Spring 2011

Our intern, Ali - an undergraduate student from Middlebury College, details her experiences from her summer with the HOT program.

Monday, July 25, 2011

Out of the Bean Bag, Into the Hard Hat

Walking down the halls of the KM on Day 1 of the cruise felt familiar for the first time. Now I walk with confidence around corners at which I used to stop and ponder before. I know the doors that are sticky and expect the sweeping rolls of the double hull chucking me from starboard to port.  My memory of the watch routine – taking samples, labeling bottles, observing the meteorology – was a little rustier than my memory of the ship’s halls. I followed along behind Reagan, the volunteer, as Cammy oriented her to these tasks and paid more attention to her instruction than a veteran HOT cruiser should.  

I became acquainted with a new part of the routine this cruise, which got me out of my bean bag chair and into my hard hat: tagging. It’s a bit like it sounds. The CTD and I play tag, except I am always it and he is always swaying back and forth trying to wiggle from my grip. Brett standing on one side and I on the other, we tame the swings of the CTD until we’re told to slip our lines and let the CTD take the plunge.  After an intermission of bottle labeling or meteorological observations, Tagging, Act II, begins. In Act II the plot thickens with the introduction of a new character: the claw extension. Known more generically as a hook on the end of a pole, in my hands it feels like an extension of my arm in claw-form. Brett and I reach over the railing to hook our long claw arms claw around the frame of the CTD and guide the CTD back on deck.

Thursday, July 21, 2011

A Lazy Sunday Morning of Lifting

The adventures of my last HOT cruise started on Sunday morning ferrying the much needed but heavily begrudged boxes of salinity samples from the storage room to the truck. Filled with the remaining water from last cruise’s CTD casts, the glass bottles were heavier than I remember. Other oddly shaped or overweight boxes followed into the back of the truck and we headed to Snug Harbor to load them from truck to ship. The most oddly shaped and overweight object of all awaited us there: the CTD. It’s taller than I am and big enough to have a party of three take tea in its round center.  While waiting between cruises, the springs that close the Niskin bottles, in which the water samples are captured, are unstrung. Before loading the CTD on the ship, we had to reattach these springs so that the bottles are ready to capture water. Craig yanked on the spring while I attempted to attach each end of the spring to the bottle caps, 48 caps in all. This involved 50 “Got it”s plus two “Don’t got it”s accounting for my two failed attempts. We carried our boxes over the gangway to the back deck for the rest of the morning. Though lifting heavy objects is not my activity of choice on Sunday mornings, any opportunity to wear my hard hat outweighs the unhappy arms.

Everything was loaded on the ship by noon. Unfortunately this meant I had to take off my hard hat. Quickly, though, my spirits were brightened when Cammy handed me the Walkie-Talkie.  It was time to test the CTD’s bottle firing, Fluorometer, and other instruments.  The CTD closes bottles on command by releasing a hook, which had been holding the top and bottom bottle caps open. Reagan and I climbed onto the CTD in the wet lab to pull on each hook until Cammy fired the bottle from the computer.  By Walkie-Talkie I told Cammy that the “Bottle fired, next.”  We tested the Fluorometer, which measures chlorophyll by light emission and absorption, by sticking our finger in front of the sensor and tested the temperature, conductivity and oxygen sensors by pouring water through. By 1 pm, all the laptops were tied down to the counters and the instruments ready for deployment, so a lazy Sunday could begin. 

Wednesday, June 15, 2011

Three Colors, Two Axes, One Timescale

Now that I am back from the ACO cruise, I am back to the office and back to my neglected friend, Matlab. I am making my brain and fingers work in different ways. There will be less pondering on the hydrodynamics of ADCP hard hats and visualization of physical things and more pondering on the algebra of matrices and visualization of columns of numbers.   I will coax my fingers out of trying to lash computers to desks and books to bookshelves in favor of tapping away Matlab commands until the error responses disappear.  The adjustment has already begun and successes in creating multicolored graphs have given me energy to pick up where I left off – that is, if I can find where I left off.

Looking at my notes from a month earlier, Matlab is again a language foreign to me. It took me the better part of an hour to even decipher what my task had been: plot depth data from the CTD against wire out data from the Caley crane to determine their synchrony.  The CTD will give the more accurate data set, so this is mainly to test the accuracy of the Caley.  Once I determined my task, it seemed simple. Almost immediately it proved much harder when the two data sets had different frequencies – one at 2 Hz, one at 1 Hz.  I needed to assign time to the CTD data set to match that of the Caley crane. Last month, I tried to stuff them into the same graph on different axes and approximately line them up. Lining them up properly proved futile to so I moved on to assigning each CTD data point a year, month, day, hour, minute and second. Year, month and day were easy – it all happened on April 12, 2011. Seconds were less cooperative because the data frequency was 2 Hz. Joseph helped me ask Matlab to take each row and assign it a seconds value equal to the row number multiplied by ½ – since each row is a step of half a second.  With a long wait – Matlab had to calculate this for over 13000 rows – I had a column of cumulative seconds. 

Just when I was about to bang my head against my computer to figure out how to assign hours and minutes to the CTD data, Craig and his magic fingers arrived. He informed me of a clever Matlab function called “datenum” that assigns a serial number to a date in decimals of a day.  Given the datenum of the start of the cast, in this case 01:16:29 April 12, 2011 is 734,605.05, I could add the seconds to it as a fraction of a day – 1 second equals 1/86400 of a day. Matlab made converting the Caley data to this form easy as well, so shortly I had two synchronized data sets. Plotting this showed an expected and somewhat boring result: the depth profile lines matched up.

Plotting wire speed – the variable that is most concerning for the safety of the equipment during a cast – would be more exciting.  The Caley crane supplies a column of wire speed pre-calculated so only the CTD data needed attention.  With a simple rate = distance/time calculation, the two data sets were ready to be plotted. To be able to reference at what depth the wire speeds occurred, I added a depth profile to the chart in the same timescale. Though this meant battling with the double axes that had been so troublesome a month before, I ended triumphantly with a graph in three colors, two axes, and one timescale.  The battles ahead will be the fancy stuff: labeling axes and giving titles.

Thursday, May 19, 2011

A Change of Plans, and of Link

As I found out on Monday, I somehow wiggled my way into a berth the ACO cruise to depart this friday about which I couldn't be more excited.  The length of time floating on the big blue, the hands on nature of much of the work to be done for the observatory, the sheer quantity of new instruments and equipment to be deployed all have me antsy to haul away the anchor and head for Station Aloha. For the next 18 days I will be channeling my enthusiasm and my blogging to that project so you can find details of the cables I get tangled in and quantities of M&M's I consume at the link below:


Wednesday, May 18, 2011

Donning a Hard Hat Always Means Good Things

A flurry is how the office felt upon returning to it after two weeks away.  I received a message from Craig a few days before saying “things have changed” and that I should plan to work outside on Monday.  This easily could have meant that the Marine Sciences Building had come crashing down and now my desk was located under a tree in the courtyard. In reality, the only thing that came crashing down was the A/C, causing problems accessing overheated and grumpy computers. What most significantly had changed was the schedule and personnel for the HOT and Aloha Cabled Observatory (ACO) cruises. The HOT cruise that had been originally scheduled to embark on Monday had already happened while I was away.  Though I missed that cruise, a vacancy had appeared on the ACO cruise for which I was trying to contain my excitement at filling.  Nothing was certain at 0900 so they told me not to get my hopes up. Trying to reel in my helium balloon of hopes was my challenge for the day.

As my desk was still located in it’s normal corner, working outside meant going to Snug Harbor with Jeffrey to help prepare equipment for the upcoming cruise.  Everyone chuckled a bit when I said that I was excited to go down to the harbor because the glass balls are very heavy, as I soon found out, and things are much dirtier than when tapping away at my computer.  New things are always exciting, however, and no one could convince me otherwise.

I started by wheeling around bicycles with flat tires trying to find a way to inflate them. Then I graduated to helping move around glass balls contained in two firm yellow plastic bowls that strikingly resemble yellow hard hats. With moving these you must be as careful as if decorating the Christmas tree with glass ornaments because no one wants chards of glass everywhere but as firm as if hoisting the weight of the whole tree onto the top of the car.

In the afternoon the spool of 200 m of cable, which will be lower to the bottom of the ocean with eleven temperature sensors attached to it, and I had a fine time rolling around the pier. In order to measure out the positions at which the instruments will be attached to the cable, I was supposed to get the cable as straight as possible. A bit like herding an oversized, uncooperative farm animal back to the barn, the spool needs constant nudging and alteration of course in order to unravel in a straight line. As dirty as a farm animal too, the spool somehow covered my legs in black and brown smudges. Had I only perfected my log rolling skills, this process would have been much easier.

The next day I got to participate in the dirty work again, starting with loading the flatbed truck with several instruments and boxes of supplies.  A forklift loaded the heavier items such as the ‘parking station,’ which is used for ‘parking’ wires as they are waiting to be connected to the observatory but which looks more like Snoopy’s doghouse. The forklift also swung the node, a large orange cylinder that Jeffrey described as a bird perch, Woodstock’s perhaps, onto the flatbed. This seems like a perfectly acceptable answer and the only thing that makes me skeptical is the logo stamped on the side of it is that of the Applied Physics Laboratory, not Petsmart. 

When we arrived in the flatbed at the harbor, I was handed a hard hat, which always means good things. It means I get to load with the rest of them and watch the happenings on the quarterdeck, which is hosting a flurry of activity currently.  Jason, the remotely operated vehicle (ROV), who will descend with the cable to install the instruments, has his innards exposed to have his wires tickled by engineers.  Swinging overhead at the end of the crane are platforms, weights, and other equipment being loaded.  I am slowly meeting all the scientists, engineers and crew involved in this project by bumping into them with boxes I’m carrying or asking them to hold the door for me.

When not loading boxes, I spent a lot of time with Nicholas in the stuffy beige tent trying to figure out how to attach two glass balls together and string a chain across them. After an hour of wrestling the hard hats together with no success, Jeffrey arrived to tell us that we needed to use the retrofitted hard hat covers shaped to fit together. Easy as pie from there. At least we got plenty of exercise lifting various glass balls.

To make this day even better, we filled the flat tires on the bicycles we were wheeling around yesterday with air enabling us to zoom around the parking lot in with alacrity and style.  Need me to grab something from the warehouse, bring it to the tent, skip over from the tent to the blue van, wait no, the PO van, then meet you over to the KM and head back to the tent? No problem.

At the end of the day, I was handed my second power tool for the day to unscrew the boxes in which some of the instruments are stored.  I helped Jeffrey set up these instruments on the observatory and in a tub of water in order to test them tomorrow.  

Thursday, May 5, 2011

A Brief, Codeless Intermission

After a busy day on Friday of scampering back and forth between Branden's room and my own trying to find the links that hadn't been updated to the new ADCP plots website and pouring over Matlab Help in an attempt to understand time conversions it feels odd now to be computer codeless. I am on vacation in Kauai this week and next with minimal electronic contact. Perhaps a detox treatment away from typing will bring me back to Matlab with a sudden comprehension of the construction of double axes -- or at least a newfound enthusiasm with which to greet my old friend. In either case, the accounts of my adventures in code will recommence on Monday May 16th, so check back then to learn more Matlab vocab.

Friday, April 29, 2011

World Wide Weblearner

I am an official weblearner. I don’t want to risk calling myself webmaster again for fear that it may induce some sort of error in the html sending me back to the drawing board. For now, I am a weblearner – but I am official. The Shipboard ADCP Plots website is linked to the HOT website now and out for the world to explore.  Please enjoy the Bulging Spry Menu Bar and engaging color scheme for yourself at:

Of course, two days ago when I claimed that the html was complete, it was not.  Many vector fields appeared, which wanted entry into the Spry Menu Bar. There were margins to adjust. There was text to be edited. Then there were margins to readjust.  All small things are worth it, though, for the satisfaction of having that html pop up on the World Wide Web in more or less the same format in which I designed it. Naturally, it does not end here. I am sure I will have the opportunity to readjust the margins at some point in the future. For now, I will focus on artistically rendering plots of wire out versus time, and crafting haikus into m-files.

The more I calculate, the more I must recalculate. I spent yesterday and today averaging and re-averaging the wire speed from the Caley crane because each time I made a new calculation, I found a problem with the last calculation.  To start, I calculated the wire speed from the total depth of the cast over the time from start to finish. However, I had neglected to take into account the starting and ending wire out values, which were invariably non-zero. After I recomputed these averages, I realized that the boundaries I set for each cast were inconsistent. All the better though, because each set of equations I concoct make me think more closely about the 68947 rows of numbers.  I have also become increasingly crafty with my use of Matlab, making up functions until one works. Craig ‘Magic Fingers’ came by and remarked at how slow calculations by hand are, which spurred me to ask Matlab to do these calculations for me. Matlab, charmingly, obliged – however, only one column at a time.  For tomorrow, the goal will be to plot CTD data and Caley data in the same figure with dueling scales on the x-axis.

Unix language lesson for today:

‘!!’                   means ‘do what I just asked you to do again, this time with enthusiasm’

Matlab language lesson for today:

‘hold on’          contrary to intuition, does not mean ‘be patient with me, I’m learning,’ rather it means ‘keep this line on the plot while I add another’

‘r’                    means ‘make this line a vibrant color red’

Wednesday, April 27, 2011

Peace with Dreamweaver, Plotting with Matlab

A peace treaty has been signed with Dreamweaver, for now.  Yesterday, with the spry menu bar back in good health and alignments of boxes, images and text on a short leash, the page was sent out for approval. Approval was granted! All that was left to do was to populate the menu bar with the rest of the available data – a simple task of copy and pasting.   For Craig, this posed some problems because he had to make the rest of the data available for me to link.  Luckily his magic fingers and head banging were up to the task and we now have a completed html with ADCP plots aplenty.

With a functional understanding of the language of Dreamweaver, I turn to Matlab, which I have neglected over the past week.  Today I worked towards verifying the calculations that the Caley crane, which lowers and raises the CTD during casts, makes for wire speed and wire out. Along the way, I am continually learning new functions that expand my repertoire of commands.  I started by calculating the speed of the wire by determining the change in wire out over time.  When plotted, this looks more like a tangled ball on the axis rather than a line because the wire speed is constantly changing over the cast. To smooth out the line I averaged the wire speed over 5-second intervals, and then 60-second intervals to see the pattern more clearly.  I learned of the possibility of plotting more than one line in the same figure, which allowed me to compare my calculated wire speed to the Caley’s calculated wire speed.

From this plot I found the time boundaries of the upcast and downcast.  Within these boundaries I can find the average wire speed when the CTD is going down, when it’s coming up, and for the whole time that it is in the water. What I found, for the first cast at least, is that the downcast is about 25 m/min and the upcast about 16 m/min making the overall speed about 20 m/min.  This shows that the heave compensation is, in fact, working to make the casts faster, but that the average speed of the wire is slower than previously thought – at about 35 m/min.

Computer language lesson for today:

‘cd’            means change directory to a designated folder
‘ls’             means list the contents of the folder
‘cp’            means copy

Monday, April 25, 2011

R2D2 Meets the Autosal

Wednesday, the Autosal and I were mere acquaintances. By Thursday afternoon, we were thick as thieves.  Duplicate water samples needed to be run through the machine to verify the machine’s salinity measurements remained accurate throughout the processing that Cammy completed this week.  I watched Craig run ten or so of these samples trying to memorize every button to press and surface to Kimwipe dry.  The key to getting to know the Autosal, apparently, is the opposite of that of any normal friendship. You must try to be as robotic and void of character in your interactions in order to function properly together. The Autosal determines the salinity of a water sample by running current in four spiral metal probes and measuring the extent to which the water surrounding the probes conducts electricity.  Small bubbles around the spirals, variations in the time the water sits in the cell, rinsing once to many or once too few times or failing to vacuum away all the water from the past sample can affect your results in small ways.  These small effects easily compound to skew your overall patterns.  After watching with strenuous attention to detail, I tried to repeat his robotic routine.  My first few runs were littered with small mistakes – forgetting to flush the water here, forgetting to Kimwipe there. But by my fourth practice run, I was feeling pretty characterless. I stayed true to the routine to the very end – even entering my results into the database, which was powered off and could care less. Just call me R2D2.

The war against Dreamweaver continues.  Naively, I had thought that I had won the war when, 20 minutes before 1700, I came to Craig’s office to show him what I had completed so far.  He did some more clicking of his magic fingers and put my page on the honest to goodness internet. Of course, it would be quite an Easter egg hunt to find the page online without knowing the URL. But that did not inhibit my excitement at being an official webmaster.  ‘Master’ turn out to be a little preemptive. The moment we opened the page, my spry menu disintegrated into a jumble of broken links.  The battle ahead will be to recreate the links and nurse my spry menu bar back to health.

Thursday, April 21, 2011

The Battle of the Bulging Spry Bar Menu

Today, I experienced great victories over Dreamweaver. These victories were equaled by moments of head banging (which, against a laptop, you have to be careful with.) Morale is up, however, and the troops are hopeful.  After our win at the Battle of the Bulging Spry Menu Bar, it seems that nothing can keep us down.

The Battle of the Bulging Spry Menu Bar extended over a day and a half, with intermittent fighting. My adversary, the code window, far outnumbered me with brackets and equal signs.  I was only armed with ADCP plot figures, which are not particularly cooperative soldiers in this kind of battle. In fact, they sometimes appear to be fighting for the wrong side when they need to be resized or repositioned. The battleground was the left margin, where I intended to place my vertical menu bar. The code window defended this territory ferociously for unknown reasons. My intention was to layout links to the data in a more compact way to avoid excessive scrolling. The menu bar can only be described as bulging because of the 70 or so HOT cruise tabs to be inserted into and the submenus to be attached to each.  Victory came when an unexpected ally, the div tag, came riding in upon a white horse and divided my page into sections, leaving the left margin open for a menu bar.  Small victories followed in the form of color-schemes and margin adjustments. A battle waits in the next valley over concerning resizing the submenu tabs.

Wednesday, April 20, 2011

Weaving Tangled Dreams

Yesterday, Craig sent me a link to a branch of the HOT website which displays Acoustic Doppler Current Profiler (ADCP) data from past cruises.  Anyone can come to this site to look through plots of current velocity and direction recorded by the ADCPs aboard the Kilo Moana or the Ka`imikai-o-Kanaloa.  Despite its noble attempts to make cruise data available to the masses, this is the ugly duckling of websites. Its first offense is its background color: beige, the internationally recognized color for blandness.  It also hasn’t been updated with new data for a while and has some functionality issues.

With the link to this website, Craig gave me the task of giving the ugly duckling a makeover.  However, the extent to which I am able to name the flaws of the ADCP page is equaled by my inability to fix them.   Dreamweaver, the software that I am using to redesign the page, has its own language wholly different from the other computer languages I have previously mentioned.   My learning process involves many trials and even more errors.  Edit > Undo is my savior as I accidentally turn the page upside time after time. My limited successes so far include inserting links to anchors on the page, or to other html files, resizing and aligning images, and my greatest triumph: changing the background color from beige to blue.
One of my successes: cropping an image.
At some point in the afternoon, after too many Edit > Undo’s for one day, Craig gave me a new project. Though this project still involves an unknown language, that of Matlab, it comes more logically to me. On the cruise last week, heave compensation was used for the first time during the casts in order to let the CTD descend more smoothly.  This means that the winch lets out the wire at varying speeds depending on the heave of the boat in order to keep the tension on the wire relatively constant. What remains to be seen about heave compensation is how accurately it reports the speed at which the CTD descends. This is where my project begins: I will use Matlab to plot wire speed from the winch over time and compare it to the pressure versus time data from the CTD.  This will show how accurate the winch data is, as well as show how beneficial the heave compensation is.

To the first twenty commands I tried, Matlab stubbornly refused to acquiesce. Matlab is quite particular, I have learned, about the use of parentheses and colons. It is training me quickly to pay attention to these details. Success came slowly and even the simplest plot gave me great satisfaction. Craig introduced me to the m-file, a text document in which I can record all of my commands and explain their functions, with whom I got along much better than with Matlab itself.  With a couple of magic movements from Craig’s fingers, Matlab ran the functions in my m-file and out popped 2 new plots. I aspire to Craig’s magic fingers someday. In the meantime, the Matlab vocabulary lessons continue:

‘pwd’               stands for ‘print working database’ which means ‘where am I?’  to which the answer is invariably an address to a database which I do not understand. I’ve got the question down, though.

Tuesday, April 19, 2011

Sifting Out the Noise to Find the Signal

Imagine you are sitting in a coffee shop, reading a book. This is a horrible place to find peace and quiet, but you are determined.  The story heated up a couple of chapters ago when someone in the library shouted, “Murder!” You are on the edge of your seat to know which character is the killer, and whether it was with the candlestick or rope.  You suspect Colonel Mustard, but you can’t be sure. Just then, the barista begins grinding a fresh batch of coffee beans. The new barista, still in training, is shouting completed drink orders across the whole room.  Your telephone rings.  It’s your mother so you must pick up.  It’s been a few days, so there is a lot to reassure her about how you’ve been getting in all your food groups. The subtle jazz music to which you had enjoyed tapping your foot has become dominated by saxophone squeaking in your ear.  A little gray-haired woman asks you if you’d mind if she sat next to you. You’re trying to determine Colonel Mustard’s integrity but the author has employed all sorts of literary tools like foreshadowing and analogy, which make the author a bestseller but now just annoy you.  The gray-haired woman is discouraged at your lack of response and begins inquiring more loudly and you’ve completely forgotten what you were telling your mother about.  Solving the murder mystery seems far afield.

After talking with Roger this afternoon for an hour, this is how I imagine analyzing a time-series might feel. It started with a question of how HOT fits in anthropogenic climate change research. The answer will not fit in this blog but the short version of the short version that he summarized for me is that it all depends on sifting out the noise to get the signals. The noise can range widely spatially, from turbulence on the scale of a molecule to global ocean circulation, and temporally from internal tides on the scale of tens of minutes to the earth’s motion on a scale of tens of thousands of years. The signals could be telling us how our climate is changing.  Identifying the patterns of noise is hard enough, and when those patterns begin to change – due to climate change or otherwise – it becomes harder. That is where a time-series becomes useful.  They attempt to give consistent data with high enough frequency over a long period of time in order to start picking out the patterns so that the signal becomes clear: Professor Plum in the library with the candlestick. Troubles, of course, include limited ranges.  You can’t measure the whole ocean and data is only available a few decades back, not thousands of years.  It is becoming clearer to me, however, that this work is ever more pressing and ever more complicated in light of those limitations.

Sunday, April 17, 2011

On Solid Ground Among Foreign Tongues

A little less rolling and heaving than the ship, but equally air-conditioned and packed with new information, Friday was my first full day in the office. I spent it trying to understand the processing through which the raw data from the ship must go in order to mean something in a language closer to English.  First, Fernando, who was kind enough to let me abduct the back desk of his office, explained it to me conceptually. Next I tried to retain this comprehension as I watched Branden, a Computer Science major light-years beyond me in the language of the keyboard, type code into Matlab to execute this processing.  Later on, I even tried my hand at Matlab, under Cammy’s supervision. Though I am not a natural born whiz at the keyboard, with a little training I may be able to rapidly type streams of gibberish with the best of them.

What come from the ship are many columns of numbers in engineering language – volts.  Every electronic signal from the instruments indicates a value in degrees Celsius, decibars, practical salinity units or micromoles per kilogram.  Scripts in Matlab are designed to perform the translation from engineering units to scientific units. While they do this, they also scan for errors in the data. A temperature that reads higher than 40°C, for instance, is an error that would be deleted.   If that were a feasible temperature to encounter at sea, I would be in trouble.

After that translation and error screening is complete, you have columns of numbers in a familiar language but they are speaking much too rapidly to comprehend their meaning. Underwater, the CTD records data at a frequency of 24 Hz, or 24 times a second. For practical purposes, this is TMI (too much information.) Run again through a script in Matlab, the data is averaged to a frequency of 2 Hz. 

Next you must account for the inherent skewing of data over the course of each cast. The skewing comes from the differences in pressure on the instrument between the downcast and upcast, giving you two slightly different data strings. Some calculations, which the computer seems to find quite simple but I’m sure I would not, match the two lines to the best fit giving you close to one single data string.

Similarly inherent to the operation of the instruments is a time lag between the moments in which each variable are measured.  The CTD works like a water slide with several loops through which water must flow. First the water enters through a pump that sends it to the temperature sensor. Next it loops the loop to the conductivity sensor and swirls on to the oxygen sensor before exiting the slide. In order to know that you are looking at the temperature, salinity and oxygen values for the same parcel of water, you must account for the time it takes for the parcel to travel from sensor to sensor.  In addition, there is a secondary slide for every variable that must be aligned temporally with the first.  There is a Matlab script for this too.

There are many more alterations to the data that were explained to me – some of which I chose not to explain in favor of the more intriguing and understandable processes, many of which escape my memory. Today challenged my capacity to follow computer commands and I am proud of what the steel trap still contains, two days later. 

Matlab language lesson for today:

‘Exit’, followed by ‘enter’ means ‘close Matlab, please’

‘y’ means ‘yes’

More to come, I’m sure.

Saturday, April 16, 2011

Without Hitch or Sneeze

My last watch on the KM was a slow one for science.  The science that remained did not involve the regular CTD deployments nor a meter net tow but something entirely new to the ship and myself.  As the wire was cranked in, a series of Plexiglas contraptions emerged from the surface and hung in a column under the A-frame. They dripped with seawater and waved ever so slightly in the wind like stubborn kites. Who knew science could be so lovely? Aside from bringing a little beauty to the back deck, these kites, actually called vanes, carefully capture water samples for iron testing. The vanes must be very careful in this capture because iron levels in the ocean are extremely low, particularly in the northern Pacific, and anything from a human hair to a speck of dust can contaminate the sample. From when I saw her at lunch, rapidly swallowing a PB&J while staring at her timer, to when I went to sleep at 0200 Jesse, the graduate student from MIT running the iron testing, looked tense.  I even felt tense while helping Cammy take apart the vanes and put the sealed water samples in a Ziploc bag – and I only had to hold the Ziploc. A sneeze in the wrong direction and all was lost, it seemed.   Luckily, the collection of the vanes went off without hitch or sneeze.

For the rest of my watch, I observed the painstaking pouring of iron samples until the whole ship seemed to be asleep.   When 0200 finally came and the last thermosalinograph sample was taken, I joined the rest of the ship’s company in sleep. 

Thursday, April 14, 2011

Paparazzi at Sea

Dave holding tension on the wire before the CTD is lowered into the water.
The CTD about to take the big plunge.

Sunset under the A-frame.

I could never tire of this view.

Dave holding the psychrometer over the port bow.

 The starboard bow, according to the port bow.
A crane in the sunset.

The CTD, back from its swim, at twilight. 

Wednesday, April 13, 2011

From Human Radio to Human on the Radio, almost

I have witnessed a great scientific discovery today.  At the end of every CTD cast on this cruise when the rosette is brought back on deck, the wire always contains between 5 and 10 turns in the wire which developed during the cast. It is quite a pain for Dave who has to disconnect the wire, untwist it and reconnect it every time. What was confirmed today was that the turns develop as a result of the firing of the bottles, either from the uneven weight distribution of closed bottles or from the resistance of the lanyards attaching open bottles.  The solution: no more water sampling. Everyone alright with that?
The green revolution continued today with apples galore. In addition to the occasional apple throughout the day, 2200 was the hour of the apple. At this time I went forward to collect a surface salinity sample and while returning I collected 3 Granny Smiths, as requested. The lab was a calm haven of crunch as Dave, Craig and I simultaneously put away our respective apples.  The doctor will most definitely be kept away today.

My water sample filling skills continue to improve. As do my cap tightening, o-ring checking and spout locking routines.  Cocking the top of the bottles has always been my favorite – the methodical stretching of the lanyard from Niskin bottle to hook appeals to my simplicity – and I have become almost robotic in this task. The struggle between the lanyards and myself over cocking the bottoms of the bottles has tamed and the victories are more often in my favor.  My repertoire is even expanding: I touched the wire today! Better wire handling techniques, I hope, will come in time.

My computational skills, on the other hand, seem to need polishing. The single digit integers are the tough ones, I find. Yesterday I graduated from bottle labeling assistant, to bottle label extraordinaire flying solo on the labeling of bottles for a whole cast, never mind that Craig only gave me a baby cast of 7 bottles.  This transition may have come too soon, for today I royally confused both myself and Dave while counting between numbers 1 and 5.  My computation skills struck again while entering meteorological observations into Matlab, the difference between 0400 and 0800 seem to be beyond me. 

Unfortunately, these errors cost me the precious opportunity to use the radio.  There were rumors that I would be communicating to the winch operator the depths at which to stop the 2100 cast for bottle firing. Communicating depths, however, requires a firm grasp on the numbers 1 through 1020, and Craig made the judgment that I was not quite ready. Next time, maybe, he says. In the meantime, I will be returning to kindergartner for some private tutoring and practicing my radio voice. 

Tuesday, April 12, 2011

Scientists and Cowboys

M&M’s and gummies did indeed get me through the end of the watch at 0300. From this experience, however, I have learned that I could probably lower the dosage of sugar from 5 handfuls of M&M’s to just one and I could limit myself to a baker’s dozen of those squishy little bears.  A combinations of my free reign on all thing bad for me and the 22 hours I had been awake made me this greedy and I hope to show more restraint in the future.

This restraint started today with apples and bananas. I even inspired my partner in crime (read: the person whom I follow around most often,) Dave, with the crunch of my Granny Smith to partake in one himself. Dave is an undergraduate from University of Hawaii working for the same project I am as well as working for OTG, the Ocean Technician Group. This means Dave gets to help bring the CTD and other instruments in and out of the water.  I don’t get to follow him around when he does this but I do get to watch.

Yesterday, the biology group, BEACH, an acronym that always evades my memory, put a primary productivity array in the water attached to a string of buoys and released it to drift as it pleased.  This evening we went to retrieve it by using the GPS coordinates it sends to the ship.  Several scientists stood like cowboys on the port side holding coils of line with giant fishhooks tied to the end.  The plan was to approach the buoy and have the cowboys lasso it in to the quarterdeck where the A-frame could hoist it on deck.  From the top deck, I watched the buoy come closer and closer then disappear from sight to the starboard side. I felt us reverse, and the buoy got smaller on the horizon. We approached again, but again the buoy ducked to the starboard side and we had to reverse. Third time’s a charm, right? Alas, the third time was a repeat of attempts one and two. The fourth time, however, was the charming one. Who ever decided three was the lucky number, anyways? Four leaf clovers are the lucky ones; three leaf clovers are dull.

As you might have surmised from my need for handfuls of sugar, twelve hour long watches are hard to make it through. Though it is often exciting to see temperature, salinity and other measurable qualities of the deep ocean being plotted on the computer screen in real time from the descending CTD, there is often little to do in the lab while deploying.  Sometime this open space leads to unusual conversation topics such as defense from zombie invasions, of which Dave is our resident expert.  Sometimes it leaves me time to catch up on my book.   Mostly I have learned that sitting in the beanbag chair is the worst solution to drowsiness at times like these and, again, I hope to show more restraint in the future.

Monday, April 11, 2011

Eagerly on the heels of others

As I am still mistrustful of the bus system, today began at 0500 to ensure that I made it to the bus stop with plenty of time to spare. As it turned out, the bus was willing to cooperate. At 0740, I eagerly scampered up the gangway on the heels of Craig and found my new home, 10 upper. The upper bunk itself is bigger than my bunk of 7-weeks aboard the Seamans in which all of my belongings and I squished. I don’t even know what I’ll do with my half of the rest of the room. Calisthenics, maybe.
After I moved in, all hands ran through emergency drills during which I narrowly missed having to try on a neoprene survival suit for practice. For the rest of the morning, my eagerness led me to the heels of many others, some of whom I could help, many of whom I could not. I am starting to recognize the balance to strike, as an intern, between reaching my hands in and learning and sitting back and observing. There are only so many tasks I can perform without extensive explanation that delays the more important tasks at hand. For instance, in the collection of water samples for the ultra-precise salinity tests to be run on shore, I can’t simply stick a bottle under a faucet and call it good. The learning curve is steep. However, I find myself rapidly approaching base camp with several skills added to my fanny pack already:  I can fill, shake, dump, and dry sample bottles properly; I know where to hold the psychrometer over the bow to get an accurate wet and dry bulb temperature reading; I can measure sea surface temperature using the bucket thermometer; and I know how to sweep up escaped mercury from a broken bucket thermometer in the case of a thermometer mishap. Mostly, I find that the scientists and crew here often delay the task most pressing in favor of instructing me in these skills and for that I am most grateful.
With the buzz of learning still percolating in my head, I found a moment this evening to go up on deck and remember some of what it feels like to be at sea. At the stern, white waves smacked against the hull and reached up to the railing. I kept my distance. At the bow, without fear of spray, I let the wind pull at my hair like a broken-toothed comb. From the starboard bow, I watched the port hull cut through clear water and remain visible underwater to its bottom.  This is a charm of a double-hulled ship that I was not expecting. Thick clouds hid sunset, but there’s always tomorrow.
The extensive stores of gummy bears and M&M’s in the galley, available to me at whim, have gotten me through the day so far and I hope they carry me through the end of my watch. In the meantime, I will be pacing the halls trying to learn my way around this maze. This morning, when returning to the wet lab from the captain’s office, I attempted to descend the stairs through the linen closet. Indeed, my grasp of the floor plan needs work.  

The Human Radio Meets the KM

The instruments I am use to deploying are no taller than my waist, no wider than twice my own width.  As I saw yesterday, while loading the Kilo Moana (KM) for my first HOT cruise leaving tomorrow, the instruments I’m going to need to get use to tower over me. On the Seamans, there are 12 bottles in which to collect water samples between the surface and around 600 meters down. The KM has 24 bottles, each one about my height and wide enough to stick my head in (I promise I won’t verify that, though) and sometimes they lower them to within 5-10 meters of the bottom of the ocean – approaching 5000 meters deep.  What they use to lower this rosette of 24 bottles is also giant-sized.  There is an A-frame the size of a 2-story building that they have used in the past, and this cruise we will be using a crane. My background is operating a crane is not too extensive so I’m guessing I won’t be lowering the rosette any time soon. The CTD, conductivity temperature and depth sensor, to my disappointment, was the same size.

When I first arrived at the dock with Craig to load, the KM was maneuvering itself into position to throw on dock lines. This meant that I got a full view of the ship as she did a 360 right in front of us. What a unique shape she is: double-hulled with a carved out center like a big upside-down papaya, very wide birth as she stretches from one hull to the other, yet not much longer than she is wide. Though my knowledge of ship design is limited, I believe this to be a very unique one.  My clarity on the design of the interior is not as strong. Craig took me on a brief tour from the wet lab at the aft of the ship to the galley forward, which I am not sure I could retrace on my own.

Once I met the enormous equipment, it was time to test it. To do this we needed to send a signal from the lab through a cable to the rosette which instructs a clip to release thereby closing a one of the 24 tubes to capture a water sample.  In order to communicate from the wet lab to the dry lab that the signal was successful, walkie-talkies are ideal. In this case, the walkie-talkies were unavailable so we proved our resourcefulness in inventing the human radio.  I stood in the hallway between the two rooms projecting messages from Craig to Cammy, which consisted mainly of variations of “Okay!” Half humiliating, half hilarious, this is a new skill I will be sure to put on my resume. 

Thursday, April 7, 2011


At 0400 on March 18th, Honolulu floated ahead of me more brightly and widely than anything I had encountered in the Pacific. As the Robert C. Seamans, a sailing school vessel of Sea Education Association, approached Honolulu harbor, and I with it, too many thoughts entered and exited my mind for me to concentrate on my given task of bow watch.  I was returning from a semester abroad studying oceanography and sustainability from Tahiti to Hawaii. After a week of finalizing work, I would be embarking on an entirely new adventure to fill an empty 5 months of calendar space.  Among the schemes that my imagination conjured, it did not cross my mind that someone might offer to take me back out to sea and teach me the many skills that I lack in the realm of oceanographic research.

Once I let the competing, unconfirmed plans settle to the bottom and the sense float to the surface, I took the uncommon opportunity to participate in research concerning the ocean’s physical properties and changing climate patterns. With this internship I will get to return to sea for four days to a week at time, on three Hawaii Ocean Time-series (HOT) cruises and one WHOI Hawaii Ocean Time-series Station (WHOTS) cruise.  On these cruises on the Kilo Moana I will be able to revisit the skills of science at sea that I learned aboard the Seamans.  However, I expect to leave with much more knowledge than I board with. 
Between these four cruises spread across the summer, I will spend time at UH in the lab and on the computer learning what’s done with the data after it’s collected. Though data collection has always seemed to me the most glamorous part of science, I am coming to realize that data is nothing without processing and presentation.  Of what use to other scientists and other humans are a couple of digits before a parts per million without context? Trends, numbers in relation to each other, are the reason for most scientific endeavors – especially this one in which patterns only become clear with many years of data.  With any luck, I will learn to determine relationships using software, Matlab, which so far seems to speak a different language than I do – just when I thought I was returning from islands of foreign tongues.  To present this data I will learn a bit of Dreamweaver to make it available online.

In addition to the practical skills and knowledge I forecast learning, I am jazzed about interdisciplinary work combining writing and physics in the form of presenting data online and blogging about my adventures. I am a physicist-in-training and a hopeful writer. My school, Middlebury College, knows me more formally as a double major in Physics and in Environmental Studies, focusing on non-fiction writing.  Most of the time these two disciplines make me stretch wide to keep one foot in each department. This summer, however, I am happy to see that I will need less gymnastic ability to stay standing with both sides of my academic pursuit.

I am expecting this summer to surprise and challenge me at all times of the day, whether it be in an office, at sea, or trying to catch the right bus.   Learning opportunities, I’m positive I won’t lack.  Though there’s a skeletal structure of familiar procedures that I expect to practice again, there’s a whole body of details and variations into which I look forward to delving.