightly to revolutionise our understanding of marine biogeochemistry and I was very excited to help deploy two of these new floats with Giorgio.

Bob and Giorgio with an Argo float

Bob and Giorgio with an Argo float

Bob and Giorgio deploy an Argo float

Bob and Giorgio deploy an Argo float

The temperature and humidity are now soaring as we approach the equator and shortly, I will be experiencing my first “crossing the line ceremony”. Meaning that my first day off in nearly two weeks will involve trying to dodge, as best I can, the dreaded consequences of passing the equator for the first time on a ship (flights don’t count unfortunately). Wish me luck!

The sampling routine

13th Oct, 2013

Sampling started on Wednesday following confirmation of our cruise route. For the last four days my routine has been intense. I am up at 5am to set up for the pre-dawn conductivity temperature and depth profile (CTD) during which the first optics cast is deployed. 

Pre-dawn conductivity temperature and depth (CTD) profile

Pre-dawn conductivity temperature and depth (CTD) profile

 

I then filter water for three hours to extract phytoplankton pigment data at different water depths, before setting up the hyperspectral radiometer (see http://www.amtblog.org.uk/index.php/1861). The filtering datasets are then logged and I then spend the rest of the morning processing the hyperspectral data. 

After lunch, I help Giorgio Dall’Olmo with second optics cast while the second CTD is deployed. 

Giorgio setting up for the second optics cast

Giorgio setting up for the second optics cast

 

Giorgio deploying second optics cast

Giorgio deploying second optics cast

 

The afternoon and early evening is spent filtering more water for pigments, particulate organic carbon and fatty acids. After dinner I just have time to call my wife and relax before crashing to sleep with the “motion of the ocean”.

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