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

Recognition

I have a very wonderful friend with whom I share many interests and pastimes. We both like the coffee shop/bookstore atmosphere, where we talk about personal drama, dancing, movies, politics and any other number of things until we get kicked out when the place closes. We dance waltz and salsa together. We watch Battlestar Galactica on his couch and make food and play with the kitten. We've only known each other for about three months, but he is by far the best friend I've made in a long time. His Christmas gift to me was a bonsai tree. It was a very thoughtful gift.

Plantses are my passion and I have a fairly extensive amalgam of knowledge about them, which I began earnestly accumulating when I was nine or ten years old. I often doubt this deeply absorbed knowledge because it doesn't appear to help me at my day job and I think it ought to. That's partly because much of this early knowledge is about horticulture and not biology, so it runs parallel to the information that I learned in college. It's not useless, but it is essentially irrelevant to phytochrome pathways and RNA extraction. However, I was so devoted to learning about gardening and ornamental plants that even details and facts I haven't reviewed in years still surface easily and these little bits of information are very much part of me. The information is so familiar and yet learned so long ago that I don't know where it comes from or even that it is there.

When my good friend gave me my present he immediately demanded to know what kind of plant it was, and I don't think he really expected me to identify it offhand. However, the moment I saw it I knew the bonsai was a Juniper of some kind and that it was about 5 years old. I knew its acerbic, piney scent from childhood, because we used to have a lot of them growing around our house and during the winter we'd accidentally sled into them and crush the branches. In the summer their prickly needles would scrape our bare feet when my brother and I chased each other around. I knew that maturity would load a Juniper with blueberry-blue berries and that Junipers hardy enough to withstand sub-zero temperatures and harsh soil conditions. For a moment I was flooded with Juniper knowledge and pleased that my guess at the age was so close. The plant was six years old.

Moments of recognition like this are always special to me, even when they are about small things like identifying houseplants on command. It takes a lot of dedication to acquire knowledge and it disappears into the brainvoid far too easily. It is nice to know that it doesn't all disappear completely. Even more meaningful is the reminder that the things to which I dedicated myself so deeply as a child were not foolish or frivolous, even if esoteric. The near-obsessive thirst to decide on the perfect plant to grow, to identify the delicate spring ephemeral, to touch the rough needles and the velvety leaves and the coarse stems on a thousand and one plants was an obsession that constitutes the depth of my knowledge. It is something that has remained with me, though it gets buried three deep under my other activities and everyday living. After hearing the name Sequoia sempervirens in the movie 'Kinsey' last night, I was compelled to look up the meaning of 'sempervirens' in my book of gardener's Latin. Another reminder of the time in my life when the meaning of a plant's name was larger than day-to-day existence.

Those times came and went and returned only recently. The internal travesties I endured adjusting to culture shock after I entered college numbed my ability to absorb and identify information about the botanical things I love to understand. Even though I participated extensively in research activities and got decent to good grades (apart from physics) I often feel that the information I carry from my bachelor's degree was mechanically assimilated and remains divorced from the rest of my psyche. Classroom knowledge continually fails me as I struggle to solve problems and piece the intellectual facts together with the practical aspects of centrifuging and pipetting chemicals in my lab work. Today, identifying a little, artfully twisted tree pulled me back to a time when I learned what I loved and seamlessly applied what I learned to the world around me.

I have taken this recognition as a quiet mandate to keep striking out on my own in the intellectual world. Devoting myself to understanding Michael Polanyi's vision of science (which is lately consuming all my spare time) is not an idle pursuit. It shares the same character of internal striving for knowledge as those endless days of my adolescence, when I stayed up late into the night reading (yes, reading) gardening catalogs and drawing diagrams of personal qualities like courage and honesty that I wanted to acquire. People might wonder how I can spend all my day time on an esoteric subject like plant biology and then go home and bury myself in an old, forgotten philosophy book. But I am convinced that through my persistent study, I will someday be able to justify my work and my life with the same conviction that Polanyi conveys in his book. That day will be a quiet victory.

Lagging

I don't feel much incentive to post lately. I've been caught up doing lab work and dealing with unusual personal turmoil. Besides, this blog hasn't been shaping the way I wanted it to. And for my work, phytochromes have momentarily slipped into the background while one research mentor is away and the other hasn't had time to set up our LED arrays for a trial run of the experiment. I keep seeing and thinking about phytochromes everywhere anyway. The plants in our first row of greenhouse mesocosms are tall and pale and developmentally trailing behind the rest due to lower light exposure (or is it over-watering?). My houseplants are pale and starved because I keep closing the shades to decrease energy consumption (and Apollo-dog "pruning" off their new leaves doesn't help either). Everywhere outside I see plants reaching for sun. I still don't have a map of how they do it.

Instead I spend my time pretending I understand what I'm doing as I learn to extract RNA from plants I heat shocked. Why is it so difficult for me to apply classroom concepts I learned in college to practical experience? I feel like I have a wall in my brain. I am constantly aware of how little I know and how badly I piece together the little I do. It doesn't help that I am so burdened lately that I have resorted to writing bad poetry while I wait for the samples on the centrifuge to spin down. I am turning into someone I do not recognize.

Image middle right: Arthurium nemesis (the redoubtable Apollo), photographed by Arabidopsisgirl

Light Ratios

Today's topic is all about light: the spectrum, the wavelengths, and what happens when light hits leaves. Most of the following info is paraphrased from Keara A. Franklin's Tansley Review on Shade Avoidance (New Phytologist 2008).

Most basic science textbooks have a bit about the light spectrum, with a picture that looks something like this:

Red light is right next to infrared (heat). Wavelength is measured from the crest (highest point of each wave) across the trough (lowest point after the peak) to the next crest and for visible light is expressed in nanometers (nm). A nanometer is a billionth of a meter. The visible spectrum of light ranges approximately 400-700 nm. Red light falls at the 625-740 nm end of that. For plant study purposes, red light is considered 660-670 nm and far-red light is 725-735 nm.

Plants don't absorb all wavelengths of visible light equally. That's why they appear green to us humans--they reflect off green spectrum light while preferentially absorbing reds and blues. A shaded plant will receive much less of these desirable wavelengths because their opportunistic neighbor will get to them first. Thus, plants have phytochromes to detect the relative difference in amounts of red and far-red light. Interestingly, plants have another way of knowing the difference between shading by a neighboring plant and the shade of, say, a building. They can also detect higher levels of the hormone ethylene around a plant. In any case, if a cell on a plant leaf gets hit with lots of far-red light and just a little red light, the phytochromes within it change their form. And that's how it all begins.

Image above: the light spectrum, from the World Wide Web

First Post

It seems trite to quote Shakespeare on anything now, but my blog title fits my intentions for this journal-of-sorts: to explore why I love flowers and plants and genes and ecology and biology--all things green and growing and photosynthesizing. I've been reveling in nature for as long as I can remember, but I've studied biology for just five years and the going gets rough. I feel a stronger sense of duty to my work now that I am at a facility where the data I collect ultimately may be used to solve practical problems beyond the realm of pure science. But I want greater clarity so I can contribute more to all the projects I work on. Lately my focus has been taking disturbingly long vacations leaving me dilly-dallying in front of the computer, exasperated at the reams of papers I've been digging through. I'm trying to piece together the molecular pathways that allow plants to detect and respond to shade. That means not just hours of reading, but hours of looking up definitions of words I hazily recall from undergrad and hours of decoding stats, graphs, and the possible implications of mutant phenotypes.

I expect this blog will stray to the "dull" side for a while as I grapple with molecular biology terms and the necessary problem of drawing a picture of a process no one really understands yet. Writing distills concrete statements from the amorphous blur floating through my mind when I read other people's writing. Maybe a few light-hearted posts will emerge later on when I understand more about what I am supposed to do. In the meantime, I will describe this thing called the phytochrome and its relation to the shade avoidance response:

Everyone thinks of plants as stationary entities, kind of like rocks, but plants do move--by growing. If a seed germinates in a shady spot, the plant can move away from the shade by growing tall and spindly. That's fine...we've all seen pale, gangly, unhappy looking plants starved for sun, but how does a plant "know" that it's in the shade and tell itself to grow skinny and tall? By detecting and responding to the quality of the light that shines on it. Plants have several photoreceptors, or types of proteins that sense light: phototropins, chryptochromes, and phytochromes. The first two respond to blue light and have to do with germination, elongation, direction of growth, and photoperiodism (the act of following the sun, like sunflowers); the phytochrome responds to red and far-red light and tells the plant to grow tall to escape from the shade. Phytochromes detect the light with a light-sensing pigment and respond to the red:far red ratio by switching the shape of their protein (zing!). This shape change affects a whole cascade of other molecules throughout the cell. Genes are switched on and off, other types of proteins are produced, hormones (plants have hormones too) are activated, and the plant grows tall, its leaves reorient upwards, chlorophyll content decreases (causing it to look pale), growth is concentrated in the main shoot (gangly and tall), it flowers sooner, and the plant produces less biomass (leaves, shoots, and other organs). If the plant gets lucky and hits a sunny spot, the phytochrome switches its shape back and all those morphological changes reverse in the new growth--the plant greens up, grows bushier, and waits a bit longer to have babies.

It's mildly impressive stuff when you think about it. Who'd have thought up a shape-shifting protein? But for me all this information is simply maddeningly inadequate both in scope and detail. How does the phytochrome change its shape? What other molecules does it interact with? Which genes are switched on and off, and by whom? How do hormones come into play? And how and in what order do all the different molecules and genes work together? I'm combing the literature trying to figure out what a hundred different scientists know about these processes. So far I am coming up with a cacophony of maybes and indirect evidence from studies of mutant lines. What I need to do is draw a picture (a pathway map) showing the step-by-step interactions of the different molecules and genes. There is so much information out there. I have barely scraped the surface of this subject and haven't even touched the unknown steps and murky conclusions about shade avoidance and phytochromes that are troubling me and slowing the map-drawing process. The review paper I am supposed to use to try to construct a basic map is one of the most confusing ones I've ever attempted to read.