Coromandel- Charles Allen

Last Saturday I visited the book fair and purchased many books.  Coromandel by Charles Allen was one of them and I read it on the flight to Chennai on Tuesday.  I picked up the book because I had read a review/excerpt in Scroll.  It was a delightful read.

Charles Allen prefaces it as a personal history and those who pick up the book to read about the various dynasties- Cholas, Pallavas, Vijayanagara, the Nayak Kings- are going to be disappointed.  The book instead follows on who were the original inhabitants of the South India (Tamilnadu, Karnataka, Andhra, Telangana, and Kerala).  So to my delight it picked up at Pothigai  or the hill of Agastya that is located in Tirunelveli, our native place. There are many legends involving Agastya- both the North and South claim him to be theirs. 

He then moves on to the origin of written language and how Ashoka helped in the propogation of the written script- Brahmi- which possibly is the originator of both the North and South languages.
If we talk about Ashoka, Buddhism and Jainism cannot be far behind.  So the spread of these two religions in the South India is discussed.  The revival of Hinduism- Shankaracharya- led to the disappearance of both these religions (Hindus, very cleverly, of course said that Buddha was an incarnation of Vishnu and adopted many of their practices, including vegetarianism).

A short detour into Orissa- Puri Jagannatha temple- to talk about how the older Buddhist and Jain shrines were appropriated by Hindus  either forcibly or because they were abandoned with the decline of these two religions. I liked this chapter because it made me think a little bit.  Our family deity is Yegnanarayana, a form of Vishnu (never mind that we are not Vaishnavites),  in a small place called Perunkulum.  The  deity is formless.  Only his foot prints are there in the temple.  Now the early Buddhists worshiped aniconic form- Buddha's footprints for example.  It made just me wonder.

The arrival of Islam- not across the Himalayas- but as traders from Yemen and Arabia coming to Malabar coast.  The intermingling was encouraged for two reasons- one because the caste taboos prevented Hindus from carrying out trade across the sea and secondly because they brought with them horses.  I also did not know that the oldest mosque of India exists in Kodungallur, Kerala.

Finally, he ends with the recent spate of rigid Hinduism.  I just want to end the post with the quotation from Ashoka's edict that appears in the book, which I think is needed at the juncture we are as a country:

"Whoever praises his own religion, due to excessive devotion and condemns others with the thought 'Let me glorify my religion' only harms his own religion."

The efficient fire alarm

None of the buildings in our University had any fire alarm.  Partly because these were built during the 70s.  But more so because the efficient CPWD, and now the RITES, that build all the public buildings does not believe in any safety procedures.

However, because the wiring in all the buildings are now more than 50 years old and overloaded, fires are very common in the Summer. Finally, after a lot of push from our end the administration decided fire safety.

Fat and thin, large and small pipes were laid through the entire school (of course without spirit level).  Each lab had a smoke detector installed. They assured us that in case of fire, the system will get activated and water, under pressure, will be released.

Well, today my student had an accident in the cell culture lab.  When I went in I could smell the acrid smoke. 

The good news: my student was not injured.
The bad news: the smoke detector did not go off.

Once again proving that L1 is the best.








Note: The Government of India believes in open competition.  That is to say, if I need to purchase an equipment or buy a consumable or if fire safety system has to be installed, then quotations have to be called in.  And the lowest bidder, known as L1, will be awarded the contract. This is to prevent corruption but...

Growing tomatoes

The past month has been horrendous but I am slowly recovering from the traumatic events and coming to terms with what has happened.  I am also sure that over time the memory of the day (especially of that one man) will fade away. 

My gardener, Nanku Ram, is an eternal optimist.  Like his predecessor Raghav Ram he too has dreams.  My father liked Raghav Ram for he was the only gardener who managed to kill the mint plant.  As my father dislikes mint, he was extremely happy with Raghav Ram and very upset when I dismissed him.

Nanku Ram has been with me for the past 12 years but I have never seen him this possessed.  We will grow tomatoes, he has been telling me ever since I moved into the new apartment.  The failure of the tomato plants in the past five years to grow has not deterred him.  So when he appeared with tomato plants this September and assured me that it will grow.  I was skeptical but did not possess the will power to thwart him.  We decided that we will plant them amidst the Malabar spinach also known as pui.  The birds and the various inhabitants of the forest around us do not eat this spinach possibly repelled by its large shiny green leaves.

The ruse worked. The tomato plants grew without hindrance. In fact they flourished and late last month, Nanku Ram said, with great satisfaction, that he will get stakes so that they would have support for further growth.  And that he would remove the pui. And, he told me, you wait. They will bear tomatoes.

He is right.  When I came back from Deepavali vacations from Chennai, there were three tiny tomatoes.  Now, there are ten tomatoes in various stages.  I look at them and gloat every day.  I do not know how many will ripen but there they are and I am happy.  As for Nanku Ram- he is extremely contented.  His dream has come true.

The Tangled Tree- David Quammen

I was led to this book by my friend who sent me a link to a New York Times excerpt from this book.  I am grateful to her.  Sitting in India, my opportunities are very limited to get access to books like this.  There is no Barnes and Noble ( I cannot forget their huge store in New York).  Unlike New York Times, or Washington Post, or The Guardian, newspapers in India do not carry a section on books. So when I read the excerpt, I ordered the book through Amazon.
The Tangled Tree, very properly, is about Carl Woese, who showed that archaea are a separate class of organisms.
The book starts with a tree traced by Charles Darwin.  This is the Tree of Life.  Above it he writes, I think. 
The branches of this tree represent various organisms.  Some of the limbs wither because they do not evolve and therefore, are unable to survive.  Life originated from a single point because the microorganisms were ignored. The single point represent all the eukaryotes- plants and animals.
But the micrororganisms exist and very soon it is realized that they are different from eukaryotes.  So the Tree of Life is modified. There were two points of origin- One that evolved into bacteria and the other that eventually led to us.
It is here that Carl Woese makes an entry.  He wants to trace the origin of life.  And he uses a technique that we still use today.  He sequences a molecule called 16S rRNA and shows that there is third branch.  These are organisms that live in extreme conditions- hot springs, extreme cold conditions etc.  He names them as archaeabacteria though we now call it archaea.  These are peculiar organisms, closer to us than to bacteria. The tree of Life, Carl Woese proposes, has three independent origins.
But it turns out that it is not still the complete story.  Mitochondria, that I talked about in last post, are really bacteria engulfed by an ancient cell and this engulfment led to the evolution of eukaryotes and eventually us.  This process is known as Endosymbiosis.  This was proposed by many and popularized by Lynn Margulis (one of the few female scientists that the book acknowledges though there are unnecessary details about her personal life.  Such details were not provided for the male scientists).  The hypothesis was later proved true by using the same technique that Carl Woese had perfected.  So here is where we diverge from Darwin's theory.  It is just not a question of survival of the fittest.
And then it turns out that this is also not the complete story.  Genes move horizontally, not just vertically.  So it is not that we just pass our genes to our progeny but also that we can acquire genes from viruses and bacteria. This process is known as Horizontal Gene Transfer (HGT).  This is how antibiotic resistance spreads.  HGT is extremely common in bacteria.  So common, in fact, that it is difficult to create a tree for them. Branches cross over and the tree looks like a web.
It is at this point, I think, David Quammen over reaches for he proposes that HGT occurs as commonly in higher organisms as it does in bacteria and therefore, the tree of life as proposed by Charles Darwin can not be created. I do not buy this argument.  Yes, HGT is common in bacteria but it is not as common in higher organisms as he claims.  We are still closer to apes than to bacteria.

The greatest show on Earth- Richard Dawkins

This book is meant for those who do not believe in Evolution.  But those who do not believe in Evolution would continue not to believe in evolution (despite the Nobel Prize for Chemistry this year) and in fact, if I were one of them, I would be offended by the tone of the entire book.  He hammers, he berates. he pours facts after facts down the throat, and he clearly shows that he thinks that non-believers in evolution are stupid.  Not the greatest combination to convince somebody.
As a scientist, I found the book fascinating.  The evidences that Dawkins presents about evolution, about Darwin's theory, encompasses a wide swathe of science- biochemistry, evolution in laboratory, fossils, anatomy... the list is endless.  Some of it I had read before.  For example, he talks about Richard Lenski's E.coli long term evolution where he has been tracking genetic changes in 12 identical populations of E.coli since 1988. 
Some of it was new to me.  He describes an experiment where freshwater aquarium fish (Guppies) were grown in different tanks with different backgrounds.  The guppies have spots over their body and these spots are changed such that the fish can merge with the background.  So in effect the spots are used for camouflage purpose.  In this experiment, he describes, the scientists use different backgrounds and watch how an initial population of identical guppies adapt to the environment.
But the most interesting chapter was the one entitled "History written all over us".  Here, he traces how the body plan shows traces of how it evolved. Very often the body plan makes no sense.  The retina is placed backward.  The brain has to perform the most intricate deconvolution to ensure we see what we are supposed to see.  This chapter, for me, nailed down why an Intelligent Designer did not create each one of us.
However, the skeptics will still argue that why we do not see the bacteria evolve into something else. Fair question. The Darwanian process is a very slow and does not completely account for how evolution happened.  In evolution, it is understood that life began with a single cell.  A bacteria.  And from this evolved everything else.
But the Darwanian theory cannot explain how bacteria evolved into yeast.  The bacteria and yeast are both single-celled organisms.  But yeast contains an organelle called mitochondria which provides the energy for the cell.  The bacteria does not contain mitochondria.  How did mitochondria come up.
This was answered in the second book I read this past month.

Is research set up for bullies to thrive

A lot of discussion has been happening on how to make the laboratory experience a happy one. Given the fact that the Principal Investigators (PI) have tremendous clout and power and that the students/post-docs are on the other end of the power equation, cases of abuse abound.  Abuse, of course, takes many hues.
There is an article in Nature on this topic this week.  It caught my attention because it described a supervisor who followed the student around the lab, shaming her, yelling at her, and in general being as abusive as possible.  There was one more such report from Germany, where a researcher who focuses on empathy was anything but empathetic to her colleagues.
My student applied for post-doc positions in India. I was curious when she rejected some of the good labs.  I asked her for reason.  She told me that the PI had told her upfront that he expects her to work long hours every day, including the weekends.  Implied in this was, of course, she should not take holidays.  My student burst out "Don't I have a life?"
Unfortunately, as I am discovering, this attitude is very common.  I am also discovering that many PI have put in CCTV as well as microchip to monitor their student's activities.  Then there are those who spy out whether a student has boyfriend/girlfriend.  Woe betide if they turn out to have one.
Actually, it makes me wonder whether such PI have a life or not.  My lab is just one part of my life.  Of course I also sometimes (like when a paper is due for revision or when the clock is running out for the student to submit a paper or thesis) restore to hounding a student out and I am sure they grumble and moan about it.  But for me, 90% of the time, lab ceases when I walk out of it at 5 pm. That is the end. 
I pay for it, of course. I do not have umpteen publications. I will never be made member of any Indian Academies. I will never be given any recognition.  But, at the same time, I want to make science fun for my students. They should do it because they enjoy it. They should come to the lab because it is a good place for them to learn.  They will make mistakes but in the end, I hope, a spark is lit.
In the end, I suppose, it is about what you want from life.

Hunting for ALS genes- STAT news

One of my Uncles died of ALS.  We watched him fade away within five years of diagnosis.  There is no cure for the disease.  Indeed there is no cure for most of the neurological disorders. 
ALS or Lou-Gehrig disease is caused because some genes malfunction.  There is no one particular gene that causes ALS but there are many genes that are associated with this disease.  Each gene increases the risk.
The disease is not inherited.  Usually.
But it is inherited in some families (familial ALS).  Especially, if inter-marriages are common.  Genetic analysis of such families can lead a researcher to identity the genes associated with a disease.
STAT News has a great article on how a neurologist is tracking down the gene associated with familial ALS.