Join the Journey!

Follow along as the researchers aboard Scripps Institution of Oceanography research vessel Melville conduct scientific experiments ranging from seafloor explorations to open ocean studies off the coast of San Diego, Calif. 

This blog, written primarily by the student scientists working at sea, will keep you updated on the science behind the adventure, and why it matters to you.

Although the artist on board on July's cruise will be away, her unique perspective can still be shared here.

We encourage you to participate in the San Diego Coastal Expedition by sharing your thoughts via Facebook and Twitter (#sdcoastex) and asking questions along the way!

Latest Blog Posts

  • Mission Accomplished, but SDCoastEx continues... Well, December 21 has come and gone and the world continues to spin1, so I guess the time has finally come to write a cruise wrap-up blog. This ...
    Posted Dec 26, 2012, 11:27 AM by Benjamin Grupe
  • Full Disclosure: Q & A with the world! Throughout the cruise, we received several questions from you via the Front Page of our website.  Cruise participant and Scripps graduate student, Emily Kelly, took the time to investigate the ...
    Posted Dec 19, 2012, 11:23 PM by Benjamin Grupe
  • College sports and Scripps science: Formula for a winning team As an avid sports fan, I still envy the collegiate and professional athletes that reach the highlight reel on Sportscenter and I roar when my team comes from behind to ...
    Posted Dec 17, 2012, 12:26 PM by Kirk Sato
  • Fifty Shades of Fantastic - Thoughts from the faculty mentor By Lisa Levin, Professor at Scripps Institution of Oceanography     All UC ship-funded student cruises are led by the students, but are required to have a faculty mentor aboard. That ...
    Posted Dec 15, 2012, 4:38 PM by Kirk Sato
  • Answers From the Deep - 7th Grade Life Science Q & A By Megan Grupe    My goals coming aboard the ship were quite different from many of the scientists aboard.  I am currently teaching 7th Grade Life Science at Granger Junior ...
    Posted Dec 14, 2012, 7:53 PM by Benjamin Grupe
  • Searching for anaerobic answers in the OMZ After a successful trip last summer, I am very happy to be on board the Melville again for my sophomore SIO cruise. For me, one of the best aspects of ...
    Posted Dec 17, 2012, 12:40 AM by Kirk Sato
  • Hungry for Methanogenic Microbes     As a member of the Seep Team, I help take samples of the seafloor mud at locations where methane gas concentrations are relatively high (in some places, you can actually ...
    Posted Dec 12, 2012, 10:45 PM by Kirk Sato
  • My scientific community: a generational responsibility      What if I told you that the funny, chaotic, selfless, twenty and thirty-somethings on this ship are the next generation of ocean and environmental scientists?  By all respects, they ...
    Posted Dec 11, 2012, 9:02 PM by Kirk Sato
  • Trawling with Zombies: Deep-Sea Creatures Up Close and Personal     Stepping onto the ship early Saturday morning was very surreal.  As a coastal ecologist, there has never been a reason for me to get on a giant research vessel; and ...
    Posted Dec 11, 2012, 12:12 PM by Kirk Sato
  • Economic implications of evolutionary and ecological interactions             From an aesthetic perspective, black shales are not the prettiest rock. They don’t form soaring spires and walls like the granite in Yosemite, or the colorful, variegated landscape like ...
    Posted Dec 10, 2012, 10:51 PM by Kirk Sato
  • Buenas Dias Amigos, desde el Melville! El San Diego Costera Expedición (Translated in English below)    Es una gran experiencia participar en un crucero organizado por Scripps y estar a bordo del R/V Melville, compartiendo actividades ...
    Posted Dec 10, 2012, 6:14 AM by Kirk Sato
  • Backyard Cruises What motivated us to take the initiative to put these cruises together? Many of us had been discussing the option to apply for ship time via UC Ship Funds for ...
    Posted Dec 8, 2012, 10:12 PM by Kirk Sato
  • Korean oceanographer, Dr. SungHyun Nam, helps lead SDCoastEx (Scroll down for English translation)학생주도의 다학제간 샌디에고 지역 연안탐사인 SDCoastEx 에 참가하면서 지난 1998년 이후로 현재까지 15년 동안 총 50회가 넘는 해상실험에 참여해오면서 각종 연구선이나 작은 ...
    Posted Dec 7, 2012, 10:34 PM by Kirk Sato
  • Any Way You Add It Up, SDCoastEx I is a Smashing Success! Tuesday afternoon marked the triumphant return of San Diego Coastal Expedition’s (SDCoastEx) science party aboard the R/V Melville to Scripps’ marine facility in San Diego Bay. Well, perhaps ...
    Posted Jul 13, 2012, 1:36 PM by Benjamin Grupe
  • The Romance of Oceanography For me, oceanography is a place for romantics that hope to change the world with colossal discovery and reach out to a vast and foreign ocean. I think every scientist ...
    Posted Jul 13, 2012, 9:11 AM by Shannon Bresnahan
Showing posts 1 - 15 of 27. View more »

Mission Accomplished, but SDCoastEx continues...

posted Dec 24, 2012, 6:14 PM by Benjamin Grupe   [ updated Dec 26, 2012, 11:27 AM ]

Well, December 21 has come and gone and the world continues to spin1, so I guess the time has finally come to write a cruise wrap-up blog. This has been such a successful expedition on so many levels, it is hard for me to know where to begin.

All of our primary science objectives were accomplished. This alone made our week at sea a success worthy of celebration! Originally, we were scheduled to have eleven days on the R/V Melville, but after a series of rescheduled and shuffled cruises (other than our own), we ended up with just eight days. We set ambitious goals for this reduced time period, including revisiting almost all our CTD and multicore stations from July, more trawls and ROV dives than during our first cruise, and exploration of the newly discovered methane seep.

We were a science party that included twenty-four graduate students (eighteen from Scripps), and at least half of us will incorporate data from this cruise into our dissertations. We are chemists and ecologists, have thesis topics ranging from fault lines to squid eggs, and represent five of the eight curricular groups at Scripps. In short, much of our science was improved out of a willingness to work cooperatively and an ability to lend each other our own expertise.

Maintaining constant scientific operations, twenty-four hours a day, was possible because members of the shelf team helped Amanda's midwater team deploy nets; because CTD team members were willing to work the graveyard shift each night; because Sarah, Kate, Paul, and others would speedily remove tubes of mud from the multicorer, replacing them with empty tubes for rapid redeployment. Most of all, we required a highly capable captain, crew, and resident technicians, always willing to do whatever it took to achieve the best scientific results.

Gabe Kooperman, one of the many graduate students that took part in SDCoastEx, attends to the CTD before one of its final deployments. Photo by Emily Kelly.

From the outset of our expedition, we have tried to emphasize outreach and education, and that continued with blogs, online picture sharing, skype conversations with a classroom, and volunteer opportunities on our science team. Many of us are driven not only to be good scientists, but to find new ways of sharing our science with other future scientists and with engaged members of the public like you. We hope that our blogs have increased your interest in the ocean environment we all share and depend on. We hope that our connections to local schools have somewhere excited a sixth grader to consider a career as a marine biologist. We hope that the undergraduates that have joined our expedition continue on in their education, passionate to discover answers to mysteries that lie beneath the surface.

From a personal standpoint, as my first opportunity to be a chief scientist, this was a different cruise experience than what I am used to. Sleep depravation at sea was not a new experience. (Just ask my lab mates.) But the need for constant evaluation of our progress, clear vocal and written communication with captain, crew, and scientists, and frequent decision-making kept my mind occupied at most waking moments. It was a relief each time a piece of equipment came back on deck safely, and I probably spent too much time fretting about the schedule and whether we had saved enough time to visit all our stations. But really, being surrounded by so many amazing scientists, eager volunteers, and more-than-capable crew members and techs made my job easy. 

If my role was similar to a coach on a sports team 2, as Kirk wrote, then it is because I was able to stand back on the sidelines, putting people in the right position to be able to make plays. Superstar athletes can make even an average coach look great, and I was lucky to have a bunch of superstar scientists on my team.

Chief scientist Ben Grupe gets a little advice from seasoned chief sci and advisor, Lisa Levin. Photo by Kirk Sato.


This week in the journal Science, the ten biggest science stories of the year were recapped. Of course, the year’s biggest scientific breakthrough was the discovery of the Higgs boson, the elementary particle that allows all physical matter to have mass. This amazing scientific discovery confirms the standard model of particle physics, represents the culmination of the careers of hundreds, if not thousands, of physicists, and generally is regarded as “kind of a big deal”.

In the editorial, physicist Pierre Hohenberg is quoted making a distinction between what he calls “science” (with a lowercase “s”) and “Science” (with an uppercase “S”).3 In his view, Science refers to the big breakthroughs, like the Higgs boson, that make it into the media, that are the product of scientific activity and the advances of many, that represent monumental leaps forward in our understanding of the workings of the natural world. Little-”s” science is ongoing, plodding along, is not always glorious, and is filled with small steps forward that eventually lead to Science, which Hohenberg describes as “universal and free from contradiction.”

Our San Diego Coastal Expedition, you may be surprised to learn, will not be listed among the top ten scientific stories of 2012. If there were such a thing as the “top ten oceanographic expeditions of 2012”, perhaps we’d merit consideration, but for the most part our cruise will stay out of the media’s limelight. As much as we would like to convince ourselves of the universal importance of our individual research accomplishments, they have no direct bearing or immediate impact on 99.9999% of the world’s citizens.

However, “Science emerges from science”, and the work we have done on our two SDCoastEx cruises will add to collective knowledge of our oceans, especially off the coast of San Diego. Who knows, perhaps data or samples that we have gathered will someday contribute to a more complete understanding of how seafloor communities respond to low oxygen, the decline of ocean pH, or global inventories of methane at seeps. Someday, part of our work may contribute to a leap forward in Science. 

But in the meantime, we will continue our work as graduate students and professors, researchers and teachers, twenty-somethings and fifty-somethings. Over the coming months and years, as our scientific findings emerge, we will have the opportunity to share what we have learned with you. We thank you for following us this far, and wish you all a happy holidays and an exciting 2013 full of natural wonder and scientific endeavors.

As the Melville comes into port, the scientists of the San Diego Coastal Expedition can be proud of a job well done.
As the Melville prepares to dock, the scientists of SDCoastEx can be proud of a job well done! Photo by Kirk Sato.



1 I hope the failure of the Mayan Apocalypse has not been a surprise or disappointment to you, as it was to these disrespectful tourists or this lady

2 Sato, K. “College sports and Scripps science: Formula for a winning team.” San Diego Coastal Expedition website, 16 December 2012. 

3 Alberts, B. “The Breakthroughs of 2012.” Science 338 (6114): 1511,

Full Disclosure: Q & A with the world!

posted Dec 19, 2012, 8:56 PM by Kirk Sato   [ updated Dec 19, 2012, 11:23 PM by Benjamin Grupe ]

Throughout the cruise, we received several questions from you via the Front Page of our website.  

Cruise participant and Scripps graduate student, Emily Kelly, took the time to investigate the answers to your questions and here they are!  

Thanks for participating this week!

What was the most exciting find on the expedition?

The great thing about research expeditions is that there are many scientists all working on many different types of research at the same time.  Some of the exciting finds have been pulling up lots of urchins from 300m, seeing squid using the ROV, and finding worms in deep ocean sediments.  I have been working on the team analyzing water chemistry and we have been able to examine the different layers of water in the ocean by collecting samples at many depths up to 1200m.


What has been your favorite discovery since you started researching?

My favorite discovery on this research expedition so far has been seeing siphonophores from the ROV camera.  Siphonophores are related to jellyfish and corals. They are colonies of jelly-like organisms that float through the water eating little bits of food that drift by them. 

What are you doing over there?

We are a group of scientists doing research.  Our work on this expedition is focused on researching cold methane seeps near San Diego and assessing the sensitivity of San Diego's marine communities to climate change.  We have five different research teams that work in close collaboration with each other.  I am working with the chemists and oceanographers, and the CTD is our main research tool since it allows us to measure and collect water from many different depths.  However, the OMZ team uses the multicore to retrieve mud samples from which they measure chemical compounds, bacteria, and microscopic animals. And the shelf and midwater teams are using Scripps' ROV to observe larger animals yet.


Is it hard to find the rocks and sediments under ground with the camera?

Great question!  It is challenging to look at the ocean floor from above the water on the boat.  Some of the scientists on board use sound waves coming from sensors on the bottom of the ship to help them see the ocean floor like the way bats can use sound waves to see in the dark.  We also have a Remotely Operated Vehicle (ROV) on board that has a camera mounted to it, and we can drive that ROV from the ship to see what is below us.  We also use tools to sample below us and bring those samples up on the ship's deck so we can look at what's below us more closely.

Do you have a sonar?

We do have a sonar mounted on the bottom of the ship.  This allows us to see what the ocean floor looks like below us.


What fish do you see in the robot?

From the ROV we can see a lot of different types of fish!  Hagfish, rockfish, and ratfish to name just a few.  We've also seen jellyfish (which aren't actually fish at all), siphonophores, squid, clams, brittle stars, and more!

How far do you guys go out on this expedition of yours?

We've traveled 75 kilometers offshore of San Diego, CA, but we've sampled within eyeshot of the coastline!

How deep is the ocean?

On average the ocean is a little bit over 4000 meters (>13,000 feet) deep but the deepest part of the ocean in the Mariana Trench is almost 11,000 meters (>36,000 feet) deep!  The deepest part of the ocean we're sampling on this expedition is about 1200 meters (about 3/4 of a mile). 


What kind of animals do you find?

We've found lots of different types of fish and invertebrates, and some scientists on the ship even use different ways of studying or seeing microbes. Check out some of the posted photos to see some of the critters we have found!

What is methane?

Methane is a gas.  You might be familiar with it as a major component of "natural gas" that might heat your stove or home.  We are interested in methane because it is one of the major fluids that comes out of cold seeps on the ocean floor.  Some microbes can produce energy using methane, and cold seeps have specially adapted communities that depend on this microbial food and are surrounded by chemicals that are toxic to us, such as sulfide. 

Are the gases harmful?

If you were exposed to pure methane, you would not want to breathe it in. However, you cannot smell methane, so utility companies add a smelly chemical to natural gas so that if there is a dangerous leak in your house, you will detect it and fix the problem. In a larger sense, methane is a greenhouse gas, so when it is released in large amounts it allows the atmosphere to trap heat, resulting in a warmer earth. Since the methane coming out of seeps is deep underwater, it is not directly harmful to a human, but some scientists are concerned that the amount of methane being released could increase as the oceans get warmer. That would be harmful to all of us.


If you get sick on the ship, what happens?

Great question!  I get seasick very easily so I take some medicine to help me from getting sick.  If you catch a cold or get another type of illness, you can get treated on the ship very easily, because there is always an officer well-trained in first aid techniques.  Sometimes ships may have to return to port if a scientist or crew member is seriously hurt or ill.


Is it really cold over there in the ocean?

It can be cold out here for sure!  Some days get sunny and warm, but at night it is almost always around 50 or 55 degrees fahrenheit. As I write this blog, I am currently wearing a hat and two jackets to stay warm while we bring in the CTD at 3:30 am. (That's right, someone has to work the red-eye shift!)

Did you find a lot of sea animals?

Yes!!! We found a bunch of animals, from different species of fish to jellyfish to crabs to siphonophores to squid to clams to brittle stars and more! Here is a picture of an Pacific electric ray!

Who makes a globe that shows underwater features like trenches and fault lines and plate boundaries as we know them?

Google ocean is a great resource! also has some great lessons on plate tectonics and other topics.  Enjoy!

College sports and Scripps science: Formula for a winning team

posted Dec 16, 2012, 10:30 AM by Kirk Sato   [ updated Dec 17, 2012, 12:26 PM ]

As an avid sports fan, I still envy the collegiate and professional athletes that reach the highlight reel on Sportscenter and I roar when my team comes from behind to win a game – it’s just who I was just brought up to be. 20 years ago, the 7-year-old me would’ve told you that I wanted to be a professional football player like wide receiver, Jerry Rice, #80 for the San Francisco 49ers, but instead, I chose another route in life.  I became involved in another field - a field of science that has led me on a different, but equally exciting journey. As it turns out, oceanography and football have a lot in common.  Despite my love for the game, my love for adventure, my earnest need to explore, and my longing for discovery took precedent. The same passion that drives any athlete to train and execute under pressure is analogous to the drive that pushes the scientists on board this ship.    

Turn on sports radio, listen to any interview with a college football player after a victory or after a great season, and you’ll hear them talk about their team.  Not just the players on the field, but their coaches, their trainers, and fans.  On this ship, we have a team that lives together, stays up late together, stands out in the rain together, laughs together, watches the sunset together, and on, December 15th, 2012, we grieved together.  We grieved for the students and victims of Sandy Hook Elementary School.

It is unfathomable at this moment to comprehend this tragedy because I grew up being able to follow my dreams and I am currently living out one of them. I am a part of a team of scientists that some might refer to as a “close knit group of colleagues,” or “early career scientists working on their own projects in a common area”, but I like to think of us as an All-Star football team; the same football team that you, your kids, or your friends go to watch on the weekend. Let me explain.

         1.    We have a coach who we all look to for direction, our Chief Scientist.  In July and for the first leg of this cruise, my labmate, Christina Frieder showed tremendous composure under high pressure situations and managed our team like Barry Switzer. Our other Chief Sci, Ben Grupe looks like he’s been to a few bowl games, towering over you like Bret Bielema.


        2.    We have an extremely supportive coaching staff, the offensive coordinators, if you will. But on the Melville, we call them the crew – the ship’s captain, the deckhands, the res-techs, the engineers, the shipmates. They help put us in a position to execute the science that we spend so much time preparing for.


        3.    We have our trainers - our advisors, our professors, our colleagues – who help us prepare and tackle the most intimidating research questions in the sea. 


        4.    Our offensive squad is made of up of All-Star caliber people - scientists, teachers, daughters, brothers, parents, divers, explorers, and naturalists; people who discover new ecosystems, people who observe natural patterns in the deep-sea and people who inspire the youth to pursue science.

        5.    We have a defense in our CTD team that some would say, “win Championships”. Our Defense keeps us in the game - they pick up our Offense when the weather is too rough for the ROV (remotely operated vehicle) to work. 


        6.    We even have Dr. Lisa Levin in the game, who would undoubtedly receive some votes for the “Deep-Sea Hall of Fame”.  She’s not just sitting on the sidelines, but is actively involved with research and mentoring.


And then there are our fans - You! If you’re reading this, the San Diego Coastal Expedition is playing for you. We are studying the ocean because we want to learn from it, to better understand it, so we can pass down this information to future generations.  We are using the ROV, multicore, and otter trawl to peer into the vast unknown of the deep-sea, and we’re finding some amazing organisms.  We’ve seen dogface witch eels, piglet squid, giant bacteria, among many others.  We are also investigating the ocean’s chemistry because, like the weather and climate, the ocean also changes. We have tracked the seasonal changes of physical features in our own backyard, like the California Undercurrent, and we have begun to ask questions like, how does this affect the biological organisms that live there?

             We returned to port yesterday after a week of sleep deprivation, hard work, and exciting results.  Next, we’ll go our separate ways, back to our offices to analyze data, write papers, and give talks, but we’ll also write proposals to continue this work, we'll go on answering your questions, and we'll keep posting photos and blogs.  We have accomplished what we set out to do as far as our research objectives go, but we will not quit following our dreams and inspiring young people to follow theirs of exploring the ocean.  


-  Kirk Sato, PhD Student at Scripps Institution of Oceanography,  Alumnus of the Burton Valley Elementary Bobcats

Fifty Shades of Fantastic - Thoughts from the faculty mentor

posted Dec 15, 2012, 4:37 PM by Kirk Sato   [ updated Dec 15, 2012, 4:38 PM ]

By Lisa Levin, Professor at Scripps Institution of Oceanography

    All UC ship-funded student cruises are led by the students, but are required to have a faculty mentor aboard. That is me.  The faculty mentor is around to give advice if needed, but not run the show.  Leading a cruise is a huge job.  It requires proposal preparation, pre-cruise logistical planning, organizing and loading gear, chemicals and equipment, and developing a thorough, but adaptive work schedule that accounts for every minute of a 24-hour day. The students on the San Diego Coastal Expedition, and Chief Scientists Ben Grupe and Christina Frieder, have done a fantastic job.  The whole team works tirelessly, with high spirits, tremendous flexibility and little sleep. Really they do not need much mentoring; they operate professionally and with considerable experience.  I serve them best as an extra pair of hands.

    This means I can enjoy the cruise in ways I can’t when leading them myself (or when I’m home teaching and attending meetings).  I can play with (I mean section and process) mud cores, spend hours sorting animals under the microscope, photograph them and look through keys to identify them.  I can eat more leisurely meals, and pop in to see what the different research groups are doing. 

    Five of my graduate students are on board… probably a record for the Levin lab, which participates in many seagoing expeditions, but often with only a subset of its students at one time. This is great fun – it allows the students to interact with each other, with students from other disciplines and with me in ways we can’t do at home in Sverdrup Hall. It also gives me a chance to see what they see, watch their new ideas emerge (as they always do when we see and handle real organisms) and for the younger students, help them formulate these ideas as thesis questions. 

    Despite the proximity of the cruise study area to Scripps, surprisingly few researchers have focused on the biology of the sea floor. The ROV (remotely operated vehicle) operations have been superb and have revealed dramatic zonation of different animal species on the upper slope. The ROV visit to the newly discovered methane seep site exceeded all expectation.  Initially there were questions about whether the ROV tether was long enough to reach the bottom there.  It was!  What a sight!  This visit ushers SIO into a new era – one in which SIO scientists can study chemosynthetic ecosystems (like seeps and vents) with their own facilities, and nearby Scripps.  All such work in the past has required use of deep submergence facilities from Woods Hole, MBARI or other from other countries.

    With the new seep only a 4 or 5-hour steam from MarFac – there is great potential for long-term observations, new teaching opportunities, and use of manipulative experiments.  Much credit goes to Bruce Appelgate, the SIO Marine Operations group, and the dedicated techs who have worked so hard to get the ROV functional.

So… here are my fifty shades – of what the students are accomplishing with UC Ship funds.

  • Access to top notch, ocean class ship operations
  • Opportunity to do great science
  • Learning to plan seagoing research – and be flexible when things change
  • Developing  leadership  skills  - how to make most of the people happy most of the time
  • Creating new collaborations
  • Bonding and new friendship arising from close quarters, long hours and common goals
  • Sharing in the exhilaration of discovery – there are endless mysteries to unfold
  • Time management – how to make the most of ship time, which costs a heap!
  • Organization skills – with endless amounts of data generated each day  there is a need to keep it all accessible and organized.
  • Sensitivity – with many putting in long long hours (including the res techs and ROV staff) schedules need to accommodate some sleep
  • Lending a hand… nearly every operations team gets some help from the others
  • Communication skills – with blogs, press releases, interviews and word of mouth the students have become SIO’s best communicators
  • Working with donors… donors at sea provides a new route to funding student research, and a chance to reach out to a broader community
  • Creating a SIO legacy… great teamwork at sea sets the scene for future student collaborative programs
  • Science is fun!  Fearsome, fantastic science goes hand in hand with a great time and lots of laughs.

 Did I say fifty???? I meant fifteen.   J

Answers From the Deep - 7th Grade Life Science Q & A

posted Dec 14, 2012, 7:53 PM by Benjamin Grupe

By Megan Grupe

    My goals coming aboard the ship were quite different from many of the scientists aboard.  I am currently teaching 7th Grade Life Science at Granger Junior High (National City) and wanted to use this experience to learn and bring back ocean science to my students.  Most importantly, I wanted to peak their interest in the deep sea, a quite unexplored (and untaught) biome in the ocean. Before leaving on this trip I asked my students to come up with questions that they would have for an ocean scientist. The science crew on the Melville were more than happy to answer these questions for you and my students.  

Question 1:  What do you like about your job as an ocean scientist?

Lisa: Overall, this job is intellectually creative, which makes work fun, challenging, and motivating, allowing me to be able to explore and ask interesting questions.  As a deep-sea or open ocean scientist, you get to travel around the world and have many opportunities to work as a team with other researchers.  There is always something exciting, interesting, and new to discover, therefore the job is hardly ever boring.  Most importantly, this job is a job of constant learning and continues to remind me that we never know everything – we must always ask questions.

Question 2: I’m scared of the ocean, how do I change that?

David: Believe it or not, I’m still afraid of the ocean a little too, but I study it!  There is so much water out there and we do not know everything that is below. My advice to you is to continue learning about the ocean and experience it.  The more critically informed you are, the more prepared you will be to embrace the ocean.

Question 3: How do you like working on a ship?

 For some, this is their first time being on a research ship:

Emily: What is fun about being on a research ship is that there are many ocean scientists asking different questions about similar parts of the same ecosystems.  This is fascinating to be a part of!

For some, this is not their first time on a research vessel:

Ally: I love being able to work with people in pursuit of quality science; it is almost like a “Summer Camp for Scientists”, but with a lot of hard work of course.

Kirk: People! People from all over the world and/or country are here representing institutions and science all in one place. This is exhilarating!  We do not always speak the same first language, but we are able to communicate the common language of science. 

The back deck of the Melville is where lots of the action happens. The A-frame guides the multicorer (pyramid-shaped frame) to collect mud from the seafloor, and also is used to pull nets that sample animals on the bottom or in the midwater.

Question 4. How long do you have to go to school to become an ocean scientist?

There is a large range on the boat.  Most all have gone or will have gone to about 10 years of college after high school.  This includes a Bachelors degree and a Ph.D.  Some have even completed a Masters degree, which takes an additional 2 years to complete.

Question 5: What things do you do as an ocean scientist on the boat?

CTD Team: Collects water from different depths in the ocean, and measures carbon dioxide and oxygen to understand how marine life and humans affect the oceans chemistry.

Methane Seep Team: Sends an ROV (remotely operated vehicle) to the depths of the ocean to explore for current day or past seeps, while collecting samples.  Most time is spent in a lab processing samples by picking out organisms from mud and water.

Shelf/Midwater Team: Uses a couple different types of trawls to collect organisms from different depths in the ocean.

OMZ (Oxygen Minimum Zone) Team: Collects water and mud samples to study organisms that are able to live in low oxygen environments.

          CoastEx scientists retrieve samples collected from 1000m deep, by the Scripps ROV.

Question 6: What cool animals have you seen on the cruise so far?

A dumbo octopus, chimera (Ratfish), Beroe (jelly-like animal), an electric ray, and many more!

Natasha Gallo  examines a hatchet fish which spends its days hiding in the dark waters, 1/2 mile below the surface of the ocean, but ascends at night to feed on unsuspecting zooplankton.

Question 7: Is being an ocean scientist difficult or easy?

Kat: Both, it is a lot of hard work because you often work long hours, but most importantly you are doing something that you think is really cool and exciting, that makes it easier.  When you love and enjoy something, it makes all of the hard work worthwhile.

Question 8: How many years have you been an ocean scientist?

We have ocean scientists on board that have been studying the oceans anywhere from 2-29 years!

Question 9: What do you love to eat while on the boat?

There is so much good food on the boat, and it is always out, including an incredible snack bar.  Here is a list of some of the scientists favorite foods: chocolate, peppermint tea, goldfish, snickers ice cream bars, dried trail mix, crackers, ice cream, and morning coffee.

Question 10: What is your favorite sea animal?

Emily: Frogfish because they are goofy looking and they always look upset. They are also well camouflaged, their fins look like little feet and they are awkward swimmers. I love them!

Jillian: Siboglinid worms because they have no mouth or stomach!

Kat: Squid! The way they move is really cool and their eye is so similar to our eye. In Danish they call the squid, the “Inkspurter”.

David: Deep-Sea Corals because they are unlike what you see when you go scuba diving (e.g. coral reefs).  They do not make colonies and are instead solitary.

Ally: Sea cucumbers because they can regurgitate their guts. I love also that they come in many shapes/sizes. Also, someone once told me that you get good luck by kissing them.

Lisa: I don’t have one cause there are so many. Whale sharks are pretty cool!

Question 11: Did the blue whale and the whale shark go extinct? If they didn’t, how often do you see them?

Actually, neither is extinct.  Keep in mind that just because we do not see some animals everyday, that does not mean that they are endangered or even extinct. 

Many of the scientists have seen blue whales right off the coast of San Diego!  In fact, someone saw a blue whale last week right off the Scripps Pier in La Jolla.

As for whale sharks, one of our scientists has seen them in the Okinawa Aquarium in Japan. Also, your teacher, Mrs. Grupe got to swim with them in Baja.

Question 12: How many sea creatures live in the ocean?

There are still many creatures waiting to be discovered in the ocean.  At this point in time, there are over 200,000 described animals in the ocean.  Some ocean scientists would say that there are still millions of species to be discovered, but we cannot know for sure exactly what number that is.

                                Some of the animals caught in today's midwater trawl. 

Question 13: How salty is in the ocean

It depends where you are in the ocean.  On average, ocean water is 3.5% salt.  However, some places like the Mediterranean Sea, are more salty while parts of the Pacific ocean are slightly fresher and less salty.

Searching for anaerobic answers in the OMZ

posted Dec 13, 2012, 6:39 PM by Kirk Sato   [ updated Dec 17, 2012, 12:40 AM ]

After a successful trip last summer, I am very happy to be on board the Melville again for my sophomore SIO cruise. For me, one of the best aspects of the two SDCE cruises has been the amount of collaboration and general support between all of the graduate students on board. One of the limitations of working in typical lab settings is that we usually only interact with other researchers working on similar organisms with similar techniques. At sea, this all breaks down – while I am looking in sediment samples for bacteria, students next to me are searching the same samples for indicators of sediment age, others are searching for invertebrates that I never knew existed, and still others are analyzing the chemical conditions found in the samples. Not only does this give me a better understanding of the environments that the bacteria living in these samples encounter, but it also allows me to observe different sampling techniques.

During this cruise I am looking for actinomycetes, a group of sediment-dwelling bacteria most famous for their production of antibiotics and other pharmaceutically relevant small molecules. I am collecting sediment cores from the Oxygen Minimum Zone (OMZ) along with my PhD advisor, Paul Jensen, and a fellow graduate student from my lab, Julia Busch. Our first multicore samples arrived on deck Monday night, and have been processed and preserved for analysis back at our home lab at SIO. By the time we offload on Saturday, we will have samples from five individual sites along the OMZ.

So far, most of my thesis work has been based on experiments using actinomycetes grown in lab cultures. These types of studies are done with samples of genetically identical actinomycetes, or a “pure” culture. From pure cultures, I can very carefully manipulate conditions and control variables, experiments that have given me some insights into how actinomycetes react to changes in their environment. In nature, however, actinomycetes are living in close proximity with millions of other bacteria, and conditions like nutrient availability, pH, and oxygen concentrations change constantly. It is difficult to recreate these levels of complexity in the lab, so it is important to test laboratory models of bacterial behavior in the environments where they really live, reproduce, and evolve.

Pure culture of Actionmycetes

In the lab, I have been studying how actinomycetes grow as oxygen levels change. Previously, these bacteria were thought to be strict aerobes, which means that they breathe oxygen, just like us. In lab cultures, I was surprised to find that actinomycetes grow almost equally as well in conditions with very little oxygen. This made me very curious about where they actually grow in the environment. Do they prefer regions with high oxygen or low oxygen? Are they equally active in both? I am hopeful that I will be able to find the answer in the core samples currently sitting in the Melville’s freezer.

Since finding out that actinomycetes can grow in low oxygen environments, I have been very interested in figuring out how they are accomplishing this. The answer may be related to the complex small molecules that they are famous for producing. Many of these compounds have antibiotic effects when they are applied at high concentrations, but the concentrations at which they are produced in nature may not be enough to kill off any of their competitors. In the lab, I have been studying the possibility that these molecules are actually produced to help actinomycetes to grow in low-oxygen environments.

Many bacteria are able to breathe alternatives to oxygen, which allows them to live in anaerobic and low-oxygen environments like the OMZ and methane seep we are visiting on this cruise. Most actinomycetes have not been known to use oxygen alternatives, but the observation that they can grow with very low levels of oxygen means that this might be a previously overlooked aspect of their metabolism. The ability to use alternatives to oxygen requires a very different set of metabolic enzymes than those used by aerobes, and this is where the production of these antibiotic-like small molecules might be important. Certain bacteria seem to use small molecules as a part of anaerobic metabolism, allowing them to live in oxygen-poor environments. In a controlled lab setting, I am trying to see if this is happening in actinomycetes, and if this might explain their ability to live at low oxygen concentrations. To examine this process in a natural environment, I will be looking at how the production of these molecules varies between oxygen-rich and oxygen-limited sediment samples.

One of the things I like most about this project is its overlap between applied and basic biology. Throughout the course of my thesis, I have been surprised at how these two seemingly separate types of studies can inform and complement each other. In this case, the search for new antibiotics from actinomycetes has given me the ability to study an otherwise overlooked aspect of their basic biology. Collaboration is really a key component of productive research, and I am very lucky that SIO fosters collaborations like the SDCE cruises. So far this trip, my own sampling is working better than ever, and I am feeling optimistic that these samples will be a valuable addition to my thesis work.

- Kelley Gallagher, PhD Candidate at Scripps Institution of Oceanography

Hungry for Methanogenic Microbes

posted Dec 12, 2012, 10:45 PM by Kirk Sato   [ updated Dec 12, 2012, 10:45 PM ]

    As a member of the Seep Team, I help take samples of the seafloor mud at locations where methane gas concentrations are relatively high (in some places, you can actually see methane gas bubbling out of seafloor). We are interested in the mud for two sample types.

    First, we collect the microorganisms – mostly bacteria, but also some called archaea – living in the mud. We want to determine which species are living in the mud, and the relative abundance of those species compared to one another. This is because the microbes are actively regulating the chemistry of the water portion of the mud, called pore water (mud is just a mixture of tiny rocks and pore water). Some of the archaea in the mud are known to eat methane, and for every methane molecule the archaea eat there is one fewer methane molecule which can escape into the ocean and, ultimately, into the atmosphere. In fact, if it weren’t for seafloor archaea ocean sediments would contribute much more methane to the oceans than they already do. We care about methane escaping from ocean sediments into the ocean because methane is a strong greenhouse gas and thus can dramatically affect our climate.

    The second sample type we collect from the seafloor mud is the pore water itself. In the water, we measure the concentrations of a variety of chemical compounds. It is important for us to learn as much as possible about the pore water because it is the environment in which the microorganisms are living. If we want to truly understand microbial seafloor populations, it isn’t sufficient to simply ascertain which species are present and in what abundance (even though that information is important). We also need to know which species prefer which environmental conditions, for example whether the microbial community is different in more or less acidic water, or if the amount of methane available affects the microbial community.

Extracting some mud from a sediment core taken in the OMZ.

    Besides my science commitments on the R/V Melville, I’m also looking forward to getting to know all the other scientists onboard. The large number of graduate students on our cruise makes it a unique opportunity to meet and get to know other young scientists doing different work in similar ecosystems to those which I study. I appreciate the opportunity to participate in this cruise, and would like to thank Ben Grupe for his generosity in inviting me and hard work in putting the cruise together!

 -  David Case, PhD student at California Institute of Technology

My scientific community: a generational responsibility

posted Dec 11, 2012, 7:00 PM by Kirk Sato   [ updated Dec 11, 2012, 9:02 PM ]


    What if I told you that the funny, chaotic, selfless, twenty and thirty-somethings on this ship are the next generation of ocean and environmental scientists?  By all respects, they seem like any group of twenty and thirty somethings...stretch pants, ironic tee shirts, laptops, sneakers, long hair, fresh faces, idealism. They look like the earnest, fun loving, at times rebellious, kids that you might see at your local coffee shop, frisbee golf course, surf-rock bar, or food co-op.


    Most of these scientists have sacrificed everything for their education, having scraped by from grant to grant, job to job; working in Moorea, Honolulu, Fairbanks, Santa Barbara, Bermuda, Costa Rica, Honduras. Most of them have two pairs of jeans to their name, know the tidal cycle for the next two months by heart, and prize their rubber boots, iPod playlist, and coveted music festival above most things. These are humble people, salt of the earth people: blue-grassy, centered, overwhelmed by narcissism, overexcited to tell stories of the recent fish, wave or clam they’ve seen.


    These are my people – and I am proud to belong to them.


    But sometimes I fear that history will not judge my generation of scientists kindly. As we strive for publications, discoveries, research funding, collaborations – we also steward a planet that is rapidly changing. And permanently. The science behind climate change is clear. Now what do we do about it?


    Historically, scientists were conveniently sequestered into a small alcove of society, where our primary tasks were: research-write-publish, research-write-publish. Wash-rinse-repeat. Inside that washing machine cycle, or vacuum, you might never move any of your discoveries into the public sphere. But now, we scientists don’t have the luxury of staying within that small enclave – more and more environmental and oceanographic research is validating and documenting the encroachment of climate perturbation. And this information is relevant to how we set carbon policy, how we inform the electorate, and how we plan for the future. You might think that an oceanographic mission to the continental margin off of San Diego isn’t relevant to climate change science - but that isn’t the case. Climate change alters the chemistry of the surface and deep ocean, it rearranges the distribution and concentration of oxygen along continental margins, and it forces biological communities to reorganize themselves. These changes aren’t temporary – they are the expression of long term trends towards an ocean with very little oxygen, very high acidity, collapsed biodiversity and drastically reduced fisheries and economic productivity. Is this an ocean, a world, which you want to pass of to your children? Or your great, great, great grandchildren?


    Never before has a generation of scientists been bestowed with such a monumental task: understand our changing earth and ocean systems AND simultaneously communicate this science to the people that need it most. My generation of scientists is up for the task. All we expect in return is to be considered open, unbiased brokers of information. We have the best intentions – and if you were aboard this ship with me, you would clearly see that in the eyes and hearts of these scientists that I am lucky to call my peers and my friends.


    And so - what we do matters. And how we talk about it matters - which is why a central component of our cruise mission is to communicate about our research, discoveries and excitement. The academic ivory tower is no longer an option for those of us that study environmental, oceanographic and climatic change. So the next time you consider scientists, especially in the polarized and distorted narrative that exists within the media and political machinations, consider our ship offshore of San Diego. Think of us around your dinner table, cracking jokes and spilling food, trying to act our age and failing at that task. Or think of us as your neighbors, gardening in the afternoon, playing fetch with our dog, chatting over fence posts and vegetable starts. We are no more, no less than that – and that is a lot.

-Sarah Moffitt, PhD Candidate at UC Davis, Bodega Marine Laboratory

Trawling with Zombies: Deep-Sea Creatures Up Close and Personal

posted Dec 11, 2012, 12:12 PM by Kirk Sato

    Stepping onto the ship early Saturday morning was very surreal.  As a coastal ecologist, there has never been a reason for me to get on a giant research vessel; and the thought of not jumping in the water to dive during a research expedition seemed bizarre to me.  I was amazed at the volume of microscopes, analytical tools, cold vans, and technology that outfitted the Melville.   This is a far cry from the BINKE nets (small nets to capture fish while scuba diving) and personal coolers filled with seawater to collect fish that I use for my research.  But I soon became comfortable with the set up and it was only a matter of hours before we were headed straight to work, decked out in foul weather gear, steel toed rubber boots, safety vests, and hard hats. 

Map of station locations in the San Diego coastal region. 

D= Del Mar line, L = La Jolla, P = Pt. Loma, SDT = San Diego Trough

    I am a volunteer for the “Shelf Team” aka the “Zonation Zombies” and our job is to collect fish and invertebrates from the seafloor at different depths (or zones) and relate that data to the oxygen minimum zone.  We use an otter trawl, which is essentially a weighted net with a mouth opening about 10 m wide.  The net descends to the benthos and collects anything residing on the bottom: fishes, worms, sponges, crabs, octopus, and echinoderms.  Our sites are mapped out using Google Earth which has been surprisingly accurate.  Knowing the distance of our otter trawls is very important because it helps us calculate the average density of each taxon during a trawl.  Our first two otter trawls were at 3 and 4 a.m. on Sunday morning (remember science does not conform to the circadian rhythms of human beings!) and they were very successful.  There is an evident difference in biodiversity among the various zones we are sampling, and it is impressive to see such high biodiversity and biomass in an area many consider to be inhospitable for organisms.  


Zonation Zombies haul in a benthic otter trawl collected from 400 m. 

Once the trawl made it back on the deck, the zombies were running around at full speed grabbing buckets, fish, brains …. oops, I mean urchins, and inverts.  We separated the organisms as best we could and acquired counts and sizes of all organisms. Total counts of organisms were being called every which way and Mike Navarro, the record keeper, would echo back the calls in confirmation.  It was a veritable round of science harmony.  Yuzo Yanagitsuru and I worked in tandem to identify and count the fishes. Natasha Gallo measured the standard length of all fishes with economic importance.  Amanda Netburn (Scientific American Blog) photographed larger animals that were too big for preservation, and Kirk Sato reserved two representatives of each species to be used as teaching aids or as a voucher species.  These specimens will be catalogued and archived into a database that is maintained by the Scripps Benthic Invertebrate and Vertebrate Collection.   The work was long, but it is so satisfying to watch sunrise standing on the deck of a ship counting deep-sea animals.

Posing with a deep-sea octopus.

    But the day was not over yet!  We still had a ROV dive planned, and another otter trawl in the evening.  The ROV performed brilliantly, with Kirk and Mike (the zombie leaders) directing the techs where to maneuver the machine.  It is interesting to see the difference in the diversity of species that we see with the ROV versus the otter trawl.  Some species, like the heart urchins (Brisaster latifrons and Brissopsis pacifica) burrow into the sediment and cannot be counted on ROV transects; but we see many of these species in the otter trawl.   Alternatively, there are mobile species that we cannot collect with an otter trawl that we see during an ROV dive. These two techniques (the otter trawl and the ROV) complement one another well to acquire accurate and comprehensive data. 

    In the evening we had our third otter trawl of the day, and brought up an even wider array of species.  As we were finishing the counts, the zombies stopped for a short time to watch the sunset as dolphins swam along the ship.  Days as long as this force upon you some introspection and I could not think of anywhere I would rather be.   This ship is decorated with Christmas lights, the company is great, and there is an endless supply of ice cream sandwiches.  What more could you ask for?

-  Katie Sievers, Masters Student in Ecology at San Diego State University

Economic implications of evolutionary and ecological interactions

posted Dec 10, 2012, 10:51 PM by Kirk Sato   [ updated Dec 10, 2012, 10:51 PM ]

            From an aesthetic perspective, black shales are not the prettiest rock. They don’t form soaring spires and walls like the granite in Yosemite, or the colorful, variegated landscape like the Jurassic sandstones of the desert southwest. Usually, they just weather into bland, monotonous, dark hillslopes. In fact, the bane of my recent research as a geologist has been finding the good stream cuts and valleys where the shales are actually exposed. From an economic and evolutionary perspective, though, black shales are fascinating. The reason black shales are, well, black, is that they were deposited under low-oxygen conditions, allowing high quantities of planktonic algae, which are normally degraded by microbes in the water column and sediment, to be preserved. This organic carbon gives the sediment (and ultimately the rock) its distinctive color. Upon burial and heating, the carbon turns into oil and gas; black shales are the source of our current carbon-based economy. How, why and where black shales form is thus a main thrust of petroleum geology.

            Hopefully as a society we are in the process of transitioning towards renewable energy sources, and future interest in black shales will be limited to those interested in their evolutionary importance. My research focuses on the early emergence of animals, an event known as the Cambrian radiation, about 540 million years ago. During a brief (by geological standards) ~20 million year window, essentially every major animal group appeared in the fossil record. Interestingly, rocks before the Cambrian show abundant evidence that they contained relatively little oxygen. The deep ocean before the Cambrian is characterized by abundant and  persistent black shales—indicating low oxygen conditions. In my field area in the Yukon Territory of arctic Canada, for instance, entire hillsides consist of black shale.


 Monotonous black shales in the Precambrian Fifteenmile Group, Ogilvie Mountains, Yukon Territory, Canada, with two geologists for scale.

Crossing into the Cambrian, though, widespread black shale horizons become much less common, and for the most part the ocean appears fairly well oxygenated. Because oxygen so strongly affects marine animal life, many geologists have suggested that the Cambrian radiation is related to the oxygenation event that occurred around the Precambrian-Cambrian boundary. Study of modern low-oxygen analogues, such as offshore San Diego, may help to inform our understanding of what happened in the ancient past. Growing recognition that oxygen-deficient zones in the modern ocean are expanding has led to increased interest among oceanographers in studying these settings (including many aims of the San Diego Coastal Expedition). My research has been focused on using new information from these settings to understand how oxygen levels affect organismal biology, and then to apply these lessons to the geologic record. Reciprocally, times of oxygen stress and warming identified in the fossil record may be able to help us understand how organisms in the modern ocean will respond to current global warming and expansion of oxygen-deficient zones on timescales not measureable by ecological experiments.

            Working with the OMZ team on both legs of this cruise, seeing the animals that live in the OMZ, and learning how an oceanographic cruise works has been one of the coolest experiences I’ve had in science. It’s been especially great to be able to learn from scientists like Chief Scientists Frieder and Grupe and Dr. Levin, and I feel really lucky to have been invited on the cruise.


Nightime deployment of the multi-corer to sample Oxygen Minimum Zone sediment.

It’s been quite a different experience from my normal geological fieldwork, though. As geologists we are used to working with the rhythms of daylight. In the field we’re usually up around first light, hiking to the outcrop, staying on the rock as long as light allows, and then back to camp, often by headlamp, to sit around the fire and talk about the day, the rocks we’ve seen and rocks we dream of seeing. Long days, for sure, but over when the sun goes down. On the Melville, the science never stops. When the OMZ team is up, it’s time to go.  My first multi-core was a night deployment. We caught a nap after dinner and then woke up at 2:00 AM to work through the dawn. In theory I knew the night-time work would be happening, but it doesn’t quite prepare you…on the plus side, the breakfast prepared by the awesome chefs on the Melville certainly beats the freeze-dried meals we eat for weeks on end in arctic Canada! Now that I’m getting used to the rhythms of science on the Melville, the experience just keeps getting better, and I feel like I’m making some progress towards a realistic view of ancient low-oxygen seafloors.   

-  Dr. Erik Sperling, Postdoctoral Researcher at Harvard University

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