July 14, 2011; 9:30 PDT
July 14, 2011; 16:30 UTC

46.209834 N
124.308628 W

I awoke this morning to a feeling of steady ground. Early this morning, we were met by a bar pilot who navigated the ship into the port of Astoria. As I speak, hatches are unlatched and shipping pallets are prepared. The gangway has been extended. I’m far from where I live, however the moment still feels like a homecoming.

It’s been a good cruise. Soon I’ll begin the real work of processing the samples we’ve collected. Right now though, I could use some breakfast.


July 12, 2011; 16:00 PDT
July 12, 2011; 23:00 UTC

47 45.677100 N
127 45.682920 W

Yesterday night, Jason was used to collect with push cores. These are just plastic tubes around a foot long and four inches across, the kind that you can buy at any hardware store. The tubes are pushed into the mud on the ocean floor, and when withdrawn they contain a plug of sediment with its original layering and chemistry preserved: a core. Holes have been driven into the push core and then covered with duct tape, so that when the cores are returned to us we can remove the tape and stick probes through the pinholes to get at the thick, sandy mud inside. We can also push the mud out the top with a plunger and chop off slices as it comes out. This is called extruding, and it’s used to take samples from different depths of the first foot of the ocean floor. The first foot happens to be an important one. We’ll probably start doing all this tonight, after Jason returns, as it’s still at the bottom, filling bags with water. At present, Jason has been on the bottom for about 20 hours, which is the primary advantage the ROV has over deep-sea vehicles like Alvin.

This seems like a good moment to offer a bit more back story on what kind of world we’re exploring. If you stand on a beach, you’re standing at sea level. The average ocean depth is 4,000 m below you, or 4 km. To put that in perspective, a 5k run is 3.1 miles, so the average depth is 4/5ths of a charity race. The bottom of the ocean isn’t a solid, flat, slab like the bottom of a swimming pool, though. It’s a bit more like the ground on land. On land, we drill ground wells to provide water in rural areas. These are just pipes that tap into aquifers. Aquifers contain water in the cracks and nooks within the rock, and even if these are small spaces, it’s enough to provide water to entire communities, so long as it isn’t drained faster than it refills. Getting back to the ocean, you may have seen pictures of hydrothermal vents, tall spires spewing thousands of gallons of water clouded with black, charred dust. The question is, where is all that water coming from? The answer is, “somewhere else”.

Hydrothermal vents were only discovered in the last thirty years. It was only a few decades earlier that geologists began to widely accept that new crust emerges at seams along the seafloor. It’s unfortunate that both of these discoveries are rather abstract, as they are evidence of the beautiful fire and might of the Earth below us. Admittedly, I myself didn’t understand the appeal of geology for quite some time. Like a piece of music, however, it is something banal until you comprehend the scale and power of it. These two regions — vents and spreading centers — are windows into the Earth. Most of the rock we encounter is sedimentary. It’s old and battered, weathered by millions of years. The rock that forms the crust is the product of real magma, the blood of the Earth. The crust at geological hotspots is even younger. It’s fresh from the interior. It’s primal.

This is by no means mere poetry. You see, the deep rock of the Earth has a trait that can be hard to understand. In scientific terms, it’s more chemically reduced than the surface. How this came to be lies at the center of the great, 4 billion year epic that is the story of the Earth, from formation until now, but what it means is that the rocks contain energy within their molecules. It’s a common misconception that the life around hydrothermal vents feeds off of the heat. The heat is important, but it is the energy in the very makeup of the rocks on which the life there relies. I don’t mean to inspire fables about mythical energies in the Earth and rocks, though I confess that such fables might be the only means of doing these stories justice, outside of a lot of very exhaustive study.

This energy is rather weak, really. It’s not something that could power your car (though it’s no coincidence that coal and oil, which can, are found deep underground). There is, however, a lot of it. Like all energy, it is change, or at least the desire to change. These rocks are the positive terminal of a battery, and the negative terminal is the minerals dissolved in seawater. Remarkably, of all the metaphors I’ve employed, this is the truest. In fact, it’s really not so much a metaphor as a literal truth. Don’t worry though, it’s not important whether that makes sense.

The overall point is that 2% of the ocean is flowing though invisible rivers deep underground beneath the ocean, where perhaps more than 10% of the life on Earth (by weight) grows. We don’t really know. If we knew more, it would inform our understanding of surface climate, the beginnings of life, and the possibilities of life outside our planet. Unfortunately, it’s behind a brick wall a mile thick, turned on it’s side and underneath another 3 miles of salty water. Thats pretty far away. Lucky for us, we’ve got some VERY long drills bits.

July 10, 2011; 10:52 PDT
July 10, 2011; 17:52 UTC

47 45.474300 N
127 45.753900 W

When I last posted on the 7th, the wind had put operations on hold. The next day, the wind had died away, leaving the water as still as a lake. At 8, local time, we launched Jason and Medea again. I’m not sure if I properly explained the arrangement yet, but Jason is a neutrally buoyant remotely operated vehicle, which neither sinks nor floats, but can maneuver with propellers. Its attached to the ship through a long tether that supplies power and data both ways. The ship maintains a position directly above Jason, however the ship always moving a few feet one way or another, and with a mile and a half of cable between them that motion could tug Jason one way or another each time the ship rose and fell with the waves. If it ever went taught, it would be under tremendous strain, too. Instead, the tether connects to Madea. Half ROV, half giant plumb, Madea hangs at the end of a taught line that gets swung and dragged with the motion of the boat, and Jason connects to Madea through a second tether 60 m long (around 100 feet).

The first dive on the 8th, dive J2-569 (the 569th dive on the second generation Jason ROV) attached a set of osmo samplers to wellhead 1352A (sorry, I don’t know how they name wellheads). There are several ways to package equipment like osmo samplers. These were boxed into milkcrates with feed lines that get plugged into outlet ports on the wellhead. Next, Jason moved to wellhead 1362B to download flow measurements, collect fluid in inflatable bags, and attach more crated osmo samplers. Unlike 1352A, 1362B has an orifice about 4 inches in diameter that continually vents hydrothermal fluid. This orifice has flow meters that measure the rate of flow out, and if we were to tap lines into ports like we did with 1352, we would divert some of the flow away from the flow meter. Instead, we attached an umbilical line that sipped water from the opening and fed it into the osmo samplers.

The next day was July 9th, yesterday as of the time of writing this. While the Jason team began dive J2-570, Gus and I set about cutting recovered osmo sampler tubing. The osmo samplers draw water into long thin tubes at a slow, continuous rate. This means that when they are recovered, they provide a history of the water moving into the sampler over the duration of the deployment. By cutting them into meter-long segments and then draining the contents of those segments into tubes, we can analyze each tube as a sample of water characterizing a specific range of time. It was repetitive work, but we listened to music and the time went quickly. Afterwards, I went to watch the dive progress on the monitor in the lab. We had returned to wellhead 1027C. This was the first wellhead we visited on the cruise, where a damaged cap was preventing us from accessing and replacing equipment inside the well. The cap had attached itself to the wellhead, and on a previous cruise the handle had broken off while trying to break it free. We had returned with a cleat that slid into grooves on the cap (known as the top hat), which gave purchase to a screw that would apply tremendous upward pressure as it was turned. The screw, called the Top Hat Extraction Tool, or THET, had done its job, lifting the top hat about 6 inches. It was assumed that the cap would come away readily once its seal was broken, but it appeared it had become stuck to the equipment beneath it, and 400-600 pounds of lift by the Jason ROV was not enough to lift it. Finally, we had returned to execute plan C. A bridle had been made that attached to the THET to Madea. Unlike Jason, which ascended by propelling itself toward the surface, Madea has no vertical mobility. She simply hangs heavily at the end of her massive cable. When a dive ends, a winch hauls all 2.6 km of cable up to the surface. With the bridle in place, all the power of this winch was firmly attached to the stubborn equipment.

Systems were go. I asked the operator, afterwards. When I was watching the top hat and data logger withdraw from the well, the cable was under 7900 lbs of tension. Madea puts about 7000 lbs on the cable alone, and the damaged gear weighed about 200 lbs, meaning that the force needed to dislodge the stuck items was about 700 lbs. On our previous try, we’d been a few hundred pounds of force short, but if at first you don’t succeed, apparently you just need to pull harder. The wellhead is now clear, and ready for refitting once the new gear is ready for deployment.

July 9, 2011; 23:00 PDT
July 10, 2011; 06:00 UTC

47 45.652920 N
127 45.681420 W

Yesterday, the space shuttle Atlantis launched on the final mission of the shuttle program. For those wondering, the shared name is not a coincidence. The space shuttle Atlantis is named for the original R/V Atlantis, the first vessel built specifically for marine research, back in 1931. In the ship’s library, there is a signed picture of an early shuttle crew, signed “from one Atlantis to the other”.

There are many differing opinions regarding the future of American presence in space. There are no simple answers to the question of what will replace the shuttle program, however it is important not to listen to hyperbole and uninformed opinions. In approaching the topic, there are several facts to remember. First, that the shuttle program must end. The shuttles are no longer ideal for the work that needs done, and they cannot be operated safely beyond their intended lifespans. It is very, very, unfortunate that a replacement program is not operational. It is a difficult setback. However, we cannot change the current situation, only what we do going forward. Second, as much as it stings, we all must recognize that there will be no interruption in human space exploration, only an hiatus in launches of vehicles built by the American government. International operations continue, along with heavy American involvement. Moving forward, we should not let petty nationalism overshadow the point of our endeavors. Obviously, there are practical concerns affiliated with reliance on other countries, such as logistics and the influence of politics on scientific research. Beyond that, nationalism shouldn’t matter. What connection do you have with an American astronaut that you don’t have with a Russian, French, or German one? Instead of focusing on the achievements of nations, focus on the progress and the achievements themselves. Many people are not aware that the images NASA captures with its cameras (including the Hubble telescope) are public domain, unless otherwise justified. They’re public domain because the public paid for them. NASA devotes a tremendous amount of effort toward reaching out to the public because the entire purpose of scientific research is to learn things and then share them. This recent launch has garnered a lot of attention, but how many people know what the mission objectives of STS 135? A space science mission is planned a lot like a seafaring science mission, and its an exciting set of successes and temporary setbacks (On that note, today, the “top hat” that had stubbornly resisted removal was wrenched free using a successful madea-assisted lift; more information tomorrow). The mission objectives for all NASA operations are available on their website, under “Missions” (http://www.nasa.gov/mission_pages/shuttle/main/index.html).

NASA wants public attention, public support, and public involvement. If you have doubts about the future of space exploration, subscribe to their twitter feed, or a mailing list. If you keep in the loop, you’ll find a lot to get excited about, and you’ll be participating in the most important way there is. When people stay interested and informed, space exploration thrives.

July 7, 2011; 13:59 UTC
July 7, 2011; 20:59 PDT

47 45.825960 N, 127 46.077120 W

The wind’s been around 26 knots since last night, so this morning’s Jason dive was postponed until the head of the Jason team decides its calm enough to deploy. We are expecting to launch tomorrow morning, however the chief scientist, Andy Fisher, has instructed everyone participating in the upcoming dive to prepare their gear and have it on the Jason platform by dinner in case the wind calms earlier than expected. We’ll be returning to a site that we postponed work on in agreement with another research vessel thats entered the area. Its the Thomas G. Thompson, operating the ROPOS ROV. You can get some details about our position from sailwx.info, under research vessels, although their position hasn’t been updated in several days at the time I’m writing this.

Today, I woke up and went up to the top deck to look at the sea for a few minutes before breakfast. Honestly, the sea can become boring on a boat. Its easy to take it for granted, as hard as that may seem. If you stop going to look at it, the ship begins to feel like a building on a pier that you don’t leave for three weeks. Plus, you don’t see many whales in the lab.

After breakfast, I watched the second half of an episode of Firefly that was interrupted when my watch began for ROV duty. Then, I spent a few minutes reading an overview of the current state of our field, followed by 20 minutes on the exercise bike. By the time I got out of the shower it was lunch. After lunch I was going to help transfer water samples, but since the Jason launch was still on hold, my colleagues decided to do some other chores and get around to transferring the water samples after dinner.

Its 2 now (9 in Greenwich). I’m going to post this brief update, then drift around a bit and see what everyone is doing. This is a surprisingly effective way to learn about what oceanographic research is going on these days or get introduced to unfamiliar techniques. After dinner, I’ll get around to the lab work and then make sure that everything is primed for tomorrow’s ROV deployment.

Another grad student just came by to ask if I wanted any water samples. Because there isn’t going on much, some people are going to put the CTD in the water. If ocean science were pediatric medicine, a CTD would be a stethoscope. Its a thermometer and salinity detector with bottles that can be triggered to capture water at selected depths. Altogether, it lets you get a snapshot of the temperature, chemistry, and a few dozen other things if you’re interested enough to do the tests on the water samples it brings up. I told her I’m good, but I might go watch that for a few minutes to see what they’re up to.

July 4, 2011; 22:05 PDT
July 5, 2011; 05:06 UTC

47 45.661260 N,
127 45.674700 W

Today we recovered our first samples. Everyone on this cruise has different experiments to carry out, however they all have in common a remarkable scientific deployment that all of them have found uses for. As recognition of the importance of the subsurface environment grew, so did the recognition of the difficulty that such investigations entailed. Any attempts to observe an environment covered by miles of rocks required drilling into it, which ruined any useful samples. The solution that emerged was to drill, destroying the usefulness, but then setup instruments to perform the investigations and facilitate the return of the natural system. Then, you wait. After a few years, the impact of the the drilling has faded, and you have a system representative of undisturbed rock, but with a window. This is the basic premise behind a corked borehole. Perhaps the most impressive aspect of a program with MANY impressive aspects is that these corked boreholes are highly modular. Once drilled, casing is inserted to prevent the hole from falling in on itself, and a string is lowered into it with packers that swell in contact with water, isolating different depths from one another. Basic instruments for recording pressure and temperature, along with hoses, connect each depth to ports at the wellhead. On this ship are chemists, geologists, biologists, and hydrologists, each with different questions, and each with their own large, complicated, custom-made devices designed to plug into the modular ports that pipe water from within the holes.
Ours are called FLOCS. This stands for FLow-Through Osmo Colonization Systems. The name is a reference to “floc”, which is a technical term for the gunk bacteria produce around themselves as they grow in large colonies. Our FLOCS are chambers containing crushed, sterilized rocks. One end is plugged into the ports on the wellheads and the other are attached to osmotically driven pumps, which are a feat in their own right. If the conditions are right, then the water flowing through them should carry bacteria that grow on the crushed rocks just like they do on natural rocks deep within the Earth, all around the world. I’ve spent several days assembling these FLOCS. We have bags of small plastic cassettes the size of film cannisters, which get filled with either crushed rocks or plastic slides with smooth rock chips. The bacteria grow better on the crushed rocks, but the smooth chips are easier to look at under microscopes. They all go into their cassettes, which go into larger chambers themselves, which are strung together in chains and placed into a cannisters several feet long and screwed onto the long, narrow plates which are the interchangable interface with the wellheads. There are many strange creations on each table in the ship’s main laboratory, but this plate is the common platform of many of them.
I wouldn’t say that building up FLOCS over the last few days was boring, but it wasn’t really exciting work, either. What IS exciting is seeing the finished product from inside the Jason control room. In the morning, that heavy mass of plastic and steel was in your hands. Suddenly, its in another world. Today we recovered samples just like those I’ve been assembling which were deployed a year ago. This is when I found what was more exciting than that: seeing it come back.
They show signs of their travels. They’re slimy, and they smells bad. Not terrible, but bad. We carried the three of them into the wet lab, where we do the messy work, and began to deconstruct them. Remove them from their housing. Discard the support padding. Leave the parts that belong to our collaborators and take the heart of the FLOCS, the rock cartridges, into the main lab for processing. It may sound odd, but they reminded me of prosthetics. Not any particular body part, just some unusual organ. This is probably because they share some qualities with prosthetics. One of the hardest parts about building fake body parts is often getting them not to do things that the original doesn’t do. There is no worry that in a living heart blood could clot on the inside of it, building up a film that could then peel off and clog an artery. A living hand doesn’t have a point where it connects to the body, where it must be fastened on. Its seamless. In the same way, the FLOCS are supposed to be in every conceivable way like the rocks a mile below them. They should have all the things those rocks have – their temperature, their pressure, their shape – and none of the things that they don’t have. They can’t include any chemicals that aren’t their normally, which could assist or inhibit growth. This is hard to do. It sounds obvious, but THINGS ARE MADE OF THINGS. You’d like to install a stint into an artery and tell the blood cells, “Just pretend that it isn’t there”, but you can’t. Plastics leach into water, especially when heated. Its minor: It doesn’t affect us to drink out of a plastic cup, probably because the process is so slow. But these FLOCS had been flowing with ancient water — water that quite possibly had not been in contact with the open ocean for centuries — for a year. A lot of care went into a design that asked as little imagination as possible from the microbes, which as far as we can tell have none. On the outside, mud and rocks. On the inside, mud and rocks. Between them, expensive polymers, precise filters, tiny gaskets, and all those plastic nuts and bolts, bringing us a bit of another world it a pristine bottle all while pretending not to be there. I had fun disassembling them, moving their contents into labeled storage vials and adding preservatives, which now told the contents to stop behaving as they would in their ordinary lives and instead to never change again. Hold that pose. Forever.
I look forward to studying them. I have time now. Maybe I’ll do it next month, or maybe long after the next forth of July.

July 1, 2011; 17:48 PDT
July 2, 2011; 00:48 UTC

47 45.360960 N, 127 43.900500 W

‘If making Rachael jealous were worth money, I’d never need work again’, I mused.

Around two (or maybe three: time slips at sea) I dropped in on Geoff to offer some help spooling tubes. He was glad to accept, as it was boring work, and suggested that Gus and I spool in the lounge where we could put a DVD on. We watched “To Kill a Mockingbird” first. Afterwards, I asked someone in the room to make a suggestion. He ran off titles and I stopped him on “Firefly”. Like “Mockingbird”, I’d been meaning to see the popular Joss Weadon series for too long. Baxter put it on, and while the first episode introduced the characters and their world, I thought back to the previous night.

Jason operations are carried out from a large shipping container on deck. At the front are 12 large screens displaying video from the various cameras. In the front row are three large captains chairs which — left to right — seat the engineer, pilot, and navigator. Each has a set of controls specific to their task. The pilot has a set of buttons and a touch screen, along with actuators that transmit his movements to the ROV arms. Behind them sits the watch leader. This is the scientist who directs the pilot. Behind them is a bench that seats the video logger and the data logger. The data logger types each action (“THET engaged”; “Rotation initiated”; “Spacer lost”) to a file that adds a time stamp. I was the video logger for the eight-to-midnight shift, which meant I just hit record on DVD players and labeled the many disks that recorded video constantly. It was a simple job, but I wasn’t complaining. I had a perfect seat with a great view of the science cam, the high def camera controlled by the watch leader. When I entered, we had reached our working site. It was so incredible to watch the team work together in the dark room lit by the glow of the dozen front monitors and the dozen other small screens and flickering lights that conveyed necessary outputs. It was even more remarkable any time one remembered that the images on screen were over a mile and a half away: straight down.

The pilot placed the THET (Top Hat Extractor Tool) over the top hat. Then, concern set in. A bolt had fallen from the damaged cap and was obstructing a cleat needed to engage the THET to the top hat. After a period of brainstorming, the pilot managed to insert the cleat at the perfect angle, and the bolt broke free. The THET was turned, and a screw raised the cleat, pulling at the jammed top hat like a medieval torture device.

The following hours were a series of small celebrations and disappointments. The THET worked beautifully, lifting the top hat several inches. This was expected to be enough to break the corrosion, allowing for an easy removal, however the top hat was still stuck. Fortunately, we had a spacer designed to give the THET more lifting power if needed. The spacer fell, though, lost to the bottom. A backup was on board, though, and it was fixed into place. More successful lifting was followed by continued tenacity on the part of the brass cap, followed by brainstorming. It continued this way until near midnight, when the watch leader announced that an elevator had reached the surface. Deck crew went into action setting up a crane. Jason crew relinquished control of the ships dynamic positioning to the bridge so that the ship could chase down the elevator’s homing beacon. Meanwhile, Jason and Medea were brought to holding patterns 80 m below the ship, safe from anything near both the bottom and the surface in the vast black benthic void.

Watching Firefly, with its roughshod, determined crew, surrounded by technology and adventure, I was reminded of the rewards of my labors. Video logger was considered a lamentable job by some. I didn’t care. To me, it was just a rung on the ladder to watch leader.

For more updates from expedition AT18-07, go to http://joidesresolution.org/blog. Its updated regularly by a team of educators who’ve come to sea with us in order to document and provide educational outreach to schools, museums, and the public. There are pictures and links to videos. Also check out the Atlantis website, atlantis.whoi.edu, which has links to live data feeds including ship location and local conditions.


14:15 PDT
21:15 GMT
47 45.44 N, 127 43.98 W

The Atlantis departed yesterday morning. We were in transit for the next 24 hours or so. This was the worst time for sea sickness, as the exit out to sea is somewhat rough in these parts. By this morning, we had arrived at our first site and deployed our first elevator. The elevators are modular platforms consisting of a grate around 4×4′ with a 10 foot mast that supports an array of floats. Once its in the water though, the base hangs from the floats as it sinks to the bottom, where it sits until the Jason ROV disengages a weight, allowing the buoyant elevator to return to the surface. The first one carried down an acoustic beacon. Once the ship establishes this as a reference point, the Jason ROV will navigate of it it, triangulating between that beacon and two others on the Atlantis (one at the bow and one at the stern).

Once we were in motion, I was feeling tenuous. I wasn’t sink, but I was aware of a subtle unease that I had no interest in seeing develop into full on nausea. I stayed away from computer screens and books, and instead went down to the forward bunks where there were two exercise bikes. Staying busy and in motion seemed wise. Afterwards, I had a hot shower and then lunch. Then, I joined several others in the lounge to watch a DVD.

This may seem like the cruise is more leisure than it is. The truth is, sea sickness is a horrendous experience, and the first days at sea are when one is at greatest risk, and its much, much harder to stop it once it sets in than it is to prevent it.

By the evening, the vague unease had persisted, but it had not progressed, and so I offered to help a colleague, Sam, assemble parts prior to our arrival on site. For lack of a better comparison, they were a set of doorknobs. Once at depth, attaching things, particularly hoses and fittings, can only be accomplished with well planned dockings that click into place eagerly and then have no desire to move. Unless you want to move them, in which case, they need to be designed to want nothing more than to release at such a time. The challenges can be enormous. Today, the first dive operation will begin with the deployment of a special cap remover. A cap placed a few years ago became welded onto the mounting it sat on because the two were of dissimilar metals, and corroded together so as to become one part. If you’re thinking that you wouldn’t have thought to worry about this, don’t feel bad. Apparently, a team of engineers and scientists didn’t prepare for it either. Whether they didn’t expect it to seal so strongly or they didn’t expect it to seal at all I don’t know, but they were unable to remove it last year, and had to design a special bracket to attach onto the cap, then turn a screw to apply thousands of pounds of force to get it off.

My colleagues door knobs were all custom, and they’d just arrived from Texas. He assembled one and gave it a try. He frowned. When it moved into the closed position, it wasn’t stable. The parts moved to smoothly over one another, posing a risk that the lock might spring from open to close if bumped. We discussed solutions, and ended up notching a several of them so that they closed with a satisfying ‘click’. I worked on filing them for an hour or so, until Sam came to tell me that the Jason operators had a mill that we could use. It was a quarter to 11, and we went out on deck to a small cargo container containing their mobile machine shop. Sam modified the pieces by 7 hundreths of an inch each and when reassembled, they clicked into place even better than they did when notched. Satisfied, I went below deck to my bunk for some much needed rest.


I’m going to be working aboard the R/V Atlantis for three weeks (from Jun 25th to July 24th). Here are some details for the curious.

The Atlantis (Wikipedia) (WHOI)is 273 ft long, and is operated by the Woods Hole Oceanographic Institute. Its the second Atlantis, and it shares its namesake, with the space shuttle Atlantis, which was named after the same research sailboat. It serves as the platform for the famous Alvin minisub (Wikipedia). You see, you can’t just toss a minisub on any boat you like, you need a lot of support equipment. The Atlantis has a housing bay designed for supporting the Alvin vehicle. On our cruise, however, we will not be needing Alvin, and so its not coming. We will be working at the bottom of the ocean, though, and for that we’re brining Jason II, a deep sea robot (Wikipedia) (WHOI). I’ll try to post a summary of what we’re doing shortly. In the meantime, feel free to click around those links, there should be plenty to keep all of you entertained. And by “all of you”, I mean my mother and possibly one other person.