Rhythmic delusions

Humans are always looking for brighter tomorrow, free from the problems of present. Every time there is a change in leadership in a country or an organization,  our expectations of better tomorrow are rejuvenated. However within a short time, the delusions are wiped off and  the same or the worser system pervade into our future too. In universities or science institutions in India, the leaders (VCs, directors, deans, heads etc) are, in my view, short-sighted with a vision limited to their own tenure period. They come and go with the least  improvement  in the system. This trend, however, has some exceptions. But, the exceptions/outliers are there in every system. Everyone is John Nash on this planet and everyone died in the road accident while returning from Abel award ceremony !  Following are my common observations on most science administrators:

1.  Their official email accounts are synonymous to event horizon. Nothing escapes to return back from this zone ! Some interpretations: i) Screw you, I don't care. You are just a  troll; ii) Come and lick my feet instead. Question: why do people take up the administrative positions when they think that they should not be accountable despite being in power?

2. Express a grievance, and you yourself will be assigned to solve the issue. Soft bullying? Interpretations: i) You got a problem, you solve it; ii) dont complain, else you will be loaded with the work.  Question: What does their office with all the staff do then? The mundane things like preparing time tables, broadcasting notices and circulars?

3. Nepoptosis (nepotism + apoptosis = programmed degradation of institution through biased treatment of employees).  Change in regime follows change in power-lobby compositions downstream. Interpretations: i) safeguarding their own tenure as pleasant and orgasmic as they want, ii) pushing their own, sometimes flawed, agendas;  iii) Feeling good about themselves by being flattered; iv) small initiatives for post-retirement plans.

My spirits take rhythmic swings,  while the delusional cycle continues...

Are we there yet? Not yet~~

My little angel likes this popular rhyme on CoCoMelon channel of youtube, while the second angel

feeds her. Over the time, I started loving this too. Perhaps, I find it soothing  and fetch some psychological comfort or perhaps it might have soothing effect on anyone.  The rhyme describes how kids got bored of long drive to picnic and how their parents engage them in fun.

Here is the rhyme:

Kids: Are we there yet? Parents: Not yet.
Kids: Are we there yet? Parents: Not yet.

Parents: Let’s play a game, Look at where we are
Won’t you look with me, And tell me what you see
Driving in the car

Parents: What do you see? Kids: A deer....

Parents: What do you see? Kids: A lake....
Parents: What do you see? Kids: A rainbow...
Parents: What do you see? Kids: A cactus...
Parents: What do you see? Kids: A tumbleweed...
Parents: What do you see? Kids: Rocks...
Parents: What do you see? Kids: A train...
Parents: What do you see? Kids: A windmill...
Parents: What do you see? Kids: A cow...
Parents: What do you see? Kids: A tractor...

Everybody:It’s so much fun, To drive so far
Let’s look outside, And enjoy the pretty ride
Driving in the car

As it radiates through our house, I feel as if this is meant for scientists or (may be for artists too or may be for everyone) who are often professionally dissatisfied with their present understanding, efforts and achievements. Everyday starts with the same intellectual dissatisfaction about what we are able to realize and an urge to know the logic or lack thereof in nature. What immediately follows is a positive vibe of how I should deal with my everyday's anxiety.  What I miserably fail to do is to enjoy the ride itself and rather hope impatiently for some elusive destination. For scientists, a piece of new information is a source of joy, which is often difficult to unearth ourselves from our own science. However, we focus too much on the discovering the truth ourselves, despite realizing that the truth  takes its own sweet time to unravel itself to us. What instead we should do, and supposedly many of us are already doing this, is to teach ourselves the new truths discovered by others: the literature reading. We often fail to read literature everyday and even if we read, we are not guaranteed to learn something interesting and appealing.  Good news is that one interesting information serve as food for thought for several days and seems perfect replacement to our anxiety . What we should make sure is that we feed our mind new, interesting and important information as regular as possible. It has worked for me at least.  

The most absurd time in scientific publishing

Denying the evidence on the face, blacking out the key findings and dismissing the novelty for no genuine reason seem routine response from science journals to me. It is very difficult to understand why and how the scientific community has become so hostile to their own colleagues. I am amazed by the innovative ways the reviewers and the editors find  reasons to reject the manuscript.  In one instance, the editor dismissed our findings by just focussing on the 1st two lines of the abstract (which are generally of introductory nature) and completely blacked out the main findings written thereafter.  Despite my arguments, the editor held on to the argument that the role of conserved noncoding elements in development is well known, while that was never the claim. The claim was that the lineage specific position-effect of CNEs, without any sequence divergence, in mammalian genome can impact the developmental trajectories of brain development and showed a link with the loss of cortical gyrations of rodent brain. I challenge if any one finds any literature evidence in that context. Nevertheless, arguing further led to editor's formal stand of applying for a formal appeal along with the a note that addressing appeals is not their priority and can take indefinite time: a trick to finally convince the authors to withdraw their submission altogether.  Consider another example: One of the reviewers argued that our finding was not novel and instead of citing the evidence or data, he/she shamelessly projected some supplementary excerpt of casual and extrapolative nature from a paper. Irony was that the other reviewer clearly mentioned that there is no literature available on such an analysis and considered the manuscript for a revision. Yet, the editor decided to go by the reviewer who had negative and rather misleading comment. How lame is that the editors do not bother of checking some facts themselves and how uninformed they can be. Reviewers hide behind the the confidentiality clause of referee's comments and lie shamelessly.   I can  project numerous more examples similar to the aforementioned ones. 

Take a break and think of converse. Often, I see articles with non-novel, expected and rather unconsolidated observations, but are published in top journals.  This is even bigger a mystery to understand. Most people reason that social ties, nepotism and lobbies fetch such outcomes. Really? Is science publishing  that worse?

There seems some serious problems with the peer review system. Why this confidentiality clause for reviewer's comments? Why I can't I copy paste those comments on social media to expose the editors, reviewers and the cooperate publishing houses? Why do journals' policies decide where my fight against editor and reviewers should end? Why don't we have an independent judiciary for science communications? And, more importantly, who should decide whether a paper should be accepted/published or not? Should these be 2-3 people on this planet? Why can't we have it opened to the community  similar to biorxiv and then open it for  review by the scientific community, cross-communications with the authors, addressing of comments and get a score for each article. Such a score can simply be a indicator of article's impact.

Your own Sansarpur?

If you think Williams sisters, Wough brothers, Tendulkar-Kambli, Boxers from Cuba are the great examples  of childhood friends/siblings playing all the way to the international levels, take a break and consider a moment when 7 childhood friends played in the same Oplympics, of which 5 represented only one country. This happened in Mexico Olympics, 1968. A total of 7 players belonged to the same small village  of Sansarpur  (Punjab) with a population of ~4000 only. Five of the 7 players played for Indian hockey team and 2 for Kenyan. In total, this village contributed 120 hockey players at national and international levels and of which 15 were Olympians. Is there any match? Unfortunately, Sansarpur is a forgotten legacy now.

(Image: 7 players from Sansarpur played in the Mexico Olympics, 1968)

Recently I thought of looking at my own Sansarpur. Where are my college mates now? It's an interesting exercise that any one can do in leisure time. With the deep connectivity of internet, I easily found mine Sansarpur:

1. Ram Pratap Singh: Gastroenterologist (MD, DM), Midland Heathcare, Lucknow 

2. Shiv Pratap Singh: Deputy commissioner, customs and central excise, department of revenue, ministry of finance, GoI

3. Vaibhav Sinha:  Senior Director, Head of Global Marketing Communications at Carl Zeiss Microscopy GmbH Jena, Thuringia, Germany

4. Rohit Anthony Sinha: Scientist at Sanjay Gandhi post graduate medical college, Lucknow.

5. Chanchal Kumar: Associate Director, Head of CVRM Bioinformatics, Astra Zeneca, Stockholm, Sweden.

6. Vidyendra sadanandan: Chief Technology Officer (CTO)), Molecular Connections, Bangalore.

7. Harkewal Singh:  Manager at Kaneka US Innovation Center, California.

8. Rahul Yadav: Engineering Manager at Strand Life Sciences, Bengaluru Area, India

Seems like a success story? But hey wait a minute, the list is biased because successful people are anyway more visible on the web.

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?