Lull'd in these Flowers with Dances and Delight

Cross-cultural Exchanges

2011-01-20T14:45:00.000-08:00

I got my hair done at this henna tatto/threading/hair place around the corner from the train station. There are four or five Indian women working there, but the woman who cut my hair was from Columbia. The first fifteen minutes or so I was there, the strains of Bollywood rang out around me. Then my hairdresser excused herself to get a comb and when she came back, the background music had switched to Hispanic radio. I made small talk. I told her I loved Latino music...salsa, bachata, meringue, reggaeton. Every few weeks I go to this restaurant/bar downtown and dance my heart out at a place called Gonzalez y Gonzalez. "But do you speak Spanish? Do you understand the words?" asked my hairdresser in broken English. --"No, I can't speak Spanish," I told her, "I just go there to dance." The woman laughed. "When I was a young girl in Columbia I listened to American music. We danced to American music and we knew all the songs. I didn't understand the words either."

Low Point

2010-07-04T15:41:00.000-07:00

When I first moved here I was so happy and the possibilities of the city around me filled me with hope and energy. But now the flush of a new start is long over and I am struggling and stumbling more than ever. I am having growing pains with my new responsibilities at work and when I struggle at work the despair comes back, stronger and blacker each time. I feel like I keep discovering new limitations inside of myself, and keep adding more and more examples to the tally of life-skills that I simply cannot seem to master. Over and over again. I don't know what to do and I am losing my will to move forward.

I miss things that everyone else sees, both in the lab and out on the street, among my friends and my roommates. I don't notice that car X belongs to person Y. I don't take that extra time to think through what the inconclusive gel is telling me or if I do, my thinking becomes muddled in tangents and I overlook the obvious. I don't know what to do. It's affecting my work, my boss' view of my work, and what little confidence I have in myself. I feel like I am adrift, without a map. Lost.

Vindication

2009-11-04T16:24:00.000-08:00

It's hard learning the ways of a brand new lab and I've felt that I am dragging along while frantically trying to process all the new information, remember the small details of how things are done differently here, and keep the different projects straight. Ever since I made the personally momentous decision to major in biology, I've spent a lot of time worrying about my ability to do science. It's always been a deep-seated fear of mine that I am not good enough for the trade. I am a slow (if careful) learner and I absorb things deeply, but it takes me time. I don't do well in harried atmospheres where I feel like I don't count and I get little constructive feedback about my performance. For the past two years I've worried and literally wept in despair about my ability to do the work of science. But today...well today I was told something that I haven't heard in years. I was told that I am doing just fine. I was told that I am a good addition to the lab. I heard the words, directed at me: "You can be a scientist."

Something deep inside of me just took a breath. The relief. It's palpable. And oh, how I love my new lab. The people are good and the science is great. It makes such a difference when the science is great.

New Beginnings

2009-10-16T15:23:00.000-07:00

I am back after a long hiatus! Since my last post, I ended my internship/temp job at the DOE lab and relocated to where I want to live: New York City. Sometime in mid-winter, a few weeks before I was supposed to sign up for the dreaded GRE, I woke up early on a Saturday morning and decided that I should move to New York and find a job instead of obsessing over graduate school and continuing my DOE work. It was a tough decision to make, with friends and mentors questioning my logic ("You want to move to NEW YORK?! NEW YORK?!! Why?! You can do your master's here and not pay anything. What are you going to DO? When are you going back to school? You are too nice to live in New York City. Everyone up there is rude. How are you going to find a plant biology job?") However, I stuck to my plan with a conviction that I rarely muster. Even though I was fearfully embarrassed about relocating without any job prospects, inside I proudly told myself that I was off to seek my fortune. Somehow, I found it.

I found a great little house in Queens to share with my sister and three roommates (and my dog and their four cats). After living off savings and babysitting gigs for a month, I landed a wonderful job as a laboratory technician in a really incredible lab in exactly the field I want. Of course, I am terrified because I am underqualified for the job and I still need to make a decision about grad school. Of course there are ups and downs no matter where I live. But for right now I feel that there isn't much I can't do.

My new job is to maintain flow and organization in the laboratory, order supplies, conduct small experiments and produce data from protocols, and grow hundreds and hundreds of plants. It will be a big step up from my limping progress of the past. Historic scientific discoveries took place and famous scientists have walked and worked there. The lab is so beautiful and looks out on the harbor. I think I will do good work. It may be impossible not to.

New York City is enormous and dirty and full of millions of people and cars and acres of concrete. I love everything about it: the good, the bad, and the ugly. I lived the first five years of my life in Manhattan and calling this city Home feels as natural now as it did when I was barely old enough to recite the address of the cramped old apartment in mid-town where I was born. The street smells of honey-roasted peanuts, the steam from the vents, garbage, rain, and the dankness of old buildings, the taste of the water, induce incredible nostalgia that makes me feel primordially real and especially alive and particularly ArabidopsisGirl. I belong here in a way that I never belonged in Chicago, Georgia, D.C., Tennessee, or even in the house far upstate where I grew up and my parents still live. For once, I made a life decision that is right.

Slump Time

2009-05-18T12:57:00.000-07:00

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.

The Other Side of Eureka

2009-05-09T22:58:00.000-07:00

I often wonder if blithe (sometimes blind) supporters of the rigid scientific method have any clue what they are talking about. Do they really have a conception of just how messy and heuristic real life research is? Would your average intellectual be half as supportive of our myriad colonies of labs if they grasped the number of dead ends and trivialities being patiently investigated? I do wonder.

I can't speak for physics and chemistry, but I know for a fact how much stumbling in the dark goes on in the biological sciences. I do a good bit of it myself. Months can go into simply figuring out how to keep the organism of study alive, not to mention developing or optimizing techniques that make studying the question possible. One of the technicians has a cartoon taped to her desk with a picture of a scientist surrounded by what looks like a failed chemistry experiment and the caption, "What's the opposite of 'Eureka?'" Indeed. What is the opposite of Eureka?

The most abundant opposite of Eureka I hear around the lab is something along the lines of (&*^$^##@$%^%&%$*((*(&^))*^%$%^#!!!!!!!!!! My current research mentor always gets mildly colorful when we inform him of a setback or failure. I had my most recent anti-Eureka moment this Friday, when I looked at my first Western blot and saw a whole lot of nothing. My phytochrome protein didn't transfer. It was not total shock and dismay because the incredibly kind and patient post-doc training me had not had any luck getting that protein to transfer either. I'd have loved to succeed at it. I literally woke up on Friday morning dreaming about washing my Western blot. It was very much on my mind, I felt responsible for it, and it ended up not working.

The opposite of Eureka:
"I have not found it!"
--"Keep searching."

That is the best opposite of Eureka I can come up with.

Prevarications

2009-04-21T06:57:00.000-07:00

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

2009-04-16T12:03:00.000-07:00

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

2009-03-14T09:47:00.000-07:00

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

2009-03-03T06:27:00.000-08:00

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

2009-02-10T10:22:00.000-08:00

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

2009-01-20T04:16:00.000-08:00

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

2008-12-30T17:04:00.000-08:00

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

2008-12-18T11:38:00.000-08:00

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

2008-12-13T22:13:00.000-08:00

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

2008-07-15T08:52:00.001-07:00

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

2008-07-02T07:36:00.000-07:00

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

2008-07-01T11:36:00.000-07:00

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.