pH and Chris Ikeda, RTC-SFSU

Chris Ikeda, RTC-SFSU

My first day on the ship, ten days ago today, there were several key scientists already hard at work. As I carried supplies, built frames, bolted down tables, and did whatever I was told to do, there was one young man that worked tirelessly by himself. The only sounds from his work area were the breaking beats of underground rap as he began a process that would take a over a week to complete.

After months of planning, Chris Ikeda another bright mind and rockstar scientist from San Francisco State University's Romberg Tiburon Center for Environmental Sciences (RTC-SFSU) systematically fed special lines from inside the hangar to outside, attached pressure connectors, and calibrated machines, both at the two

Dr. Bill Cochlan, chief scientist
and principal investigator for our research
RTC-SFSU

computers as well as the multiple sensors and meters. While I took breaks at night, always making time to eat, Chris continued to work, asking for a plate instead to be saved. Many nights, after our work was done, Brian Bill (NOAA), Chief Scientist (ChiSci) and lead Principal Investigator (PI) Dr. Bill Cochlan (RTC-SFSU) along with Co-PI's Dr. Mark Wells (University of Maine) and Dr. Charlie Trick (Western University, London, Ontario) could be found outside with Chris discussing these instruments and working through challenges along the way. Any observer could see that this was important work, crucial to the mission of this laboratory at sea. 

Co-principal investigators:
Mark Wells, Univ. of Maine
pictured right, Charlie Trick, Western
University, Canada

This set up is the result of months of planning and testing in the lab; then, a week of work day and night to get it running as planned. Chris Ikeda (RTC-SFSU) is the one responsible for this important work.  

Besides a few asides about his taste in music, Chris quietly worked and politely refused any help from me and others for the most part, and when he was finished, I could see why. The amazing result of plumbing and electrical innovation had to be precise, as he was reading one of the most sensitive and critical pieces of data for every experiment on board: pH.

When I asked Chris about the science, that's when he really opened up. The passion for the marine science is evident in his enthusiasm and seriousness of purpose of his work. I listened and took notes intently as he spoke.

Oceanic acidification seems to the buzz phrase that is becoming more important to the global science community with new research warning of the repercussions of an increasingly less basic ocean. The ocean will never truly be an acid, but when we talk about oceanic acidification or OA as it's termed, we are talking about the gradual movement of the ocean's pH lowering closer to neutral than ever before. The pH scale measures the amount of hydrogen ions available. A lower number on the pH scale is acidic; higher numbers are basic or alkaline. The numbers range from 0 to 14 with the extremes of this range being the most powerful. Bleach would be a strong base at pH 13; stomach acid (HCl) would be a strong acid nearing a pH of 1; and pure water would be neutral right in the middle with pH 7. Our global ocean has an understood pH value of 8.10 and was 8.21 before the industrial revolution. 

Coffee in the morning tastes better
with this kind of entertainment!

Our work here is important analysis of the ocean. "We are taking the pulse of the ocean," as Dr. Cochlan describes it. I will go into more depth about this global OA movement and our work at sea in the coming posts. Chris's pH reading contraption is connected to two incubators, one as the ocean is now and another artificially manipulated to simulate the ocean in the future according to the readings from our samples. It's really fascinating, so check back tomorrow for more details!

Remember to check out Denis Costello's perspective on the day to day here at sea as well: socalcostello.blogspot.com.

No Dentist on Board

Grin and bear it.

This isn't the first first time that I've broken a tooth. In fact, my front teeth have been through a lot from contact sports and a full contact life. My dentist and friend, Chad Owens, has had to work on this same incisor more than once. But, I didn't realize that I'd need him here at sea. I'm long ways from any medical staff, but I did find out that this vessel has a medical room, complete with gurney and equipment for emergencies. Apparently, my "emergency" is not one that their prepared for; in fact, the captain said that this is a first that anyone had ever asked him for a Dremel to do some dental work.

Medical room on board

I could make up a cool story about how a narwhal got too close or even that a wave swelled as I was carrying samples above deck. But, no. I was simply doing what I do best: eating. As I bit into the French baguette, I felt and heard the snap. I ran to the bathroom to see the damage.

I didn't panic. I just needed to get it glued back in ASAP, so I cleaned up the recovered tooth and the cavity. Super glue should do it, I thought. So, I scraped with my knife and dried it to prepare for setting. A few drops of glue on the post and in she goes. It worked! Temporarily.

Pirates of the Pacific

Next meal, it breaks again. I'm back following the same procedure, but this time it won't sit correctly at all. After short work with my knife, (quick aside: Don't ever try this, especially on a rocking boat. Stupid, but made sense at the time.) I thought if I only had a rotating multitool like my dentist...
It seemed logical to me to at least ask, so I went to the bridge and just smiled at the Captain. He gasped. Then, we headed to the "hospital" to see what toys could fix it.

Before getting to the medical room, I did get a Dremel from the Res Tech and tried just using the grinding bit without the motor. It tasted like motor oil even after dipping it in alcohol. I really thought that it was going to work. After unsuccessful efforts, I tried various other instruments, such as forceps with varying degrees of stupidity, all while Captain Wes Hill grimaces, chuckles and makes jokes all while making sure that I don't cause a bigger problem or emergency.

Not mouthwash!

I rinsed with isopropyl alcohol, you know, for sanitary reasons; this is another act high on the Richter scale of stupidity and one I will never do again. All of this for naught. Nothing worked, and I'm a month at sea without one-half of my front upper bite.


I asked the Captain for an eye patch while in the infirmary. He looked confused until I grinned and said, Arrrrgh, matey!

Yes. I'm from the South; but I really didn't want to perpetuate any stereotypes while working with my new Pacific friends. However, it's just part of the adventure, and I can assure that everyone will remember the toothless teacher from Tennessee.

If you haven't already, check out my shipmate's blog, Denis Costello, fellow teacher-at-sea. His blog includes other perspectives of the same excursion. I will be focusing on the science and shiplife in the future. This mishap is part of the whole science at sea experience: really important, serious science research mixed with fun and laughter. I'm just beginning to grasp the magnitude of this research, and as I understand it more, I'm compelled to share it with all that will listen. I'm taking notes daily and putting it altogether for you, the reader. Please share with others so that we can reach a broad audience.

Inorganic Nutrient Analysis

Julian Herndon (RTC-SFSU) 

When you think of what a potted plant needs to grow, what do you think of? 

Fertilizer (soil), water, trace metals, carbon dioxide, sunlight... Similarly these are the components of growth in the oceanic primary producers. Yet, ocean water doesn't have soil. It does, however, have the same necessary nutrients for the photosynthetic algae that populates the seas: nitrogen and phosphorus particularly.

Reagents

Julian Herndon through the Romberg Tiburon Center for Environmental Studies at San Francisco University runs the analytical lab in a room just forward of the main lab. For days (and nights), he has been carefully setting up the lab, calibrating the instruments and preparing the reagents that are needed to get a complete profile of the ocean water, those necessary nutrients: phosphate, nitrate and silicate which is used by diatoms, the most common phytoplankton, to make their intricate frustules, their porous cell wall. The amount of care that goes into the programming and plumbing is astounding. The nutrient auto-analyzer is made up of four spectrophotometers, a peristaltic pump and a robotic auto-sampler and pipette that does what any good technician would do: it transfers a constant volume of sample, mixes it with a predetermined volume of reagent, records the results and clears the Teflon tubing with pure water--ready for the next sample. It repeats at a rate that would not be obtainable manually.

Automated nutrient analyzer

Basically, the instrument measures the "disappearance of light" as the light is absorbed by the specific compound. Visible light is actually a mixture of different wavelengths, each a different color that is seen as light. What the "spec" does is control the wavelength of light to transmit a particular ray at a specific wavelength through the sample. The reagents react with the sample to allow the machine to read and record the amount of that wavelength that passes through versus that which is absorbed. As an analogy, think of the compounds as stained glass windows, each one a different shade, absorbing that particular color, wavelength, of light. Light passes through, but we only see the color of the glass because its absorbed.

Julian Herndon, research associate for RTC-SFSU, ensures
proper protocols are followed for sampling.

Robotic autosampler system

Each type of stained glass has an associated wavelength of light, transmitting a different color; therefore, the spectrophotometer shoots a specific type of light through the sample and records the amount of that very specific color that makes its way through the system. If the stained glass represents nitrate (NO3, a pinkish red color), then the number of nitrate molecules is proportional to the number that is absorbed and unable to pass. Each element or compound absorbs a color. The greater the concentration, the less color passes through to be read by the detector. One of Julian's jobs is to change the "stained glass" needed to measure that particular compound in the sample by creating a new product through a chemical reaction so that it reads that very specific lightwave emitted by that one specific element or compound of interest. By doing this, we can determine the amounts of each of those important nutrients for growth and photosynthetic processes present in the ocean water being studied. He has meticulously set up the robotic machine and computer to do this work for him.

Automated spectrophotometer with cadmium column
 that strips the oxygen, turning nitrate (NO3) to nitrite (NO2)

As a man that has traveled the world in the name of science, Julian is man rich with more than just knowledge of his chemical craft, but he is one of the most interesting people that I have met. His expresso maker sits in the corner with classical music one hour and classic rock the next. With his lab assistant (pictured below), Maribel Albarran, I've never seen such careful attention to detail, cleanliness and consideration of contamination and safety--especially in this raw environment and rough seas--but then again, I've never been a part of something so important where every slight variation counts so much.

Maribel Albarran, student researcher (RTC-SFSU)

I have learned a lot and have a lot to learn. Julian has patiently explained his laboratory practices and the science behind his work, and I will be taking his teaching to heart and practicing these same methods in my classroom from now on, for safety and precision. I am honored to work and learn from him and all of the professionals onboard.

This standard spectrophotometer measures
one sample at a time.

Don't worry Mom; they're feeding me well, very well!

Everyday Bob and Mark get up early to begin their 12 hour shift from 6 to 6 to make the crew and science team happy. Very happy. At 7:30am, 11:30am, and 5:00pm, the line begins to form for the buffet style meals that are prepared for us. And, these meals are good, nothing like I thought that I would be sacrificing by leaving the world's greatest "cooker" (as my children say) at home. However, when we were being fed pork ribs, salmon, prime rib, and seafood gumbo each night, I realized that I was in good hands, and I made immediate friends with the masters of the grill.

Bob Seeley, retiring this year after 23 years

Mark Smith, 19 years of service

Today's dinner:
Tuna steak, brussel sprouts with bacon, red potatoes

Mark Smith, a former Navy man, has been working for Scripps for 19 years, preparing foods aboard ships in the fleet. Bob Seeley from Iowa far from any port is retiring this year after 23 years of service, most of which has been on the Melville. That's a long time to work in one place, which means two things: one, they do an awesome job at what they do; and two, the job is worth the long hours and time away from home. They work these research cruises for four months at a time with three months off, traveling the world. Literally. Mark told me that he's been every possible place imaginable with a port: South Africa, Galapagos, Samoa, Chile, the Philippines, and beyond. 

Dessert is not an option!

For this research cruise, they spent $15,000 for the food to prepare the meals. They don't necessarily make a menu ahead of time, but instead, they take turns making what they know well. Mark said, "When I get to cook something I really like, I hook it up." And, I couldn't agree more. It's like the way my administration allows me the freedom to be creative and be a professional--"I hook it up" too.


We will go through 55 gallons of milk and 1,980 eggs before this trip ends with very little if anything going to waste. Bob said that they purposely choose foods that can be repurposed into the next meals without feeling like we're eating leftovers. I know this magic trick firsthand from home with my wife--It's ALWAYS the best thing that I've ever eaten.

Our rolling galley, where table tops have lips and everything is secured to the floor

These men make this journey bearable and even enjoyable for all of us. I will be focusing on the important science happening all around me on this ship, but these are the guys that play an important role as well for so many years of service. Thank you, Bob and Mark. I'm getting hungry just thinking about it. 

"I'm feeling a little woozy here."

The ship's crew laughed when I said that I was feeling the effects of the constant movement of the ship. In the calm seas that we had experienced, they knew that greater, more powerful surges were inevitable. And, they were right. Yesterday marked the first day of stronger winds and larger waves. The power of these waves amazes me. This ship is about the size of a football field and made of more steel than I could imagine, yet it moves back and forth like a cork on a line. It began to rock and roll quite violently yesterday afternoon and hasn't slowed down as of this morning.

I retired early while the veteran, Denis Costello (check out his blog at: socalcostello.blogspot.com), stayed up to write an entry. He is a teacher at sea as well, teaching high school chemistry in Houston, TX. This is his fourth research cruise, so I look to him for guidance in these foreign affairs.

The shower was the most challenging part, trying to keep my feet without slamming against the cold steel walls or the concrete floor. Ship showers are different than showers at home: you get wet; turn off the water; lather up; rinse off quickly; and get out. We conserve water.

The captain stated that the winds were 30 knots which is 34.5 mph but were localized, meaning that the waves were NOT as high as they could be (and most likely will be). This will be a challenge for sure. There aren't any breaks; even when it's calm, the deck moves. Performing experiments with this kind of movement will be interesting. Stay tuned for that update...

First steps: collect the water

I'm working with Dr. Mark Wells, our principal investigator from
the University of Maine here, collecting water samples at various depths

Denis and I wake up early to set up the filtration lab station (Can you find it in one of the pictures in the previous post?) and the CTD Rosette submersible (pictured left); CTD stands for conductivity, temperature and density. Through coordination with the ship's crew and science crew, the CTD is lowered to predetermined depths by the scientists. At each, the canister or bottle, called a Niskin, fires, closing the top and bottom to collect the water at that depth. There are 24 Niskin bottles, and we usually make 2 collections at each desired depth.

The large A-frame (pictured above the CTD) moves forward, along with a crane and winch, to place the submersible into the water. As the CTD returns to the surface, it captures water samples by releasing the line and snapping closed the Niskin bottle from a computer system in the main lab. In real time, data is collected on the conductivity, temperature, density, salinity and dissolved oxygen. These data points will be farther investigated in the labs on board.

Notice how each bottle is attached to a release line.

Rachel Vander Giessen, University of Washington and NOAA-PMEL, communicates to the crane operator and us outside on the deck when to stop the CTD and take samples. 

Retrieving the CTD with carbon fiber poles and lines,
"Res Tech" (resident technician), Keith ensures safety.

With the line attached, now we reel it in.

Denis and Andrew preparing filters for measuring chlorophyll. One of many tests to be done from this one CTD cast.

Multiple labs onboard; efficiency is everything!

Everyone on this vessel has a job and a station. There are labs set up all over, both inside and outside. Every lab is testing for different chemistries of the sea water; it truly is amazing to see it all in action. We begin the day very early, and it doesn't end until very late. We still have a collection to make tonight which means there will be data collection and analysis for hours afterwards. These are the labs that we have set up.

What do you think that we are testing at each one?

Comment below. I will be reporting about each one in the future.

My Station on day 1 

Main Lab area

Darkroom Lab

Lab on rear deck outside 

Outside deck, multiple sites

Rad Van mobile lab

The "Clean Room"

Auxiliary Lab

In

No turning back

After there days of hard labor, we have finally set off to sea. There's no turnin back now. I'm writing this now because once we leave this area, phone service ends and I will have to work with a slow connection to relay back to you. I have been posting Vines and tweeting pics, so check those out @t3joyner.

Well oiled machine

The ship runs off of two things: diesel fuel and coffee. There are crew members working 24 hours a day in shifts to keep the ship running smoothly. It's very structured and organized (I'm number 59, see above). It has to be. In case of emergency, we have to know where to go and what to do under each circumstance. Fortunately, the crew in charge is experienced, most that I have spoken with have been working with Scripps Institute ships for over 15 years. Obviously, they know they're job well and somehow even have patience for newbies like me.

"Look below deck on the starboard side in the forward compartment," says the Res Tech. 

"Yes sir," I respond confidently before turning in confusion. Then I go to someone else and ask them what all that means!

I'm learning a lot and have a lot to learn--exactly where I love to be.

Clean Room

This is where I have spent a LOT of my time. The Clean Room, or as I call it, The Bubble. One group of scientists will be testing samples for trace metals; therefore, there cannot be ANY metals in the air to contaminate the samples. That means that the room had to be scrubbed clean before building a wood frame and hanging plastic from ceiling to the floor with everything covered. We then had to clean the plastic twice and install two HEPA air filter systems to filter the air inside the room. I have spent nearly two days on this one task, building and cleaning, long before the first sample is even tested. I'm ready for a new job. The smell of plastic wrap on a rocking ship is not the way that I want to spend the next month! But, I do as I'm told and work hard to pull my weight because everyone around me is working hard too.

Building a bubble reminds me of the movie E.T.

1st impressions...

Simply amazing.  The massive ship with busy hands hard at work to set up is the scene. I was put to work right away which eases any apprehension as I like to work. I have a lot to learn but am with some truly patient professionals that are wiling to take the time to explain both the science and the ins and outs of preparing for life at sea. 

Here today, gone tomorrow.

I normally have closure with my students, field day, picnic at the park, and fun labs, but this time, I was rushed to close out for the year as I embarked on this incredible journey. It seems like a whirlwind of a way to end a year; I'm going to miss them and the last days of school.

With the mad rush to close out the classroom responsibilities, I spent far less time than I normally do with my family. My wife, Laura, has been in cosmotology school for most of the school year. This means that everyday I have had the new responsibility of getting them to sports practices and games, fed, bathed and tucked in. And, homework! I always forget that one! The respect, love and appreciation for my wife were already high, but now I KNOW firsthand what she has done for all of these years. It's amazing how you can long for something that requires so much work. Being away from them and my wife will be the biggest challenge that I face.

This is what I left this morning. Four sleeping beauties. 

I love my students...

As my last day with my 8th graders before, I leave on this trip, and they move on to various high schools, I am a bit saddened because it seems so sudden. Please feel free to interact and comment all along the way.

Times-Free Press: "Science at Sea"

How cool is this.. http://www.timesfreepress.com/news/2014/apr/28/science-sea-normal-park-teacher-spend-month-pacifi/

Digital Docents

Digital Docents

This is just a little taste of what we do in our classrooms. We create exhibit-worthy projects that demonstrate the students' understanding through art and other mediums. In this video, students are explaining what they have done and what they have learned. We created QR codes that take visitors to explanations by the students.