I have been making good progress in my quest to analyze all of the summer cruise footage and have all but finished organizing the winter cruise data in order to make easy use of the data toward the end of my research. I should be able to reach my goals in analyzing each video within three weeks and may be able to finish up sometime before that deadline as my process of analysis has been speeding up steadily through practice. I have observed few pyrosomes in the videos that I’ve reviewed so far, so future footage may prove more time consuming when more begin to appear. I decided to start my analysis on the final CTD cast from the summer cruise, working backwards toward the first in order to account for some mislabeling. The final few CTD casts where performed in very choppy water and I have been able to identify surprisingly few pyrosomes near the water’s surface in these casts, regardless of water depth, distance from shore, or time of day. Pyrosomes are known to perform diel vertical migrations (meaning a migration over a 24-hour period) that place them nearer to surface water during the night, something which appeared to be supported by my experiences during the cruise. I would sometimes find pyrosomes floating directly at the surface during the night when the sea state was calm, but the general lack of them represented in the footage taken from rough water may hint at a connection between sea state and pyrosome distribution. I have also observed a fairly concentrated population of macroscopic zooplankton such as jellies and krill, and the presence of several schools of fish in these videos, which may be evidence of another connection between zooplankton, fish, and pyrosome abundance. The frequency of pyrosome consumption by fish is not something which has been researched in depth at this point in time and, while I predict that the lack of pyrosomes in fish populated waters has more to do with sea state and distance to shore than to direct interaction between animals, I will be interested to document fish and pyrosome abundance in the future.
An example of pyrosome sizes found during the S18 cruise.
The passing of the fifth week marks the half-way point for the interns of the REU program and with it, a more focused approach to our various research projects. Research proposals have been created and reviewed for strengths and weaknesses, and clear questions have been formed to act as an anchor for our remaining work and studies. The question I am asking is how vertical distribution of pyrosomes is affected by environmental parameters including oxygen content, salinity, temperature, and fluorescence (a measure for phytoplankton productivity in the water). This question will most likely be edited somewhat over the coming weeks, but the framework is present and I am able to begin the work that will fill the majority of the coming weeks: counting pyrosomes. All of the field work for my research was completed during the cruise once the final footage was recorded, but now that information must be transformed into numbers if any conclusions are to be reached. Until somebody develops an automated pyrosome-counting technology, that process of transformation resides in good old-fashioned human observation and recording.
One extremely useful aspect of data processing that I am currently immersed in, is that I am forced to critically evaluate the way I present information and whether the information is actually useful. I have known for several weeks now that my research will focus on the relationship of pyrosome distribution and environmental conditions outside of Oregon and California, but I had yet to put real thought into how collected data could be presented in a way that highlights that relationship. The questions that I am asking myself now are those like ‘What data do I ultimately need to take away from each sampling station?’, ‘How can I summarize huge volumes of data without altering it?’, ‘Is every parameter going to tell us something useful when processed?’, and of course, ‘How much data will I actually be able to process with the time that I have available?’. The question of time constraints is one of the most pressing as it will ultimately serve to force me into deciding one way or another which questions I will be able to approach and which of those I will have to dismiss. I may not have time to compile the data for the primary and secondary sampling of each station during the day and night, so I have the option of leaving out the secondary sampling, which in turn may cause me to miss an important trend. These are tricky questions to answer and have given me greater insight to the sort of issues that a researcher can run into when trying to explain or apply their data.
The cruise has come to a close after 9 days of productivity, one day earlier than was scheduled because of further equipment problems in combination with rough seas along the Newport, Oregon transect. We were fortunate to have completed nearly all intended sampling, due in large part to the tireless effort put forth by the R/V Sally Ride research technicians, who worked with the science crew around the clock to keep the cruise on schedule and make up for time lost at the outset. We were also fortunate to have experienced extraordinarily calm waters in both the Newport, Oregon and Trinidad, California transect lines for seven of the nine days at sea. This was made doubly apparent when compared to the experiences of the crew of the Winter, 2018 cruise who had to work around consistently rough seas while handling heavy sampling equipment. The ship docked early on the morning of July 12thand, by the end of the same day, all of the equipment used during the cruise had been dismantled and sent off to storage or repair and the science crew settled down for a well-earned drink at the local brewery. Now, by the morning of the 13th, we prepare ourselves for the coming months of analysis that will give purpose to the physical and fiscal cost of running a large research vessel from Oregon to California and back.
The frequent equipment issues that plagued the cruise were mostly involved with the operation of the MOCNESS and ISIIS systems, and, in spite of a camera lost overboard near the end of the cruise, we were able to collect several hours’ worth of camera footage in the water column during CTD sensor operation. The footage revealed a variety of jellies and fish that inhabit the waters outside of Oregon and California, but surprisingly few pyrosomes were encountered in the beginning few days of the cruise. Many more pyrosomes began to appear towards the end of sampling and quickly began to fill our MOCNESS nets, where they packed in like Vienna sausages. There were enough to necessitate a dedicated pyrosome counting and measuring station! During a night with especially calm, almost glassy seas, hundreds of the creatures floated by the ship in a leisurely way so that they could be picked out of the water with hand-held net. I found it absolutely bizarre to see hundreds of pink pickles floating by the ship, passively filtering microscopic meals out of the water. More were seen when reviewing footage of the water column and, while the footage has not yet been compared to the accompanying CTD sensor data, evidence of daily vertical migration of pyrosomes appear to be consistent with previous findings, as well as their tendency to aggregate at the lower end of the surface mixing layer. With luck, more trends will emerge when analyzing the footage that might help us better understand these tubular invaders.
Two days have passed since setting sail on the R/V Sally Ride out of Newport Oregon. I slept through the ship’s departure in the early hours of Tuesday, the third of July, and spent much of the first day adjusting to the world in motion through a Dramamine-induced haze. I am excited to finally have an opportunity to put into motion the camera system that I have been preparing for the last two weeks!
The activities of the ship and science crew can be divided roughly into those which require the ship to be moving and those that need the ship to be still. The main activities which require the ship to be moving forward are the deployment of the In Situ Ichthyoplankton Imaging System (ISIIS) and sampling by use of a coupled MOCNESS net system. The ISIIS looks something like a child’s rendition of a fighter jet, with torpedo shaped floats and adjustable ‘wings’ that control the position of the system in the water and allows us to take a continuous slice of images for the purpose of observing plankton. The MOCNESS net system is essentially a series of enormous plankton nets attached to a large metal frame, which we can remotely open or close in order to take samples of organisms at specific depths. Much of my work on the ship will consist of sorting through different taxa of organisms obtained via this system by physically picking through them. The samples will be processed later to determine what they have been eating. Counting the pyrosomes that get caught in the MOCNESS nets may prove to be the easiest or a very difficult part of this process depending on how many we come across, which has been surprisingly few so far. Unfortunately, we have been plagued by equipment failures since initially successful testing and so haven’t done much of picking and sorting just yet.
Those activities which require the ship to be still include sampling by use of a comparatively small plankton net which is lowered vertically over the side of the ship and collecting data though a CTD sensor array that carries the stereo camera system. So far, we have done one CTD cast and the footage from taken with the camera system looks good! Some small adjustments to the angle of lights and timing to start equipment were necessary, but some adjustment was expected. I can look forward to a long period of sorting through footage after completion of this cruise.
I find myself consistently astonished at the many comforts that the R/V Sally Ride has provided so far. Everything from high quality of the food to the wideness of the passageways seems to me like a special treat when compared to the cramped conditions of a Naval vessel. Both the science crew and ship’s crew are dedicated, open people who clearly love their work and will talk you about it at length when not asking to hear about your own. The going has been slow for many of the scientists aboard due to the equipment failures but, where an excess of unstructured time has appeared, I find nobody spending their time unwisely. I can say both about the crew of the research vessel, and about the population of interns and researchers back at the OIMB: it is a pleasure to work with so many motivated and enthusiastic people.
Only two weeks into the summer, and already time is beginning to fly. The previous week’s effort provided me with the necessary tools to take video analysis into my own hands while attempting to lift the veil on the mysterious life and habits of Pyrosoma atlanticum, and now begins the final days of preparation for the upcoming research cruise. My remaining responsibilities in preparing for the ten-day cruise mainly revolve around developing a method to fix the new stereo camera system to the outer cage of the CTD (Conductivity, Temperature, and Depth) sensor which will be lowered into the water repeatedly over the course of the cruise, and to learn the necessary steps in preparing future footage for effective analysis.
To understand the basic concept of the dual camera setup you must look no farther than to your own eyeballs. The two cameras will look outward, tilted very slightly toward each other to allow their fields of view (FOVs) to cross over and cause images at a specific distances to perfectly overlap when footage from the two cameras is compared; thus allowing a computer program to determine the distances between objects in a similar way that your brain does when you are trying to throw a ball or judge the distance of an oncoming car. If all goes well, then any footage we take in the next two weeks will be ready for synchronization and subject to the scrutiny of the computer program. If all doesn’t go well, then we will simply have twice the useful footage which will be analyzed by good old-fashioned human counting and comparison!
I’m willing to bet that many of you readers are getting pretty curious about this cruise that I keep going on about, so let me fill you in! This is actually the second of a four-part series of cruises being put into action by the National Science Foundation (NSF), following a proposal to observe mesozooplankton (which include species approximately 0.2 to 20 mm in length such as small jellies and fish larvae) in the Northern California Current. The first cruise occurred in winter, 2018 and just happened to provide an avenue for the Sutherland Lab to observe the little-studied Pyrosoma atlanticum that had been quickly making themselves comfortable in northern waters. To help demystify the life of a researcher, I will let you in on a small secret: research can be expensive! It isn’t cheap to run a 238-foot (in the case of the R/V Sally Ride) research vessel up and down the pacific coast and so as many tests and observations as possible are squeezed into a venture wherever the opportunity is presented. In the case of pyrosome observation, a lot of good information was gleaned by simply attaching a water proof camera and light to the cage of a CTD which was going to be lowered into the water anyway. This technique turned out to be pretty effective, so we are doubling down by trying out the stereo camera system which may provide us with even more information than the first recordings.
The days that remain promise to be packed as the lab hurries to finish preparations for a busy voyage of pyrosome pilfering and observation that will bring us south, halfway down the length of California and back before we’re though. Keeping pace has been a challenge and will surely remain that way for the final months of summer, but it’s a challenge that keeps me intrigued and involved throughout.
I would like to share some thoughts that I’ve had recently on agency and the importance of programs like OIMB’s REU. An element of research (and work in general) that has not been properly expressed in my experience in several colleges is the need for flexible thinking and the satisfaction that a person can gain from expressing their agency. What I mean by agency is most simply explained as a person’s ability to affect or change things around them for the better. You might also interpret it as solving problems or utilizing accrued knowledge. Here is an example. During the last week of cruise preparation, I have looked through a variety of different protocols relating to experimentation, analysis, and equipment operation. While reading these protocols and training for video analysis I observed a basic issue: nobody thought to record the times of any events in the footage from the previous cruise. The basic consequence of this is that the footage must now be meticulously combed through and compared to the accompanying environmental data in order to stitch together a picture of when the CTD and attached camera are being raised and lowered in the water, all so that we can match the time that readings began to the relative time in the video. This is a very time-consuming process and, in response, I quickly typed up a set of instructions that details the important events that should be timed with a stop watch. This was by no means an inspired or difficult process but the very act of observing a problem, coming up with a solution, and then implementing that solution was very gratifying!
This gratification is something that I have observed in my fellow REU participants as collectively, we discover that You! Yes You, the Undergraduate, can develop creative answers to real world questions!It is an experience that simply cannot be taught in the classroom but must be experienced through implementation of the knowledge we have accumulated throughout school and throughout our lives. I think this is understandable considering the volume of information that a person must ingest during their time in college, especially in the sciences, and I have had the pleasure of studying under a number of teachers who try their very best to express the usefulness of knowledge found in the classroom. Even so, I can honestly say that I am more interested and more involved after eleven days of research at REU than I have been in two years of full time education, and I don’t believe that I can drive home the importance of this program any more eloquently than by communicating those feelings. Whether testing a new camera system, collecting crabs in the local estuary, or simply sitting at a desk and writing protocols, I have felt dynamic and involved in every task. I believe this is the importance of programs like REU, to teach new generations of people to recognize their agency and to teach them to love expressing that agency.
Hello there! My name is Matthew Gimpelevich and I am currently an undergraduate student in my third year of oceanography and engineering at Seattle Central College in Seattle, Washington. I’m lucky enough to be working in the Sutherland lab at the Oregon Institute of Marine Biology where I get to formulate my own methods of studying the pyrosome, Pyrosoma atlanticum, which has recently migrated up the Pacific coast from warmer waters! As an REU intern, I look forward to developing research techniques and methods of organizing and maintaining my own projects!