Reconceiving the gene- Frederic Lawrence Holmes

When I joined SLS, I was asked to teach genetics. My heart sank. I had never done genetics. Vaguely, I remembered some classes during M.Sc but it never made any sense- more on how little I learnt in M.Sc. later.  But the point was I did not know anything beyond Mendel's law- something I learnt in school.  The senior faculty who coordinated the course was also emphatic that I should teach Benzer's experiments.
I sat down in the summer break to learn genetics.   In an attempt to understand Benzer's experiments, I turned to the internet and thereby learnt about this book.  I purchased it couple of years back and finally read it.

Frederic  Lawrence Holmes was Professor and Chair for the Section of History of Medicine at Yale University. He draws on wealth of information to present an engaging picture of the emerging field of molecular biology.  At the turn of last century, the nature of the hereditary material was plaguing the biologists.  Thomas Morgan began using, what we call as classical genetic tools, to address this question using Drosophila.  It was in his lab that Alfred Sturtevant, an undergraduate student forgetting his homework, built the first chromosome map one night. (This is a story I always tell my students!).  Morgan himself was not comfortable about chromosomes as the unit of heredity- he preferred to use the term factors.

But was chromosomes composed of?  And what was being transmitted?

Holmes paints the picture of those days- Muller's experiments with radiation to understand the nature of the chromosomes.  The discovery that radiation induces mutation and what really is a mutation is something that Muller is obsessed with. He journeys from America to Russia to Scotland, changing the location of his labs as he bombards radiation on the chromosomes in a bid to understand the nature of the genetic material.

Into this milieu, Max Delbruck is sucked in after listening Niels Bohr's talk. He established the phage group- scientists working on bacteriophage in an attempt to understand genetics.

Seymour Benzer completes his Ph.D in physics and joins them as he wants to work on biophysics.  He is enchanted with the phages and after a period in Delbruck's lab and a year in Paris with Andre Lwoff, he starts his own research group in Purdue.  It is here he stumbles into a method to map the rII region (gene) of the T4 bacteriophage.  It takes him from 1954 to 1961 to create a genetic map of the region.  He shows that the rII gene is possibly divided into two regions and recombination between the two regions as well with a region was possible. This was the biggest contribution to the field of genetics.  

But what most fascinated me was that fact that he kept a detailed record of that period.  The work done everyday was recorded, analyzed, and a map drawn based on the results.  Something I wish my students would emulate.

The second most fascinating fact was the usage of the word 'gene'.

Gene was first coined by Johannsen but geneticists could not agree what the term meant.  The discovery that DNA was the genetic material followed by the structure of the DNA  did little to dispel the fuzziness of the term.  Benzer begins by using the term gene but is dissuaded by Alfred Hershey (of Hershey and Chase fame).  So he coins three terms- Recon to define a unit of recombination, muton to define a unit of mutation, and cistron to define a unit of physiological action.

Unfortunately, Holmes was ill and dies before he could complete the story that he had originally conceived. So the book sort of ends abruptly with the question still hanging as to when did the word 'gene' find acceptability.

In most modern textbooks, Benzer's experiments are either not mentioned or are mentioned too briefly to understand its importance.  Possibly in today's time, when sequencing so commonplace, it is not important. But his experiments were a major stepping block to our understanding of what a gene is.

Young Sheldon and would it happen in India

I have been watching Young Sheldon- the spin-off  of the Big Bang Theory.  This one features Sheldon and his family as he grows in Texas absolutely confident that he would win the Nobel Prize one day.  The series begins with the school recognizing that Sheldon is a genius and promoting him to the middle school.  Today episode was as usual hilarious.  A NASA scientist visits Sheldon's school and manages to put him down.  Sheldon sets out to prove that he is right and the NASA scientist is wrong.  The episode ends with a visit to the NASA center where the scientist admits that the idea (or rather the Math) is fantastic but they do not have the technical capability to put it into action.  Then a shot is shown of space program conducted by Elon Musk, essentially showing that Sheldon's idea has fructified.
But as the episode ended I wondered whether it would ever happen in India.  If a child was bright, would he/she be promoted or put through a special program for such children?  Would a child be encouraged to think out of the box?  Would such ideas be welcomed by our scientists?
I asked this especially as I got the feedback forms from my students yesterday. Till this year one of the senior professor was the coordinator of the course and he never took the feedback forms. But he retired and I became the coordinator of the course and of course, initiated feedback forms.  I took feedback both on the course and teaching methodology.  As I read the feedback, I was elated and sad. One of the students had written that this was first time he/she had been encouraged to do problem-solving and he/she was now getting the hang of it.  This reminded me of a student few years back. After she got into IISc that it was because of my teaching that she was able to answer analytical questions at the time of the interview.  Over the years there has been many such episodes. After one exam a student told me that it was so different from any exam she had taken for this was the first time she had been asked to think and analyze a piece of data.
"I enjoyed it so much, Ma'am," she said and I can never forget the joy on her face.
It is so sad. This is something they should have been encouraged to do right from school. It should not take a Master's level course to learn how to think or how to work around a problem or to analyze data.
As we dream of Nobel Prizes, we might want to get our basics right first.  Unless our children are allowed to dream and unleash their creativity, we are not going to get anywhere in the near future.

Lessons not learned

It is that time of the year again.  A heavy greyish pall hangs over the city.  My eyes are burning and breathing is difficult. We had one year to set at least some things correct but of course, every one was too busy and Delhites cannot be bothered to obey rules.
The state government was busy fighting elections in other states. It is only when they lost heavily in Punjab and Goa that the chief Minister turned his attention to Delhi. Consequently, the public transport system has not been strengthened.
Haryana is busy dealing (or not dealing) with the various deras and babas.  Punjab has a new government and they are too busy putting the blame on the center.  The central government is always in election mode. They are more worried about the upcoming Himachal Pradesh and Gujrat elections.
Also, today is the one year anniversary of the demonetization drive and newspapers/media are busy covering that.
We are now used to buying our own water purifiers because no government can promise to deliver safe drinking water. We will also buy our own air purifiers. The economy will at least be uplifted, right?
The Supreme Court and the National Green Tribunal tried to do some thing. But the people of Delhi believe that they are never in wrong.  Anyway, don't you know who I am?  You are asking me to travel by public transport? Me?
So there we are.  One year later, no lessons learned. That is us.

The Raya Sarkar Post

Harvey Weinstein sexual misconduct case has had numerous fall outs.  One of this was a Facebook post by Raya Sarkar, a law graduate student at the University of California, Davis.  She named two Indian academicians accused of sexual misconduct and then invited other victims to send her the names of Indian academicians who have sexually harassed them.  Not being on Facebook, I did not see this post.  But it caught my attention today when I saw that prominent feminists have put out a statement against Raya Sarkar.

Curious, I searched out the list and scrolled down through it.  The following are my thoughts:

1. The list contains names of mostly social scientists.  There are no scientists in that list. I am not surprised. The science students are not brave enough to name their professors. Their career (read: future grants and positions) are dependent on their professors.

2.  After reading the names I was also not surprised by the statement put out by the prominent feminists.

3. One of the questions asked or suggestion proffered is that the victim should use the institutional mechanism available to them to complain against the alleged harasser. I agree that would be the wisest course. However, the reality is different. Where the powerful are concerned, no action will be taken and in this case, all attempts will be made to shield/protect the harasser.  Instead, the victim will be shamed.  May be this is one of the reasons that these victims have chosen to speak out in this way.

4. The institutions- even the courts- have not really given any solace to the victims that their voice will be heard and justice will be done. In case of Mahmood Farooqui, the Delhi HC let him off by saying that a feeble No can mean yes.

5.That said, the major problem is that it names the name but no explanation is offered.  No chance is given to the alleged harasser to explain his stance.  That is really worrisome.  One of the names on the list shocked me.  Why did the person name him?  Is there any truth?  Who investigates?

I do not know what will be the outcome of this list or what Raya Sarkar hopes to achieve.  All I know is that the list has left me deeply disturbed.

I will just end this with a personal anecdote.  When I worked for a company in Bangalore, a girl intern approached me. She was deeply upset.  Her supervisor was mentally abusing her- basically telling her that he does not like to hire women because they are insincere and they do not work. They always make excuses as to why they cannot stay late and if some body talks to them harshly, they will start crying.  I went to the HR and told her that irrespective of the position the man holds, he has no right to harass anyone.  Next thing I knew- I was pushed into resigning from the company.

Guns, Germs, and Steel by Jared Diamond

It all began with an observation I made to my brother: Why did India lag behind so much in scientific advancement?  And my brother who can generally be relied to answer such questions told me to read Guns, Germs, and Steel by Jared Diamond.  At least it will partially answer your question, he said.

Funnily enough the book begins with a similar conversation that Jared Diamond has with a New Guinea citizen. 

Diamond's hypothesis is that the nations where agriculture flourished along with domestication of cattles became more technologically advanced as compared to the other parts of the world.  Agriculture began in the Fertile crescent and spread into modern day Europe as well as into India.  This was facilitated, of course, by the availability of wild plants that could be easily domesticated.  The spread was across the latitude where the temperature was uniform and thus, plants domesticated in one area could be grown in another area.  In contrast, the availability of such wild plants in American Continent was less and further, after domestication of few available plants, the spread was slow because it had to move across the longitude. There as a greater variation in climate making the spread slow. 
He uses the same argument to explain why domestication of animals happened much earlier in the Fertile crescent as opposed to the other continents.  And then he explains how domestication led to human diseases like small pox that could decimate populations not exposed to these germs.

This is the basis of the entire book. He uses this argument to explain the spread of Europeans to America, Australia, and Africa.   He also acknowledges, fleetingly, that some cultures were more open to innovation and ideas while some cultures that were open to innovation initially became more closed later.

If you read the book you get the feeling that human intention had no role to play in the colonization process.  And that left me with a dissatisfied feeling. Surely, it is much more complicated than a simple explanation of how agriculture and domestication of cattle led to the colonization of almost the entire world by the Europeans by 19th century.  Partly yes.   Development of agriculture and domestication of cattle led to the formation of cities and complicated governments.  However, there was also human agency at hand and it was not all that passive as Jared Diamond portrays in the book.  

Trawling through the net I learnt that a later book by Jared Diamond explored the human angle.  I do not know whether I will read it or not. For the time being, it is on the list of books that I should read.

Teaching science to school children

When I did the site visit to the teaching centers of the NGO we support, I found that the 10th class girls were reading their science book. I squatted down beside one girl and discussed some of the things that she was reading.  Seeing this, the coordinator of the NGO asked me to come and teach the children some day.  I rashly promised.  But when the day came, I was quaking with fear.  Teaching M.Sc students is one thing.  School children are a completely different ball game.  I would have to get down to their level.  Language was another thing. I knew that these kids were not comfortable with English. Teaching Science in Hindi?  I did not any of the terminologies.  But a promise is a promise so I went out there last Saturday.
The kids were equally apprehensive.  Would I scold? Would I shout? Would I be strict?
And so we met. 
The first rule in my class, I said, was that they had to ask questions.  I cannot teach if questions are not asked. 
The children stared at me.  Disbelieving.
I had looked through the 9th class text book as the coordinator had told me to.  But the 10th class girls decided that they wanted their syllabus to be covered.
We covered a lot. We started with photosynthesis, moved on to processes like nutrition, transportation, and digestion.  Along the way the children lost their apprehension. Questions came fast and furious.
How is cancer caused?
What happens when memory is lost?
And then one girl asked:
"Why do hormonal changes happen? Why do we have to grow up?"
I wanted to comfort her. And tell her that it was the same question Jo, from Little Women, had asked. But of course, she had not read Little Women and I did not have the book with me to read it to her. 
Two hours went fast. They were not exhausted but I was.  I learned a lot:
1. The NCERT text books have improved a lot.  Each science section comes with set of easy experiments that can be done in the class room.  In fact, instead of memorizing the facts, the children can understand the concept if they were allowed to do the experiment.  I do not blame the teacher especially if they have to teach 40-60 children at a time.  But if we had more schools, if the class size was limited, and if the children were seated in groups, and if the teacher was enthusiastic and allowed the children to ask questions, science would be fun.
2. I learned the Hindi version of some of the science terminologies
2. The children were eager to learn. Once they had lost their fear, they asked all kinds of questions.  Generally, it takes my M.Sc class more than a week to start asking questions and then too it is of limited nature. Some of them ask interesting questions that make me go back and read more but generally, the questions are of limited scope. But these kids were really fun to interact with. It is such a pity that we are depriving them of a good education.
 

Quartet in Autumn- Barbara Pym

I picked up the book in the book fair as I had heard a lot about Barbara Pym.  This is her penultimate book.  It is the loneliest book that I have ever read. Loneliness seeps through every pore of the book.  But it is not a sad book for the story is told with just a dollop of humour. It is just lonely.
Four office workers- 2 women and 2 men- share an office. It is never made explicitly clear as to what they do. Indeed even the office seems unsure of exactly what they do.  It is the 70s Britain and computers are beginning to make their presence felt.  The office is clear that these four people will not be replaced.  And the four are nearing their retirement. Plans have to be made. Two of them- Marcia and Edwin- have their own homes.  Letty and Nicholas live in a bedsitter and thus, their position is precarious.  Letty's position becomes worse when her landlady sells off her house to Nigerians and Marjorie, her old friend with whom she was planning to retire to a small cottage in the village, decides to get married.  Edwin, whose hobby is to attend Church Services- indeed he makes a list of all the Church related events through the year- finds her another bedsitter.  Letty moves into this place as she has nowhere else to go. This move coincides with her retirement.  Letty makes plans for she knows she should never let time hang heavy in her hands. She decides to read books on Social Studies but finds them too heavy and too boring...
Meantime, Marcia too has retired.  Her life moves in a different direction. Spurning everyone, becoming depressed, ultimately, she stops eating.
On her death, the remaining three find that Marcia has left her house to Nicholas on whom she had a crush long time back.
The book ends in a slightly upbeat mode.  Marjorie, Letty's friend, informs her that her engagement is at an end and would she come and live with her.  Letty realizes that life holds infinite possibilities. She might or might not move back.  Nicholas might or might not sell the house. Marjorie might or might not find another partner. In fact, life is alright. There are so many things to look forward to.

March for Science India

The Breakthrough Science Society called for "March for Science, India" 6 months after the event was held globally.
I marched.
There were about 100-200 people who marched from Mandi House to Jantar Mantar in Delhi.  For the number of institutes and universities located in Delhi (including the NCR), the participation was pathetic.  Most of the number was made up by non-science faculty. My own school was represented by two of us and handful of students from one of the lab (the faculty was marching and he asked them to come).  And when I think of the demonstration the students held on Science day couple of years back demanding for fellowship, I really do wonder about priorities.  I also wonder about our (teachers) priorities.  We grumble and groan about fund cuts, about poor quality of students, about life as a scientist but really, aren't we ourselves responsible for the abysmal situation?  When it comes to crunch time, when we have to speak up, we don't.  We back out.  We worry about promotions, about membership to various academies, we worry about grant (oh, if we speak up the funding will be cut.  It does. I have had first-hand experience in this matter but...)...in general we worry about everything but about science. 
So the government continues to spend 0.8% of GDP on Science, knowing fully well that there will be no protests.
Rubbish continues to thrive. Vaastu Shastra masquerades as science. People flock to astrologer and numerologists- change the spelling of your name and your fortune will change. As my brother pointed out, only the English spelling seems to be targeted. There are astrologers who promise that fortune will change if one uses their particular brand of ash (vibhuthi).  Then there gemologists who promise that the fortune will change if one wears a ring of particular stone.  Wait a minute. I know of scientists as well as students who wear these rings.
I rest my case.
 

The unanticipated problems that we sometimes face

I have been associated with an NGO partner for almost 10 years now. Initially, we funded them as part of Asha-Delhi project. But when our funds dried up, we found them new funding partners. I continued as the point person and have been visiting their project for many years now.
When we started, the children were in primary classes. I still remember the project director telling me that her realistic goal was to ensure that the children remain in school till class 12th.  They focused on girls as they were the most vulnerable. There are many reasons why a girl will be pulled out of the school- there are younger siblings, the economic situation in the house, the mother needs her help with the household chores, and of course early marriage.  So the goal was straight-forward. Let us ensure that the girls remain in school. The way to ensure it was to provide free tuition in the afternoon. It would also be a safe place for the girls to spend time. 
There have been successes. The early batch of girls- 3 in number- have now graduated from school. One is working and studying. The others are studying. All the 3 have enrolled in Open University.  We feel happy.
And then there are unexpected situations.  Today, when I did the site visit, the director gave me the first bad news. One of the girls- she is in the 12th class- had been married off in the Summer. The family went to their village and there was a mass community marriage organized in the village. The lure the organizers dangled was that they would pay the dowry and bear the costs of the marriage. It was a good offer as the mother is the sole bread winner. She agreed and the daughter was married off. She has been pulled out of school and sent off to live with her in-laws.  The entire visit I was haunted. Lot of publicity has been done about the evils of child marriage but the laws and the publicity have only limited impact. The family weighs in many factors- the safety the girl is paramount. What if she gets molested?  What if some body kidnaps her?  Wouldn't it be better if she is married off? Also, it would be one less mouth to feed.  And then somebody is paying the dowry and bearing the cost of the marriage (I really wonder about these organizers!  Did they bother to check whether the bride and groom were of legal age for marriage? Shouldn't they be held culpable?).  So child marriage continues.  I have no clue how to deal with this issue?  Of course, the girl could have protested. The media reports at least one such case every day where the girl refused marriage. A student of mine, I am really proud of her, told me that she fought with her Uncles when they were planning to get their daughters married. She got her cousins to Delhi and got them educated on her  Ph.D. fellowship. How many such girls exist?  How do we raise them?  How do we teach the girls coming to the tuition centers to protest if their parents force them into early marriage. Of course, the NGO has done plays with them, talked about these issues but theory and practice are entirely two different entities.
The second bad news was about a girl who was kidnapped by her neighbour and molested. Fortunately, her parents were able to recover her back. But she has now dropped out of school. She comes to the center but she is traumatized and scared.
As the girls grow up and as we add boys to the mix (the center has now expanded their attention to the boys too and I am culpable for it. I felt that the boys too needed attention and badgered them into opening their centers to the boys also), I wonder how do we handle this explosive mix. The media, the freely available internet has ensured that the world is no longer as innocent as we thought.  So now we are facing unanticipated problems and charting a path that we have no clue how to navigate.

Army tanks and Vande Mataram

I think we have lost it. Totally.
The VC decided to celebrate Kargil Victory Day.  He called in bunch of retired Generals, the administration decided to hold a Flag march and a ceremony of sorts. I gave it a miss. This was not my cup of tea and I have objections to celebrating victory days in University campuses.
Then came the news via the newspaper.  The VC wants an army tank to be stationed on the campus so that the students and faculty are inspired and become nationalistic.  One of the Generals also said that now the JNU "Fort" has been breached, only Jadavpur and University of Hyderabad Forts remains to be taken/breached.

This is deeply problematic.

First: if students do not debate and discuss, how do we ensure academic growth?  We might not agree with all their viewpoints but they have the right to discuss.  Dissent does not mean that our students/faculty are not patriots or nationalists. The academic environment is the place for debates.  In fact, I wish our science students would debate vigorously when they read a scientific paper. They tend to accept whatever is fed to them, which is detrimental to their growth as a scientist.  So if we want ideas to flourish, we want academic excellence, we have to give space for dissent, for debates, and for discussion.  It would also do good for the VC to remember that the University of California, Berkeley was the scene for vigorous protests against the Vietnam war.  UC, Berkeley continuous to be one of the premier Universities and the protesters by no means were anti-nationalistic/anti-patriotic.  At least I knew one of them when I was a post-doc in Charles McHenry's lab.  Art was just fun to talk to.  He believed in America and he was proud of his country. But he had also taken part in the protests.

However, our VC seems to believe that we should not debate and discuss but accept whatever is given to us.

Second: Army tanks do not belong to University campuses. Agreed, many of the Defence institutions are affiliated to us and get degree from us, yet the fact remains that we are an University.  Army tanks can be placed in Defence institutions to inspire their personnel but not in University campuses.

Third: Just because there are dissents does not mean that the Universities are forts meant to be breached.  The statement is so problematic that I do not even know where to begin.  Does the General even know what he is talking about?

Just as I was wondering where we were heading to, the Madras High Court today gave an order that Vande Mataram should be sung at least once a week in Schools and Colleges.  I love the verses of Vande Mataram but why make it compulsory to sing?  What will it achieve?  I remember that in School we had to take a pledge every morning. It went something like India is my Country and we are all brother and sisters....something, something. I said it for 12 years, I still do not remember that pledge. It was a joke.  However, not doing it/remembering it does not make me less of a citizen or less patriotic or less whatever.  The point I am trying to make is that one does not need all these aids to be a good citizen.

A tiny, little guava

The guava sapling was planted by my upstairs neighbor. Nanku Ram, my gardener, and I took care of it, providing nourishment both in form of fertilizer and water.  We pruned and watched it grow into a tree. Understandably he was upset when random people plucked all the fruit last year.  Sumitra, my  house help, was also upset.  They could have left at least one, didi, she lamented.  I was not upset. I am not too fond of guava.
This year too the tree flowered and very soon the fruits appeared.  However, I did not hold out any hope. I was sure that the random people will soon appear and pluck them off.  And then yesterday when I went into my tiny garden to get the flowers for my mother, I saw this tiny, little, ripe guava on the ground.  It was so perfect, the first fruit off the tree.  I picked it up to show it to my parent.  Of course, my mother wanted to eat it.  I photographed it first though and then sliced it.  My mother liked it.

My mother with the first guava

Thus, endeth the saga of the first guava.
But it was a good omen. My student's paper got accepted and she can now submit her thesis.
There are many more fruits on the tree. I hope I get to save at least two- one for Nanku Ram and one for Sumitra. 

The Gene- Siddhartha Mukherjee

This past month has been a difficult time.  Two thesis to read.  One student whose thesis has to be submitted this year does not have a paper and the University declared that she will not be able to submit her thesis. We have been attempting to get it published since last November but journals kept rejecting it. We modified as per the comments given to us. Each time it took us a month to do the experiments and incorporate them into the revised manuscript. Finally we submitted to a journal who were kind enough to say that the paper can be resubmitted after revision. I got the entire lab working on the paper- we have resubmitted it and are waiting for the decision with bated breath. UGC thinks everyone should fit into one mould. Yes, there are too many Ph.Ds without a paper but just by putting a rule that there should be a paper before submission does not solve the problem. In fact when I talked to the University and when we approached the VC with the problem, remarkably, they had the same solution- submit it to one of the pay and publish journals.  Why do you need to submit it to a good journal? 
My jaw fell open.  Does not the VC know that most of the pay and publish journals are fake? That it is better to wait and publish the work in a good journal than in a dubious journal? Are such rules more important than getting a good publication? And exactly what are we trying to solve here?
Anyway, my only relaxation was reading and I finished reading The Gene by Siddhartha Mukherjee.  The book traces the history of identification of gene as the inheritance material. The early part was really enjoyable. He talks about eugenics, the horrifying experiments on twins done by the Nazis and the lasting impact it had on genetics. The latter part was I too felt rushed. And it is not the author's fault. The field has expanded so much that it is difficult to compress it in one book.  There are too many strands and each strand requires its own book.  That said, some of the early history I do plan to incorporate into my lectures for the M.Sc. students.

Nate's podcast- What is CRISPR?

Nate Butkus is 6 years old and he wants to become a biochemist when he grows up.  Meantime, he is a podcast host who talks about science because he likes science.  What he would like to do for his homework is to create a creature that has flaps of skin on its face, antennae on its head, and spikes on its back like a hedgehog.  And on his podcast, he wonders whether CRISPR can help him do it. 

CRISPR is the new exciting technology on how we can change the genome.  We are planning to use it in our laboratory to create knockouts so that we can learn what the gene we are interested in does in a cell.  But obviously its use extends far beyond that.  One of the things that the technology can do is to change a bad gene into a good gene and thus, effect gene therapy.

But listen to the podcast- the explanation is much better than what I am offering.

The Right to Silence

We are fond of noise.  Living as I do inside the campus, I thank every day for the sound of silence. On a cold winter day, just stop and listen to it.  It is so soothing and refreshing.  In the summer, early morning, I go for a walk.  The only sound I hear is that of the birds chirping. It is blissful, such a lovely way to start the day.
Stepping outside is a hazard- horns of all kinds being tooted randomly.  Every vehicle is in a rush. They have to move fast, fast, faster and what better way to do than to blow the horn. As loudly as possible.  The pedestrian, the lowest form of human being, has to make way for the moving vehicle. It does not matter what age the pedestrian is.  The old and the young, the able and the disable- all have to make way for the vehicle. It will remind you by blowing the horn, deafening you in the process.
Then there are all the religious establishments who have to reach out to the faithful and to God.  The jagrans are other thing- the all night jagrans, the nine-day puja during navaratri, the list is endless. The loud speaker is put at the highest possible volume so that no one gets sleep.
And don't get me started on Deepavali- a festival completely ruined by the high volume, highly polluting fireworks.  Without that noise and smoke how could the festival be complete?
We also have student events- fresher's party and the Hostel nights- neither of which are complete without the loudspeaker.  The Hostel nights coincide with the board exams of the children on campus. I often wonder our students have also gone through those torturous time of board exam.  Don't they remember how irritated they would be if any body made noise? Then what gives them the right to put loud speakers at high volumes during exam time?
My sympathies with Sonu Nigam, though the original statement he made could have been made little bit more diplomatically.  It is not the mosque only- it is every religious shrine.  The thing is I have the right to Silence, to be not bothered by raucous noise.
Will anything come out of it this controversy?  I doubt.

Three interesting links

1. The first one is about HeLa cells. As almost all in biological sciences know, HeLa were the first cells to be successfully cultured in the laboratory.  The cells were taken from Henrietta Lacks, an African-American woman suffering from cervical cancer, without her knowledge.  Those interested should read the book "The Immortal Life of Henrietta Lacks" by Rebecca Skloot. I read it my cousin's place in one night- well, I was leaving the next day and I had to finish the book. It is riveting because it touches one of the issues that we rarely talk about in Indian Universities- Ethical practices. To return back to the point, STAT News has an interesting article on HeLa cells- 5 important ways these cells changed medical practice.

The second and third links are something I found on Nanopolitan blog. 

2. First of this is for the academics- Get a life.  I loved this message at the end of the article.  It is so important for all of us.  I often find it incomprehensible when I find some of my students working all sorts of hours in the laboratory. It is almost as though they have no other life other than the laboratory. Of course, there are things that they are interested in but I do not think many of them have a serious hobby that they take time out to pursue.  I also do not think many of them pay attention to their physical health. So for all of them- Go Get a Life and you will find that rest is easy.

3. The third link..well...I will leave it to you to read.

Of this and that

The past month has been difficult.  For one, Summer arrived with a bang. Overnight temperatures shot up giving us a taste of what was in store for us ahead. I am so not looking forward to May and June.  The mornings are cool, for now.  On walks in the morning, I can hear the koels, the barbets, and the oriental magpies.  The peacocks look magnificent as they perch on trees modeling their tails. This year I have been lucky to have caught sight of Shikra- last year I missed them.  The bougainvillea have just started blooming and the winter flowers have faded away.
On the garden side, we have planted the usual summer suspects- Bhindi (okra), Brinjals (eggplants), spinach and amaranth.  Ever optimistic, Nanku Ram has planted tomatoes once again. He thinks they will fruit this year. My mother, who is staying with me at present, was happy when I gave her the first brinjal.
On the university side- the rankings have rated us once again as the 2nd Best University (one spot behind IISc) but I cannot help think how long we will remain so. This year most of the schools are not accepting Ph.D. students. Only our numbers remained unslashed- this was due to the decision that we took about 4 years ago.  When the Supreme Court ruled that there would be 54% increase in seats, it was taken to mean at Ph.D. level too.  We ended up admitting 60-70 Ph.D. students per year which translated into 2-3 students per lab per year. After two years of this policy, it became evident to all of us that this cannot continue. We needed laboratory space and more important we needed enormous funds to support these many students.  So we requested the University to reduce our numbers. Needless to say it caused great consternation but we persisted and finally got the numbers reduced. As a result when the University decreed that we have to follow the UGC guidelines (8 Ph.D. scholars/professor; 6 scholars/Associate Professor; and 4 /assistant professor) we found that we were within the limits and thus, can admit students. 
But the question remains- how many will apply and how many will end up coming to us.
For the rest- a blanket ban has been put in place till the number of Ph.D. scholars reduce down to the UGC defined guidelines.  While it was truly mind-boggling to think that there were faculty with 20-30 students (how do they manage to guide these many students and ensure that they did good research work is something no one is talking about), yet a blanket ban will adversely affects us.
It is thus, a season of despondency as we ponder on what will be the impact of these guidelines on us.

GIAN Courses

The Ministry of Human Resources Development conceived this idea soon after the Modi government took over. The idea was to invite faculty from abroad to teach courses for 2-3 weeks in India.  The MHRD offered them total honorarium of USD 12,000 that included air travel. The program was named as Global Initiative of Academic Network (GIAN).  The implementing agency was IIT Khargpur  JNU, of course, decided to take up the offer and soon invited applications for GIAN course.  Under this initiative  I and my colleague conducted two GIAN courses.  And here are some of my thoughts:
1. The success of the initiative really depends on the guest faculty.  If the guest faculty puts in the effort and time to prepare a good course and is an excellent teacher, the program offers great value.  We had an excellent guest faculty and, indeed, I learned a lot from her about teaching. She made the students read papers, discuss them, and interspersed her lectures with discussion points, puzzles, and in general, made it an interactive session which the students valued.  I was little apprehensive whether the students would read the papers but they did. And not only that, some of them offered to write a term paper to get extra credit. This is big because motivating the students is something many of us are not good at.
However, if the guest faculty does not engage the students, the course becomes boring and the students end up getting a certificate without gaining any knowledge.
2.  The GIAN program is supposed to offer courses that are not offered at present in colleges and Universities/or courses that add value to the existing courses. The problem is then of integrating these courses into the existing course structure and ensuring that the students (undergraduate and post-graduate) get credit for it.  This usually means that the GIAN course has to be approved by the faculty and the board of studies. This is a long process and many times we are unable to do it because the program is of short duration and evaluation is problematic.  However, this is an issue that each College/University has to solve on their own.
3. The Indian consulates are clueless about the program.  The GIAN program states that the guest faculty need to get a business visa but the paper work required for a business visa does not match with the papers provided to the guest faculty.  Further, each consulate seems to be operating on an independent and autonomous mode. So they have different requirements for the same visa (I observed the same thing with student visa when I was the foreign student advisor) and the guest faculty and the host faculty scramble around trying to fulfill the requirements.
4. Accommodation and food- In JNU, our guest house is in shambles and generally people are advised not to stay there. This then brings up the problem of where do we house the faculty?  If we book a hotel, then the payment comes out of the honorarium given to the guest faculty.  By itself, it is not a bad idea but it is not made clear to the guest faculty at the time of applying.
5.The GIAN program itself has nothing for the host faculty. Fortunately, in JNU, the program coordinators made sure that the host faculty also get a token honorarium. 
I am not sure if GIAN is evaluating the courses or evaluating the program itself to make it more effective in its deliverables. In its present format, as we rolled out the program, the problems became visible and needs to be fixed.
But I will reiterate: Given an excellent guest faculty, the program offers tremendous scope as it can be taken by anyone.  We had an undergraduate student and a faculty from a Delhi college this time taking the course. Each one benefited in their own way.

Landour Days by Ruskin Bond

It all started with a book that I purchased at the airport en route to Chennai in December. The bookcover was fascinating- it was covered with flowers, a lady sitting in the middle, and a boy standing near her. The title of the book was "The Prospect of flowers" written by Ruskin Bond. I will confess. I purchased the book solely for the cover as I had already ready the short story "The valley of flowers" in Reader's Digest long back. I had loved that story.  The volume contained some stories that I had not read before including "The Blue Umbrella" that was made into a movie by Vishal Bhardwaj.
I went on to purchase two more books- Rusty Runs Away and Landour Days- at the book fair.
I like Ruskin Bond because of the language he uses (simple not convulated) and the stories he tells of people you and me meet every day on the streets. Sure some of the stories are recycled.  The Prospect of Flowers was also present in Rusty Runs Away as an incident that happens to Rusty.  I also felt Rusty was semi-autobiographical, a story of a school boy who is an orphan for all practical purposes. He has a guardian whom he dislikes He is sent to a boarding school and the book tells of his adventures.  It ends with Rusty leaving the guardianship and striking out on his own. It is set in the pre-partition India and the most evocative story was the friendship between Rusty and Omar.  On partition, Omar moves to Pakistan and dies in India-Pakistan war.
The final book that I read was Landour Days. I read this book sitting in the UGC office while waiting for my turn to present before the committee. Ruskin Bond is an inveterate dairy writer and I enjoyed his reflections.  The best part of the book was his musing on Landour, the writers who flock there, the houses built by the colonists that are empty and decaying now, John Lang-the lawyer to the Rani of Jhansi- who is buried there, and a gentle pace of life that is missing in the cities.

UGC M.Phil/Ph.D guidelines 2016

The new guidelines for M.Phil/Ph.D are in and woe betide any university/institute that does not follow these guidelines.  We have been breaking our heads over the guidelines for the past few weeks. At the outset let me state that some of the guidelines do make sense given the way Ph.D. degrees are handed out but if the UGC thought that the new guidelines will make our Ph.D. system more accountable and productive they are way off the mark.  While the entire guidelines can be accessed at the UGC site, I will just point out the most problematic one out here at least for the scientists:

"All students will be admitted to M.Phil program only. They have to do 2 years M.Phil and then only can go for Ph.D.  Further, to complete the M.Phil program successfully, they need  course work and one paper.  Peer-reviewed." 

I do not know whether to laugh or cry.  Our students do course work the first two semester. The first semester is tough and they spend their time in the class room and in the lab, learning the techniques. They start working in the lab in the next semester. But they also have to write a term paper and present a paper.  So the time spent in the lab is not sufficient to generate any data.  They really start working only from the Summer break.  It takes a student (all of us went through the same thing) at least two years to understand what we are doing. The first few experiments always fails.  A hypothesis starts forming somewhere in the third year.  The speed picks up in the fourth year and by the fifth year, you have a paper written up. Then you start plugging the loop holes, you submit it for review, the reviewers ask for more experiments, you do it, and somewhere towards the end the fifth year, a paper in a fairly good journal gets published.  So how does the UGC expect a good publication from a M. Phil student?  On one hand they want to categorize journals and want us to publish in good ones (there are incentives built in for promotions) and on the other hand you are going to force us to publish half-baked work in shoddy journals.

The students are freaking out.  The faculty is upset.  But who is listening?  If a student does Ph.D from India and wants a faculty job, they need a certificate stating that all the rules and regulations were adhered to at the time of award of degree. The administration will not issue such a certificate unless we adhere to the norms.

So there it is. I do not know what will happen in the coming days. All I know is that it is scary.

Disability and invisibility in India

Long time back, I edited a book for Ali Baquer who was the President of Concerned Action Now (CAN), an advocacy group for the disabled.  At that time Delhi was getting new bus stops and it was publicly touted to be disabled friendly.  Prof. Baquer and I discussed how misleading the publicity was because none of the bus stops really are wheelchair accessible.
In India the disabled are invisible in many senses.  Accessibility, support groups, diagnosis, medical help...the list is endless.  I am not going to say much but am going to provide a link to a write-up that explains it all.

The Philadelphia Chromosome by Jessica Wapner

The Philadelphia Chromosome is a poster-child for chromosome translocation.  This is the example most students will give when asked about chromosomal translocation. I was taught this in my M.Sc. and I teach it to my students in Human Genetics when I talk about diseases caused by chromosome translocation.  The importance of this translocation is underscored by the type of cancer it causes- Chronic Myeloid Leukemia (CML).
The DNA in our cells are present in the form of 24 chromosomes. Each chromosome has a specific set of DNA sequence. It is same in every individual.  Occasionally, two chromosomes can exchanges pieces in a process known as Chromosomal Translocation. This is bad because it can result in loss of information.  In case of Philadelphia Chromosome, it results in the formation of a rogue gene that results in cancer.
Jessica Wapner has traced the discovery of this chromosome and the cure for the cancer it causes- Gleevec.  The story begins in 1959 when David Hungerford discovered that one of the chromosomes was too short in the blood samples of patients suffering from CML.   At that time the concept of chromosome translocation was unknown.  The minute chromosome was named Philadelphia Chromosome in honor of the city of its discovery.
From there, the story traverses across continents and laboratories wherein it was firmly established that the Philadelphia chromosome is due to exchange of DNA between chromosome 9 and 14  and this exchange results in the synthesis of an abnormal protein known as Bcr-abl that causes cells to divide indefinitely.  This abnormal protein is a kinase- it transfers a phosphate group from ATP to proteins causing them to become active.
The discovery that an abnormal protein kinase causes cancer spurred researchers and doctors- in particular Brian Druker- to push for an inhibitor that would specially block the function of this abnormal kinase. Today we call this strategy Rational Drug Design and it really begins with knowing the structure of the protein. However, for Bcr-abl, the structure was unknown and the scientists working in Ciba-Geigy synthesized chemicals and screened them for inhibition activity. Gleevec was discovered in this screen.
Ciba-Geigy was purchased by Novartis.  Not many people were convinced that the inhibitor would be a good drug. Further, there was the cost factor- CML affected too few people to make it an attractive market.  However, Druker persists and finally, Gleevec was approved for drug trials.  And of course finally for medical use.
Gleevec is that rare chemotherapeutic medicine that a patient can take at home with very few side effects.  It is effect also against c-kit, which causes GIST cancer.  The only caveat is that Gleevec has to be taken for life- at least till now that is the story.
Jessica Wapner traces this 40 year old story and I enjoyed it tremendously. 
As an aside: There was a dispute over the drug in India which Novartis lost.  Jessica barely mentions it though it was landmark decision where the Supreme Court of India ruled that Novartis cannot patent Gleevec in India allowing for the generic drug to be manufactured.

Finally: Nothing to do with Gleevec. Winter did arrive in Delhi albeit late. 

Sweet Potato soup and winter of discontent

This time too the winter has played hooky.  It has been unseasonally warm.  Usually, we get a week of really cold spell with the day temperature going down to 12-14oC and the night temperature plunging to 3-4oC.  There would be a watery sun that would perhaps bravely appear around noon to promptly disappear by 2 pm in the afternoon.  But this year, just like last year, it has been sunny throughout the day much to our disappointment as it just means that the summer will arrive early with its unbearable heat.

The garden has done okayish in spells. We had trouble with the usual suspects - peacocks and nilgai.  Then this year the fox and the hedgehog decided to put in an appearance.  The methi, spinach, cauliflower, and lettuce were much appreciated by these two animals. We have now fenced the entire area but I am quite sure that the animals will figure a way out.

I went to Chennai as usual for the winter (or whatever weather was prevailing in Delhi).  When I came back, the crysanthemums had flowered, bringing much needed colour to the garden.  This week I cut some and put it in flower vases. 

Their season is almost over. Next week, we will remove them.  Hopefully, the dahlias will flower soon.

In this mild winter one does not even feel like making soups. However, I did have one opportunity to make it. My mother invited her brother's family over for dinner before they went back to Canada.  As we had some sweet potatoes, I decided to make a soup, which was much appreciated. My aunt asked for the recipe and I gaped at her. That day I had been distracted as I was writing a rebuttal to an editor who had rejected our paper (the rebuttal was rejected as expected).  So, I had just grabbed whatever was in the fridge and put it into the soup. The recipe always varies depending on my mood. That day, I gave a tadka of jeera,and fried some onions, added chopped carrots, sweet potato, and peas.  As an afterthought, I added a piece of red chilli. All this was boiled with plenty of water in a kadhai (I do not like to use pressure cooker for soups).  After the vegetables had cooked well, I cooled it down and then pureed it in a mixer.  Just before serving, it was heated with salt and pepper.

Sometimes, I added a piece of garlic. Sometimes milk. Sometimes curd. The interesting thing about soups is that the variations are endless. It just depends on the cook.

Happy New Year!