Game of the Genomes by Carl Zimmer

The human genome was sequenced in 2001. I still remember how skeptical many of my professors were at the beginning of the project. Whose genome are they going to sequence, was an oft-asked question. And then there were others who were enthusiastic about the venture. They felt that it would answer a whole lot of questions about our genome. In particular, they were sure we will know for sure what makes us so different from other animals.
Well, the 2001 paper raised a whole lot of questions rather than answering them. In particular, it was disappointing to know that the number of protein coding genes was about the same as that present in mice.  And that whole lot of our genome (in fact 98%) did not code for proteins. In fact, a majority appeared to not to code for anything.  It was called as junk DNA. 
The picture has changed a lot in the past 16 years. We now know that most of our genome codes for something. The trick is to understand what these do.
Over the years, genome sequencing has become popular. It can, after all, tell you whether you are at risk for a disease.  But what else can it tell you?
This is the question Carl Zimmer is trying to find out.  He got his entire genome sequence and then got the raw data from the company that did the sequencing.  Now he is getting it analyzed to understand the information stored in his genome.  The Game of the Genomes is an interesting read.

Poor Ruby Rai

I feel sorry for the child. All she wanted was to pass in second division. She told that to her father who ensured that she came first in the subject, a subject she clearly has no idea about.  I do not know what the father was up to.  Did he not realize that the whole thing would blow up on their face in this era of instant sound bytes and TV  hunting for stories? 
I have no idea what the authorities are planning to achieve by arresting Ruby Rai. When she needs them most, her parents are on run.  The Minister who wrote a big list of achievements few days back on her Facebook is silent on this issue. She can, of course, claim that education is a state subject and therefore, under the purview of the State Education Minister. Bihar is fortunately not ruled by BJP and therefore, everyone in the Center can wash their hands off.
The rot in our education system run deep and every state is in a mess.  The cut-offs for admission to colleges in Delhi University are a joke. Seriously, they expect some one to get 99% in English?  What kind of examination was administered that a child could score 99% in English?
But who cares? Those who can send their child abroad. Those who can't...well, do they really matter?

What they do not teach you in grad school

The past month I have had couple of requests for an inhibitor molecule that I discovered when I was a grad student. Not many bothered me about it for these past 20 years or so but ever since we published a paper showing its effectiveness against triple negative breast cancer cell line there has been increased demand for the molecule.  And it dawned on me (my advisor pointed it out to me actually as I am still naive about these matters) that I better get Material Transfer Agreement (MTA) signed before supplying the molecule.  As I do not work in the lab anymore and it is my students who make it, I have to protect their interests. Therefore, I wrote a letter to the VC (after all he has been tom-toming about how we should foster interaction between the industry and the academia) asking for legal help.  It snaked its way through the Registrar, the academic branch and finally the legal cell who sent it to the lawyer for advise. Finally, the paper came back to me. Yes, I need a MTA and I should the needful.  I stared at it blankly and then I called up the legal cell. Very politely they told me that I should draft the MTA and send it to them through the VC.  They will go through it and let me know whether it is okay or not.  I was about to tell them that I am not a lawyer when it dawned on me that I am a lawyer, an accountant, a manager, a teacher, a researcher, a scientist, an editor, a writer....In addition, it is also my responsibility to get money in for research.  Unfortunately, the graduate school does not prepare you to be anything except being a scientist. The rest of the skills you have to develop yourselves and if you are in an Indian University, with no help from the administration.
As it happened, I googled, picked up few MTA available on the internet, and put my own version of MTA together.  The legal cell approved it.

Orphan train by Christina Baker Kline

I picked up this book at the book fair.  The book claimed that it was #1NY times bestseller.  That should have warned me.

But first the history:  The orphan trains transported many children from the East Coast to Midwest in the US between 1854 and 1929.  It was organized by Children's Aid Society in order provide home (?)  to many orphan children.  The family that took in the child had to provide education, home and food in return for labor, though a lucky few were adopted. Of course things never worked out as imagined. So many children ended up in bad situations and changing homes many times. In many cases, their names were also changed- thus erasing part of who they were.

Christina Baker Kline uses this as the background for the story she tells in her book "Orphan Train".  The book was page turner- I finished in in three hours.  It was also cliche-ridden and I could predict exactly what was going to happen as I turned the pages.   She uses two characters- Molly, who is for all practical purposes an orphan and is living in a foster home, and Vivian, who was transported in 1929, after she lost her home in a fire, to Minnesota.  Molly has to do  50 hours community service as she was caught stealing a book from the library and her boy friend, Jack, gets her work in Vivian's house where she has to clean up the attic. Molly, who has been into many foster homes, has developed a thick shell in order to protect herself,  unravels Vivian's story for an English assignment and in the process finds herself warming up to her.  The ending was bleah...kind of abrupt, unrealistic...almost as though the author was ticking all the right boxes. 

It was a good one time read.  I got to learn some history but this is not a book that I would re-read.

The new UGC regulations

In the last pay commission, the UGC introduced the Academic Performance Index or API as it is (un)popularly known as. The UGC had decided to quantify the teacher's performance and it was, and continues to be, bitterly resented by teachers. I, personally, had no problems with the form once I, along with my colleagues, figured out the teaching workload section. Typically, a college teacher has more teaching as compared to the University teachers. But the University teachers have research scholars working with them.  So we figured out the teaching hours and once this was figured, the form is pretty easy to fill.
Now, the UGC has decided to modify the API.  The workload of the teachers has been increased. An assistant professor has to have 18 hours direct teaching plus 6 hours of tutorials/administrative work/blah...blah... This translates 4 hours of teaching per day for an assistant professor. The associate professor has to put in 22 hours of teaching and the professor has to, I think, put 18-20 hours of teaching.  The other major thrust is on student feedback.  The new API form has also eased the requirement for publications and UGC is going to bring out a list of acceptable journals.
Predictably, the teachers are up in arms. Regardless of what Prof. Thampu thinks, the modified teaching workload is disastrous.
Yes, there are teachers who do not teach, who use the same notes year after year (I remember my Chemistry teachers possessing yellowed notes from which they taught us) but you cannot penalize the entire community. Nor will the teaching improve by increasing the teaching workload. I typically put in 5-6 hours of preparation for a 1 hour lecture. If I have to prepare slides, then the preparation time increases.  If I have to teach 4 hours every day where will I get time to prepare for classes? The notes that I prepared last year will be recycled this year and next year and next year and ad infinitum. The UGC has failed to come up with a method to motivate our teachers but I think the problem starts from recruitment where very often the one who is the most syncophantic is the one appointed as teacher. And then are Indian states where recruitment as a teacher means greasing of palms.  I agree that not all teachers are motivated to teach but our recruitment process cherrypicks those who have absolutely no interest whatsoever in teaching/research and possess zero sincerity. They only know how to be a good syncophant.
On student feedback I agree with both UGC and Prof. Thampu. The teacher associations are scared of student evaluation and yes, they are right that the system is open to abuse. But world over teaching is evaluated and promotion depends on student feedback. So how come only we cannot have feedback because it will be abused?  But to understand the fear read the previous paragraph.

 

Summer harvest

And here is the harvest from my garden:

Okra, brinjals, Tori, and bitter melons...all my favourite vegetables.
Today I will be harvesting the amaranth greens and possibly spinach.
And the lemon tree has couple of lemons and guavas are developing on the guava tree.  All in all it has been a good Summer. Now if it would only rain a tiny bit so that the temperature goes down a little bit...

Don Camillo in Soviet Russia

My mother having given us the ultimatum that she cannot take care of our books anymore is now watching  hawk-eyed as we are slowly emptying all the accumulated books.  They have truly accumulated- right from 1950s when my father used to purchase Imprint magazine (now defunct) to 70s when we purchased Reader's digest and sundry other books from pavement stalls and book fairs.  It has taken my brother and I numerous trips to slowly trawl through the books, weed out what we don't want, and transport the remaining to our places. There are books that were dumped by our cousins-which as I told one of them-cannot be thrown out because of the memories associated with them. Then there are books that were dumped by other people- again  cannot be thrown out for sundry reasons unless they are truly unwanted.  And then there are books like Mother by Maxim Gorky-unreadable but we share memories of it and are undecided what to do with it.  (Un)Fortunately, we got rid of the Russian lessons that my father purchased in a fit of enthusiasm- he was going to learn Russian and Russian Center was offering them for pittance.  The time never came and my father reluctantly decided that he will never learn Russian.
Anyway, I was going through Imprint magazines printed in 1950s and 60s, deciding which ones to throw away.  And there it was-Don Camillo in Soviet Russia.
Don Camillo was the character created by Giovannino Guareschi. I do not remember where I found the first books of Don Camillo but I truly loved Don Camillo and Peppone and the voice of Christ as he dispenses advice to the hot-headed Don Camillo.  Don Camillo is a Catholic priest and Peppone is the Communist party leader in a village on the banks of River Po. Both are at odds with each other though Peppone does get his children baptized and attends the Church (just so that he can keep track of what Don Camillo preaches). 
In this gem of a book, Peppone and his party members are going for a visit to Soviet Russia.  Don Camillo gets himself included in the trip much to Peppone's consentration (but there is nothing much he can do about it other than scream blackmail).  And so begins a hilarious journey where Don Camillo manages to solemnize marriage and baptize children, create havoc amongst the party members and promote a love match. 
The Don Camillo books are available in Amazon but tad bit expensive. For the time being, I am keeping the old editions of Imprint magazine.