Lockhart's Lament and The Physics of Lenses

Week 12, Day One

There's a centrally bulging piece of spherical glass mounted on a stand with a curved depression to hold it. A wooden box with a triangular hole houses a tiny bulb with a cord plugged into the mains. The box is placed 30 centimeters from the glass. A white screen is placed at the same distance on the other side of the glass. The light is switched on. The magic begins.

Unfortunately, science lessons in schools do not begin in the lab, rather, on a chalkboard. The fast pace of life is no excuse to forget that Newton started thinking about gravity after the apple fell to the ground before him, not the other way round. Everyone with a secondary school education knows that convex lenses converge light rays and concave lenses diverge them. How do they know this? Because they're told. They're told what happens before they had a chance to discover. That's what science has been reduced to. Replication, not discovery. Drab fact regurgitation. Well, close enough.

Think about the description in the first paragraph. When the light was switched on, was there an image on the white screen? Think about the things that could be done with that set-up. Logically. The centrally bulging glass can be replaced by a flat piece, or a centrally thinning one, maybe a wavy one too. Or whatever else. The screen and box can be moved relative to the centrally-placed glass. The screen could be moved to the other side with the box as well! If the image caught is enlarged or shrinking, the trends can be recorded- where does the image start shrinking? At what distance from the glass piece are the screen and light box? Are they on the same side, or opposite sides of the glass? Granted, it'll take longer to beat well-established facts out of schoolchildren. What is harder to fathom however, is that the widespread understanding of the delivery of science and mathematics education has come to mean anything but self-discovery? And frankly, even if that comes at the cost of knowing lesser stuff within the same period of time, it would be totally worth it. How logic has come to be divorced from science, I don't know and couldn't care less about. What I do care about is why it should be rectified, and how.

A widely (and yet not widely enough) circulated little paper of the nature of school education is Lockhart's Lament (PDF file: http://www.maa.org/devlin/LockhartsLament.pdf). I came across this wonderful piece of work a year ago, and re-discovered it in my pile of keepsakes a few days ago. Curious about the man who spoke about the flaws of current school education in a manner similar to my own thoughts, I google-d Paul Lockhart. Not the astronaut. Paul is a mathematics teacher at Saint Ann's School in Brooklyn, New York. His article has been circulating through math-ed communities since 2002, but he never published it. It is one of the best critiques of current K-12 mathematics education, made no less important by the fact that it has been written by a first-class research mathematician who elected to devote his career to teaching schoolchildren.

What drew me to his work was the utter semblance of what he said with my own experience and consequential understanding of learning science. Having come from an Indian school before I went to McGill for a Bachelors, I can safely say that I was in a deep rut when it came to understanding science, particularly biology. See, Indians make for amazing workers. Only the Asians could give us any competition in clocking study hours. We have tiny, error-laden textbooks, and 3-4 reference books that are so humongous that the only way they can fit into a book bind that isn't breaking apart is to have ultra-thin pages with alphanumeric page numbers. The easiest way to kill, KILL, our own version of O and A-levels is to work on over 20 past exams per subject. While this needn't necessarily involve rote learning, there are no traces of independent thought. Shame.

The average science student is first compelled to do full-blown independent work at the graduate level. Through schooling and undergraduate years, they can slip conveniently through the cracks of small-scale independent work, failure at which can be more than compensated by the fact and formula-based tests and exams. Even labs are a sham. Independent work, with less reading and more hands-on lab or field work, and informal sit-down sessions with the professor where ideas are beaten out...these should be the foci of primary testing. Having no background in the variety of education systems of the world, my viewpoint reflects strictly one side of the argument. It is nonetheless a strong one because if students feel unprepared for the scientific process, or daunted by the seemingly copious work, then there is a serious problem. Education communities should seriously exchange notes and hammer out a feasible and flexible solution that addresses this issue. I wrote notes for students in Physics, Chemistry and Biology as an undergrad, and realized how easy it was for people to get everything they needed to get a 3.0+ GPA without the effort, and honestly, without the fun. So most science graduate students, unless under the tutelage of a phenomenal supervisor, will be left to replicate someone else's study by changing one tiny factor. It's enough to get published in an obscure journal, but what was new? What was learnt?

Science is about progressing, in painfully slow steps. Not a lot of scientists have leaped, not even most Nobel Laureates. The Nobel-worthy culmination of decades of work starts with an obscure idea that doesn't receive much endorsement. It's only when the results start to show that some support starts to flow in. What about the investment that goes into work before the monetary support? Until results don't show, scientists follow their instincts. Instincts that are obviously based on logic-derived hypotheses. However, given that many logical explanations can be drafted for any phenomenon, trusting one of them to be the focus of your work, is a gut-thing.

Halfway into my flailing research, I was told to look up an alternative, short experiment to complete so I could at least get a publication for all that labour. Last week, the sixth week into perfecting and testing my experiment design, I got a result that gave an indication of the system finally working. No more meter hiccups, no leaking, no dying tadpoles, no clogged tubes, no toppled cages with escaped tadpoles. Nada. One smooth run with distinguishable difference between the two treatments.

Were the fast-piling failures, the uncertainty of the sustenance of the system design, the doubts at probably aiming too far, was it all worth it? Oh Hell yes.

Cough, sputter, sputter.....hiccup

Week 11, Day Three

A black cylinder, 10 centimeters long and barely over 1 centimeter in diameter ends in a thin, thin glass nib housed in a teeny transparent plastic cup. A squirt of distilled water and an abrasive rub later, it is plunged into a yellow solution droppered flimsily into the small plastic cup. The cylinder is inverted, its wiring carefully set aside. The curved end of the 1 centimeter diameter plastic cup is draped with a membrane held in place by an ultra-thin rubber ring made visible only because its black colour is conspicuous against the transparent background. So far, so good. The last leg involves pushing this delicate assembly of rubber, plastic and glass into a cylindrical hold barely larger in diameter than the cylinder itself. The membrane and rubber ring assembly go in unharmed, the black body of the cylinder starts to move in. And then gets stuck. No amount of force can get it in, the only way out is pulling it back out and destroying the little membrane and rubber ring assembly. Dratted, dainty little equipment that costs over 2000$.

Another hour of re-doing the whole process, and my supervisor successfully installs it in the holder. The holder goes on the clamp, the wires into the meter. Switch on.

The manual says it draws its numbers every 18 seconds. Mine takes 60 times that time. Multiply by six experimental set-ups, and I'm sashaying around the meter for almost an hour and a half. Not to mention the predicament of comparing numbers from the chamber measured at 10:15am with those from the one measured at 11:30am.

Six concurrent set-ups and one precariously functioning respirometer.

Everything here is old school, and not in a good way. With no software for the meter to record the readings all day for weeks, a lot of trials were underway to determine the appropriate timeline for making the recordings. And it doesn't help that the meter sputters like an old engine that just refuses to die and thus be better used as scrap metal.

One, Two, Three, One, Two, Three

Week 11, Day Two

I underestimated kinks. Kinks are interesting. Kinks keep monotony at bay. Once the kinks diminish, there's no...fire! The burning curiosity to find a solution so you can move on keeps the bulb inside burning, keeps things fresh.

Now it's all routine. The counts are at half-hour intervals, the feeding every 24 hours. Uber thin tubes glued into the glassware making for water entry and exit. The tubes go from the tanks to the pumps, the pumps to the glass chambers, the chambers to the meter. The glassware rinsed with fresh, warm, distilled water with its flush-distill-flush-distill prep routine. Nets scooping up the scurrying tadpoles. 60 milliliters of aged tap water in beakers with five tadpoles weighing below 100 milligrams each poured into the little glass chambers. Six glass chambers neatly fitted into their seats on an iron stand, one set of tubes bursting out like a single spout of water from atop one set of glass arms. The hum of the now-running flow pumps. The water slowly surging up the tubes from the tanks, into tinier tubes hidden behind the opaque pump, into visible tubes flowing into the glass chambers, and emerging as dew droplets from their make-believe fountain heads. Pitter patter, plop.

Twenty hours later, the first recordings are drawn. Another in two. After twenty-fours hours, the flow goes off. And I watch as in each chamber, five little critters frisk about, from tube to tube, still hoping to exit their small, crowded (and temporary) lodging. I hope the meter can catch what obviously happens: oxygen depletion. Just to be sure, I put in five of them into one chamber, yet I hope they breathe fast enough and the meter is alive and kicking so it can catch the oxygen decline substantially well. Lower numbers make my heart swell.

Four hours later, the flow goes back on, running overnight. Pitter patter, plop.

Meet the cast

Week 11, Day One

Pictures and videos of the lead cast:

A 100 milligram Arabian tadpole:

Several dozen, actually. Plus, a 100 milligram dragonfly larva:

The tadpoles are stored in small tanks with small rocks as refuges and anchorage points for both algae and tadpoles:

After several casualties- upstream swimmers that got caught in the multiple sponge and cloth layers in the filter- wire mesh was used to cover the inlet and outlet pipes. Sometimes though, the odd mini tadpole finds its way into an alternate tank in the array of tanks.

Some unfortunate tadpoles will wind up as dinner, like this one:

...others just get the aftertaste.

I basically watch what they do once they've got a whiff (literally) of the dinner I fed their predators. Amphibian young are famous for their ability to detect the presence of predators through little chemical cues dispersed in the water. These cues have been found to be quite specific, and reveal both qualitative and quantitative information. It tells them which predator is nearby, how near it is, if it's been killing their kin or is just an opportunistic feeder, and varies with time as well. Sound and smell have always been the best developed senses in all aquatic creatures.

So, I keep tabs on any behavioural or morphological changes in large set-ups like these:

I'm also trying to figure out if their respiration rate rises, which is the hard part. After much reading, hunting, improvising, tweaking and testing, I concocted this set-up:

Water is pumped out of two tanks- one without any predators, and another with a predator in its cage fed at regular intervals- into identical glass chambers with five tadpoles and the controls without them. Based on previous studies, the larvae predators release chemical substances as do the dead tadpoles. These diffuse through the water and alert the tadpoles of the impending danger. Once the tadpoles in the glass chambers sense this in the water that's flowing in, their respiration rate should rise. The tubes coming out of these chambers are periodically attached to the meter at the end that records oxygen concentration. Should the decline in oxygen be significantly different between the predator tank and control tank, it would constitute a viable experiment.

The whole idea behind setting this up is to get small doses of pesticides and metals into the tanks as well. If respiration increases, toxin uptake will increase as well, resulting in mortality. Given the (still) widespread use of pesticides, such studies are strong scientific evidence that specify appropriate (if that's what they are!) concentrations of such potent chemicals in natural water sources. And for the fast declining amphibians water contamination can be a death sentence because of the synergistic effects of predation and toxin intake.

Labour day

Week 9, Day One

It's hot, dry-hot. And the glare is astounding. Summer is officially here.

I try hard not to focus on the tiny, excessively rusted- and therefore creaking- pushcart I'm wheeling on my three kilometer trek from the lab to the greenhouse, but the stillness of the air muffles not an iota of the rasping and grating. To think this was the best of the lot of wheelers available. Empty carts go easy on the inclined planes, but thankfully drivers here actually adhere to speed limits. I get some respectful passes as the they let me take my noisy machine and wincing face across the street and up the next inclined plane. The last one goes up to the greenhouse, all the way behind the closed gate. No parking spot. Yay, windfall. I walk up, swing the noisy green gate open, block it with the massive boulder, and slide down to where I left my creaky companion. I haul it up, and meander it through the narrow paths with way too many right angles and park it in front of the tents housing the plants and tanks. I sniff around for aquariums. There is a mountain of dirty ones, brown-dust-and-dry-leaf dirty ones. I have no idea where to hold it without breaking it or collapsing with the sheer weight. After two minutes, I grasp two edges of one, pushing its entire bottom against my chest, secretly thanking the one stroke of luck I've had all day: my labcoat. I walk half inclined myself, reach the cart, and make another incline with my legs over which I slide the aquarium down onto the cart. Five more trips to go.

Another three kilometers and one more respectful driver later, I reach the lab. My pile of aquariums, all neatly balanced on top of each other with no edge sticking out, now poses another hassle. A little forethought, and I start manage to remove them without toppling the whole darn pile over. The aquarium just about fits into the sink where they're to be scrubbed and cleaned. I fold up the arms of my sleeves and dive in with a metal scrubber, dishwashing liquid, pure ethanol, and very, very hot water. Two hours later, they're all done. I squirt some ethanol onto a cloth, followed by a bout with distilled water as finishing touches. The clear, glistening aquariums are my pride and joy.

I wheel them into the lab, assemble them on the shelving unit, hoping they don't crash, now or ever. My back is as hard as a rock right now.

10-minute walks in the warm sun and dry warm breeze are never enough to satiate the back stiffening that comes from a combination of hard labour and excessive air-conditioning. And bending over aquariums for nearly three hours, netting tadpoles as little as 4mm long to those over 30mm and sorting them right after that, makes it worse.

Which is why you cover the connecting drains through which they escape and- if lucky enough to survive- enter other aquariums BEFORE you add them in the first place.

And despite desperate measures to prevent casualties, I killed two and nicked the tails of three others in the process. Between this, and my tadpole-prodding episode from two weeks ago, I have acquired a ticket to hell.

My two-inch Frankenstein

Week 7, Day Two

It fell three feet to the ground. Again. The tail wriggled and momentarily stopped me from bending down to pick it up.

It was supposed to be dead.

I gave it another minute, but the tadpole lay lifeless in a tiny pool of water on the floor. My heart sank all over again and I picked it up gingerly. I scooped it up on the foil and lay it stomach-down on my palm once again. The beady black eyes were always motionless against the equally black, shiny body. But the nostrils don't flare and no suction on the ventral surface, the tailspin a far cry. I rubbed the pad of my forefinger against the bulgy part of its body, the slimy surface soft, pudgy. Carefully. As if it were still alive.

Less than two months ago, they were barely a centimeter in length. You could just make out the pin-sized head and wriggly tail. Three weeks ago, they'd all grown to more than twice that length, lateral bulk now added. A week ago, they were five to seven times that length; eyes, nostrils and suction cup-like mouths obvious. I got curious, and after handling them during wadi sampling, tank transfers and set-up construction, I got accustomed to the wriggling on my palm. So I scooped one up from the storage tank to have a closer look. I nabbed a rather feisty one because he jumped right off my palm onto the floor over three feet down. Oops. Took me long enough to find something flat yet thin enough to slide between its belly and the floor and once back on my palm, it wriggled and then curled into a jet black oval, motionless. A hint of moisture from the spray bottle, and it sprang back to life wriggling in the newly deepened pool. The suction began as it swam from crevice to crevice in my cupped hand. I opened my palm wide, straight, and then watched the eyes, the cheeks underneath bloating and sinking quickly with gulps of air. I lowered my finger and barely touched the surface. Satisfied, but more wary of the stress that may have been invoked with its high jump, I lifted my eyes off my palm, hunting for a beaker in which to deposit the creature.

I grabbed one and looked down, and there was no movement. No suction, no makeshift cheeks. Oh god.

I touch the sensitive tail hoping for a reaction. Nothing. I touch the head, spray some water and dunk it into the beaker, sitting still for a minute. Nothing. Nothing. I lift it out of the beaker and onto my palm, remembering the two dead tadpoles from the wadi samples that had to be dunked into the drain. I can't throw this creature there. I killed a tadpole. I killed the tadpole.

I must have killed a dozen insects every few weeks unknowingly. This one dead tadpole is making me more miserable than all those dead insects in two decades. Since I couldn't bare the dark, smelly burial ground, I dunk it into the storage tank instead, half hoping it springs back to life. Nada.

I follow it as it sinks to the bottom like a wisp of snow, my face wrinkled.

Two minutes later it joins the other milling tadpoles.

Grey checkered American Eagle ballet flats

(for SATURDAY, March 20)

Week 7, Day One

There's a part of the Muscat landscape we don't see much of. Industry. With all this open sandy land to use, the concrete maze grows horizontally here. And the mills get built far, far away. But on the impromptu trip to a new wadi, we take the Nizwa freeway from Al-Khoud towards the township of Sa'al. And I discover one of Muscat's industrial pastures on the way. Lone, white and steel structures rising from the sand, seemingly lost amongst the many orange mountains.

Sa'al is built near an oasis under the foot of a comparatively large mountain, the summit gleaming, sharp, sun-thrashed. The drive ends halfway up a dirt path and we get out into the crazy afternoon sun. It is deathly silent. There are no date palms in sight, no towering hills for shade. The fifteen-minute walk to the wadi is traumatic when you're not dressed for the occasion. My grey checkered American Eagle ballet flats have long run their course, but I had no other alternative on this impromptu trip up to the wadi. So I walk past the stinging needles of the desert plants that are hoping to land their seeds near the vernal pools by latching onto the thin, really thin, spun cotton on my feet.

The elephant grey rocks housing the intermittent pools of water run like frozen waves along the entire length of the stream. Somewhere beneath all those hard rocks must lie tiny gullets linking the pools. Red dragonflies buzz between pools, sampling their prey. Fish and metamorphosing tadpoles dart between pebbles, not much silt here anyhow. The pools are relatively transparent. We hunt for pools housing newly-spawned tadpoles. The terrain is death sentence to my cute ballet flats, and I'm afraid by the time I'm done with this little trip, my beloved American Eagles will topple into their graves. I don't care if they die bravely. I want them to be preserved.

The combination of the silence and the heat is shockingly calming. But it's still March. The boiling, blistering heat is yet to come. A goat bleats in the distance. But it's hard to see where, what with all the jutting mounds of grey blocking the only view spared by the blinding sun. I get back to the tadpoles and I hear it bleat again. I can't resist cocking my head up to look again. I get my fill of tadpoles, skip from rock to rock, and collect more stinging needles on the way back to the car.

My legs will be crying tonight.

Eureka! and other romanticisms in research

Week 6, Day Two

Research is four parts planning, two parts reading, one part experiment, two parts re-planning, and one part analysis.

The task at hand is understanding stress physiology in individual tadpoles exposed to predators. The actual experiment would be, at maximum, a 3-4 day vigil on the behaviour and metabolic activity of tadpoles exposed to chemical cues from predators. Prep time: four weeks. It's like cooking butter chicken. The chicken is doused in two marinades with dozens of ingredients and kept for over four hours, but spends less than thirty minutes on the flame. The raw chicken takes its time to soak in the melted butter, oil, yogurt, lemon and spices. It's the same with most Indian meat dishes. Hours go into preparing it for the short quick assault of hot oil.

In India, high schools spend no time, none at all, in preparing future research enthusiasts for a large chunk of their work life: preparation. Lab classes- in rare cases, field work-is about telling the students what they're supposed to be looking out for, and then showing it to them. There are those concentric layers in cross-sections of roots and stems of every imaginable plant; the ink blue colour after adding iodine on the succulent leaf filled with starch; the eight and eight legs only on the spider.

Science education is supposed to inculcate the joy of discovery. That means I should not be told how to place my transects in a four acre-field filled with patches of daisies whose numbers I need to estimate within a day or two. Or that I am going to find a larger number of metamorphosing tadpoles in the hot, exposed waters of a shallow pool rather than the deeper, clearer, cooler, possibly fish-infested ones. Or that there are four parts of a flower, because yes, I see the purple petals, the green sepals below them, the tall blonde stems with the creased bulbs at the ends, and the singular pale green structure with the bulbous bottom and the sticky head. I teach a young Omani girl in a school following the IGCSE curriculum, where it took them three months to teach basic ecology. But she can answer that transect question better than most freshmen high schoolers her age. They took three months to teach her about the dynamics of eating and being eaten, but they developed independent thinking. A component most developing nations lack in their school curriculum. By the time you work hard and get used to doing well by reading and regurgitation, developing critical thinking becomes harder than steering a bull by its horns.

Science is an extension of logic. Newton got curious about the falling apple. Steam engines were conceptualized on steam pots. Sure, it took longer then, and time is...well, everything, including money. But good science is more than in-depth information. It's curiosity and efficient, logical search for reason. And we're in dire need of those virtues in scientists. I'd rather schools spend some time initiating good search and critical thinking habits in students. There's always time for competition and mass accumulation of information. Even Einstein said that it wasn't that one needed to know everything, just where to find it. Knowledge is everywhere. I wish I could say the same for curiosity.

So anyway, after a weekend of scanning 1711 Google Scholar search results, I have accumulated 741 pages of literature related to my experiment. The idea is to read all of that in time for the piece de resistance a month from now.

First up: 48 pages on Amphibian respiration and olfaction and their relationships: from Robert Townson (1794) to present.

Gum Boots

Week 6, Day One

This land is merciless. Hot, parched. It's a wonder so many organisms survive here. Every nook and cranny with a hint of moisture is swept up by some amphibian, fish or insect. In a thirsty land, fresh water comes only from above, down the fortresses of fiery rock, collecting in vernal pools on flimsy floors of cobblestone and sand. And there are plenty of takers.

Hot red dragonflies buzz loudly in the silence of an uninhabited wadi. Schools of little black fish scatter with the eddies from my gum boots in their living space. A successful steer from the bright hot sunlight under an ample boater allows focus on the pint-sized leaping Arabian toads. They don't seem to like the water too much. Opportunists. Hard to imagine that in some places, they're seriously endangered. Near the mouth of the wadi are small stagnant pools abounding in metamorphosing tadpoles and more leaping toads. I spot some unusually large fish in the deep ends of the otherwise clear, shallow waters. Invasive cichlids, Tilapia, from Africa, introduced as aquarium fish and for aquaculture (Tilapia is a common food choice), that managed to escape and conquer the few fresh water sources in Oman.

I look down at my gum boots. There's small chance of overflow from the wadi waters, so I inch closer to the deep end in my search for bacterial mat-infested stones. But there's been some heavy rain six weeks ago, and the disturbance from construction nearby for the development springing up as a by-product of the region's first botanical garden makes it impossible to find viable samples for the experiment. We return empty-handed.

On the rocky drive back, the landscape looks like one of islands of hard grey rock in shallow, almost-opaque seas, strawy green sprouting from the unexposed nooks between rocks. In between the sounds of the wheels over the pebble-laden ground and the construction trucks, there's the cawing of a few egrets. The bright red-orange dragonflies are clearly visible on their bare flat rock perches, and the heat amasses through the windows despite the air-conditioning in the four-wheel. I become conscious of my damp feet.

Damn gum boots are always leaky.

Transparent Accounting

Week 5, Day One

Sometimes we study so much as students of science, and work so much on our own in the initial (study) stages of our career that we tend to forget about scientists being human, subjective too.

Research is 60% individual work, and 40% collective effort, if not downright half and half. It is naivety to assume otherwise. This morning, I was faced with a little situation that had me wishing that research was just about identifying a question, generating a possible answer, collecting resources and designing experiments to clarify the accuracy of the answer. Period.

I sometimes find it hard to explain to my parents that thesis-based graduate degrees are just like a regular job. Only harder, longer hours with menial pay, and more ambiguous. For instance, you get a whiff of the tussle between individual interests whether or not you're the sole investigator, because there are vested interests. In most schools, particularly ones with minor budgets, grants are poured into a particular research team with expectations. Suffice to say that professors in turn would expect work of a certain quality to come out of their research teams, so you're walking on eggshells until you're sure what they want.

If there was ever a time I understood why Waterloo showcased a joint Bachelors in Accounting and Biology, it is now. Have you ever seen a grant application?? They have courses to explain how to go about that work! I'm certain it tops the list of the most tedious work done by researchers. But accounting classes might be beneficial in more ways than that, I think. Getting the prices of the glassware and chemicals down to the T is just log-keeping. Some relatively subjective accounting requires gauging interpersonal interactions, expectations. Even a simple Masters thesis is a major collective effort. The professor and department invest their resources in you, and it's a tough call between the process that had proven results and the other- always the more cooler, riskier- one you've been dying to test for hope of a mild eureka moment. Plus there are the undergraduates and technicians you invest in yourself. Clarity and honesty will go a long way in supporting your niche in that web.

In my experience, professors in North America are fantastically accustomed to the whole research process, glitches et al. You're treated like the adult you are, no overt displays of reverence necessary. That attitude helps if you're foolhardy, or impatient, or otherwise, since the responsibility for failure-like success- rests on your shoulders. Plus, there are very few professors who'll shoot down everything you think of, or do. So don't worry about sounding like someone lacking knowledge, or worse, downright foolish. Through all the fresh- sometimes unpleasant- reality-checks I get a dose of, I still maintain that science is rooted in curiosity. So long as curious George isn't latching onto broken vines. Do your background research before any discussions. Do it regularly, do it well. At the outset, be clear about the domains of the project. Be practical in your definitions, and always leave room for more. Don't binge, don't spread yourself too thin. Better may be less, but more is certainly not better, and that is the distinction between work that gets published and work that doesn't.

This clarity is doubly crucial when defining the roles of advisor and student investigator, and the expectations both have of each other. There's bound to be compromise by both, but never let the equation tip over. For either side. We're twenty-plus year-olds by the time we get to this stage, so gauging unvoiced issues is a skill I'd assume we've acquired. If there's something substantial not out in the open, get it out asap, whether it's something you want, or the other person. If it's significant to one, it's significant to both. Everyone is making a commitment, so you're just as much responsible as you are rightful. But like every right, you've got to know when the rope's stretched too far, when you're maxed out in terms of compromise. And be conscious of how much you're pulling as well.

Lack of clarity can be an awful situation, especially since time is an investment on which you don't get returns. I've had to move bases myself after this morning, so no more molecular work. Tomorrow I start a new project with tadpoles and dragonflies. On the bright side, there's more pictures! And I'm going to try and lasso one of the flying critters like my dad often did, and report my results on this blog, hopefully shielded from the animal police.

P.S.: Just in case there is a PETA enthusiast around, I'm all for ethics on this issue. Honestly, I'm better with dogs than babies!

R-E-S-P-E-C-T

Week 4, Day One

I have a feeling that among scientific circles, the wars between researchers and techs is the stuff of legends. Researchers complain about the lack of efficiency on the part of techs, while the techs rant about the lack of patience and disrespect for established bureaucratic procedure by researchers. I recently developed a new-found respect for the work techs do for us, but to be fair, they really suck at basic math!

Now, molecular work is very deceptive. You don't get a good inkling of the prep work that goes into the raw materials needed.

At McGill, we had the regular undergraduate lab courses in molecular biology and microbiology. The ones where everything you need is right there at your workstation. The plastic and glassware, the dippers and ice and vortex, the shared PCR machines and spectrometers, and solutions in just the right amounts. I even worked at a protein lab whilst there, but since my work involved assisting the post-doc in his work, I spent those seven months pretty much working on DNA extraction, PCR, electrophoresis, and DNA extraction, PCR, electrophoresis and more. Over and over again. Most of them were repeats of those with insignificant results. He was a sweetheart though. He always told me what I was doing, which samples I was using, and what I was searching for in those electrophoresis gels mounted with extracted and amplified DNA. That was as far as the variety went.

Either way, even that work wasn't as close to monotonous as that of the technicians. Every little protocol, standard everyday work like extraction, quantification, PCR, and all kinds of electrophoresis, require an average of three solutions. Solutions besides the regular bench materials like ethanol and distilled water. Solutions weighed and measured in every way possible. Just the right pH, the exact volume down to bare microlitres, not an iota of froth, perfect temperature, some filtered on millipore papers. Solutions that, as luck would have it, aren't versatile enough to be used for more than one procedure! And if you're really lucky, each of those solutions will require three more solutions for prep. And neither one of those nine solutions have any exotic colour. Windfall, yay.

It takes nearly three hours to collect the material, that's how slow things get in some places. Once there, it doesn't go any faster. You have standard protocols for solution prep, and you move progressively. There's the math you need to do to determine what quantities you're using, then the weighing and getting individual ingredients to be in the exact state you need them to be, and finally, the mixing, filtering and autoclaving.

In my lab daze I start to think that the toolbox I've been working at since hours now, is pretty diverse and visually appealing. The lovely Erlenmeyers and graceful long-necked conical flasks with their neat graduations, valves, suction pumps and individually wrapped filter papers. Love who you work with.

Even then, it's only interesting for the first or second time that you're doing the prepping. I do this once, and I'm good for the next 4-6 months. They do this every day. Excruciating.

We're done by five, and it's time to go. I can't believe a whole day went in prepping solutions. It's good to know ahead of time, that you can't take these things for granted when you're doing research. Prep work is lengthy, monotonous and rickety. But, there's always a ton of logging to do to get a tech to do your grunt work, and even then, they work at their own schedules because you aren't the only one they work with. So if you don't plan and book, chances are, your work could either be left stranded or left to waste if it has a short shelf life.

It's also subtly revealing of the investment risk that goes into getting techs to do the base work for your research. You cannot afford to use incorrectly prepared solutions for fiddling with something invisible like DNA when samples are few and hard to come by, which is aways the case, isn't it?

Heavyweight

Week 3, Day Three

Hours more of dirt sifting for eggs, and then I get to the actual project I signed up for!

After lugging 12 kilos of rocks and containers to the lab in three shifts, I get down to unpacking and taking stock. There are big food delivery containers and sealed bags full of brown and black rocks painted in a sea of green, pale yellow and brown. I bet if all that scenic photography on the big and small screen was developed from constructed landscape models, they'd select these rocks. These were picked up from Wadi Al-Khoud, near Muscat city, Oman.

A wadi is the Arabic term for an intermittent stream or a dry riverbed that contains water only during times of heavy rain. Oman's wadis shot to wider fame during the summer of 2007, when Cyclone Gonu struck Omani coasts causing unprecedented- and unpredicted- destruction, as the wadis overflowed immensely causing MASSIVE floods. It was a Category 5 cyclone (read: windspeed >250 kmph, storm surges 18 feet-high), the strongest tropical cyclone on record in the Arabian Sea, and the nation's worst natural disaster. I've lived here since 1991, and the city plan is spectacular! Not strangely, the only thing it didn't account for was drainage. During the very, very brief rains in Muscat, some of the roads get blocked due to these dry land depressions getting filled with water as flash floods are caused by the accumulation of water running downhill and collecting in the depression, sometimes overflowing onto the roads nearby. Over the years, you get to know the susceptible roads and the kind of showers that can result in their getting blocked. Muscat's low-elevation Corniche area saw arched waves hit the famous jutting man-made rocks. The city lost power, and all the regions near major wadis, like Ghubrah, close to where I live, were badly, badly hit.

Wadis have not been studied all too well in this region. Oman itself has no academic record in this arena. It is also a known fact that around 80-90% of the bacterial species are unknown. Tapping into bacterial energy dynamics is environmentally significant. Also, wadis are consistently disturbed habitats. For most of the year, wadis are dry. Come rainfall, and these get filled with water that is lost slowly, and mostly by evaporation. Hence the ecological significance of studying an unexplored ecosystem. They are also sources of sustenance for several local nomadic tribes, and thus economically important.

Back to the rocks I was scraping for samples. Living micro-organisms are generally preserved in large freezers at 20 degrees below zero celcius. My first job was to collect samples representative of all the microbial colonies on these rocks, and store them in little plastic vials in the freezer. Armed with a scalpel, I began cutting chunks of growth off of the rocks, chopping them, and dunking them into 1.5mL vials. It's much like grunge work in the kitchen. There's the tiresome peeling, scraping, chopping, collecting and pouring. And then the mess generated afterward, minuscule particles of gunk hiding under everything fathomable.

Mats of microbial communities are strewn all over the rocks. A few rocks down, and I'm seeing patterns in the morphology of these growth mats. Cuts into the still-frigid surface of the colonies reveal neat horizontal layers in mint, pale yellow and dark green. Some are single layers; brown and green, mostly. There's the odd one looking like clusters of miniature orange-coloured mushroom caps. Some are little finger-like projections, jutting out vertically in hundreds. Pale brown. Rocks with these don't seem to house any other kind of growth. An hour into the prodding and probing, and the rocks get slippery. Some bulbous green growth releases bubbles and water as I attempt to chop. So I tweeze the fibrous material out. A beautiful flat rock from one of the sampled ponds has snail shells scattered within the growth. The thawing releases them from the stronghold, and they scatter all around. I pick up the shells- a maximum of 4-5mm in length and imagine the little creature that lived. I bring the shells closer. And then I try and wrap them back into their green cradles, hoping they won't fall out.

Some detours make for good stories

Week 3, Day Two

One of the lessons you learn as a Research Assistant is this: you do quite a bit of random stuff to get through slow days. Ideally, you wouldn't want to, because you don't know where this is going, and time is of essence. But when you're a graduate student, it allows you to mingle. So it works. I'm interning as an RA at a university in Muscat, Oman, for four months. Sprawling campus, quiet 30-minute drive to campus, and lovely Islamic architecture. Most importantly, something to keep an otherwise useless post-graduate waiting on graduate applications busy, in a generally quiet town.

So this morning, like a few other mornings, I dive into non-project-related work. Skills are skills after all. I'm supposed to sift through bags of silt from a lake bed in Australia, looking for eggs. Tiny, microscopic eggs. Translation: hours spent squinting into a version of Leeuwenhoek's greatest gift to biology. I plug in the lights and set up the toolbox: miniature airtight jars, tweezers, probes, droppers, petri dishes and glass beakers, and squeeze bottles filled with water and ethanol to euthanize the little critters.

You learn quickly that the key to getting through the tons of monotonous days and tasks is an iPod. I don't know how scientists got through without them earlier, because in those days instruments were large enough, and rooms small, to leave no space for a bulky record player. Sometimes you want to hear the quiet humdrum of the machines in the room, but it's earphones all the way.

I prepare my samples for viewing, sit on my backrest-lacking throne and start sifting.

I see a little asteroid explosion on my dish. The pale yellow background of the light underneath glistens through the large and small chunks of brown, dark brown silt. I'm looking for something that looks almost exactly like the debris its buried within. I need to break these mounds with the probe to find the eggs. Tap, tap, tap. Trouble is, when you break one chunk, it sets tinier chunks flying in every direction. I start a one point, and move the plate clockwise to cover the entire area without oversight. With every little task, you establish a regimen. Neither lab class nor field trip. This is the excruciating path of research. So I probe, lift, twirl. And then again.

There, in the midst of that chaos, I find my treasure.

Even if you've been doing this a small while, you'll know a living thing when you see one. So I find that smooth-edged, shapely, mustard-brown egg, almost glowing red sandwiched between the dirt chunks above and the light below. The circling stops, the area around in cleared, the dropper dives in and sucks the little critter in it's temporary haven right out. I put a strike on the sheet with the details of the sample. The circling starts again. And I continue to break mounds of dirt for that fiftieth chunk that will yield that golden egg.

Tap, tap, tap, tap.

When one song flows into the next, I don't realize. But I'm constantly humming. I've unknowingly memorized these songs. Until the next set of 100 that I take the week to memorize.

The tapping stops. I think there's a fatality. I gingerly tap again, and the dirt disperses. False alarm. Sometimes, I'll admit, I am more afraid of ruining the shape of the beautiful critters I'm fishing out and into the ethanol that puts them into a permanent sleep, than I am of killing them.

I found another. Three actually. And after seeing no results for ages, I actually yelp. Out loud. On such occasions you're glad that there's no one there but you, and those that are, have earphones. I repeat my fishing routine. Stop, clear, suck, spit, return. I smile as I watch the alcohol from the dropper tip starting little eddies in the water. See the several teeny possibilities of getting lost in the mundane everyday tasks?

The dish takes too long to rotate. It's taken me four hours to sift through 6 grams of soil. 42 grams to go.