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Core sampling in Kochi

Greetings from Japan.

The Expedition 353 team is currently in sunny Kochi, in the southern part of Shikoku island, about 600 km SW of Tokyo. We’re here for the so-called “sample party”, which probably sounds a lot more relaxing than it really is…

Screen Shot 2015-10-18 at 17.35.40     Screen Shot 2015-10-18 at 17.35.46

Our job for the next couple of weeks is to take all the individual samples from the sediment cores we collected back in Dec/Jan, so we can take them back to our home laboratories and carry out experiments. As I’ve said before, actually getting the mud from the bottom of the deep blue sea is the fun part, but it’s only half of the scientific process. The only way we can answer the big questions we have about how the monsoon behaved in the deep past is to carry out sophisticated experiments and generate multi-proxy data that we will use to test our theories.

But taking all 47,000 samples that have been requested by the expedition participants is no mean feat.

The cores are being stored at the Kochi Core Center (KCC) where they are kept cool and safe by the expert team of curatorial staff. The team are capable of sampling the cores for us, but with so many samples to take, and with their placement within the core being so crucial, it’s best that the scientists who are requesting the samples come and take the samples for ourselves.


Racks of cores in the white D-tubes, waiting to be sampled on the table. The team is working hard to make sure everything goes to plan

So here we are, spending from 8am til 6pm every day in the windowless lab working on the cores. It’s just like being on the ship (except that you can go out and get a beer in the evening…).

We have all prepared our sample lists in advance, and the only thing left to do is actually take the samples and bag them up. We pull out the core sections one by one, carefully check that they are labelled correctly, before using either metal or plastic knives and scoops to take the samples from the exact depth in the core that they have been requested from. We replace the sediment we have removed with polystyrene to hold the core together and stop it moving about.

cores5     20151013_145344#1                                                    20151013_110316

We look quite serious, but that’s just because we’re concentrating hard on not mixing up samples. We also manage to have some fun, even if some members of the team think is is acceptable to play Genesis loudly from their laptops (they are mistaken…).

After sampling, some of the very popular cores have barely anything left in them, and are more polystyrene than mud!


As well as being here for the physical grunt work of taking the samples, the sample party is also a really good opportunity to talk to the rest of the 353 team and finalise our post-cruise science plans. We are all applying for research funds from our home institutes and funding bodies (NSF, NERC etc.), to carry out the important work on these samples over the coming years, and it’s important to make sure our efforts are coordinated between different labs.

Sample party kochi

It’s also just generally very nice to see our shipmates and friends again, and to be back in Japan to sample the amazing food, hospitality and culture of this beautiful place.


Nearby Kochi castle in the October afternoon light

Yee ha! It’s editorial meeting time

Hello monsoon fans,

Just an update to remind you that even though the super-fun, nautical part of Exp. 353 is over and done with, that doesn’t mean the work has stopped. Oh no indeedy, it’s just the beginning!

This week a crack team of iMonsoon participants has assembled in College Station, Texas – the (somewhat unlikely) beating heart of US-IODP operations – in order to get our shipboard reports spruced up and ready for publication and digestion by the scientific community at large.

IODP editing team

4/5 of the IODP Exp 353 editorial team on our last day of report editing. Go team!

You might remember me telling you that while we’re at sea we write the detailed site reports as we go, in between describing and analysing the cores and collecting the data. While this is certainly the most efficient way of getting the reports done, while the material is right in front of us and it’s all fresh in our minds, the high-pressure nature of the day-to-day work means that there’s not always time to get the reports 100% right while we’re at sea. No matter how much you love your science, in week 7.5 of an 8-week cruise, you’re a bit too tired to write coherent sentences and make beautiful figures. We’re only human.

So here we are, in a massively air-conditioned room in Texas filled with coffee and energy bars, sitting down together to fix up the reports. One to two members of each team (sedimentology, paleomagnetism, biostratigraphy etc.) has been invited, along with both our co-chiefs. So it’s not the whole jolly gang, but everyone on iMonsoon has had the opportunity to comment on the reports by email in the previous weeks and give feedback to their representatives.

IMG_6596      IMG_6597 Well, I never promised that this blog post would be a visual treat…

It’s great to see everyone again and look over all the great work we did last winter – gosh I’m proud of what we achieved on this cruise! – and it’s nice to know the Proceedings will be published soon so everyone can have a look. (The shorter Preliminary Report is already out there, but the real meaty stuff is yet to be released). This is also a great opportunity for us to talk about the follow-up science projects we are planning with the Exp. 353 material and to shore-up our collaborations. Everyone is busy writing grant proposals to their respective funding agencies (so, NERC for me, NSF for the Americans, etc.), and we’re hoping the funds are forthcoming to support the great work we’ve got planned.

The extreme heatwave in India over the last month, and the terrible toll this has taken on people’s health and livelihoods, is a stark reminder that understanding how the monsoon will respond to ongoing climate change in the future is of major societal relevance. We hope that the new knowledge about the past behaviour of the Indian Monsoon this Expedition will bring, will contribute to this effort in the coming years.

The Exp. 353 team be meeting up again in Oct 2015 for the sampling meeting in Japan, this time to get our treasured mud samples(!), and I’ll tell you all about that later on in the year, but for now it’s over and out from me. Wish me luck with the track changes and my steady diet of Texas tacos.

Meet the…. geochemists!

Hi folks,

Well, what with the ~2 km of core we pulled up in the final days of Exp. 353 there really wasn’t time to upload the final interviews for “meet the scientists” before we hit shore. So here is one of our esteemed geochemists, John, giving us his two cents about his role on the ship… (sorry it’s 3 weeks late, John!)…


Well hello there, and who might you be?

JK: I’m John Kirkpatrick from the USA, and I’m sailing as inorganic geochemist. My home institute is the University of Rhode Island where I’m currently a postdoc.

John waves1

[John sporting some fabulous facial hair around NYE, which sadly became more normal and respectable towards the end of the expedition….]

Jolly good, and what do you do onboard the mighty JR?

JK: I’m sailing as an inorganic geochemist: our main job has to been to extract porewater from the sediment and analyze it for many things, including pH, alkalinity, salinity, dissolved ions (e.g. sodium, magnesium, potassium, calcium, chloride, bromide, sulfate, et cetera), and other elements such as metals.

Ah I was wondering what you were doing when you were squeezing big pieces of the core in that giant vice – you were extracting the pore waters!

johns arm1

[Lab Tech supreme, Vinny, (and John’s hand), show the vice being used to squeeze porewaters out of a “squeeze-cake” taken from the base of each core]

So why exactly is inorganic geochemistry important to the expedition, and why in particular should we care about porewaters?

JK: The dissolved components in sediment porewaters reflect the history of the sediment, its composition, and how the composition came to be – for example, at our earliest site, U1443, there was a lot of carbonate. Where that carbonate came from, though, if it formed organically or inorganically, if it is currently dissolving or precipitating – those are questions that water chemistry can shed light on.

Interesting stuff. I guess we can also see other important things like the depth of the sulfate reduction zone, which will be related to the amount of organic matter in the sediments, among other things, and which will vary from site to site. (See, I do pay attention when the geochems are telling me stuff!).

So tell us about your area of research back home.

JK: My shorebased research involves tying this sort of chemistry to  biological data, typically DNA sequence data. We don’t sequence DNA  onboard, so all of that work is shore-based; plus, DNA analysis is now restricted to samples from international waters or samples that we first obtain permits for.

Yeah, it’d be nice to be able to see exactly what cool bugs we are pulling up from the “dark biosphere” in our cores, but I guess that’ll have to wait for another expedition…

John lab1

[John managing to do an excellent evil scientist impression whilst analysing the porewaters…]

So what is the scientific question you are most hoping to answer with the new material from Exp. 353?

JK: My own pet project, or topic of specific interest, involves the removal  of nutrients – nitrogen – in the sediment by forming N2 gas. Removing nitrogen can take that nutrient out of the biological cycle for a very long time (since N2 gas just floats around in the atmosphere where it is mostly inert). Of course, gases are very ephemeral and so to do these analyses we need fresh, active sediments to incubate and measure under highly-controlled conditions. 80% of the gas in our atmosphere is a
potential contaminant for these measurements!

Yikes, well good luck with that!
So what is the best part about being at sea on the JR for you?

JK: Being away from the day-to-day hustle and bustle of work at the university, the meetings and conferences and emails and stress – we  have a LOT of work to do here on the JR, but it is all focused on a single set of goals; I relish being away from the feeling of being pulled in a hundred directions that I get in my office. Plus, it is a lot of fun getting to know new colleagues!

john twister

[John getting to know new colleagues through the medium of “Microfossil Twister”, surely the most fun game ever (re)invented!]

Good getting to know you too John! And I fully agree with the part about the hustle and bustle – now a full 2 weeks after the end of the expedition, I still have another ~200 emails to plow through before I’m all caught up. Ergh!

Apart from the long hours and the hard work, what do you think is the worst part about being at sea? What do you miss most from home?

JK: I’ve never been apart from my wife this long since I first met her (we  got married last year). Actually now that I think about, never this far apart either – literally on the opposite side of the Earth! I also really miss being able to stretch my legs and go running outside; that always makes me feel better when I’m too busy to think, or feeling a bit down. We have exercise equipment on board, but a treadmill ain’t the same.

Yup, missing loved ones is the pits – hopefully by now you’re all fully reunited, well exercised in the great outdoors and enjoying a break from the office 🙂

Thanks for the insight into the world of the shipboard geochemist, John. Hope to sail with you again!

Coming up soon (well, when I get through these 200 emails, and the rest of the mountain of work that has built up since November!):

-What happens now that the expedition part of Exp. 353 is over?

-When do we all meet up next?

-What are we going to do with all this mud??

Go with the (core) flow

Howdy folks,

We’ve arrived at our next Site, U1444 in the Bay of Bengal!

Indian Ocean map3

It’s not quite where we were originally planning to be coring, but as Steve said in the last post, nothing ever completely goes to plan at sea and you’ve got to be prepared to be flexible. Looking forward to having more core on deck soon, regardless of the location!

We arrived at 07.30 this morning (while I was still fast asleep), thrusters are down and we’re tripping (lowering) pipe to the seafloor now. We’re in 3000 m of water out here, so the first core on the floor is not anticipated until around 7 pm this evening…

So this seems like a good moment to explain what we call “core flow” to you all. Basically this is the order in which measurements and descriptions are taken from the core as it moves through the core lab – our specialist deck on the JR for handling the precious mud. [We will hear more about the various specialties, like “phys props”, “sedimentology”, “geochem” etc., and the people on board who do these jobs in later “meet the scientist” posts].

CORE FLOW: A beginner’s guide:

  1. After the drill pipe is lowered all the way to the sea floor at the bottom of the ocean, the core is cut from the sediment pile (this is the steel-straw pushing into the mud, if you recall). The mud gets pushed up inside a plastic core liner inside the pipe, which is then pulled all the way back to the surface 3+ km above with a really strong wire. The 9.6 m-long core liner full of precious oozes is then received on the drill floor, before being carried to the “catwalk” where the curator (Chad) and technicians (Chieh, Heather, Colin, Maggie, Aaron etc…) cut the core into more manageable 1.5 m sections. Everything is very carefully labeled using triple-redundancy pens, stickers and laser engraving – the order of the core sections is super-important!


  1. While the cores are still on the catwalk, the “core-catcher” (the sample at the bottom of each 9.6 m core) is sampled and given to the biostratigraphers so they can get to work straight away. They will look at the micro- and nanno- (really tiny!) fossils in the mud, which can tell us how old the oozes are and how deep the seawater was when it was deposited. At the same time our microbiologist John takes some samples and wraps them up tightly in sterile containers (and freezes them) so he can search for cool “deep-biosphere” bugs later. The geochemists also take a few “whole round” samples from the cores, which they will then squeeze in the lab downstairs to sample the “pore waters” that exist within the sediment pile. The leftover bits of mud from this are called “squeeze cakes”, which I rather like. Nom nom nom.

microbiology sampling

  1. The core sections are then given over to the physical properties team (or “phys props”) whose job it is to scan the cores for a variety of parameters like magnetic susceptibility (how magnetic are the minerals in the mud), p-wave (how dense is the mud), gamma ray (how radioactive is the mud (don’t panic, the answer is always “not very at all”- You get more radiation from spending 15 minutes near the Cornish Granites!)).
  1. After scanning, the cores are left to “equilibrate” for a few hours – this means they have time to come up to room temperature (it’s cold down there and warm up here) and do any expanding they are planning on doing (there’s a lot of pressure at the bottom of the sea, and not much up here, so sometimes the cores get bigger while they’re sitting in the lab!). After equilibration, the cores are split in half lengthways using a piano wire – truly high tech stuff. Now we have two halves – the “working half” which people are allowed to take samples from, and the “archive half” which is to be left untouched for future reference. Some extra samples are taken from the working half for geochemistry measurements before it’s put away for the rest of the cruise.


  1. The sedimentologists now get their grubby hands on the archive half of the cores and can begin the exciting job of describing them. What color are they? (hint they are not always creamy-white like in the photo above!). What are they made of? How big are the grains? Can we see any structures or macrofossils? All of this info is carefully written down in the database so we can make beautiful diagrams and plots of the sediment characteristics later on, while we try to figure out what’s going on.
  1. Last to get the cores are the Paleomagnetists (or “paleo-magicians” as we affectionately call them). These guys measure the ancient magnetic field direction and strength preserved in the magnetic minerals in the mud, which can be really useful for telling where we are in time. [This is pretty complicated, so we’ll let one of the magicians explain it themselves in a later post].
  1. After all this, the cores are boxed up and put in the reefer (the big fridge at the very bottom of the ship), where they will stay until they are unloaded again in Singapore at the end of the expedition, ready to be shipped to our IODP Indian Ocean repository in Kochi, Japan. In about 4 months time, we will all meet up again in Kochi and take our personal samples to do further experiments on the mud – one of the perks of sailing is that you get a 1-year head start on everyone else to do some science on the cores from your expedition, before they are opened up to the whole scientific community. Tick tock…

So that’s about it for core flow. T-minus 4 hours to next core on the floor, so I’d better get back to work!

Next update: meet the (super awesome) sedimentologists…