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

A place of comfort

Springtime is almost, almost here. There's a mist of green among the understory trees and shrubs clustering the property lines behind the house. It has been raining since yesterday. My friend (now more than a friend) BG is off somewhere in the button-round hills leading a hike. I am following my usual Saturday rituals. Saturday is my day of relaxation. I've finally learned to give myself one of those. I get up late and unhurriedly. I let Apollo out of his crate and into the yard. After he does his sprinting and sniffing routine, call him back into the house with me, where I make myself some breakfast, usually hot cereal simmered slowly in milk. Then I clean the house.

I rent from a middle-aged single father whose teenage daughter lives here most of the month. I have two small rooms and a bathroom on the right-hand side of the house, along with access to the kitchen and living room for both myself and Apollo. Gigantic dogs shed hair, so part of the agreement for renting here is that I vacuum after him. I do a more thorough job than anyone here expects--usually dusting and tidying, a little extra scrubbing in the kitchen.

Renting here has had its ups and downs, but on days like these I especially aware of why I choose to live in close proximity with a family in a private home, instead of some little apartment off the interstate. The truth of the matter is that I don't do very well on my own. Mind you, I think I'm a pretty mature 24-year-old. I have a full-time job as intern/technician at a national lab. I pay all my bills and college loans and help a younger sibling with college tuition and living expenses. But living alone just doesn't work out very well for me. It seems I must have people to come home to in order to retain my sanity and compassion. Life for us humans was meant to be lived together and I am a rather vulnerable example of that.

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.

Death in the greenhouse

If you're the type to be struck by little things, poignant moments occasionally happen, even at national laboratories. Sometimes I'm that type.

I was feeling discouraged and distracted at work one day this past July and to try and get my mind back on science I did the usual and visited Greenhouse 1. Greenhouse 1 contains mesocosms full of Arabidopsis plants that are supposed to shed light on the problem of scaling, essentially how a change in one important gene can translate across multiple ecological hierarchies. I was not thinking about ecological hierarchies, though. I am a student intern and I don't get to worry about those things. I had a different problem: my plants were flowering too early, making collection of all sorts of important data pretty much impossible. I wandered in and out of each row and stared at my precociously flowering babies til I got to the last row, row 6. There's a door that goes outside just beyond row 6 and no one ever uses it. We all come into the greenhouses through the headhouse. I even didn't notice the door when I first started working here and I still forget about it a lot. That day I re-noticed it and while I was staring aimlessly at it I spotted a tiny skeleton on the floor in front of it. A little toad or frog had somehow got in and died there, crouched a foot or so away from the wall between it and freedom.

For some reason this struck me as a deeply poignant moment. I was having a super-rough day and that might be why it impressed me so much. Whatever the case, it was a moment and to keep a memento I carefully picked up the skeleton and took it back to my office. I keep it sitting on my desk, near my luxuriantly beautiful African violet. It is pretty well preserved, having dried up and the flesh decomposed by innumerable microorganisms, though some skin and membrane dried stretched across the tiny bones. It is so light, just 1.1774 g, and fragile but tough at the same time. It is a nice little specimen--more or less a complete skeleton I think--but I keep it more for the evoked emotion than as a curious scientist. If I were a poet, I might have written a poem about it because it seems to me that such a moment begs to be poetized about. But I only write "poems" when either a nice string of words occurs to me or I am so upset that no other emotional outlet seems possible.

Though no haiku is forthcoming, I did want to tell this story because whenever I think about it, I feel a sort of universal sadness. The little toad didn't know it couldn't survive in the big, cold, concrete-floored greenhouse. It wandered in somehow, perhaps through a hole or squeezed under that forgotten door. I clearly remember it was positioned facing towards me, away from the door, as if it had slipped in and found a quiet place to die. It dried up huddled in the same crouched position and remained there until I reached for it. I often pick it up off the desk and cup it in my palm, examining the intricacies of its figure. I think, in fact, that no poem is needed. The skeleton is so meaningful in itself.
















Image above: the lonely toad, photographed by Arabidopsisgirl