On a molecular level...

How well coordinated is this science research cruise?

Dr. Bill Cochlan, RTC-SFSU, SciChi

Our Chief Scientist and lead Principal Investigator, Dr. Bill Cochlan (RTC-SFSU) has put together an amazing team of scientists, students, and teachers with one overarching goal of analyzing the effects of oceanic acidification on the lipid (fats/oils) synthesis in the ocean's keystone organism, phytoplankton. As the foundation to the food web, phytoplankton, particularly diatoms, are extremely important to the quantity and quality of the entire web, leading to us the consumer. I will go more in-depth in a future post on Dr. Cochlan and his work, but until then, I will continue to focus on each of the specific experiments on board and the unique groups that delve into their particular research.

Joselynn Wallace, URI

Joselynn Wallace, URI and
Heather Richard, RTC-SFSU taking a break

Joselynn Wallace and Laura Filliger traveled from the University of Rhode Island to gather samples at sea that will make their way back to the labs back on the East coast. Their advisor, Dr. Bethany Jenkins, in their Ph.D. program, Integrative and Evolutionary Biology (IEB), was unable to attend this cruise because she had just spent 65 days at sea earlier this year. So, she called on her two top students: Joselynn in her third year, Laura in her first.

Laura Filliger, URI

Joselynn and Laura, fun on the fantail

Joselynn is the veteran. This is her third stint at sea, researching phytoplankton and comparing data from each new area of the globe--it's research that matches her expertise: microbiology.  Laura is the newby to this floating laboratory but is learning fast from Joselynn and seems right at home on the R/V Melville. Laura's learning curve is steep because she's sailing solo in November--three weeks to Antarctica! Together, they run their lab with precision and great care, all while keeping a positive attitude and adding to the "vibe" of this cohesive unit on board.

Their work is unique on board. They are the only ones researching the phytoplankton on a molecular level. All of the other focused experiments are physiological, which makes sense as a lab at sea. But, this goes to show the genius vision of the Chief Scientist, Dr. Cochlan; each of the labs are selected to shed new light on the ultimate mission of the research and the reason that it was funded. Like the layers of an onion, each separate experiment reveals more from another angle, allowing the scientists on board to compare data from different methods. This check and balance system pinpoints possible errors earlier as well as shedding new light, helping us to better understand what is exactly happening to the phytoplankton as the ocean's acidity level rises in nutrient-rich but iron impoverished areas--the direction of the global seas will one day be at our current rate.

left to right:
Hannah Glover, NOAA-PMEL
 Kit Angeloff, NOAA-PMEL
Laura Filliger, URI

These "gene jockeys," as Dr. Cochlan quips, are a valuable piece to the research puzzle. On a molecular level, Joselynn and Laura are researching a phytoplankton genus, Thalassiosira, that is found all over the earth's oceans from the sub-tropical to the polar regions and are "key players in all of those systems" (Wallace). By focusing on this universal genus with different species all over the world, they are able to compare the DNA and RNA from each of these communities. They use a filtering system similar to the one that Denis and I are using to extract chlorophyll to gather the biomass; then, they have the coolest step to any experiment on board. Literally. They use a dewar of liquid nitrogen, -321°F, -196°C, to flash freeze these samples, locking their genetic makeup until they are ready to extract the DNA and RNA in the lab back in Rhode Island.

Dewar of liquid nitrogen, LN2

According to these "gene jockeys," DNA differs from RNA in a similar way as a football team has starters and those on the bench, ready to come in and play when the conditions are right. The DNA is the whole team; the RNA is the actual players on the field. I think that they realized that a football analogy for me would be the best way to explain a very complex process; and it worked. Basically, DNA is all of the possible options, while RNA is that which is actually activated--the gene expression that is metabolically active. By comparing the RNA from different members of the same genus, they can see on a molecular level how the organism has adapted over generations to survive in different environments. Our focus here is on those that have been starved of sufficient iron (i.e. iron stressed). From Joselynn and Laura's current work and the past work of other molecular scientists, the RNA of coastal species is different than those in open ocean. Coastal regions are nutrient-rich; open ocean's have limited nutrients. The open-ocean species have adapted to become "iron scavengers," grabbing this necessary component for photosynthesis and nitrogen fixation from every source possible. Coastal species would not survive in the open waters. Diatoms' ability to scavenge iron from different sources may change with seawater pH.  Since they are the foundation of the marine food web, this information is critical for understanding how the ocean might respond to climate change and elevated carbon dioxide. All of this research is dependent on each other. I guess I could say that the chemistry of the science crew is just as important as the chemistry of the ocean. Joselynn, Laura, and the University of Rhode Island are integral part of this chemistry of thought and discovery. They will be able to compare their findings to those of the other teams onboard.

*I will be writing about Brian Bill, lead research associate for NOAA, and his taxonomy work of phytoplankton in an upcoming post with another on the complimentary work of Dr. Charles Trick and his team, using different methods to draw conclusions from the data independently before comparing.

Water Sampling: Go Flo

CTD in front, Go Flo in hand on the table

Everyday begins with a similar routine with workloads that depend on the amount of water that we are sampling. "It's like Groundhog Day," joked Dr. Wells this morning, "everyday seems like a repeat of the day before." I haven't felt quite like that yet since part of my job is to report something new to you everyday. I really enjoy the work of reporter on board; I get to know more about the people and the work that each person is doing which both are incredibly interesting to me.                                                                                                                                                                                               I'm on the team that deploys the CTD (see previous post and socalcostello.blogspot.com for more info on that method). We "cast" the CTD twice, once at depths up to 200 meters with samples taken throughout the water column and a second cast that only samples from 5 meters, since the majority of our study is from depths that utilize the sun's energy the most. These samples are collected by each group for their focused experiments. We have it down, well, to a science, running smoothly and working together as a unified team.                                                                                      

Keith Shadle, Res Tech with Dr. Mark Wells
University of Maine

After the CTD deployment, we need to collect water samples without any contact with the surface. These special samples are needed for the more sensitive work that is being done in the "Clean Room" (see previous post). The work done by Dr. Mark Wells (University of Maine) has to take every precaution not to contaminate the water sample with any outside metals, quite a feat on this steel vessel. Dr. Wells equated this work of past scientists that did not take such precautions, as "measuring flour particles in a lab located in a bakery." Data in the past in this area, especially in iron content, has been tainted by experimental procedures that have led to his practices today. I'm blown away by the care of every procedure and the ingenuity that is required to procure such clean samples. Before the sample ever enters the "clean room," it has to be collected.

We have to go below the surface because the tiny film that covers the ocean, and all bodies, has dust that includes particles of iron, the target of Dr. Wells' study. Therefore, we deploy from the winch a 200 plus pound weight 10 meters below the surface. We use the "A-frame" to bring the line in close enough to a heavy table that we move and bolt down everyday. Once the weight is deployed far below the surface, we attach the "Go Flo" to the line. Dr. Wells has to make sure that it securely fastened and that the spring-loaded ports are open before sending it down to 10 meters farther below the water's surface.

This is why it's called an "A-frame."

The way that this thing works is quite impressive. It's engineered to stay open until triggered to close. The increased pressure from the 10 meter depth pops a rubber cork, cocking a lever that is the key to capturing the untainted seawater. In order to trigger this lever, Dr. Charles Trick (Western University, Ontario) brings in the A-frame so that Dr. Wells can attach a heavy polycarbonate weight that is denser than the salty water below. He sends it down like a messenger to the Go Flo to slam its ports. Thirty liters of water is now trapped in the Go Flo, and zero outside contaminates are included. We reel it all in, detach the weight and Go Flo, and carry the treasured sample to the "Clean Room," before moving it all back until the next site. 

Dr. Charles Trick, Western University, Ontario
mans the A-frame controls.

I'm realizing daily more and more the extensive lengths that we have to go to in order to assure that every precaution is taken--the integrity of the data depends on it. These principal investigators take their job and their work seriously to present the best indication of the health of the ocean. It is an incredibly big responsibility with global impacts if only we'd listen to what they have to say. It is not their opinions; it is the data. It is the evidence that supports a claim that effects us all. The food chain begins with the phytoplankton, healthy phytoplankton, healthy food chain. 

Between 40% to 60% of all of the earth's oxygen comes from these as well; that's more than any other source (Cochlan).   

Lifetimes are spent in this study, "taking the pulse of the ocean," as Dr. Cochlan, RTC-SFSU puts it. with the greatest care and precision.

Shouldn't we listen as we get the prognosis of its health?

Chief Alex Rodriquez inspects the controls with Dr. Wells.

"A-frame out"

Fitness at Sea: "Steel Beach"

Exercise room with weights secured for travel

At home in Chattanooga, Tennessee, I stay pretty active by getting up early everyday and driving across town to meet up with about 30 other guys, fighting gravity and age by doing some phenomenal workouts. It's called the RRL or Fitness Truth, and there's a daily blog and Facebook page that describes it better than I can. What I do know is that it's a brotherhood of guys from every walk of life, and one that I miss here at sea.                                     

Wood chucks have been crafted to keep the bar from rolling as the ship continually rocks.

Crew member, Paul Martin, OS (left);
Hannah Glover, UW, NOAA-PMEL

I have tried to work around the busy schedule of sampling and analyzing, but it has been difficult between inconsistent hours, the continuously moving ship, and the results of motion on the body--it's physically exhausting just to stand and do lab work because of the constant grappling with gravity to regain balance. There are plenty of workouts that are options while traveling, so I was prepared to do a lot of these. Surprisingly, I didn't have to break open a "deck of cards" workout or resort to repetitive bodyweight movements. There's a gym on board! Well, it's more of a closet with weights, bars, and fitness paraphernalia, but it's perfect for life on the ship. I was even more pleasantly surprised to find a pull-up bar, several stationary bikes tucked throughout the lower and upper decks, and even a rower (Concept 2), which is my favorite cardio on board.

"Steel Beach"
deck 50ft above sea level, pull-up bar
in the background

Paul Martin in action during a fire drill

Our science crew schedule is variable with one day being completely slammed for 14+ hours and the next relatively chill after lunch, so our girls and guys workout when they can. Hannah and others hit the cardio machines before everyone wakes up, while Dr. Wells has been spotted on the rower before dinner.

Crew: Paul, Keith and Heather

"A-Rod" Alex Rodriguez, 54,
Chief Engineer and lifetime salty sailor 

Tom Brown, Oiler

In my short time onboard, I have not only made quick friends for life with the fellow scientists, but I have also made friends with the ship's amazing crew. There's a "vibe" as Tom Brown, 25, from San Diego put it that makes this ship special. He has two other brothers on Scripps' sister ships (and at one time there were four brothers all working for Scripps). Tom comes from several generations of sailors and knew that he wanted to work at sea early on. At 25, he's now a permanent employee and engineer, working his way up by hard work and experience at sea. Tom's a former football player at Santana High; 6' 1", 230 pounds, he was an ideal tight end. Now, he continues to train. Every morning at 0600 (6am), he views his workouts as "his coffee for the day" with the lifetime sailor, Chief Engineer, Alex Rodriguez.

"A-Rod" or "Chief" as he's known on board is 54 and still trains daily. After graduating from high school in Missouri, Chief made his way back to sea. From his early teens, he has spent time on ships as either a fisherman or engineer. He has a college degree in Fisheries Biology from the University of Alaska where he spent most of his saltwater career. Now, he's the head engineer on this vessel and others in the fleet.

Keith Shadle talking with Rachel Vander Giessen, NOAA-PMEL

Our "Res Tech," residence technician, Keith Shadle, 33, and new shipmate, Paul Martin, 25, choose the afternoons instead. Everyday at 1600 (4pm), they hit "Steel Beach" as they call it. They spend the better part of an hour before dinner is served lifting weights and mixing in different movements, all on the rocking deck. Heather Galiher, a young 2nd mate (like an assistant captain, piloting the ship, charting the course, etc.), also finds time to workout during this hour, doing her own version of pilates, yoga, and core exercises. 

Everyday, the science team depends on Keith. As the Res Tech, he is the liaison between the ship's crew and the science team. He's available 24 hours a day for emergencies and keeps us up and running in the lab. His first priority is our safety. Everyday as we deploy the CTD, the Go Flo (blog upcoming), and any of the other actions that require us to sample the water, he is there to instruct us on the proper protocol and keep us from doing anything that would risk anyone going overboard or being hit with anything overhead. We don lifevests and construction helmets and use lines to guide the devices into the water safely. Keith has a commanding presence yet is patient as he has to teach every new group how to run the machines, tie the knots, hook the CTD, bolt everything to the deck, and much more. 

Retrieving the CTD with Res Tech, Keith Shadle in control

Despite his seriousness of purpose while doing his job, he also shows an interest and aptitude for the science that we are doing--and no wonder, he has a degree in marine biology! After graduating from the University of Maine (the same school as our own co-PI, Dr. Mark Wells, coincidently), he worked as a biologist in Alaska on fishing boats. After four years of that tough work, he applied to Scripps and has been working here ever since. Now 6 plus years later, this kid from Indiana has seen some exotic places--working out on the deck with the Philippines' crystal clear water and white sandy beaches in sight. The greatest challenges that he faces, however, are the language barriers that occur when working with foreign scientists and the time at sea. This is his third 30 day research cruise since October, and it can take its toll. If there is any weariness, we wouldn't know it. He has been on point everyday, professional with an engaging personality. 

Fitness at sea comes in a variety of different methods all throughout the day. I'm just glad to be around so many that make time for it as often as possible. The attitude of the ship is positive and fun; and I guarantee that regular exercise plays a huge role in that "vibe." I know that it does for me.

In case anyone is wondering here is my workout from today:

5 rounds with 3 minute rest between each round,

20 pull-ups

30 pushups

40 situps 

50 air squats

*The workout is called, "Barbara." Comment if you want the times. :-)  

Watch my hand shake when the fog horn blows!

Ocean Acidification: Batch 1 Sampling

 Near incubator, control group; far incubator, experimental group.

 All the principal investigators and super techs gather
for the big day--the results will be exciting, either way.

 Sampling: acid wash, rinse with ultrapure water three times,
rinse with sample three times (note: don't forget the threads!),
then fill your container to the neck, no more, no less.

Dr. Cochlan, lead PI, knows best; Chris Ikeda assists.

The two carboys (large bottles) on the ground are limiting the trace metals
 that are being analyzed in depth in the "Clean Room".
The process for collecting that water without contamination is incredible in itself.

Today’s the big day! Months of planning lead up to this experiment. We analyze samples from our most focused experiment of our fieldwork: the incubators. From the tireless work of Chris with his pH meter mash-up, Julian’s inorganic nutrient auto-analyzer, and so many on board along with the landward labs leading up to this research cruise, the incubators outside on the ship’s fantail have been monitored and the phytoplankton have been growing as expected. “It’s just like grass, it grows to a certain point until it runs out of nutrients,” Dr. Mark Wells, University of Maine, co-PI, explains. These incubators have been running for days with seawater and all of the organisms within from the first site. Methodically, each container within the incubator has been stressed in different ways as we may see naturally. The independent variable in this experiment has been the amount of available nutrients: nitrates, phosphates, silicates and iron. 

Limiting iron availability of a sample while modifying the pH
with infused carbon dioxide (CO2), just as we would see naturally.

One of seven pH meters used to monitor the acidity of the sample.
When the meter reads above 7.6,
CO2 is pumped through the lines to lower the pH back to 7.6.

Each line is fed from the carboys in the incubator to the computer
for recording and monitoring by Chris Ikeda (RTC-SFSU).

There are two incubators. One is the control; and the other is experimental. The control is seawater sampled while at sea. The experimental has same seawater with the pH controlled through a simulation of the natural process: by infusing CO₂ to lower the pH. Both are introduced to the same stressors at the same rate, limiting all undesired variables—a sign of a solid experiment.

Pressure gauges for each carbon dioxide tank.

With the introduction of more CO2 in the atmosphere, the acidity level of the ocean changes. "The chemistry of the ocean is dependent on the chemistry of the atmosphere" (Cochlan). Therefore, more carbon dioxide emissions in the atmosphere, more dissolved carbon dioxide in the oceans. Carbon dioxide in the ocean, a necessary component for plant life, turns to carbonic acid, slowly lowering the pH (raising the acid levels of the seas). The 100-year projection is a pH of 7.8 by 2100, causing problems with shell-bearing organisms and much more that is still unknown. This is ocean acidification.

We have intentionally targeted areas of upwelling along the Pacific Northwest because these are "sentinel sites that indicate the future" (lead PI, Cochlan, RTC-SFSU). There are two currents: surface water and deep water. Surface water currents (the first 100m of water) travel the earth’s surface in roughly five years, driven by the winds. Deep water currents (100m-4000⁺m), on the other hand, move slowly, taking 1000 to 1400 years to circulate. Oceanic deep water conveyors in the intermittent layer does resurface every 50-100 years in upwelling zones; therefore, by sampling from these zones, we are able to observe the future chemistry of the ocean. Unlike the surface water that reaches equilibrium with the atmosphere through interactive processes, the deep water continues to become more acidic at faster rate because the CO₂ is trapped under the blanket of surface water. The water sampled this week at our first site was nutrient rich, low in iron, and had a pH of 7.6. This water hasn't seen light since pre-industrial revolution—an indication of the ocean’s future normal in 20 to 50 years, not 100 as previously projected, according to co-PI, Charlie Trick, Western University. There is still a long way to go before making any substantial claims, but it does perk great interest. Upwelled zones naturally have a lower pH, but this may be an indication of the acidity level in the future. 

And, this is why we are experimenting: we simply want to sample cleanly, analyze honestly, and use methods in experiments that model the future accurately. The end result will be a presentation of the results. One of the mantras of the PI's onboard is that of Joe Friday from Dragnet, "Just the facts, ma'am." These men of integrity are prepared to title their peer-reviewed scientific paper as their results support their hypothesis or their results do not support their hypothesis. Either way it is one step closer to understanding the current path of our future and the steps that we can take to change that path. This is science. And, I would never know this without this experience first-hand.