Slump Time

It's one of those times when I'm not feeling very motivated to do anything. This extends to my personal life as well as my work life and it's frustrating and demoralizing. I'm not sure why I so often seem to hit a lag spell in late spring, after more busy and productive winters (though a trend of unfortunate spring/summer romances could correlate). You'd think with all the busy photosynthesizing going on outside I'd be inspired.

The past couple of weeks I've simply been hauling myself to work and going through the motions. The high point of my day today is going to be a waltz lesson at 7 pm, because dancing always brightens my mood. But before that I have Apollo to walk and primers to design for a gene that we're going to be cloning. I also have to do mesocosm work, which isn't exactly inspiring or fun and RNA extractions for a very particular technician. Sundry and various miscellaneous tasks are also beginning to pile up. Let's have a resounding headdesk for my miserable lack of enthusiasm. I hate it when my life turns into shades of gray.

On the bright side, I do have a Brugmansia suaveolens seedling that finally germinated after almost a month. I planted about fifteen seeds and only had one pop up, but one plant is really quite enough anyway--the plants can get quite big. All the other seeds molded or were consumed by little larvae, perhaps partly because I kept the soil too moist. In any case, the germination was a victory for me and something small to be happy about. Maybe inspiration will hit tomorrow.

Prevarications

How to appreciate the growing, blooming, alive, respiring plant and probe its innermost workings at the very same time? How do you describe the real world in such a way that you construct an accurate model? How do you understand both the whole and the parts? Ever since I brought my African violet, Murphy, to work and rediscovered my love of cultivating plants I've been pondering these questions with little success.

I bought Murphy at Kroger's the second night I moved to my current job at the labs. Murphy was the prettiest of the group on display, with delicate, purple and white flowers and nice, firm leaves. At the checkout counter the clerk accidentally sliced off several of the largest leaves, leaving the plant with a lop-sided appearance. Oh well. I put it on my windowsill and promptly forgot to water it for a week or so. After discovering that my violet was looking a bit limp, somehow, during the 10-foot trip from my windowsill to the sink, I managed to drop my violet plant-first on the ground. Somehow, I managed to do this several times over the next few weeks. Needless to say, it lost soil and I didn't get around to replacing it. But it struggled on. I switched apartments after a month and dropped my plant again. Then I moved again, to cheaper accommodations and relegated the plant a low table, where my newly adopted dog blithely knocked it over with his magnificent tail. I watered it occasionally and shifted it around the apartment, musing that its lighting requirements weren't being met. At some point, I realized that my plant had had a most unfortunate life ever since I'd bought it. Still, though admittedly ragged and unhealthy looking, it was alive, and I named it Murphy, after Murphy's law. Last summer I finally decided to bring it to work with me, thinking that perhaps it would do well under the fluorescent light at my desk.

To say that Murphy did well would be an understatement. Murphy flourished. Having the plant in front of me all the time was encouragement enough to give it some much-needed TLC. I added some soil to the pot and gave it a bit of 10-10-10. Most importantly, I kept it stationary on my desk instead of traipsing around with it. I recently re-potted Murphy in a larger pot and Fafard mix and have been enjoying almost uninterrupted blooms ever since. I am not modest about Murphy. I love talking about my plant and showing it off to people and telling the story behind the name.

For me, plants are far more than simply the taxonomic group I've chosen to do research on. I love them and always have. When I'm driving, I unconsciously identify trees and wildflowers on the roadside. At art galleries I am drawn to the intricately tiny plants Medieval and Rennaissance artists painted in the backgrounds of their classic renditions of Madonnas and saints. I am also fascinated by the disjoint between the methods and principles of botanical study and the art of growing plants; for you can do one with excellence and fail at the other. You can love you some molecular biology and care less about that random field flower you carelessly spotted while trying to figure out why the fragments in your gel aren't the right size even after redesigning the primers. You could recognize and appreciate close to every single plant species growing in a forest, yet have not a clue about the staggering array of busy mRNAs and proteins massed in a single cell of one plant among those myriad species.

I sit at my desk, with Murphy and various other favored plants that I feed, water, and fuss over between gels and protein assays in front of me. How does the science I do on frozen leaf tissue dissolved in chemicals fit together with the simplicity of my alive and entire African violet plant, faithfully flowering away?

Image upper left: Murphy, after luck turned, photographed by Arabidopsisgirl

Southeastern Springtime

Another springtime finds me here at the labs. Another springtime finds me slipping out of my office to dawdle along the paths and take pictures of wildflowers. Here are a few woodland/edge species common in this area.

Being blue, the little iris is my favorite. I used to want to grow these in my garden in upstate New York. I was disproportionately thrilled to discover them growing wild here in the South last spring.

Botanizing in the hedges is way too much fun. Must get back to work! Lab meeting to attend and protein assays to do.

Image upper left: Iris cristata, the miniature wild iris of the South; Image upper right: Lithospermum canescens; Image above right: Trillium luteum, photographed by Arabidopsisgirl

The Listless Flower

A peek at my desk at work will clue you in on the real reason I do research: I love plants. I'm already growing hundreds of Arabidopsis, soybean, poplar, and switchgrass plants in greenhouses and growth chambers, but I still keep two African violets and three Pothos rescued from my renter on my desk, along with various cuttings soaking in a plastic juice bottle full of water. I also have a rangy begonia, which is unfortunately not flourishing like the others. Begonias aren't that difficult to keep alive and with the right conditions they can be stunning. Mine is not. My begonia has straggled along for months now. It grows, but the new leaves emerge oddly curling and twisted, and those lower on the stems progressively yellow and fall off, leaving long, bare stems that sprawl gracefully from behind my computer (this is classic shade avoidance phenotype--elongating, non-branching, sparsely-leaved shoots). My plant also flowers, and in classic begonia fashion the flowers are short-lived and shed often. The fact of the matter is that begonias are particularly messy plants to grow and mine is no exception. However, I rather like this aspect of my plant, particularly on very quiet days like today, when few people are around and the loudest noise you hear is the steam pipes rattling in our ancient building. At random times throughout the day the stillness is interrupted by the softest of sounds: the fall of a flower.

Points for Science

It turns out that committing to read Michael Polanyi's book Personal Knowledge for my discussion group was just the beginning. After I finished it last month, all the unanswered questions and uncertainty about his case for personal knowledge consumed me to the point where I ended up doing a bit of a literature review to find out what kind of standing he has in the scientific community. It turns out that not only does he have one, but that his views are at least a little bit familiar to established scientists in a variety of disciplines within the biological sciences. I am thrilled to find his name being quoted with respect in major review papers. I admit that I am also a little smug about this.

The small discussion group I've managed (with help) to pull together is composed of a variety of people from different backgrounds. A couple of the philosophical types have what I feel is a bit of a condescending attitude towards the natural sciences. Polanyi directly attacks pure reductionism and its derivatives in his book. While there is no doubt that pure reductionism has driven much of modern scientific inquiry, tides are turning on the linear thinking approaches originating from the more extreme reductionists (I'm thinking of Crick, I suppose). Now we have papers written on systems biology, emergent properties, and new conceptual approaches in areas like genomics and molecular biology. I think the philosopher crowd is mostly unaware of this shift in scientific thinking. That is understandable given that this movement is only now gathering numbers and developing research projects that utilize these concepts practically. But the undercurrent attitude of some philosophers that scientists need to be spoon-fed metaphysics because we are too buried in exploring some trivial molecular pathway is irritating and (I believe) inaccurate. I think it is just too cool that a couple of scientists have picked up Polanyi and started self-critically integrating his ideas into research while in the meantime philosophers have more or less forgotten all about him. Teehee!

Down Time

Thoughtful mood today, sitting at work watching the progression of a 543 nm laser inching down a microarray slide on a computer screen. The growing image is beautiful: it looks like little squares of the night sky arranged to form a larger square. A mini-fractal, so to speak. Of course, what the image really represents is a group of carefully spaced DNA fragments attached to a chemical matrix on a glass slide, with the bright spots showing where DNA fragments recovered from heat-shocked Arabidopsis plants have hybridized to their matching sequences among the probes on the slide. The results will help us understand which genes are active in our plants.

Being one half of the resident cheap labor for my project, I'm the one who gets to sit in this icy corner on the third floor, making sure the images from the two lasers (543 and 635 nm) coincide in brightness. I actually like this job. I get to stare at a pretty picture, tinker with it in the name of science, and think. I have a down jacket that is just preventing my hands from turning blue with cold. I also have a stack of papers that I am forever planning to read and this stack of blank paper for notes. I never turn down "thinking time" tasks at the lab. I've spent a lot of the past hour and the past weeks thinking about Polanyi's ideas.

Polanyi's view of biology has me both deeply intrigued and deeply unsettled . I love his book. It hits some key, rarely-addressed aspects of biology unflinchingly. Most importantly to me, he acknowledges that our human foundations of knowledge have their roots planted most unquestioningly in our biological heritage. He does no dabbling about the role of evolution and the place of this critical theory in our quest to understand ourselves. While reading the book I never got the sense, as I do from proponents of intelligent design theory, that he's going to spring some gotcha revelation about the Biblical origins of the human race on me. He's trying to understand the real universe.

Yet in some ways this questing of his is what troubles me the most. He has left me with many more questions than he raised in the book and not much insight to answer them. How do I, an aspiring researcher, frame questions in my routine research based on his view of science? Where does this vitalistic "force" he proposes towards the end of the book originate in the history of life and what is it anyway? How can we integrate our understanding of different levels of biology in order to glimpse a more complete picture of ourselves and the rest of life? The thread of these questions can be traced through stacks of systems biology papers. They pose a gargantuan problem to modern biologists. Are these questions outside or beyond the scope of Personal Knowledge or did I miss something critical when I read it?

Image upper right: combination of microarray images scanned by 543 and 635 nm laser, image scanned and saved by Arabidopsisgirl

Close Calls of Mice and Men

Living life carries incredible risk. It is the risk of death.

There's something about being slightly nomadic, young and single, and focused on an objective where you can confidently talk yourself into doing all sorts of foolish things. I'm not one to drink myself senseless at a bar or experiment with illicit substances, but I've taken my share of other risks, living in sketchy neighborhoods, walking alone any time of the night, and driving through bad weather. On the way up to my parents' place I lost control of my car on a bridge and ended up halfway into a snow-drifted ditch. Not two weeks later, shortly before New Year I spontaneously decided to change my plans from spending the rest of the holiday at my parents' house to driving over 300 miles through the night to spend it in New York City--without checking the weather ahead of time.

It was a nice drive for the first 2-3 hours. I chatted with my sister and played my Celtic music and mused about life. Apollo made himself comfy in the back seat and eventually my sister dozed. I'm fond of long, quiet drives. They vindicate my fondness for thinking and I like being occupied while I think. I was settling in for a nice, 7-hour drive when enormous snowflakes started trickling down from the clouded sky. There are two ways to get to The City from my parents' house and I'd chosen the somewhat longer, but (I thought) safer way. I was shortly reminded about lake effect snow off Lake Champlain, Lake George, and the Hudson. Slush piled up on the road and it got worse the further south we drove. I had to turn my music off and shift every ounce of concentration to the road. Other than a few big rigs I was practically the only person on it.

Blitheful spontaneity no longer seemed like a good idea. Upstate New York is sparsely populated and we were miles from family and friends so I decided to press on as far as I could. I got about halfway to Albany before I detected a change in the road in time to slow to a 15 mph crawl. The bridge was all ice and the car simply slid all the way down until I managed to brake it to a halt in the slush on the left lane. On the right side of the road across from me a less lucky vehicle was askew in the snowdrifted grass with emergency lights flashing. That was it for me. After shakily pulling back into the tire track path in the right lane, I got off the highway at the first exit I saw and found a 24-hour gas station. Inside, a couple of bona fide upstaters were conversing about the state of the road and the mindset of people with 4-wheel drive. The storm was worse further south and there was black ice until Albany. I knew I wasn't going anywhere soon.

I went back to my car, where my sister was somehow managing to catch a nap in an impossible position in the front seat and there was Apollo, curled up cozily on our luggage in the back. I, on the other hand, was on overdrive. I've always had trouble sleeping before and during long road trips. A mix of apprehension and excitement rev up my adrenaline and I do these six- to fifteen-hour drives on practically no sleep. After almost crashing into a guard rail, sleep was out of the question. So I picked out two pieces of cinnamon gum and watched the road for the snowplows and the sky for snowflakes and the gas station for unscrupulous individuals who might want to pick on two sleepy girls in a car. It was a long, long time. A few snowplows came and went. A few people came and went. The snow fell harder and harder.

Eventually someone else parked an SUV ahead of us and sat with the engine running for a very long time. No doubt they were waiting for slightly better travel weather as well. In the meantime, I was charmed to see a chipmunk skittering around in the snow. I love chipmunks. They are adorable and chirpy, harmless and lovable. Someday I'll tell you the story of Chippy the Chipmunk, who lived under the backroom in the house where I grew up. But this little chipmunk should have been asleep in a warm tunnel underground, not scampering around a gas station during frosty December snowstorms. Did you ever think of the inside of a tire as a cozy hideaway? This chipmunk did. It seemed to be looking for shelter, darting up the sidewalk and around the ice chest and garbage can. Then it spotted the left rear tire on this parked SUV and darted into it. It stayed there for several moments and then decided to try the right rear tire. It preferred the left one and went back to it. To my horror, not a minute later the brake lights on the vehicle lit up and it started moving.

I couldn't look away. As the person slowly backed the SUV towards me, I could see the chipmunk running inside the tire like a mouse in an exercise wheel, going faster and faster, trying to keep up. At the last minute, as the monstrous contraption paused to turn the front wheels and pull away, Chipmunk managed to jump out and dash safely back to the gas station. I let out a sigh for both of us as it disappeared around the station corner, unharmed and hopefully wiser. For some reason, at the time, intervening didn't enter my mind. In retrospect, I suppose I could've woken my sister and Apollo by bouncing out of the car and waving my arms at the unsuspecting traveler, hopefully getting her to stop and let the chipmunk escape. Happy for my conscience that Chipmunk was lucky and quick enough to jump out all on its own.

I ended up waiting two hours before venturing back onto the highway. I took things very, very slowly and pulled over several times. By the time I hit clear road I was so tense that my arms hurt and I couldn't tell whether the unsteadiness I felt on the road was black ice on the road, the blasting wind, or my lack of sleep (in the end I figured out that it was the wind). It was a rough drive and it took me a few days to recover my usual equilibrium. Chipmunk and I should've known better than to take midnight trips in the dead of upstate New York winter. It will be a while before I risk so much to get somewhere.