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Land ahoy

Jeremy, Tuesday, November 11th, 2008

Nearly over. After six weeks the cruise has ended, at least as far as we are concerned. We have got to the Falklands safely and docked at Port Stanley. The Falkland Islands invite rather mixed comments on ship but they looked beautiful in the early morning sun as we arrived, and to remind us of the naval history a frigate was anchored in the entrance to the sound.

Heading towards the Falklands

Heading towards the Falklands

HMS Iron Duke in front of Mount Tumbledown

HMS Iron Duke in front of Mount Tumbledown

The last few days have been rather dominated by weather as we have gone through a series of gales alternating with calm sunny intervals. The sunnier intervals allowed some sampling in these waters and we have been rewarded with green soupy water rich in diatoms, copepods, some rather unpleasant gelatinous gunge and a few whales.

A whale's tail

A whale’s tail

Coccolithophores have remained common and surprisingly diverse but the layers of different populations are no longer distinct – they now look pretty similar throughout the water column.

The zooplankton samples have been interestingly variable. Plankton net sampling has been cancelled several times but the samples which did come in made a very useful addition to the material I have been collecting.

However, science stopped completely a couple of days ago so that we could get packed before arriving in the Falklands. The first task was tidying up and sorting out the samples. There is a decent haul – we have collected from about 70 stations and accumulated about a thousand filter samples, four hundred microscope slides, eighty bulk organic samples for DNA analysis, two hundred filter samples prepared with a special buffer to allow labelling of cells with fluorescent markers, and hundreds of pteropods and ostracods picked from the zooplankton.

After that the main dismantling of the labs and packing up took place on Saturday afternoon, just as we hit particularly bad weather. To make things worse we were sailing south whilst the wind and waves were coming from the west, which made for rather chaotic ship motion and the occasional spectacular roll of up to 30°. So packing was sporadically interrupted by the need to grab something solid with one hand while restraining what ever one was trying to pack with the other hand. The rolling also added a certain something to the end of cruise dinner, and especially to the dancing in the crew bar.

A wash bottle serving as an inclinometer to record the ship's motion, although I did not manage to photograph it during any of the larger rolls

A wash bottle serving as an inclinometer to record the ship’s motion, although I did not manage to photograph it during any of the larger rolls

So that is about it for the cruise, although we will have a lot of work to do on the samples over the next few months. It has been a great experience, we have learnt an immense amount and had some excellent evenings. The RRS James Clark Ross is a fine ship and everyone from galley staff to the captain has made us welcome. It’s nice to see dry land but we will be sorry to say farewell to the ship.

Jeremy & Martine, Port Stanley.

Representative objects

Jeremy, Tuesday, November 4th, 2008

We have worked our way across the southern Atlantic gyre sampling intensively as we went and have now left the tropics and run straight into a force 8 gale. This has stopped the science, so, there is finally time for us to catch up on the blog, starting with a little discussion of some objects representative of shipboard life.

The coffee carrier from the UIC

The coffee carrier from the UIC

The coffee carrier: The “Underway Instrumentation Centre” (UIC) where our microscopes are based is a nice dry air-conditioned environment, in contrast to the warm and wet labs below. Along with the microscopes are computers controlling various machines, and scientists tending them. Now, scientists need coffee to sustain them and coffee comes from the bar one deck up and quite a way along (see photo of ship). Carrying cups of coffee by hand is a bad idea, since the ship rolls and a golden rule on board is one hand for the ship and one for yourself, i.e. you have got to have a free hand to hold onto the ship. So, one of the most useful pieces of kit in the UIC is the coffee carrier which allows us to transport cups of coffee in total safety – it may not look very clever but on a rolling ship a hanging tray works perfectly. It is also a nice example of the economy of ship-life. There are no shops around so making things yourself is the way to go, hence objects like biscuit tins, rope and copper piping get re-used and workmanship is valued (look at the neat way the ropes are tied off).

The RSS James Clark Ross, showing the relative positions of the bar and the UIC

The RSS James Clark Ross, showing the relative positions of the bar and UIC

The scientist's beaker

The scientist’s beaker

The scientist’s beaker: Along with improvised construction another way to get things on ship is by searching and borrowing, and people are remarkably generous in lending each other stuff. This beaker was leant to me by Paul Mann from the Plymouth team, and it filled a severe gap in the arsenal of multi-purpose objects I remembered to bring with me. The little chap next to it is also Beaker, from the Muppets, in honour of whom scientists on board ship are generally referred to as “beakers”. So, our humble pyrex vessel is “the beaker’s beaker” and hence arguably the smartest thing on ship.

Scones similar to those made by our doctor © Wikipedia

Scones similar to those made by our doctor © Wikipedia

The doctor’s scone: The ship also has an impressive range of human resources, including our very own doctor, Nerys, who is responsible not only for our well-being but also for the ship’s official blog, or web diary. As part of her research for this she has been investigating the different parts of the ship, including the galley where she was put to work making scones. We had them for pudding at lunch recently. Very good they were too, just like my mother makes, or in the words of Alex (the third mate) marine-grade ballast scones.

Nerys' mother's crayons

Nerys’ mother’s crayons

Nerys’ mother’s crayons: Martine, I and the other scientists will be leaving the James Clark Ross when we get to the Falklands in a week or so. The officers and crew will be staying for three more months till the mid-cruise crew change. So our lovely doctor, Nerys, will be the only person staying on the ship until it returns to England in May. Which means she is away from home for eight months. Her mother was obviously concerned about this and has given her a series of date-marked parcels to open at Christmas, New Year and other such important dates, as the cruise progresses. Yesterday was the 31st of October and Nerys had a parcel containing, hallowe’en chocolates, a witch’s hat, and a set of face-paint crayons. The crayons looked innocuous but they provided the catalyst for some flamboyant artwork.

Evidence of the talent and ingenuity aboard: from left to right, Vas Kitidis (scientist), Nerys Lewis (doctor), Ben Tullis (the ship's IT specialist), Mike Gloistein (Radio Officer), Paul Mann, Mario Vera and myself

Evidence of the talent and ingenuity aboard: from left to right, Vas Kitidis (scientist), Nerys Lewis (doctor), Ben Tullis (the ship’s IT specialist), Mike Gloistein (Radio Officer), Paul Mann, Mario Vera and myself

Jeremy, South Atlantic

Day in the life

Jeremy, Tuesday, October 28th, 2008

Dawn sky. Almost a nice sunrise this morning.

Dawn sky. Almost a nice sunrise this morning.

5.15 Alarm goes off, Martine and I have worked out we don’t need to both get up early so we are alternating this, and unfortunately it is my turn for an early morning.

After getting up I nip across to the bar, conveniently just around the corner from my cabin, for a coffee. Then down to the lab where one of the Plymouth Marine Lab scientists, Carolyn, and chief scientist Malcolm, show me a large black insect that was found on the deck this morning. This is rather strange as we are more than a thousand miles from land.

Since I come from the Natural History Museum they hope I may be able to help identify it. It looks like a big black grasshopper to me; I take a set of photos and promise to ask an expert.

5.45 As I finally get to our corner of the lab the CTD and rosette sampler are still going down on its water collecting mission so I have time to wash and rinse our bottles and prepare the syringe filters we are using to take reconnaissance samples.

6.15 The CTD comes back on deck so it is time to collect the water – attaching hoses to the bottles on the sampler to fill up our jerry cans. This is really the only outdoor job we have so one of our favourite tasks. The sun comes up as we are sampling and a big frigate bird comes to visit, circling over the ship a few times.

6.45 Sampling over, it is back into the lab to do the syringe filter preps and start the main filtration process going.

7.30 Breakfast – a very welcome cooked breakfast (and more coffee), we are well looked after on the ship.

8.00 Start the main work of the morning: Processing the filter samples generated from the day before - we are collecting from 9 water depths in the morning and 13 in the afternoon.

There are two filters from each depth, as we are taking different filter types for light and electron microscopy, so there is a constant flow of filters to look after.

The filters for electron microscopy simply need to be transferred into petri-slides and labelled. For the light microscopy filters, I also make up microscope slides.

Part of the days haul of filters ready for storage. The square bits are where I have cut out a portion of the filter to mount for microsocpy.

Part of the days haul of filters ready for storage. The square bits are where I have cut out a portion of the filter to mount for microsocpy.

9.00 Take a break to send an email to a couple of entomologists in the museum to ask what the grasshopper is. I can’t remember who specialises in this group but I am very confident someone will know (especially as it is a big distinctive insect).

Then back to the microscope to check on the samples I collected this morning. We are near the equator now, the sea is getting more productive, and the coccolithophore communities are slowly changing – especially, and this is something of a surprise, the communities at intermediate depths around 50m.

Gryllus bimaculatus, our grasshopper stowaway.

Gryllus bimaculatus, our grasshopper stowaway.

10.00 Get an email reply from George Beccaloni explaining that our grasshopper is ‘an adult female Mediterranean Field Cricket, Gryllus bimaculatus. This species has a very wide distribution from Africa to Asia and it is also bred extensively in captivity for live food for reptiles etc, and as a lab animal. This species may have flown on board, but it may also be a stowaway. I had one recently brought in to the museum which jumped out of someone’s suitcase in the UK when they got back from Egypt.’

The fact that it is a common species is something of a relief, since Carolyn was very unhappy with the idea of me preserving him for the museum collections – a dragonfly which died on the deck a couple of days ago has ended up pickled in the fridge.

10.45 Reconnaissance of these morning’s filters is finished so I complete the sample labelling and take the trays down to the lab to start filling up with the next set of filters.

Start a more detailed examination of the afternoon filters from yesterday – the basic aim is to do a count of coccolithophore abundance in all the samples and note the dominant species but for the afternoon samples I am usually able to do a more detailed analysis.

12.00 Lunchtime – like I said they look after us well and lunch is a three course meal - with quite a bit of discussion of the grasshopper and other visitors. Then a half hour break for a relaxed coffee in the bar and a little wander round the ship.

The ship stopped after lunch for more sampling

The ship stopped after lunch for more sampling

12.45 Prepare for the afternoon sampling. Martine has decided that this is a good time for an extended sampling so we can collect bulk organic matter samples for DNA analysis through the water column. This means pressing all our bottles back into service.

After washing the bottles, time for a bit of a stroll and chat as the CTD goes out. The lunchtime (or more technically ‘solar noon’) halt is rather impressive as in addition to the CTD midships there is a plankton net deployed further forward and an optics rig near the stern so with three cranes out, the ship looks like it is undertaking large-scale fishing.

13.30 The CTD comes out of the water and sampling gets back in earnest. With about 120 litres of water to collect there is a lot to do – and it is hot and humid outside.

The afternoon’s haul of water (and it all needs to be filtered)

The afternoon’s haul of water (and it all needs to be filtered)

14.00 After half an hour of work in the sun the samples are safely lined up in the lab, and I am in severe need of a shower.

14.30 Back to the microscope to finish off the analysis of yesterday afternoon’s samples – there is a lot of really nice stuff in the samples, but the day is getting a bit long and around this time I find microscope work pretty hard going; a bit of music helps and luckily there is an impressive system in the UIC (Underway Instrumentation Centre) where we have set-up the microscopes.

Our insatiable filtration set-up

Our insatiable filtration set-up

16.00 Start my turn of the day’s filter work. Filtering water is pretty much the coalface of oceanography and there is a lot of it going on on the ship. The basic principle is that you pour water into the top of the filtration apparatus it gets pumped through the filter and into a receiving carboy and the sample gets left behind on the filter.

So the filtering process basically involves pouring water in, ticking off how much has been filtered, watching till the water level falls near the bottom (running the filter dry is a bad idea), closing the tap, pouring in more, re-opening the tap and so on in (hopefully) a nice steady rhythm for as many hours as it takes to get all the samples done.

17.00 Science meeting – there are 18 scientists on board, and although we are in separate small teams, it is very useful to meet once a week or so to discuss plans for the next few days sampling, and debate any interesting results (are low surface-water salinities here a result of Amazon outflow?). Today’s meeting also includes a briefing on the crossing the line ceremony that is getting close and becoming a major focus of discussion.

17.20 Back to the filtration – rather tranquil as the sun is low on the horizon and comes in through the lab windows, through which every now and then I can just about see a shoal of flying fish jumping out of the water.

Further away, there is less tranquility, as the engineering officers have got out their new inflatable swimming pool.

This is tempting but Martine and I still have a lot of work to do as a result of the extended sampling today.

18.20 Stop the filtration, change for dinner (no t-shirts or shorts allowed), and, as the sun is now definitely over the yardarm, its time for a medicinal G&T in the bar.

18.35 Dinner

The all important bar (and coffee machine)

The all important bar (and coffee machine)

19.30 Time for an after dinner coffee and chat in the bar – the bar has a bar, obviously, but it also has lot of comfortable seating space, tables, a darts board etc. and is the social centre for the scientists and officers (there is a separate crew bar which seems a touch anachronisitic but no-one on the ship wants to change that).

After dinner is probably the busiest time of day in the bar with most of us there, a lot of open discussion, and usually a group attempt at doing the crossword from the shipboard paper. Later on the numbers decrease as many people are working shift systems, or retire to their cabins, or like Martine and I tonight, have work to finish off.

20.15 Finish the last bit of filtering then spend an hour or so picking through the day’s zooplankton sample for pteropods– this is a particularly pleasant and relaxing task which I will have to explain in another blog entry.

21.30 Rejoin the bar group for a wind down at the end of a rather longer than average day.

Jeremy, nearly at the equator.

Sunday news

Martine, Tuesday, October 21st, 2008

Sunday 19th October, 10 pm
I’m outside by a nice clear night, writing from the hammock set up out of my cabin. It is the end of the weekend and there are not many people awake onboard… apart from Alex (the third mate) and Kevin (watchman) at the bridge to check there is nothing in our way and everything is working fine.

It’s Sunday evening, however there is no real weekend onboard as we are sampling everyday. This weekend was especially busy with a deep sampling, down to 5150m on top of the normal 2 stations. We even ran out of containers to collect the extra samples and had to use the collapsed carboys.

Still just usable, one of the carboys we collapsed through vacuum pressure

Still just usable, one of the carboys we collapsed through vacuum pressure

This supplementary collection means for Jeremy and I about 290 litres of seawater filtered instead of the usual 160 litres per day, and about 20 extra slides to look at during the day… But it also means souvenirs as we sent down a team of expanded polystyrene cups attached at the top of the rosette sampler in socks (special thanks to Glen and Jeremy who provided the socks).

Preparing the important scientific experiment – cup-filled socks are attached to the rosette-sampler frame

Preparing the important scientific experiment – cup-filled socks are attached to the rosette-sampler frame

At 5000m the pressure is about 600 times that at the surface and our valiant team was shrunk to a fraction of their previous size – this also meant that our swift marker-pen cartoons were rendered into finely detailed pieces of art.

Our cup team before and after meeting the AMT-Abyssal Challenge

Our cup team before and after meeting the AMT-Abyssal Challenge

Busy and fertile because most of the samples we collected over the weekend were really nice, and quite distinctive and thus worth having! We also had a nice barbecue-style party on the deck in the evening to relax and enjoy.

After dinner in the very dark night (no moon) some of us had the chance to observe bioluminescence (pictures to come later if we remember a camera next time) around the ship, the best observation spot was at the bow on the forecastle. The galley telegraph subsequently carried rumours of nocturnal entertainments near the kitchen (I’ve no idea what that was about, honest)…

Martine 11.13°N 32.06°W

Sampling

Martine, Monday, October 13th, 2008

Already a week since we left the stable land for the not-so-quiet sea. Time flies out here even though we have already gained 2 extra hours by sailing west, towards the sunset.

After a rough beginning of the week, the weather cleared up and the sea is more gentle now. We have settled into a sampling routine, usually with 2 sampling stations a day, one before dawn (unnaturally early according to Jeremy), the other at midday.

Sampling begins with the rosette sampler being lowered down through the upper 300m of water. It carries 24 bottles, each of which has an individual firing system to collect the seawater at specific depths.

The rosette sampler and other devices for recording water properties

The rosette sampler and other devices for recording water properties

Because the weather is now better, we can secure the rosette on the outside deck between samplings. This makes our life much easier when it comes to recovering the water. When the weather was rough, it had to be secured as soon as possible in its ‘cabin’ where it fits tightly, and half a dozen scientists would try to get in as well to recover their samples.

The rosette sampler returning to the deck at dawn this morning

The rosette sampler returning to the deck at dawn this morning

After recovering the seawater, our main task is to filter it. We have to do this in several different ways depending on what we are trying to find out. First of all we look at a small syringe filter under the microscope to decide the volume of water to filter. We use membranes with holes that are 0.2 or 1 microns wide (a 10,000th of a centimete) to filter the water. The process takes place in a vacuum and we use a recovering flask called a carboy.

While Jeremy set up the microscope in the dry lab, I played with tubing in the wet lab to set up our filtering system. Unfortunately our carboys were not delivered in time, so I tried (unsuccessfully) to use a fermenting cask. It collapsed. Then I tried a thick plastic flask. It also collapsed. We managed to borrow a 20 litre heavy duty carboy from Glen Tarran (a colleague from Plymouth). Fingers crossed, this one is still alive and healthy…

The sampler is relieved of its watery load

The sampler is relieved of its watery load

Because our 2 filtering ramps are on 2 different benches I had fun playing with tubing, connections and taps to connect everything. The best thing is that Jeremy loves to come and watch all the bubbly tubing!

We have now tried all our protocols and are ready for intensive sampling to produce LM (Light Microscopy) and SEM (Scanning Electron Microscope) slides, bulk and probe DNA samples, and other samples, during the second part of the cruise, south of the Azores.

A happy Martine surrounded by the filtration kit in her lab

A happy Martine surrounded by the filtration kit in her lab

Martine, off the Azores

We’re off

Jeremy, Monday, October 6th, 2008

Our ship, the James Clark Ross

Our ship, the James Clark Ross

We’re off. After several weeks of increasingly hectic shopping, and other preparations, we are now sailing down the English Channel (well actually we have stopped off at the Isle of Wight to practice sampling).

The photo below shows our equipment and supplies being winched onto the James Clark Ross. The pile looked very large as it was filling first Martine’s office in the Museum then the car (in fact it only just fitted) but it looked minute on the quay next to the ship, and insignificant next to everything else being loaded onboard.

Our equipment being winched into the James Clark Ross

Our equipment being winched into the James Clark Ross

Winching equipment

Winching equipment

The main reason the James Clark Ross goes south each year is to resupply the British Antarctic Survey bases and the ship is carrying tonnes of equipment and supplies for the scientists in the Antarctic. Mostly it is in crates but there is some pretty cool stuff on deck. In addition there is the party of eighteen scientists, including ourselves, for the slow cruise down to the Falkland Islands studying ocean life and processes as we go and they have a lot more equipment.

Once our little pile of gear had been put on the ship, we then had a day and a bit to unpack, set-up, and fix everything down securely – lots of drilling, screwing, and strapping. We also of course had to nip out and buy a whole lot more stuff, but we are now safely isolated from all shops so Martine will have to make do with whatever we have got.

Actually the shopping trip was curtailed by the need to get back for the safety lecture where we learnt what to do when the ship sinks (unlike the Titanic there are as many lifeboat places as people on board). Then on Friday, after one more lifeboat drill, we sailed out of Immingham docks (just next to Grimsby) and down through a surprisingly lively North Sea.

Leaving Immingham

Leaving Immingham

Jeremy, The English Channel

Posted in Equipment

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