EngulPhD

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Courtesy: Chris Schlag

A 3-episode column on PhD life written between 2008 and 2012

EPISODE 1 – Now, what’s with my brain?!

The life of a scientist can be fun, hilarious and eccentric besides just maddening. With research it is always the craziest ideas that make the best papers, nonsense thoughts that stumble into stunning discoveries and poor jokes with a scientific temperament that give the scientist his identity.

It is common in a lab to interact with co-scientists to sneak into their ideas not to have them mask our own but to occupy our leisure with “entertaining” science thoughts. On such occasions, it is not quite unusual to use transferred epithets like, “your DNA sample”, “my gel”, etc. so much that it goes unnoticed even if we said “my pups are being delivered today!” Well for the non-biologists, it just means that I have bred some mice for research and they have borne babies today. I personally dislike this idea of owning biological samples “strictly meant for research purposes” as it sounds rather embarrassing to state in public that “my kidney cells don’t grow” (they are the HEK 293T cells, a cell line developed from an embryonic kidney…well, somebody’s kidney, not mine!) or “her blots are so blobby and not good for publication” (to describe the results from a Western blot) or in the worst case, “she’s out exposing  in the dark room” (well, exposing an X-ray film for a Western blot). Such possessiveness, however, is not dispensable when it concerns my colleagues. Not forgetting to mention that English is not the language that they are conversant with.

In my first year as a grad student, I was introduced into primary culture of neurons which required mice dissection. Thursdays are meant for primary culture when I, the ‘responsible’ person, gently, swiftly and sympathetically sacrifice new born mice to get out their cerebral hemispheres (something to do with the brain) to subsequently grow brain cells on a plate. It is not an easy job though not really nasty. P0 pups (new-born) as we call them, are tiny, one-third the size of our little finger and calm and less agile than the bigger mates. It took me quite a few tries before I got the art of uprooting the intact cerebrum. The procedure doesn’t stop there. I then carefully pull out the meninges (a thin layer covering the cortex) again making sure I do not disturb the gross morphology of the structure under the microscope and finally drop the clear cerebral hemispheres into a new petri dish with..whatever.. media. I have performed this dissection less than a dozen times now, so I still call myself an amateur in mouse work.

My turn this week came yesterday. Half past one, 6 pups, all game and I started the work. The usual. Cut off the head, hold the snout with big forceps, cut open the skull, pinch off the cerebral hemispheres with fine forceps, under the micrscope, clear the meninges, drop the hemispheres in whatever media. 3 pups and as always, I never got the hemispheres intact. They were either dislodged from each other or disfigured or even slurried. The fourth head. Splendid. Even after all the processing from above, I realized that this one looked amazing. A blind man (provided he is a biologist) could identify this structure under the microscope as belonging to some region of the head. Exemplary! I was so ecstatic with the production of my masterpiece held between a pair of forceps when somebody slammed the door of our tissue culture room. It was one of those non-English speaking colleagues. I know not for what reason she was here but the moment she entered she was all screaming…”Oh my God! Look what you have done!” Apparently I was so confounded with her entry that I had no clue what has been happening all along with my masterpiece. And she exclaimed, “Your brain is on the floor!”

Well. Not quite.

Published online LabTimes Oct, 2011

 

EPISODE 2 – Tips to get to your discovery

Food, water and shelter…are these the only indispensables for man? Well, not for an eccentric man – I mean, a scientist in the making. Years of fidgeting in the lab can mean nothing in the end if that ‘one’ thing’s missing. Struggling with your pipettes all through the wee hours, turning up in the lab on sunny weekends, yet not reaping the benefits of “hard work”, you lapse into a feeling of numbness. It’s the kind of feeling that overwhelms you when, at the end of a tiresome day, you are so paralyzed by work that you hit the sack without a trace of appetite. It is a kind of satisfaction that you are forced to perceive with all the discontentment buried at the back of your mind, when nothing has worked out the way you had planned. But as a PhD student, I learned a few tricks to keep things rolling, to look at the brighter side of the wrecking lab life…and I believe this will some day help me touch my finish line charmingly.

Food has been a major contributor to the success of my experiments. Though I try to keep calorie-checks, the thought of a food-break has always stirred me up. Sponging up some chocolate to forget an experiment that flopped, scurrying to get my hands on leftover cakes from a neighbor lab’s birthday party (unashamed of the “help yourself” notes) and crashing a lecture for the sake of free food has become routine. Besides feeding my overworked brain cells, a food-break has always been a key motivator… it is the time when everybody gets out of the lab (as far away from it as possible) and cries out his/her worries about lab life. Beyond whining, we get down into hot debates on virtually anything that can keep our minds off the lab – America’s next president, the German tax system, Indian mythology…what not?! It is then that we come up with the craziest of ideas like having meal-size energy capsules to save cooking time or calling the urgent need for clone-slaves for each of us to share our workload (but not the authorship on papers). Though such entertaining conversations are unfortunately thwarted by screaming timers indicating the end of ‘incubation times’, our coffee-breaks have always been some of the best and intimate moments that I look forward to every day.

The second great thing that has cleared my brain fog is music. Earlier I had disregarded music as a ‘distractor’ and kept it away during working hours. But when I’m bogged down with work I find music a great help. When listening to my favorite music, I get fizzy and end up with an enormous amount of positive energy and a “nothing is impossible” attitude. It is not uncommon to find my mates walking around the lab with head phones stuck to their ears donning a “I don’t belong to planet earth” look. One of my colleagues is particularly notorious for having startled a technical representative by a loud karaoke. Apparently, this colleague had had her head phones on when she was imaging at our fluorescence microscope. The ‘scope’ room, as we call it, is a dark niche in one corner of our lab. With the heavy curtains that confine it, it is hard to guess if anyone is imaging unless one looks at the ‘login’ list. The service person from the microscope company, obviously oblivious of this design, walked into this space only to be shattered first by a shadow in the dark and second by the loud and unevenly pitched singing. What followed was an hilarious afternoon!

A PhD is quite a trying time. But just as every cloud comes with a silver lining, PhD life has its own share of fun. A light heart makes it easier to appreciate science. Life is a miraculous creation with so much complexity that there’s no wonder it takes so long before making your discovery. But enjoy the scenery en route.

Published online LabTimes Dec, 2011

 

EPISODE 3 – Savoring your Eureka moment

If I turn back time, I can recount the D-day, about two and a half years ago…

It took me several tries and months of disappointment until I finally had a break through with my project. It was a year and a week of grad student life when, late on a Friday afternoon, I sat down at the microscope to analyze my staining. As usual, I was expecting a repugnant set of neurons that simply refused to light up (fluoresce) on excitation, let alone, light up my lugubrious lab life. But no, this day was unusual. Even as I scanned my slides under the epifluorescence ‘scope’, it seemed like the neurons were talking to me in a language that I had put forward in my research proposal. The same words; I heard them repeat! Wait…was I dreaming? After getting my PI to confirm my findings whose remark, “Madhu, you have magic hands”, still reverberates in my memory, I safely concluded that what I just witnessed had been my life’s first Eureka moment .

Daring a little frolic at my finding, I went on to jot down my work in my lab book and successfully reproduced the results before raising a glass. Convinced that this had been the kick start into my project, I sketched our working model and set out to do the simple rituals… I mean, experimentally prove every detail in the model by following an even simpler drill: perform an experiment a dozen times to standardize conditions, another dozen times when a part or whole of the experiment cannot be completed (you find antibody aliquots empty only on the weekend during an important experiment) and finally, at least three times to get concordant results. This way, I carefully worked my way through the model…indeed, with several failures, some breakthroughs, a few detours and sacrificing many weekend parties. Eventually, two and a half years down the line, here I was with a piece of research, which I held onto as my masterpiece… until we came to publishing my work for peer-review.

“It is your little piece of art, if you’ve done your best and you think it is complete, the reviewers too will find it complete”, I was misled by the opinion of an anonymous professor. He was probably referring to an era that has already lapsed. The age of Einstein, of Darwin, of Cajal. I wouldn’t dare say they had no critics or opposition but, at least, they had all the time in the world to be the “first” to describe a phenomenon; they could write their books for the sands of time and did not have to rely on papers and their impact factors to launch a scientific career.

Today, discoveries are made in the order of minutes and if it takes too long to tell your story, you can be sure of being swept over by your competitor. After three rounds of submissions, rejections and re-submissions (to successively lower impact factor journals and with several rounds of experiments to refine my study), I have come to call the publishing process a gamble or precisely, Russian roulette, with the odds simply not in your favour. Though the peer-review process is laid with the idea of inviting constructive criticism, there are several instances when you feel that the reviewers simply condemn your idea for no apparent reason. As a grad student, I know I can do nothing about it and I do realize that publishing will only get tougher but I cannot brush off the statement, “the reviewers were not too enthusiastic about your study and we cannot offer to publish it” (it reads to me, “your work is much too sloppy to get in here!”). It is a funny thought but why would anyone want or not want to be enthusiastic about my work? In that case, can I not be done with it by publishing it on my blog? But alas, “fighting is normal” comes the consoling annotation from my colleagues. Yes, “fighting is normal, success is sigmoidal, rejection is logarithmic and now, I am eccentric!”

Published in LabTimes Feb, 2012

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