An ill-conceived question

I am not a representative of any committee, if exists, that works upon the genuity of questions in the entrance exams or interviews for PhD admission at IISER-Mohali. Nor I expect neither I will be entertained if I try to correct the questioners on the spot. However, I can be vocal enough on my blog.  Dear PhD aspirants, please beware of following question if asked in the IISER-Mohali's PhD/int-PhD interviews:

Cell size in nature remains constant, but the cell number increases. An example of human and elephant will be projected

The statement proves the popular notion in quantum mechanics, "Everything that can go wrong, will go wrong if you wait long enough". However, I did not need to wait long enough to wait see the wrong. Since I joined my present institution, I see this question popping up in one or the other interview.

Cell size is not a constant property of living beings.  In eukaryotes only, it varies by 300,000 fold. Throughout biology cell-size/shape matters. It is under adaptive selection. Think of a blood cell that has to pass through thin capillaries and think of a axon that spans through your spine. Think of a oocyte and think of a sperm.  Think of xylem, think of phloem. Think of stomatal guard cells, think of root hair cells. Think of collenchyma, think of sclerenchyma.  One can argue that comparison between same cell-types in different species should be made. Fair enough, think about cardiomyocytes of human and mice? And hold on, I have not been extreme in my examples, else I could cite the comaprison of amoeboid to a virus cell.  Cells are different in size and shape for the obvious reason, perhaps not that obvious to questioners, this thing called adaptive selection in evolution. Sounds familiar?

But then why the question is being asked and what answer are the questioners looking for? I do not frankly know the correct answer to "why", may be a typical case of verbal diarrhea or an ignorance of utterly arrogant nature. The answer they are looking for is the surface area to volume ratio of the cells. If the volume increases, surface area increases rather slowly and therefore transport rate, and hence the growth rate, will be compromised. However, the nature had other plans.  The observed decline in growth rate is very very shallow, suggesting that  either the transport rate is not the limiting factor or it is compensated by higher production of transporters and channels.

If at all, you are looking for a cellular property which largely remains constant, it is "karyoplasmic ratio" and again not for the reasons they cite. It is to keep the balance between nuclear and cytoplasmic processes like transcription and translation rates. The news for the questioners is that the noncoding DNA seemingly expanded or contracted in genomes to keep the karyoplasmic ratio constant!

The champions of bullshit

Science administrators are my all time favourite bullshitters. But when it comes to science speaking, some young investigators are the big time champions of bullshit. ABSOLUTELY NO CONTEST !

Inflated claims amplified by overconfident tone for rather obvious and expected results is common. Uncommon are the new ideas and hypotheses. Same old stories of role of a gene/protein or few in a particular process. Assumption that deleting a  chunk of protein will keep the physiological properties of protein intact and others will have some impact in the manner they test it, seems too naive to be interesting and enlightening.  Claiming desired change upon knocking down common signal transducers, transcription factors or epigenetic modifiers  is like expecting an animal to survive after acute dehydration.  Some even tinker temperature and expect no response as null ! Well, my phone also hangs up when heated up! Wonder about the source of motivation and the nature of excitement the young PIs cherish in doing so. Bullshit stinks when someone claims that the deletion of quack quack domain has a role in blah blah interaction, while other domains are dispensable. Really? Thanks for the insight ! Would you kindly elaborate  the changes in  biophysical properties of the that protein? Does it still fold? Does it still phase separate? Are the cells fine, why to shy away from normality of cell-cycle curves.  Biophysics, the bullshit pours in again, peeing something onto proteins and voila the conformation changes ! Thanks, I experience that every morning when I flush. And, the protein-protein interactions, we need to be in awe.... yeast two hybrids with >50% false positive rate seems the favourite toy, validating through partial col-localization of some clumps inside (and sometimes outside) the cell that is sandwiched like an omelet between two glass pieces, the immunofluorescence, as if both the techniques are complementary to each other! They are not even self compatible. Despite severe flaws, not working out an alternative approach seems so un-enlightening. Yet the bullshit is stuffed in the ears as the work is likely to cure the human diseases in future, though not done on normal human cells at first place.

Get a life !

Plunderage of most scholarly type and the making of assholes

I experience a sense of duty mixed with fear (of being late and penalized) when it comes to income tax filing. Most of us, as citizens of this country, feel accountable towards the law of the land. But, where is the accountability of the government funded science institutions? I express my agony against the severe lack of accountability for the use of public money in science and higher education. The recent funding crunch in country’s science is no excuse to plunderage of past. There are institutions having poorly managed multiple copies of the same expensive instruments. Some are kept as backup for more than a decade. One can spot these lying in the corridors in unboxed parcels loaded with termites and rodent shit.  Each of such instruments cost a few crores of INR and the plunderage is not an inappropriate term to be used. One might disagree and counter-argue this view. However, why these arguments are needed at all if there can be a transparently managed official platform for the accountability of public money in science institutions. Since most of the instruments and other facilities are funded by the very same handful of agencies, a database can be managed and made public. Surprisingly, many of these institutions do not even declare these facilities on their official web-pages. The institutional reviews by external peers appears a formality and no real issues are assessed. It might not be appropriate to argue on why these facilities do not fetch even a single cell, science or nature article, the real issues are the ignorance, arrogance and the severe lack of co-operation. Why can’t these facilities be limited and why can't these be shared democratically among the seekers? After all, these instruments are not discovered by scientists in their backyard neither they diffused in from parallel universe as an investment by aliens in Indian Science. Why do most scientists become assholes? 

Which Smad?

Welcome-Trust/DBT interview:

X: “Which Smad are you talking about?”

Me: “Don’t recall the variant precisely, but I guess it is Smad2 or 3”

X: “You mean you are not sure which Smad you are going to study?”

(and X looked around towards the other panelists with an ill-conceived smile as if to convey “see I caught him”)

Me: “No I do, the Smads, or any other known signaling proteins for that matter, which interact with CTCF, are my interest”

X: “It is generally the function that determines the genome structure, why do you propose other way around? Your hypothesis seems flawed”

Me: “No I did not, not sure how you got that impression.  We simply don’t know the answer. In my view, genome is self-regulating feed-back system, where structure and function are interlocked with each other and may be it is not appropriate to look for a starting point. Chicken or an egg problem!”

X: “Why do you want to study the bivalent marks?”

Me: “Well bivalency has huge significance in development. It is known that ………”

X (interrupted): I am not asking what the bivalency is? Why did you choose bivalent mark to study?

Me: “I did not. It is the observation. We find association with bivalency and therefore we want to study it.”

X: You mentioned that you will use various matrices of differing elasticities to grow the stem cells. What is the SI unit of elasticity?

Me: Well, I do not recall it right now.

[again X looking around the panelists with a expression of “how was that?”, as if it was a cool physics question and my whole project will depend on that! ]

X: “With whom are you competing?”

Me. “To best of my knowledge, nobody is working on this question, I am not sure if I want to compete with any one. I am just addressing one scientific quest that appealed me.”

X: ”Why did you choose that your post-doc PI should not be contacted for this project”

Me: No I did not.

X (repeated):  ”Why did you choose that your post-doc PI should not be contacted to review this project”

Me: No I did not.  I am not sure if there was any such option in the application form [Indeed, there wasn’t any and I confirmed this from my colleagues]

X (repeated):  ”You chose that your post-doc PI should not be contacted”

Me: “Not sure if I did it. If at all my application conveys so, it is genuine mistake on my end. You can contact him any time”

PS: I don't think I signed any agreement for confidentiality of this interview which happened sometime in 2013.

Social media, the stripper of characters

Imagine if Lance Armstrong, the elite biker, was your role model, what could have been your emotion when you discover that he was doping. This indeed was case the situation for many youngsters. Lance was subjected to medical scrutiny that led to the exposure of reality. Unlike Lance, many of our celebrities are not subjected to such scrutiny of their deeds and characters. In contrast, they are exposed by themselves, through the trail of their own posts on social media and to some extent through social punishers like wikileaks. One can pick the example to convenience.  Then whether  these are personalities/pages followed/liked by OR abuse, lies, flip-flops, contradictions, quarrels, fake-news posted/tweeted by our colleagues/relatives/politicians/icons, more visible you are on social media, greater is the accessibility to your reality.  It teaches lesson, a lesson which is not new as such, but now the realization comes from global experiment in  a powerful manner. To judge someone's  suitability as your associate in any relevant sense, you must provide free space, just the free space, to let the person express his character in full and the naked truth will be staring at you. Some of my icons/role models got naked in that manner and sooner I learned not be follower of personalities, but of realities.

Dr. Mukhopadhyay: India's own Alan Turing

While I always mention about my all time intellectual hero Alan Turing in the introductory class of the courses I teach in IISER-Mohali,  mentioning of  Dr. Mukhopadhyay (well not samrat mukhopadhyay, its Dr. Subhash Mukhopadhyay) during my epigenetic class is irresistible.

Many youngster are not being liked of being too critical of old headies in administration and bureaucracy. If any one wants to find out why, one of the best documented examples I could recommend is the case Dr. Mukhopadhyay. In fact, you can find a movie on that "Ek doctor ki maut" played by Pankaj Kapoor. He could have been the first in the world to make IVF successful, for which Edwards was awarded the Nobel Prize in 2010 and there could have been a possibility of sharing the Nobel with him, havent he been been harassed by government bureaucrats. Later, he committed suicide and his wife could not take it and got paralyzed.  As Dr. Sudarshan Ghosh put it, just like in IVF, the embryo does not survive if you put it in bad culture media, a bright scientist will not survive in an environment of negligence and harassment. Damage done, but where is the apology from the Indian government? Will they repeat what Gordon Brown did for Alan Turing? Will they ever?  

Faulty ideas to plundered systems

'Only the change is persistent' is the popular saying encouraging to induct and accept potentially positive changes in the system in the favor of collective welfare. It's a lesson that very few of my fellow countrymen seem to have ever followed in real sense. The 'change' mentioned here is not in the context of mundane changes to accept technologies, like that of cell-phones, without which we are left behind in time. We are good at that. It's a change related to culture, attitude, habits, policies and administration.

The issue of corruption remains unarguably the foremost problem of our society and I do not assume any need of elaboration on this. However, I find the the irony of morals very striking. I recalled how my parents narrated a story of a young police officer visiting my home for the back-ground inquiry of me joining as a class I officer in a central government institution. The officer removed his shoes outside the main door and when my mother told him not to bother and come inside with shoes. He arrogantly said "hamare sanskaar hume anumati nahi dete" (my morals do not allow me). What would have happened during the inquiry checkup is a no surprise. My parents had to pay bribe multiple times in order to keep the inquiry report OK. It was not as if they were willing to pay, they feared the sabotage which could create problems for me. It was clear that asking for bribe was not in his morals. Examples goes on. Mundane and rather irrelevant things like going to temple, touching our elders' feet, keeping the home tidy are in morals, but littering, spitting and peeing in public, abusing, jumping red light, taking bribe etc are all OK. If we trace back the history of this attitude, I will not be surprised that such attitude would have escalated after British liberated us. We still cherish the festivals, which are sexists: Kadwa-chauth, Raksha-bandhan, Bhaiya-dooj and Lohri (vibrantly celebrated when a boy is born) to some extent. These festivals are tightly hardwired to our society and emotions and are here to stay for centuries to come.  The least damage these festivals do is to remind at-least a few times a year that the males are superior to the females through several different interpretations. One could argue on correct or incorrect interpretation, but the fact remains that the the celebrations are gender-biased.   My brief experience as a scientist in India taught me that the new institutions follow work culture and policies of existing age old institutions, as if those had been great examples. It is immaterial to discuss the whole repertoire of cases. More important is the quest why is that so? Carrying over the faulty ideas from generation to generation is the bottleneck, which needs to be broken collectively through immense courage and effort. Ideas of our constitution deserve more respect and should be implemented as antidote to faulty morals. One would say this can best be achieved through our politicians. Well, another faulty idea that we inherit! If that was to happen, 68 years of independence was sufficient enough time. This will only happen through us, the people.  We need to change. Change ourselves, change our politicians through our votes or in less likely scenario through joining politics ourselves. One reason why Imran Khan is my all-time role model and why I appreciate Arvind Kejriwal and team. Not for what they could achieve, but for something that they dare to attempt.