Sunday, May 26, 2013

Monday, May 20, 2013

Its In The Syllabus

From PhD comics:

The tables can very easily be turned on you, the faculty, when a student goes over the syllabus with a tooth comb and then holds you to every dot and comma in it.

My friend who is an igneous petrologist and faculty at a local university here in Pune saw the nasty side of the syllabus centered education. As a researcher, my friend is highly enthusiastic about his work and often launches into long excursions about it during lecture time. He didn't think the students minded until he posed a question about his research in an exam. There, some students objected... it was not in the syllabus you see!  They took their complaint to the Vice Chancellor of the University and had the exam annulled.

This happened at a post-graduate level i.e. these were students studying for their Masters degree, a level at which students should be learning not just the fundamentals of a subject but also exploring the boundaries of knowledge about a topic by diving into the research literature and hungrily biting at anything extra that comes their way. It makes you wonder about the motivation and mindset of these students that they so quickly and vehemently protested against a faculty who actually wanted to go out of his way and teach more than is required of him.

I hate to think that the narrow minded focus on rigid syllabus and passing exams has reached such a level that it is destroying any curiosity to learn more.

Thursday, May 16, 2013

Again! Charles Darwin Was Wrong.. About The Tree Of Life

Well.. I guess the headline "Darwin Was Wrong" always sells!

But The Guardian should have thought a little before publishing this. It is an article which appeared sometime back but is the most viewed in the science section and is about how the recognition of lateral gene transfer i.e. the transfer of genes aross taxonomic groups is proving Darwin's idea of a tree of life wrong.

Read this passage:

Evolutionary biologists say crossbreeding between species is far more common than previously thought, making a nonsense of the idea of discrete evolutionary branches.

I don't think their science correspondence Ian Sample thought enough to see the contradiction in this passage.

Cross breeding between species implies that species exist in the first place which in turn means that there has been in existence discrete evolutionary branches i.e. long periods of independent evolution of different populations so as to have accumulated unique features recognizably different from other populations. Its only when there are discrete unique branches is it possible to recognize lateral gene transfer between the two!

For example, coyotes and wolves are closely related animals that occasionally interbreed in the wild. But the fact that we can recognize coyotes from wolves means that these are two discrete lineages having diverged from a common ancestor at some point in the past and have since followed separate evolutionary trajectories accumulating unique traits along the way. Occasional interbreeding between the two does not wipe away all these differences. They remain two distinct branches on the canid family tree.

Gene trees are not the same as species trees. Gene trees reflect the evolutionary history of a gene which may be transferred across taxonomic groups by a variety of processes. Early in the divergent history of populations genes may be exchanged through interbreeding. Or, for example a not so insignificant portion of the genome of mammals is made up of fragments of genes from other species transferred into us long ago by viral infections. However, that does not change the historical fact that the coyote and the wolf, or for that  matter humans and chimps diverged from a common ancestor. Species trees or the tree of life reflects this history of speciation. So, Darwin's tree of life idea is about diverging populations from a common ancestor. These populations despite occasional transfer of genes maintain reproductive integrity and become different enough over time. Life has become diverse over time by such branching. Darwin was not wrong about that.

And what does one make of this confused para- Last year, scientists at the University of Texas at Arlington found a strange chunk of DNA in the genetic make-up of eight animals, including the mouse, rat and the African clawed frog. The same chunk is missing from chickens, elephants and humans, suggesting it must have become wedged into the genomes of some animals by crossbreeding.

Does that mean there was interbreeding between mouse, rats and the African clawed frog? Ridiculous!

Update May 16 2013: There is another potentially misleading passage in the article:

But modern genetics has revealed that representing evolutionary history as a tree is misleading, with scientists saying a more realistic way to represent the origins and inter-relatedness of species would be an impenetrable thicket. Darwin himself also wrote about evolution and ecosystems as a "tangled bank".

Now, the "tangled bank" has nothing to do with lateral gene transfer and interbreeding at all. It should not be conflated with evolutionary relationships being described as a web or a thicket. Darwin was describing the complex inter-dependencies in an ecosystem as organisms compete and co-operate with each other for resources.

Tuesday, May 14, 2013

Genghis Khan And Interdisciplinary Research

State of the Planet has quite a readable account of how a period of warm climate in the early 1200's may have produced an abundance of grass and livestock in Mongolia, fueling the expansionist ambitions of Genghis Khan.

Here is an interesting passage from the article:

In 2013, Avery Shinneman, a biologist at the University of Washington, will analyze sediments at selected lakes in order to estimate abundances of livestock over time, using varying levels of fungal spores that live in the dung of grazing animals, and algae fertilized by that dung. The data will be fed into a model developed by Hanqin Tian, an ecologist at Auburn University in Alabama, who studies the weather of modern Mongolia and its relation to grassland productivity. The Mongols left few written records, but Nicola di Cosmo, a historian at the Institute for Advanced Study in Princeton, N.J., will look into contemporary accounts from China, Persia and Europe for clues to climate and military events. From all this, the researchers hope to develop a picture of how sun, water, soil and animals might have created an energy system that the Mongols could have tapped into.

Biologists, theoretical ecologists, historians... increasingly big projects like this one become interdisciplinary by necessity.

If you have been following my posts on the controversy over a paper by Giosan et al on the geomorphology of rivers feeding the Harappan that was a big project involving geomorphologists, climate experts, paleobotanists, sedimentologists and geochemists. The paper had 15 authors. You could have confused the author citations for the abstract! :)

Friday, May 10, 2013

OF Flies Mice And Men- Francois Jacob 1920 -2013

The great French biologist Francois Jacob died on April 19th 2013. I started this post and left it lingering in draft. I want to post it now.

 Carl Zimmer at The Loom  has an essay which outlines one of the key moments of Jacob's career- when he realized how cells turn genes on and off.  That formed the basis of understanding gene regulation and laid the foundation of the field of developmental biology. For that work he shared the Nobel Prize in 1965 with Andre Lwoff and Jacques Monod.

Francois Jacob also wrote beautifully about evolution. His description of evolution as a tinkerer has become a popular way to think about how evolution builds novelties and puts together complex structures and traits. From his elegant essay on evolution and tinkering published in Science in 1977 :

Natural selection has no analogy with any aspect of human behavior, However, if one wanted to play with a comparision, one would have to say natural selection does not work as an engineer works. It works like a tinkerer - a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him whether it be pieces of string, fragments or wood, or old cardboards; in short it works like a tinkerer who uses everything at his disposal to produce some kind of workable object. For the engineer, the realization of his task depends on his having the raw materials and the tools that exactly fit his project. The tinkerer, in contrast, always manages with odds and ends. What he ultimately produces is generally related to no special project, and it results from a series of contingent events, of all the opportunities he had to enrich his stock with leftovers. As was discussed by Levi Strauss (5) none of these materials at the tinkerer's disposal has a precise and definite function. Each can be used in a number of different ways. In contrast with the engineers's tools, those of the tinkerer cannot be defined by a project. What these objects have in common is "it might well be of some use". For what? That depends on the opportunities.

I enjoyed reading his books; The Statue Within and Of Flies Mice and Men.

Here is a passage from his book Of Flies Mice and Men where he describes the fear and excitement of changing course midway through his career:

The word "courage" is not too strong. The daily interaction over years with a living organism, however humble, entails a certain familiarity. You could almost say that you acquire a certain tenderness for it. After 15 years of working with a particular colon bacillus, I had accumulated hundreds of mutants. In each of these mutants, one or another of the cellular functions, many of them indispensable to the life and reproduction of the bacteria, had been altered. To abandon this work and all that it offered; to renounce the kind of intimacy that comes with the knowledge of little unwritten quirks, the folklore that surrounds the work of any one organism; to start again from zero with another, unknown organism whose idiosyncrasies I would have to discover - all this was a considerable sacrifice. It was a little like leaving a loved one . But, at the same time, the new project was an exciting one. It would mean entering an unknown world, beginning a new life, becoming young again....

Thursday, May 9, 2013

Summer In My Neighborhood

Its been a blazing week with temperatures over 100 deg F. Pune this past few days has been as hot as I can ever recall. Time for ice tea and cool stewed mango drinks. Evenings are very warm too. We are giving our rugby kids water breaks every 10 minutes.

But walking through the small lanes near my house are sights like this one:

Summer can be glorious too. And the alphonso mangoes and cold beer is helping!

Wednesday, May 1, 2013

V.K Gaur On Earthquake Research, Jaitapur Seismic Risk And Role Of Scientists

The Hindu carried an interview with Vinod Kumar Gaur, seismologist with the Centre for Mathematical Modelling and Computer Simulation. His work on the seisimic risk at Jaitapur southern Maharashtra where a nuclear power plant has been proposed was criticized by the Indian government and his colleague Roger Bilham denied entry into India on the grounds that he violated the terms of his tourist visa. I share the suspicion of many that the Indian government is too sensitive and insecure about anyone raising questions about nuclear safety and reacted pettily by banning Dr. Bilham.

Some excerpts:

You have been vocal in your scepticism of Jaitapur as the location for a proposed 10,000 MW nuclear power plant...

Not for the construction of the plant, which can be designed with safety features. But India’s western coast, a well-recognised zone of potential seismic vulnerabilities, is likely laced with ancient faultlines buried under sediments and waiting to spring back like a piano accordion under continental compression. It is intriguing that Jaitapur [on the Maharashtra coast], the chosen site for the world’s biggest nuclear power plant, should have been declared seismically safe without refuting these possibilities.

My concern is that the various geological proxies of faultlines around Jaitapur and their possible implications on the plant and public safety have been neither adequately studied nor communicated. A clear picture of Jaitapur’s vulnerabilities and their quantification, needed in order to calculate the level of safety measures to be incorporated, is missing from the earthquake hazard assessment of the site. 

What, in your opinion, prevents a more thorough safety analysis of Jaitapur?

We have every technological possibility to exhaustively investigate the subsurface geology of Jaitapur including high resolution seismic imaging that can be carried out at a fraction of the project cost.

Scientists tend to downplay earthquake risks. It is convenient to do so. You keep everybody happy when you maintain status quo. But science only grows by addressing challenges, by considering alternative views and designing incisive experiments to prove or refute conjectures.

 and he has some harsh words about the lack of outreach role played by Indian scientists.

....Sadly, our scientific culture lacks responsibility and rigour towards public safety, and so denies society the advantage of information, and consequently resilience, against the natural disaster.

Read the full interview here.

My previous posts on this topic:

1) Politics And Pettiness In Indian Seismology
2) Note To Indian Govt: It Is Pointless Banning Seismologist Roger Bilham