The final week of summer research is here, and the experience feels simultaneously as though it passed by in a flash and at a crawl. At the time of writing, the research symposium already passed and the interns of OIMB have demonstrated their research with passion and clarity, proudly sharing the product of two months’ effort while successfully defending their methods and data interpretation from the steady flow of questions posed by fellow researchers and science enthusiasts. The experience was enjoyable, and far more relaxed than many of us had expected as we prepared for criticism in the days leading up to the symposium. I would describe the questions posed to us as being much closer to friendly interest than real criticism, but the idea of seasoned researchers picking apart our hard work was powerful motivation to ensure we were caught up on our organisms and able to clearly explain the elements of our research. The posters themselves were designed elegantly and I felt that they fully expressed the effort poured into them during the preceding weeks.
My own poster was aimed at expressing the vertical distribution of pyrosomes by several measures while explaining the purpose and methods of the research. Demonstrating the relationship between pyrosome abundance and environmental parameters was accomplished by reviewing the 33 summer videos for the depth in each video that contained the highest number of pyrosomes. These depths and associated environmental data were then used as data points to show if there are any parameters which pyrosomes favor above others. The closest association revealed by the data showed that the depths containing the highest amount of pyrosomes tended to fall within 8 to 11°C, with some outliers placed closer to 17°C from a cast outside of Newport that had unusually high seawater temperature. There also appeared to be a fairly strong relationship with fluorescence, a measure of phytoplankton content, in which most of the depths containing the highest amount of pyrosomes appeared close to 0. This seems to indicate that the pyrosomes were mostly placed below the surface mixing layer where fluorescence drops off rapidly. Pyrosomes have already been observed to accumulate near the bottom of the surface mixing layer and this observation was reinforced my own data. It is also apparent when looking at a representation of every pyrosome’s location by depth that their vertical positions varied quite a bit during the day, while accumulating near surface water at night. Unfortunately, I was not able to incorporate the winter, 2018 cruise data into my research because I did not have time to process the videos from both cruises, but I am beginning to process those videos now in an effort to continue research past completion of my research poster. I had previously been under the impression that fewer pyrosomes were observerd during the winter cruise due to a confusion with the data that I had in my possession, but the case seems to be quite the opposite as well over a hundred pyrosomes regularly appear over short depth intervals rather than the ten or so that I typically observed in the summer footage. I am interested to process the remaining winter footage in the future see how it compares with the summer footage.
Several weeks ago, I posted an entry into this blog regarding my feelings on the REU program as a whole, and those feelings have only been reinforced since that point in the program. I spoke about how the program allows a participant the chance to think creatively and practically about their area of interest, and about the rewarding experience of seeing one’s own effort come to fruition, something that I get to experience fully at the end of the program. I believe that this sort of experience is a major benefit to anybody wavering in their education or career plans, as well to those who are simply feeling worn down by their long journey through the sciences in college. Of course, a research experience looks fantastic on a resume and I think that coming into this program looking forward to that reward is fine, but I strongly believe that this should come as a secondary concern to the experience itself. I think that the same is true of coming into the program by treating it like a summer camp. To anybody reading this blog with the intent to participate in the OIMB REU program, trust that you will have enough time to make friends and some fun memories while you are here, but I urge you to think first about what it is you actually want to work on! What actually interests you? If you could work on anything for 2 months, what would it be? This is one of the rare opportunities for your interests to take center stage and the more interested you are, the more your efforts will shine.
The OIMB Summer REU program is coming close to the end and so the final effort for finalizing data and constructing a poster has taken up the last several days. I had expected the actual creation of a poster to feel like a puny task in comparison to several weeks of dedicated video analysis, and my expectations have been proven wrong. All of the ingredients for a quality poster to represent my summer research are on hand, but it turns out that organizing those ingredients into a concise and coherent display that allows a passerby to understand months of effort at a glance is no easy thing. I am actually still in the process of finalizing my display and I am finding it particularly difficult to fit all of the graphs necessary to express my results in an elegant way. It is easy to lose time on the process of poster beautification, but the organization of a science poster really is important to expressing the elements of research coherently to an audience. The best presentations I have seen in poster rough drafts so far tend to organize their data into columns of descriptive elements, data presentation, and conclusions, while separating major sections with their own containing boxes. My poster creation is made somewhat more urgent because it happens to coincide with my final data analysis and I am finding myself bouncing back and forth between my poster and my data, trying to develop a logical way to present my data while ensuring that it fits nicely into the presentation. This has been a confusing process, but I have found it somewhat helpful in thinking of ways to display my data as any graph that I put together must be immediately judged for its effectiveness in the final product.
Another productive week of video analysis has passed, and I am getting closer to finishing with this stage of my research. I found dramatically more pyrosomes in the water outside Newport, OR than outside of Trinidad, CA, but I currently have no ideas as to why that is the case. I have also noticed that the pyrosomes recorded very rarely mixed in with water layers containing significant numbers of visible zooplankton such as krill and jellies, which tend to exist together. Typically, these species can be found in deeper water during the day, at around 50 meters or more, but during the night may be found close to the surface. I have noticed that very few pyrosomes can be found at all in cases where zooplankton and jellies are near surface water, but these cases usually occur when filming relatively close to shore in shallow water, from about 60 to 150 meters deep. In relating this to observations that I made in the previous week, I believe that the presence of these dense zooplankton populations are a more likely factorof pyrosome absence or abundance than predation by fish, but I cannot rule out the idea that sea state has a role to play as well. It is also possible that there are other factors at work determining the depth and abundance of pyrosomes and zooplankton, such as phytoplankton abundance or water currents that may push certain species further from shore than others. I have begun to record the general density of visible zooplankton at depth during video analysis as a reference for myself and as a possible avenue for further research. With luck, some patterns will appear that relate environmental parameters to pyrosome and zooplankton abundance.
In other news, the Charleston Marine Life Center research show case is scheduled for tomorrow at 11am and I have spent much of the day preparing a display for my project. My display will include some interesting footage taken from the July cruise, a jar of preserved pyrosomes for visual reference, and a pyrosome that I constructed out of thick plastic mesh and bubble wrap for tactile reference! I have found that an assumption many people have about pyrosomes is that they are very squishy and gelatinous, and while this is true of a pyrosome that is dead or dying, they are actually somewhat crisp and hold their shape well when they are fresh out of the water. ‘Sea Pickle’ really is a fitting name for them because they will crunch in a way that is distinctly reminiscent of a pickle when they are healthy. This is the sensation that I am attempting to capture with my false pyrosome as hopefully the plastic mesh will give people an idea of the solid but collapsible tunic of a real pyrosome while the bubble wrap will give a sense of their crunchiness as well as represent the zooids which compose the creatures.
My constructed model pyrosome atop a jar or the real thing preserved in ethanol
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.
I finally arrived at a sunny Eugene airport on Saturday, the 16th of June for my long awaited REU experience! I arrived, stiff bodied from a short flight in a crowded plan from Seattle, Washington, to be greeted by several other eager REU interns corralled together by our responsible supervising graduate student! We loaded two months’ worth of luggage into a nine-person van and began a three-hour journey to Charleston, Oregon for a summer of adventure and education (with a break for lunch, of course)!
I originally hail from California and only moved to Seattle in the last two years for school after a four-year enlistment in the Navy. I was initially pursuing a degree in psychology with hopes of acceptance into the University of Washington but switched focus within the first year to seek an education in one of the fields of oceanography after experiencing the excellent tutelage of Marina Halverson in an Oceanography 101 class as Seattle Central College. I have loved being near the ocean for as long as I can remember, no doubt strongly affected by the sparse sailing trips that I experienced as a child. The thought of a career that might allow me to share my time evenly between educational pursuits in the lab and field appealed to me very much! Over a year has passed since that shift in educational goals and I have since changed focus again in the direction of engineering, following experience that I have gained about where my talents lay and the sort of work that I enjoy in school. My ultimate hope is to combine these two disciplines and eventually serve the needs of marine scientists through development of technologies to aid in research and maintenance of the world’s oceans.
Following three hours of conversation on the road, the good interns of the OIMB arrived on campus under darkness and quickly found our way to the dorms where we would spend the next nine weeks sleeping, eating, and hopefully having some fun as well! Fast-forward two days into Monday, and we were introduced to both the various facilities of the campus, and to the mentors who will guide us through our summer of research. I received the honor of working under Dr. Kelly Sutherland in the pursuit of knowledge about marine invertebrates, specifically the recent visitor of the Northern Pacific Ocean: Pyrosoma atlanticum. Pyrosomes are typically a tropical or subtropical planktonic chordate that spend their days aimlessly drifting through warm-ish water, passively sucking up microscopic plankton and look rather like a pale, floating sausage. For those of you who don’t already know, a chordate is a taxon of animals who are specifically defined by the presence of a few morphological features that can easily be searched for online if you’re curious. Need an example of a species representative of chordates? Then look in a mirror! You are more closely related to a pale floating sausage than you are to an octopus!
In several weeks I will be joining a cruise on the R/V Sally Ride to take samples, video footage, and other data on these squishy invaders and have so far spent my time here in the Sutherland Lab preparing for just that. I have learned a lot about pyrosomes in the last four days, including aspects of their morphology as well as how they strayed so far up north by means of a large patch of warm and stable water appropriately dubbed ‘The Blob’, which appeared off the pacific coast several years ago. I have spent a lot of my time learning how to analyze video data taken during the previous winter cruise to determine exactly where pyrosomes like to live in the water column and have been trying to assist in developing a method to take further footage using a stereoscopic video system (utilizing two cameras at a time) which will hopefully allow us to determine the density of these organisms in the water. Finally, I am trying to determine how to house these plankton temporarily during the upcoming cruise and, more importantly, what to do with them once we have them! Whatever techniques and idea I am able to develop here, I have a good feeling about the following eight-and-a-half weeks!
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!