We live in perpetual motion around a star. As a metaphor, deity and mystery, our star’s various memetic incarnations derive from its constancy of power and presence, yet we still know precious little about it. The long life span of trees relative to that of humans makes studying them difficult. Similarly, understanding the life of a star is an infinitely more daunting endeavor and in many ways an eternal puzzle, one that we can only observe indirectly, mediated through technology, projecting ourselves into the future and past, and only in the briefest of blinks. We know that our star is not magical, that it obeys known laws of physics and nuclear chemistry, that it is incredibly far from us, yet we can feel it on our skin, and as we consume the products of its excitations and marvel at the games it plays, we continue to spin around and around its eternal light. A place of constant origin, only one of an infinity of others that speak to us from the night sky. A contradictory and alien being, our sun.

On Monday I watched our moon eclipse this star from a field in Corvallis, hundreds of people laying or sitting in the grass with lawn chairs and blankets, drinking morning cocktails, chasing rambunctious dogs and kids, telescopes and cameras trained to the sky. As the light dimmed and the world changed color, the shadows through an old redwood sprayed a hundred crescent suns across the ground, all of us wondering at the fascinating pattern of light and shadow in the dirt. At the moment of totality, cheers and gasps filled the air, life holding its breathe on the cool wind, wonder and fear echoing back through thousands of such events throughout human history.

Intellectually I was aware of the process as a consequence of orbits, relative distances and coincidental alignment, but the animal within howled. I stood there in the stop-time of fear and curiosity so common to the human animal, wondering at what I was seeing, not with my eyes but with my being. A part of me knew that I was looking at the corona of the sun, but such explanations have no bearing on the emotional component of such an event. In that moment I felt an awesome and terrible presence. I can now understand why such events have inspired panic and sacrifice. I have only once before felt something similar about the sun, my first morning in the sands of Kuwait, the sun rising as a pale blue disc on the horizon, its visible rays feeble and weak, yet its power all around me in the 120 degree air. The sun as an embrace, a holy gesture of an ambivalent god, a passing terror, a perpetually unknowable entity driving art, religion, science and life together under its rays.

I am becoming a scientist. I am the recipient of a vast canon of knowledge about the world we live in, a gift from our ancestors. I have been given many tools to inquire about the workings of nature, to ensure that I am not seeing only what I want to see, or the spirits of habit and superstition. I have a community of passionate and experienced scientists from around the globe that I can call on for help and guidance, yet this is a relatively recent state of affairs. Staring at the sun and moon in alignment I found myself remembering all of those who came before and confronted such phenomena without science. They possessed the same mind and intellectual powers as I, an inheritance of knowledge and experience to keep them alive, and a cultural narrative to order the why’s and how’s of the world, but no science. Those people put stones in circles, piled them high toward the stars and consecrated them with human blood in the effort to understand and control the powers of life and death. I remember and honor those ancestor’s efforts, the generations of sacrifice and confusion that led to here and now, to me. Confronted by the mystery and terror of an eclipse, I must have felt much as they did, quaking at the sight of the sun blotted out by the moon, an event that shouldn’t be.

I have struggled both intellectually and emotionally this summer in pursuit of science. Standing before a wonder of life on planet earth, I was reminded that a part of my being remains untouched and untouchable by science and intellect, that at some level I am unable to completely integrate what I know from science with what I feel with my being. Like the sun, I am a mysterious power of contradiction that defies explanation, even as I seek to explain this condition and the world around me. Much remains hidden in the light.

This last week has felt very relativistic. I’m not sure what happened to all of the hours, which depression in the fabric of space-time continuum I rolled into. No one went to the field, every one retreating to their respective labs and offices. Politics continued to get crazier, NPR hard to listen to on the morning commute. Fred Meyer staged their eclipse survival supplies by the front door of every store. It even rained on Sunday! I continue to feel like a slinky on an escalator; the end near, while never quite arriving.

My proposal to stay on at the EPA as a volunteer and continue my work with respiration rates has been approved. I feel good. I have one more week to go in this internship, and then I’m on my own with the BOD bottles, data sheets, and the strange state of informed ignorance that doing science puts me in. September is coming, a time of beginnings and ends. 12 years ago, September found me with a canteen and a rifle patrolling a New Orleans devastated by Hurricane Katrina. Ten years ago, I held back the tears as the bus drove away from the barracks, taking me and my brothers to an airfield and Iraq. If my old sergeant major could see me now, he’d probably shake his head. “Jennings, how’d you end up a geek, a fish-squeezer, a civilian?” “It must have been my people skills, sergeant major.”

For the last several days, my main task has been the construction of a poster for our final presentation this Friday. I was somewhat surprised to find that no one enjoys writing them. From the number of posters mounted along the walls of every hallway in the building, you might think otherwise. Many folks told me that they enjoy the process of preparing papers for publication, even the revision process, yet there was universal disdain of science posters. The results of my informal survey pointed to several issues: the lack of space to properly fit relevant items, the difficulty in keeping fonts and formatting from going screwy at the printer’s, and the seemingly impossible demand to turn quantitative analysis into sophisticated cave drawings with minimal text and maximum cool factor. Despite the odds, I managed to complete my poster by the deadline (Monday), and I took advantage of the many excellent examples around me to make the best poster I have ever made! To be honest, it’s only the second one I have ever made, but it’s a significant improvement over the last. I found excellent conceptual diagrams to use and minimized confusing figures or charts.

It feels good to make something that will be manifest in meat-space reality. It will be a tangible thing, unlike so many things that I make as a student. It’s a strange process, being a student who remembers mimeographs and typewriters: I conduct research and reading digitally, type a paper digitally, submit the assignment digitally, and look for my reward, a number in the “grades” tab on a website that means “good job” or “uh oh”. The dominance of the digital realm sometimes leaves me feeling empty, bereft of any proof that I have been, that I have felt, that I am here on planet Earth doing things. Posters erupt from the binary and claim their place among the living, reminding me that we are still just sophisticated animals that need to stare at things together, point and go “Hmmmm. What?”

This week, I finally made a stop at the Tillamook Cheese Factory’s visitor’s center and had 2 scoops of caramel butter pecan ice cream. It was an unusual 88 degrees in Tillamook that day and we were headed to Garibaldi to install sensor rigging beneath a pier and collect water samples. It was a nice break from the car ride from Newport and the already long day. I had spent the morning learning how to analyze cholorophyll samples with the Turner Designs 10AU fluorometer. While not especially difficult, making sure to do every thing in the right order with the right checks conducted can get confusing fast when you’ve only had 5 hours of sleep. Analysis is conducted under low-light levels, and the fluorometer gives off a fire-red glow from it’s power button that is both sinister and sedating. It was a long morning with too little coffee, the 10AU glaring at me like the frighteningly incomprehensible machine that it is inside the dull black, ruggedized case. Science apparatus can often-times look quite frightening for no reason at all. The 10AU says, “I might explode,”, it’s red light screaming, “look out”. The fluorometer is just a fancy lamp, but it sure doesn’t look like that or feel like that when you’re sleep-deprived and concentrating on doing things right because the samples are not practice samples. Why can’t it look like an ipod?

After the welcome ice cream break, we launched the boat and tied up beneath the pier of interest. The installation of the sensor rigging and test package went off without a hitch. I took pictures to document the project, and collected water for BOD incubation and nutrient analysis. The test package, with a somewhat sacrificial sensor, will be retrieved shortly to check the data and see how the whole set up did with the tides.

My respiration runs have yielded interesting variation in rates, and as the time to present this research and talk about its implications comes near, I am forced to admit that I am intrigued by what I have found so far but cannot explain it or say just what it means in terms of pH, carbonate chemistry, or nutrient pollution. Perhaps the most important knowledge gained at this point is a sense of the magnitude of change involved in respiration rates, how those rates might change spatially and temporally, and how best to measure them.

I am incubating the last samples taken from beneath a pier in Garibaldi near the mouth of the bay. The three samples were taken over the time that we were there installing the rigging, as the tide changed. It will be interesting to see the results. The last sample was taken as sea water was rushing back in to the bay and was super-saturated with oxygen, unlike any sample incubated so far. Exciting!

A beautiful day on the Wilson River.

The Tillamook area is quite beautiful. There are moments during a busy day of sampling when I suddenly forget what I am doing and feel the blue sky, beautiful water, birds and the breeze. This is a job that actual people have, and that I could have some day too. It’s not a bad life.

I am currently incubating a batch of water samples taken earlier this week in lower Tillamook Bay. This incubation is special because I decanted the samples in the BOD bottles within hours of collection, rather than keeping the samples in a cooler over night before filling the BOD bottles. The respiration rates from the two previous incubations show significant variation by geographic location, and it will be interesting to see how the 4 most recent samples I took look in comparison with the others, and if the rates are still consistent with this batch and storage hasn’t influenced the rates from the previous incubations. My mentor Cheryl has been mapping them in ArcGIS and it is neat to see the data depicted visually on the map of the Bay. It affords a completely different sense of the data than a bar graph or scatter plot.

On our last trip to Tillamook, we employed a hover craft to get around. It sounds fun, and it is, sort of. Mostly, it’s a nail-biting, loud and wet ride. The most redeeming aspect of the hover craft is that it makes who ever is in it look really cool. I had the pleasure of spotting a van on the highway come to a complete stop to stare at us as we were heading back to the boat-launch. Of course, minutes later, we almost nose-dived and crashed when the tail wind started giving us a little too much help, and I had to scramble on top of the ice chest to put as much weight on the rear of the craft and get sprayed with water. That did not look cool. Good thing the van wasn’t watching.

My next trip to Tillamook will involve assisting with the installation of rigging to secure an instrument package beneath a pier. The planning and design that has gone into this is significant, as are the challenges. There are cables, pulleys, huge bags of stones, and power tools involved. The trick will be in not getting smashed by the pier or boat, as the work must take place from a boat beneath said pier. I will also be collecting a time series of water samples to test for variation in respiration rates as the water changes with the tides.

I leave you with a couple pictures of the latest rig we have employed on water sampling trips for maximum efficiency.
Cheers!

Filtering water with the peristaltic pump.

Pumps make sampling fun!

I have spent an awful lot of time hunched over vats of acid washing bottles and syringes this week. Oddly, doing the dishes, whether with soap and water or 10% hydrochloric acid solution, is drudgery. The only excitement to be had was when my right glove began leaking. I expected the worst, but after rinsing with Milli-Q ultrapure water I was unharmed. I had the pleasure of throwing out the scary old gloves and donning a beautiful new pair that I can love and trust for the rest of the summer.

The experiment incubating pure water in plastic containers to look for an increase in the dissolved oxygen occurring as a result of leaching yielded interesting results. The 2 gallon ziplock bag showed quite a large increase in dissolved oxygen level in the ultrapure freshwater over several days. Unfortunately, the ziplock bag containing sterile seawater drained empty at some point during the incubation. The data on the logger from the drained bag showed a similar trend to the other bag, but the plot went wonky when the water started leaking. The five gallon carboys of pure water and sterile seawater showed much lower rates of leaching than the ziplock bags. Hmmm.

The glass BOD bottles are working out nicely. On Wednesday I went to Tillamook and collected water samples at low tide from several points in the bay that represent different mixing zones. I began incubating them on Thursday in BOD bottles. Temperature and light exposure have been difficult to control due to laboratory limitations, but wrapping the bottles in aluminum foil and storing them in a cooler in a dark room has helped keep them at a stable temperature and prevent light from triggering photosynthesis int he phytoplankton.

After 24 hours of incubation, we took oxygen readings and compared them to the oxygen levels in the water in the bay when the samples were taken. We noted significant decreases in oxygen, meaning the microbes were consuming oxygen at a rate that could be easily measured in a single day. This information answered key questions about the required size of bottle and length of incubation required to measure respiration rates in this environment. While biological oxygen demand has been measured in BOD bottles for many years and is a standard practice, measuring estuarine respiration rates in a complex system like Tillamook Bay is not the usual application. Knowing that we can use small samples of water and get results in a couple days is very helpful. If the oxygen decrease in the bottles levels off, it has been suggested that I add glucose to see if the microbes take off again and are carbon limited. Exciting!

Now I just need to prepare more BOD bottles. Back to the acid.

Last week’s water incubation experiment was useful. The plot of the dissolved oxygen levels over the weekend showed clear declines in all of the samples, but there was some strange “noise” at around the same point in the plots of both of the ziplock bags. There was no way to determine an accurate respiration rate from the data. Additionally, the magnitude of change in the dissolved oxygen was much greater in the ziplock bags than in the carboys. My mentor, Cheryl Brown, found an interesting paper in which similar methods were employed to determine respiration rates, and the researchers found that enough oxygen would leach out of the plastic containers and into the water to confound their results. They carried on using plastic containers for incubations, but incubated additional “blank” containers containing ultra purified water to determine a rate for the oxygen leaching from the plastic so that they could correct for it.

I am currently running several incubations of ultrapure water in carboys and ziplock bags to see if leaching could be the source of the noise in our dissolved oxygen plots. We also went to Tillamook and collected more water samples that are now incubating in glass BOD bottles, glass bottles specifically designed for the purpose of measuring biological oxygen demand through incubation. The oxygen sensor we are using for the bottles is optical like the HOBO loggers, but much smaller and designed to fit into the mouth of the bottles. The sensor does not take a time series of readings, and will be used to take only initial and final readings of dissolved oxygen.

The main purpose of this week’s Tillamook trip was not to collect water for incubation experiments, but as a trial run of the bi-weekly water sampling plan of Tillamook Bay and the tributaries that will take place over the summer. Two teams with boats went out on Friday and collected water samples to measure the carbonate chemistry and nutrients of the bay and the tributaries. I rode along with the team sampling the tributaries. We did a little boating in the lower end of a couple rivers and went out only a short way into the bay before pulling out the boat and driving to all five of the rivers to gather water samples both above and below the agricultural zone. It was a long day, and aside from the pungent smell of dairy cows, or “the smell of ice cream”, I saw juvenile salmon leaping out of the water eating bugs in the morning, green herons and pairs of bald eagles, and even one large juvenile chinook in a pool up the Miami River. We will be doing these sampling trips every two weeks for the rest of the summer and I hope to observe and learn more about the ecology of the Tillamook region as I continue to learn about the science of water.

Collecting water with a Van Dorn sampler.

Nutrient sampling on the boat.

A beautiful morning on the Trask River.

I have begun my experiment. To tell the truth, it is not a glamorous affair. It wasn’t even my idea, though I wish it was. It consists of nothing more than 5 gallon plastic jugs, black plastic, duct tape, and several HOBO U26 dissolved oxygen data loggers. The idea came out of a planning meeting where the desire to get more precise measurements of microbial production in the rivers flowing into Tillamook Bay was one of many topics discussed. The method proposed was to incubate samples of water in the dark for a period of time, and measure the change in dissolved oxygen from start to finish. Any decrease in the oxygen level should be the result of organisms in the water respiring, eating or decomposing organic material in the water.

It is important to know how bacteria change the conditions of the water, changing the amount of nutrients that flow into the bay and the concentrations of both oxygen and carbon dioxide. The ocean is warming and becoming more acidic, bringing increasingly acidic water into the bay with every incoming tide. The nutrients that flow into the bay from the surrounding watersheds lead to increased bacterial growth that close the oyster beds in the bay to harvesting, as well as further acidifying the waters, as dissolved carbon dioxide increases in the water as bacteria release it as a waste product of their metabolic processes and it reacts with water to form carbonate, bicarbonate or carbonic acid. The relationship between higher nutrient inputs into marine waters from terrestrial systems and increased acidification is not just a bay or estuary problem, but a coastal problem as well. The EPA, along with the Navy and many other players, hope to assemble the big picture of how Tillamook Bay works with respect to all of these issues so that the people of the region can better plan for climate change and mitigate potential problems, as well as improve the health of the ecosystem and the lives that depend on it.

There was a considerable debate about how best to go about incubating the water and how to measure oxygen changes in a scientifically valid manner. The issue with the incubation lies in the transporting of the water to the lab. Changes to the temperature of the water will effect the solubility of oxygen in the water, as well as the rate of production of bacteria, affecting the results. Maintaining water samples at a constant temperature remains impractical and a concern, but a greater concern is with the Winkler method. The Winkler method is a method of analysis that allows for measuring the dissolved oxygen at a single point in time, but not continuously, but the measurement can be more precise than that of a datalogger. It was proposed that only initial and final oxygen measurements would be used to determine the total change in a sample, and the incubation period would be short, a few hours at most. As the experiment was discussed, it became apparent that such a short period of incubation may not adequately capture microbial growth, and that a time series of measurements would be the only valid method of determining a rate of microbial production. Thus, the 5 gallon jug trials, to gather a time series, determine a proper incubation period, and as a basic proof of concept.

Friday we drove to Tillamook and collected samples, though not as many as we had planned to. We are also evaluating an alternate incubation method using 2 gallon ziplock freezer bags kept dark in a cooler. The samples have been incubating all weekend. On Monday I will download the data from the loggers and see what there is to see. I may even have a graph or two to share next time!