Tag Archives: summer research

Cloning, Harvesting, 117 Grilled Cheese … and Counting

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Ryan Apathy photo Grand Park, Mt RainierWeeks before the summer even began, Dr. Bryan Thines, PhD, my research advisor and a professor of biology and genetics at Puget Sound, challenged me to a beard-growing competition. “I like to have friendly games within our labs,” he told me after I received my research grant. “It encourages both competition and camaraderie.” I had already been pranked once by my lab after I misspelled the word “assess” on a poster for a presentation, so I should have assumed that our summer work would be just as mischievous as the previous semester.

I and two other students, Lily O’Connor and Tina Chapman, are working hard to characterize F-box proteins in Arabidopsis thaliana through molecular, genomics and bioinformatic approaches. Through weeks packed with genotyping, gels, culturing, cloning, harvesting seeds, and extracting DNA, we have finally begun to identify knockout lines, develop gene constructs, and locate brand new candidate genes for further study.

Throughout the hard work we’re putting in at the bench, our lab has found additional ways to entertain ourselves. Any given day often alternates between lab meetings discussing research progress, thesis writing sessions, miniature genetics or molecular biology lectures, bench work, and discussing how many grilled cheeses we have each eaten since our research began (I’m in the lead with 39).

Lily, Tina and I are entering our final year at Puget Sound, and we collectively decided to capitalize on our mentor’s time by bombarding him with questions about scientific writing, life after college, applying to and attending graduate school, how to make the best cup of pour-over coffee. As we enter the penultimate week of our ten-week grant program, our lab has collectively grown countless pots of plants, run dozens of gels, eaten 117 grilled cheese sandwiches, and grown two significant beards.

Ryan Apathy’s summer science research at University of Puget Sound is supported by the M.J. Murdock Charitable Trust’s Science Research Program.null

And So it Begins

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It’s official – summer has arrived at the puge. The flowers are out, the birds are chirping, the rain has been absent for well over 7 days now, and students – myself included – are beginning research.

Which is crazy to think about. Because between school and finals and OLE, I was not able to fully process the fact that research is upon me. I always knew it was coming. I’ve prepped this entire semester for this moment – I’ve written a proposal, created images plotting what my plan for this study is, and have had multiple hour-long conversations with my advisor/professor/role model for life, Carrie Woods, about bryophytes and epiphytes and life itself. The days turned to weeks which turned to months, and there was always something else to do before I could focus on the research I was doing this summer. And, like so many things about college life, it snuck up on me – but unlike many things about college life, this sneak-up was pleasant.

Because now I am here. I am sitting in the sun (!!!!!!) in the courtyard of Thompson on this beautiful Friday, after my first full week of undergraduate research (which included learning mosses, extended walks through Point D, climbing in the rafters of Harned, and over-complicating things in the typical college fashion). And I know that, for once, everything I worked for this semester has paid off. All the stress the proposal put me under, all the hours I spent reading paper after paper about epiphytes, all the mini-breakdowns that occurred all too often in Carrie’s office about “What-am-I-doing-Where-am-I-going-I-don’t-know-what’s-going-on”, all the people who told me that it wasn’t possible for a freshman to get a research position here, everything – everything – has boiled down to these 10 weeks.

And I couldn’t be more stoked to spendthe summer doing the thing that I love, with the people I adore, in the place that I can officially call home.

The first prototype of the bags that are going to be used to hang the bryophyte samples. Super over-complicated, as per usual.

The first prototype of the bags that are going to be used to hang the bryophyte samples. Super over-complicated, as per usual.

The second prototype for the mesh bags - this one took far less time and makes far more sense.

The second prototype for the mesh bags – this one took far less time and makes far more sense.

My view for the past few days

My view for the past few days – look at that beautiful bryophyte!

 

On the Road

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In late May, two weeks after the school year drew down, I drove south from the San Juan Islands to my home in the Bay Area. The drive, fourteen hours with an overnight intermission in Eugene, OR, began a journey on which I planned to drive quite a lot: some ten-thousand miles all told, on a trip that would neatly circumnavigate the country. The while, I would be researching state energy policy. It was a sponsored trip, a university research grant doled out in a single check for the amount of $2,750. An additional stimulus of $500 was to come at the end of the summer, as soon as I had submitted my research and earned the money.

In June and July, I worked my way from California to New York, beetling by a circuitous route across nineteen states and over thousands of miles of backroad highway. My trip plunged, first, into the sunstroked American southwest. Abbey country: Utah and Colorado, where landscapes are scrubbed Desert Solitaire pinks and purples and where, perhaps by some southwestern ordinance, every bookstore seemed made to own at least one signed copy*.

Sunset (not so pink) in Joshua Tree, CA, the last California stop before true SW.

Sunset in Joshua Tree, CA, the last California stop before the true SW.

As a guy who’s only ever lived by a body of coastal water (at the very least by a sound) I was beginning, somewhere in Utah, to go a bit crazy from the dryness. So, like a thirsty migratory bird, I winged my way northeast, stopping first in Texas before traveling up through the soggy South. Misssissippi, Alabama, Georgia, the Carolinas. State by state I absorbed then sweated back out the monsoon humidity of the region, the annual baptism of the South in mid-summer.

I arrived in New York in early August, days unshowered and tanner than ever, my skin crisped a yellow mud color. I had spent most nights** sleeping on the road in the back of my Subaru, a stalwart hatchback of some 200k+ miles whose back seats I had replaced with a platform bed. Four nights on a couch in a friend’s NY apartment, then, felt sadly palatial. The couch was not even very comfortable; it was simply not located in the back of my car.

Wheel

The worn leather of an old wheel.

Four nights were all I had in New York. A nagging internal voice kept reminding me that certain parts of my research were yet-undone. I needed to get home, but I was on the wrong coast.

After some ribbing, I convinced another friend, Robin, to make the drive home with me across the three-thousand-mile width of the U.S.-of-A. We would travel through: Pennsylvania, Ohio, Indiana, Illinois, Wisconsin (briefly), Minnesota, South Dakota, Montana, Wyoming, Idaho, and, finally, Washington. In Washington we would stop, stay for a week before driving south to California.

As an aside, I have known Robin nearly my entire life. Our mothers met in a pre-natal group when we were yet unborn. We grew up together, in proximity until he moved to the East Coast in the first grade. We have managed a close friendship since then, upkept by summer visits and an annual backpacking trip.

The smell of gasoline in the morning.

The NY-WA stretch was, is, a long one. According to google maps, the drive alone would require just over forty- three hours of car time. We figured another twenty for sleep/gas/bathroom stops. A ratio of 3-1, driving-to-not-driving. Respectable and manageable. The notion of such speed across such distance had, we thought, a certain sex appeal about it. The appeal of crazy endurance, of comfort foregone for greater speed. Of two rugged dudes racing the very sunset across the spine of the country—of the evening redness in the West—of the lonely flatness of the American interior—of something like that.

Highway Morning

Morning on 90-W: The lonely flatness of the American interior.

And how better to transmit all that steam, we thought, than by an Instagram account?

On the 13th of August, departure day, we make the account. At precisely 1500hr (auspicious because it is the exact time we had planned to leave, which never happens) we pull out from Robin’s driveway. Our first post is a picture of my car with a sentimental caption, and it is yet fresh as we merge onto Interstate 84-W.

Robin takes first shift behind the wheel—first of many, many—and I look out the window, scouring our surroundings for second-post-worthy content. Something exciting, something sexy. I find very little of this: road signs with graphics a touch silly; advertisements one could not imagine would work on anyone; all sorts of funny looking humans, our fellow travelers. But nothing remarkable.

In the aggregate, spoken of in elevated terms—“thousands-of-miles,” “number-of- states”—our journey promised to be grand indeed. Peering around at the highway, no particular thing seemed worthy of it.

Really, though (to be ponderous and altogether less fun), no journey is taken in the aggregate. The aggregate, after all, is an aftereffect; a glittering highlight reel that requires the forgetting of lots of unsexy things—speed limit signs, off-ramps never taken, one-pump stations in anonymous, sad little towns. The aggregate is a retrospective deal. It is only in retrospect that a huge stretch of common driving—a series of McMuffins, refuels, farts—can take on the high romantic quality of the trip, the quest: of the Big, Sexy Journey.

We bought dinner here, sandwiches: two patties, a piece of roast beef, nothing else.

We bought dinner here: two patties, a piece of roast beef, nothing else (no mustard, even!).

The journey (the Big, Sexy Journey (BSJ)) is the story of whatever you want it to be. You can be who you want, on the BSJ, so long as you have a good imagination and are creative with your camera, pen, etc.

Perhaps on the BSJ you are a drifter type. The BSJ is for you the story of a rambler. You are a study in hip, chilled-out nonchalance. Neck bandanna’d, man-bun pinned up sloppy, obscure tee dusty from the wear-’n’-tear of the road, your vibes are alive, on the BSJ, and resonating in all the right ways.

Otherwise on the BSJ you are a wandering sage, a poet taking the temperature of the Heartland. Or else the BSJ is more cynical: You are a sneering anthropologist, gathering about you a sneering ethnography of the towns (cultural voids) along the highways linking East Coast to West-.

Robin and I finish our drive, 3,012 miles in total, in fifty-three hours, arriving in northern Washington a bit more than two days after departing from New York. We do this by stopping exactly nowhere interesting, except twice in South Dakota—once at the Badlands Nat’l Park and again at Mount Rushmore.

The Badlands National Park, South Dakota.

The Badlands National Park, South Dakota.

If we had taken more time for own Big, Sexy Journey, perhaps it would have been sexier than it turned out to be. But our BSJ was flaccid indeed. These inane things, among other inane things, comprised it: fifteen gas stations, 1/3 of Steven King’s The Stand audiobook (a 62-hour-long beast), and a nearly constant patter of dull but diverting conversation.

When we turned off the engine for the last time in The Evergreen State, our Instagram account was populated by exactly one more photo than it’d been when we’d left The Empire. The new addition was a picture of a dusky, alien landscape in the Badlands, SD, the only really remarkable shot taken during the entire trip. Not shown: three-thousand miles of westbound highway 90.

Not shown, at least, until now.

Somewhere in Ohio (or was it Pennsylvania?), I started to shoot footage. Mostly from the passenger-side window. Of passing trees, passing cars, the passing road. A gas station. A rest stop. Another gas station. Another gas station. Another gas station…

Another gas station...

Another gas station.

After working the footage for a couple of days, I made a film of the trip. Having never made a film, this project was a bit out of my wheelhouse, but nevertheless fun to do. The agenda of the film (that is to say the agenda of its creator, of me) included all the usual goals of travel stories: to relay some version of the truth—to make a narrative at once universal and unique—to tell a story.

Yes, this: to tell a story: to string bits and pieces—images, noises, scenes—together into something more than a mere collection of parts.

What departs our travel story from the typical one is the nature of the parts we did collect, those which made the final cut. If other travel stories have a range of parts—some smooth and some sharp, fun because the collection is so eclectic—ours is like a bucket of wing nuts: repetitive, hard to lift, possibly beginning to rust from last week’s rain.

This film focuses on the parts of the drive usually cut from the journey. It lingers for sometimes uncomfortable durations (in mimic of a real drive) on the stretches where absolutely nothing of note happened at all.

This film is very boring; that is basically the point. I hope you enjoy it, though I expect you to not.

*I had left my copy (unsigned) at home and, though I’d already read it, I bought a new one out of a weird feeling of peer pressure, only to not pick it up once over the following months.

**—with the exception of an unmentionable two in Jackson, MI, when the air had been so palpably wet that I caved, rented a motel room and watched Grimm, perhaps the all-time worst show, late into the night.

A Star-studded Summer

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A clump of healthy Pisaster ochraceous on San Juan island

Sitting here in the sun with my feet pressed familiarly against Harned’s red brick patio, I can’t help but be overtaken by a strange feeling. It seems as if the summer is flying by ever so slowly. The past two months spent conducting summer research here at Puget Sound have been a kind of exhilarating whirlwind that I could never have anticipated during the frantic weeks I spent writing my proposal in the winter. On one long drive between study sites, I was shocked to realize that in the past two months I have seen about 2,000 different sea stars. This sheer number has trained my eyes to instantly identify the species of a sea star and evaluate its health with a sensitivity that only repetition can offer.

But perhaps I should retrace my steps and introduce my research. My name is Haila, and I am a rising Junior majoring in Biology with a minor in English. I’m currently working with Dr. Joel Elliott and fellow student Katie Pyne to evaluate the effects of sea star wasting disease. This aptly-named marine epidemic has traveled up and down the western coast of the United States, brutally dissolving our beloved celestial echinoderms. The cause of wasting disease and the way in which it is transmitted is still very mysterious, although researchers get closer to finding an answer each day. Fortunately, Dr. Elliott and his students have been closely monitoring local sea star populations for years, providing us with solid baseline data to which we can compare the condition of present populations.

San Juan Island photos 264On the days of the month with the lowest tides, Katie and I venture out to the rocky intertidal, GPS and measuring tape in hand, and collect data on every sea star we can find along a previously established transect. We try to collect as much data as we can so that we can be prepared to answer as many questions about the disease as we can. For each of the 2,000 sea stars mentioned above, we have data on species, arm length, color, GPS coordinates, tidal height, arm loss, and sickness level. We then randomly sample the area of the beach in which we expect the sea stars would be feeding, usually in the mussel zone or the barnacle zone. Since sea stars are keystone predators (they are integral to the diversity of their communities because they prey on and suppress hearty organisms like mussels and barnacles that might otherwise dominate the inter-tidal), we would expect a change in sea star populations to set off a change in the populations of their prey items. However, this change will likely occur more gradually than can be observed in the length of a summer, so we hope to provide a baseline for comparison in the future. When the tides are less than ideal, we return to the lab to study the behavior and physiology of baby sea stars, but we’ll save that project for another blog post.

So far, Katie and I have had the privilege to explore some of the most rich and beautiful intertidal zones that Western Washington has to offer, from  the locals sites in the Tacoma area to the beautiful shores of San Juan Island  to the rugged points of the Olympic Peninsula that house the largest organisms we’ve seen. Personally, I am infatuated with the intertidal zone and the organisms that inhabit it, and this research seems so suited to my love of the outdoors. I spend my time sitting in tide pools, climbing slimy boulders, and crouching down to peer under rocks. In a way, it has given a focused direction to my time spent surrounding myself in wild environments and examining, with wonder, nature.

I have always seen science as a place for mystery-solving, elucidation, and exploration. In the past few months, sea star wasting disease has wriggled itself into the public eye with the flashy appeal of its mysterious cause and its gruesome, zombie-like effects. While to the general public sea star wasting disease is a devastating condition destroying a highly recognizable and culturally significant organism, I feel fortunate that I have been given the opportunity to spend time examining the disease from a scientific, ecological perspective. To me, this epidemic is incredibly complex in its effects and implications.

A wasting Pisaster ochraceous on the Olympic Peninsula

A wasting Pisaster ochraceous on the Olympic Peninsula

Although community interactions are so elegantly intricate and important, they have long been the ecologist’s foil. An animal living in the intertidal is affected by a myriad of different factors: abiotic influences like temperature, wave action, and substrate type can vary immensely among sites, within a habitat, and even from one rock to the next. And, to add to this, all of the organisms that share an environment are connected in dizzying webs that are undoubtedly even more complicated than we understand. And this is what has made our research simultaneously frustrating and interesting, providing us with an abundance of questions and few answers. I’ll try to provide you with a snapshot of where we are at right now. Sea stars are wasting, and the culprit is likely a virus. It seems simple enough, right? But once we ask one question, it only sprouts more and more opportunities for inquiry. We might ask, how do sea stars contract the virus? Can it be transmitted through water? Through contact? Through the shellfish that the sea stars eat? We are seeing huge variation among different habitats, and different types of sea stars seem to be differentially affected. So, is the disease aggravated by temperature? Wave action? Prey source? Are certain types of sea stars affected more than others (are small ones more resistant)? Are the sea stars that we see without lesions completely healthy, or does the virus have a substantial incubation time? We see a high recruitment of baby sea stars. Will they be healthy, or will they become infected when they grow up? If the disease results in a large loss of sea stars, which are keystone predators, what will happen to the communities they left behind? Will the mussels and barnacles dominate?

Perhaps most frustratingly, it is likely that each location will respond differently. Differences in mussel population in different habitats could be the result of differences in settlement, differences in food levels, and differences in the availability of good places to live. All of these factors are likely to effect the response of a mussel community to the absence of sea stars due to sea star wasting disease. However, even with the seemingly daunting lack of control that ecologists face in the field, we are not discouraged. These questions remind me of how much we still have to discover, and this opportunity for contribution (combined with pure curiosity) acts as the fuel for a researcher’s motivation. This summer has been a lesson in flexibility, careful planning, and persistence. I can already tell that the skills I am gaining now will be valuable in the remainder of my education and beyond. Thanks for reading!