Vindication

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

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

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

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

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

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