Tuesday, September 29, 2009

Professors must put in 40 hrs/week

The UGC has apparently released new guidelines for the professors. The new guidelines states that the teachers must clock in 40 hours a week and be present physically at least 5 hours a day.

My father has a favourite pastime when he visits me. He stands in the balcony and clocks in the movement of everyone. He faithfully tells me the movement. This professor went to the market, this professor stayed at home, this professor met his children at the bus stop...so on and so forth. Rarely, he will tell me, this professor went in the direction of his department and returned back in 5 minutes.

With this guidelines from UGC, I am looking forward to the next visit. Will my father clock in 5 hours for each of the professors?

PS: My father, by the way, makes it very clear that the worst place to do PhD is in my lab. This professor, unfortunately, has a habit of getting to the lab at 8.30am in the morning. Actually, my father should blame my advisor. Joel gets into the lab at 8.00 am in the morning. That is where I got the habit of getting into the lab early. And habits are hard to break!

Saturday, September 26, 2009

A long journey

Eleven years ago, serendipitously, I discovered a new molecule that showed anti-tumor properties. As my adviser reminded me yesterday we are half way into our patent life. It is has been an excruciatingly long journey trying to figure out the structure-made even more tough by the fact that we have no way of estimating its amount. So all we know is that it inhibits a protein and that is all we can use for measuring it or detecting it.

We made this darned thing from forty liter reaction. Dried it down and gave it for NMR. And you know what? The only signal we could see was from contaminants picked up during purification. I can see a signal which I think is from the inhibitor but it is so low that I have no clue what to do.

We are now back to the drawing board, trying to figure out how to purify it away from these contaminants. We think we have a way but will it work? That is a million dollar question.

Meantime, I know a lot more about this inhibitor. I know how it interacts with the protein and why does it inhibit it. I think I also know why it causes cell death though we are trying to finish up those experiments. But what I want to know-the structure of the molecule-is a journey that, I suspect, will continue for some more time.

In these three months I have made inhibitor from 80L reaction and still have nothing to show for it. I have purified protein about dozen times just to have it aggregate so that I cannot crystallize. It is absolutely frustrating but it was during such frustration that we discovered the inhibitor. I just have to keep myself reminding of that one fact and keep plodding.

Wednesday, September 23, 2009

Tale of Two proteins

I work with two proteins. One of them is of bacterial origin and the other is from mammalian cells. The bacterial protein is nice and manipulative. The mammalian one is finicky and hates being manipulated. It especially hates being produced in E.coli cells, the workhorse of molecular biology.
Therein lies the problem.

I express both the bacterial and the mammalian protein in E.coli. The bacterial protein is produced in tons of amounts and is easy to purify. I use it produce the inhibitor. The only unknown thing, and therefore of interest, in this entire process is the structure of the inhibitor. We have managed, after two months, to produce enough for NMR. Will I get the structure? That is something I do not have confidence in.

The mammalian protein is the one which is of tremendous interest. The inhibitor binds to it in an allosteric site and blocks its activity. I need to get at the structure of the protein. But the protein is so difficult to purify and concentrate that in these two months I have just managed to standardize conditions to purify and concentrate it.

With all the proteins being overexpressed in E.coli, lot of technique is mumbo-jumbo. We really do not understand. How does the plasmid get into the bacteria? Why does the bacteria retain some plasmids and throws others out? Why some proteins are produced in large amounts and why some are produced in tiny amounts? We can theorize. This is toxic, this is eukaryotic, this is that, this is that...but, honestly, that is lots of handwaving. We just have to accept what we get.

Wednesday, September 16, 2009

Austerity drive

The Congress has gone bonkers. The new mantra is austerity. Which has been interpreted as traveling by economy class on flights and taking trains. Do they realize the extent of disruption they will be causing thanks to this idiotic decision? The amount inconvenience that they will cause the rest of us who have to travel by trains or by economy class?
At least Tharoor was honest enough to say that the economy class is cattle class. It is with so less leg space that if you happen to be tall you wonder how to fit in your legs into that tiny space.
I have never understood this romanticization of poverty. We in the University for example do not ever talk about increasing the hostel fees because the poor students will suffer. The end result is that the hostels look like slums. I have never figured out how the students can live in those hovels. But they do and they take great pride in living a simple life (or their interpretation of simple life).
If the congress wanted to really talk about downsizing their expenses, how about paying their electricity and phone bills out of their pocket? How about cutting down on those endless security for themselves or paying for it out of their own pocket instead of dipping into the taxpayers money?
Of course tokenism is easier!

PS: Finally figured out was going wrong with the protein purification. Whew! It is a relief to know that I was not going crazy.

Tuesday, September 15, 2009

Going Crazy!

The first five protein preps were beautiful! I knew exactly where the protein eluted. I could see it. And then Wham! It has stopped working. I have no clue and I am absolutely going crazy trying to figure out what has happened.

The day starts at 7.30am in the morning when I open the lab. Very often it ends at 7.30pm when I pack up and leave. And after 12 hours if the protein purification does not work, all you feel like doing is wailing.

Bah!

Friday, September 11, 2009

Dogsitting this weekend

I am dogsitting Bella, my housemate's dog while my housemate has gone to a cell biology retreat.

Bella is a fox terrier, a small bundle of endless energy. She believes that human beings have been made for her sole entertainment. Therefore, she knocks on my door asking me to come out and cuddle her for a bit. And for those who are wondering how can a dog knock on doors, I can assure you she knows not only how to knock but also to open the door. Unfortunately, she refuses to get 100% house trained and therefore, in her excitement she is apt to dirty the carpet which we then have to clean.

Today, my housemate told me to keep her confined to one room and give her toys to play with. In spite of them, she ate up my dinner while I was not looking. No amount of telling NO has made any effect on her. She just looked at me with her liquid brown eyes and an innocent look. What me?

My housemate will be back on Sunday and my duty ends then.

Wednesday, September 9, 2009

The chalta hai policy

We are firm believers of chalta hai policy. Everything is chalta hai. If things break down, we will do a shoddy job of quick fixing it and saying chalta hai.

The entire medical center at UVa is undergoing renovation and it is a lesson for us to see how it is being done. The sidewalks were cordoned off one week because they were digging for something. The moment the work was done, the sidewalk was repaved. Part of the road too had been dug up. The road was immediately relaid properly.

Outside JNU there is a sidewalk. It is unusable. It is dug up often but never relaid properly. Stones and mud will be plied up on the sidewalk making it impossible to walk. As an aside, of course in India we believe that the pedestrians do not exist. So what is the need for a sidewalk/footpath? Why should the drivers stop and allow the pedestrians to cross the road. Why indeed should they drive carefully. The road after all belongs to the mightiest. The net result is that there is never a place for the pedestrian to walk.

To come back to the point of the blog, the chalta hai policy has completely ruined us. We never take anything to completion. Everything is done so haphazardly and so shoddily that a new building looks as though it is at least 100 years old.

The miasma is all prevalent. It is not very difficult to publish papers in good quality journals. We just need to do the experiments carefully and diligently, chasing it all to completion, taking pride in the final product. Since we believe in chalta hai policy, half-baked experiments are taken as completed. Why would a good journal publish this work?

Tuesday, September 8, 2009

On why I love UVa

This blog is dedicated to the student who commented that I seemed to love UVa a lot.

I do. I came to UVa from an institution run by a certain person, who can for the purpose of this blog can be simply Dr.X. The only thing I can remember of that place was that it was a nightmare. I do not know if anyone saw The Devil wears Prada. Dr. X. was truly awful. She was running this show where she was the supreme commander and everyone had to kowtow down to her. It was a dictatorship. None of us students had any access to her. She was never there to discuss any problems or any results. The research was bunkum and I know many of the results were fabricated. No one was interested in research anyway. We sat around chatted, did some pottering about and left the lab in the evening.

Then I came to UVa and it was like a different world. Faculty and students were at par. It is not that I can call faculty by his or her name, it was the fact that my opinions were solicited, and that I was allowed to think. I could tell my adviser that he was wrong and not get reprimanded.

The best part was the classes. I had done my M.Sc in biotechnology and had hated every minute of it. I could not remember the facts or wrote long essays for short notes. In B.Sc I had done Chemistry and the question paper was absolutely analytical. We had to solve problems. Here I was not expected to do any analysis. Remembering the Biochemical pathways was torturous. No one taught the logic of it.

But at UVa, in none of the exams I was expected to write long answers. I was expected to read papers and analyse the data. I was expected to design experiments. Oh, many of them were rubbish experiments that I designed but hey, at least I was allowed to think.

There were other things. Yujie, Vanicha, and I went driving across the country, we attended operas and concerts, we had potlucks, we went for hikes and got lost. It was fun.

I grew up a lot. I do not know if I made right decisions in life but I do not regret one bit of my UVa years.

Sunday, September 6, 2009

The Football match

Yesterday was the season's opening football match- UVa versus William and Mary.

Matches are great events. My housemate threw a party yesterday and went to watch the match with her friends. This has to be only school where students dress up to go to football match. So you will see boys in tie and girls wearing their prettiest dress.

UVa is not one of the greatest teams. But there were great hopes for yesterday's match. William and Mary is a small college in Virginia and they are not believed to have a great team either. And UVa is a big University. Our team has to be better than theirs.

Only...oh well, we lost.

Reminds me of the the tortoise and the hare story.

Friday, September 4, 2009

Where libraries are a pleasure

When I joined the University in India as a faculty, I went to the library to get books. I was appalled to find that the library still used an antiquated system for cataloguing its collection. The books were in a mess. The whole stacks section was dusty and musty. No one knew where the books were...Anyway, I lamented about the state of the library to a friend of mine who incidentally was a student of the library. She was amazed that I dared to criticize such a wonderful library. I was out of mind, she declared. You should go to the eighth floor and browse through the wonderful fiction section.

Well, I am back in UVa, and I am sitting in Clemons library. I have my laptop on and I am typing this blog sitting in the library.

This was the place I would come to when I had to take my 4 hours Genes exam. The library has study sections where one could sit in peace and take the exam. The library also has a wonderful video collection. My brother and I had once sat here and watched Kathalika neramilai.

Clemons is just one library within the university system. The main library is Alderman's and then each school has its own library.

None of our Universities have libraries like these. Where it is a pleasure to sit and read, or browse, or do your homework, or take your exam.

I wish we had...

India says no to HIV drug patents

The Indian Patent office has rejected the claim to file patent for an HIV drug, giving the rights for Cipla to create a generic version of the drug.

Indian pharmaceutical companies are excellent in creating generic versions of any drug. We possess very capable organic synthetic chemists who can figure out how to make an existing drug as cheap as possible. Some might call this jugaad technology but truthfully, we need these generic drugs.

One of the reasons that the cost of a drug goes up is because of patent. Yes, it is very expensive to do research and discover new drugs but the companies also push up the cost because they lock up the method to make the drug under the guise of patent.

Oh, we need patenting laws. I am not saying that we do not need to protect inventions. But it is a thin line when it comes down to medicine. There are poor people in this world who need medication when they fall ill. But very often the drug price is exorbitantly high. So what do we do?

Cipla and other Indian pharmaceutical companies are the life-savers as they create generic drugs and sell them cheap. I, at least, do not believe that we need patents for life-saving drugs. These are medicines that should be available cheap to people who need them.

There is a flip side to all this. While most pharmaceutical companies abroad have an active research program running, the Indian pharmaceutical companies have almost no worthwhile research program to discover drugs.

Wednesday, September 2, 2009

Delhi to banish beggars

This was the headlines in Times of India yesterday. You can read the article here:

Delhi has beggars at every red light. Many of them are migrants from adjoining states. Most often you see women with children. You also see lots and lots of children. They are great gymnasts (if I can use the word) and entertain the passerbys with their antics. None of the children go to school.

So Delhi Government has woken up to the problem of these people now that the commonwealth games are upon us. Does this mean that the government wouldn't have given a damn if the games were not scheduled? And what does the government plan to do? Oh, send the children to juvenile homes and the adults to jail. What a fantastic solution! Of course, once the games are over, the government can forget about the problem.

There are couple of NGOs working with beggar children in Chennai. What they have realized, what has often been articulated, and what was also portrayed in Slumdog Millionair, is that there is a cartel involved in this business. The begging is a business. The children are kidnapped and made to beg. The adults-those you see with grotesque limbs-are also held at ransom by this cartel. The cartel itself comprises of goondas. Police knows this as do the politicians. If any outsider tries to interfere in this matter, their life is at threat.

What we require is a way to break the nexus. It is not the beggars who belong in the jail. It is the cartel leaders- the men who hold children and adults alike at ransom and dehumanize them- who should be shut up in prison. Forever if possible.

Tuesday, September 1, 2009

Classes in the morning

The medical school classes start at 8.30 am in the morning. Whoosh!

If our classes started at 8.30 in the morning, neither the teacher nor the students would be present. I learnt this the hard way. I think once I made a time table such that the 4th or the 2nd semester student started their day at 10 in the morning. There were no classes at 9.00am. As usual, I like to get the classes done and over with, I had the first class. So I went to the class at 10 am and guess what? No student was present! They sauntered in, some rushed in breathless, well past 10 in the morning. Nothing can be done! You can scold them, cajole them, plead with them, tell them to be punctual. Nothing works. The Indian Standard time says half hour past the scheduled hour and that is what they would adhere to. Finally, I learnt the bitter truth. What ever I do, the students are going to be late. Sometimes I tell them that they cannot enter the class but even that does not help!

The medical course is being seriously revamped. Of course they are spoon fed but that is not the point. The point is that there is a conscious effort made to improve the teaching methodology and course content.

Well, we too did a serious effort to revamp our teaching. After one year of deliberations, we restructured things. On paper it is very nice. In practice? Well, most of us cannot be bothered to change the way we teach, the kind of questions we ask, or the course content. So everything remains same.

I usually ask analytical questions in my exam. I want to know whether the students can analyze the data and whether they can design experiments. After all they are going to be scientists. However, some of the faculty members have been asking me to stop asking analytical questions. They feel it is too tough for the students. I try to explain to the concerned faculties that students can think if you allow them to. It is only when we tell them to regurgitate whatever they have learnt that they stop using their brains. Of course it does not wash with them. They keep telling me to stop asking analytical questions.

Maybe they are right. Maybe the questions are too tough. I do not know. The feedback I get from most of my students is that they enjoy these questions. Of course it is tough for some of them but then if they are going to do M.Sc and then PhD, they have to learn sometime to start thinking.

Actually, that is not the real reason I give such questions. Honestly speaking, I never know how to evaluate the essay type questions and the short notes. Am I supposed to go by the length? Am I supposed to be impressed by their ability to memorize? Am I supposed to marvel at their ability to write so much in such short time? What am I supposed to do?