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.
 

The River of Consciousness- Oliver Sacks

My M.Sc. student gifted me this book when his project got completed.  I am grateful to him for it is a wonderful read.  Published posthumously, compiled during his final illness, the book comprises of set of essays covering a whole gamut of topics.
He starts with Darwin- not the usual Origin of species but covering Darwin's experiments with plants and making the argument for evolution and natural selection.  So timely given the cacophony emanating from many of the right-wingers. I always used to be proud of the fact that Evolution and natural selection used to be taught in India without interference from religion (unlike America) but of course, I had reckoned without the right wing coming to power.  They, of course, do not believe in Evolution.
Oliver Sacks then talks about speed and couple of other topics.  But my favorites were towards the end.  There was one on mishearing. When he starts to lose hearing, he also starts to mishear. I showed it to my father who is now suffering from lose of hearing.  My father was deeply appreciative of this essay.
Then came the one on The River of Consciousness where he makes the case that what we think of one continuous stream of thought is in fact frames of thoughts stitched together into one continuous frame.  A remarkable power of our brain
The final essay was on Scotoma: Forgetting and Neglect in Science.  Many of the discoveries are neglected during the scientist's life time.  Take for instance Mendel.  He publishes his discoveries in a journal.  No one pays attention and then in 1900s, the laws are rediscovered.  And now Mendel is celebrated as Father of Genetics.  Or Barbara McClintock who discovered the so-called jumping genes.  No one paid attention till it turned out that these genes are important component the genome and contribute a great deal to variation.
All in all it is a book my father says he would like to read.

On the relationship between waterbodies and us

This past week I was in Hyderabad attending a conference.  Our hotel was opposite the Hussain Sagar Lake.  The driver told me that the lake was visible from the hotel rooms and I was lucky enough to get a room that faced the lake.  At the conference, one of the members told us that the government had created a nice walk around the lake.

So on the last day of the conference, I went out at 6.30 am for a walk.  The lake itself is lovely filled with water.  Common Coots were having a swim.  Nice and wonderful.  But...
The thing that hit me most was the stench that reminded me of Cooum river in Chennai.  My uncle used to have an apartment overlooking the river and everyday we were reminded of the river, thanks to the stench.
The lakefront had boards put by Hyderabad Municipal proclaiming the need to keep the lake clean but garbage (plastic bags) was strewn around the edge.

The lake front garden was small and unimaginatively built. Four stray puppies were gamboling.  There were no women.  The entire park had been taken over by men.  I had a quick walk and then turned back to the hotel chased all the way by the smell.
Which brings me to our relationship with water bodies. At this point there are no water bodies in India (maybe excluding Indore and Bhopal?) that is not highly polluted.  Garbage is one menace but the greater threat is untreated sewage and chemical waste that is dumped into the water bodies without a care. So while each of our river is worshiped, each of them too turn into a dumping ground for all waste.  None of the stakeholder is serious about cleaning up the water bodies- panels and measures are regularly announced but...

Standardized online entrance exam and biometric attendance for teachers

Now teacher attendance is mandatory. As usual I do not understand either of the two decisions.  What is this going to accomplish?  Will it force the non-performers to teach and do research? All it will do is that once a day they will make a trip to their center and sign in.  Big deal.  It will waste little bit of petrol but if it satisfies the powers, what can one say?
The other issue is even more mind-boggling.  Apparently, our exam is going to be now conducted in multiple choice questions. How do you evaluate a language or a social science student  or a international relations who is applying for Ph.D in multiple choice format? How do you evaluate their ability to make an argument and defend it in multiple choice format?  In sciences itself, where it is easy to design questions in this format, we struggle with the kind of students we get. Most often they possess absolutely no communication skills, many of them do rote-learning, many of them do guesswork, and when they join the program it becomes an uphill task to make them read, think and ask questions.  But in social sciences or languages...I give up!
As usual there will be no debate on this issue. It has been decided by the administration so we just have to follow it.
Ugh!