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.