Wednesday, December 02, 2009

Back to blogging with Darwin, India and scientific peer review

It has been a nice long break away from the blog, but hopefully regular weekly programming will resume shortly.

Till then, I'll leave you with these.

First up, a lovey article by the always excellent Vikram Doctor in the Times of India (yup, even the Times sometimes publishes something worth reading) on Edward Blyth, a self trained zoologist and contemporary of Charles Darwin, who was the curator of the Asiatic Society Museum in Calcutta at the time. He corresponded extensively with Darwin, and his exchange of letters with Darwin reveals much about the lives of fortune seeking scientists of the time who weren't from the privileged upper class. The article is well worth your time.

Also, here is an excellent writeup by Suvrat Kher digging deeper into Darwin, Blyth and Alfred Russel Wallace.

Finally, in lieu of an apology for being away from the blog for so long, I'll leave you with this hilarious spoof video of scientific peer reviewing, circa 1940's.

Wednesday, October 07, 2009

2009 Nobel for telomeres and ribosomes: answering basic questions in life

It’s fair to say that there were few surprises when the Nobel prizes in Medicine and Chemistry were announced. Chemists might again quibble, since the prize again went to biophysicists/biochemists for their work on a biological problem, but other than that, the prizes deservedly recognize magnificent work in two areas of basic biology that reveal very important ways by which life, literally, goes on.

Also, for the first time, there are three women scientists winning the prize in the sciences. While the prizes themselves are “gender neutral”, it remains a fact that (at least until recently), women have been massively underrepresented in the sciences, and only a handful of women have won Nobel prizes (a reflection of that underrepresentation). If not anything else, these prizes will at least inspire many more women scientists (and the winners have all been great role models, not just for women but all scientists).

Now to the prizes themselves.

The medicine prize went for discovering how one of biology’s most important processes is enabled by a quirky unit called a telomere. People realized early that DNA, which encodes all our genetic information, was packaged into chromosomes inside cells. Later, proteins called DNA polymerases were discovered, and these proteins were responsible for making copies of DNA, which would allow the DNA to replicate and be propagated. Scientists observed very early that there would be trouble with this copying process, cine the polymerase would leave tails of DNA at the ends, and that chromosomes would slowly shorten. But if that happened, how could all the genetic information be passed on correctly over generations? And then, was there a relationship between this chromosome shortening and the lifespan of the organism? Over the years, the winners of the medicine prize, Elizabeth Blackburn, Jack Szostak and Carol Greider went on to show how all of this was made possible by telomeres, the capped ends of chromosomes. Telomeres were shown to stabilize the ends of chromosomes, and proteins called telomerases synthesize chromosome ends inside the cell. The Nobel website has an excellent short summary on the discoveries.

Here are two general comments. The first is that all these discoveries were made in two organisms that seem as different from humans as possible; the humble yeast, and a common fresh water microscopic protozoa called tetrahymena. Though some people often question the purpose or use of studying these organisms, basic biological processes (like chromosome maintenance and telomere function) are perfectly conserved across evolution, from these simple bugs through humans. So the findings that came out of these organisms were directly relevant to human and mammalian cell function. Model organisms have taught us a tremendous amount of biology that has been directly applicable to humans.

The second general comment is that when Blackburn, Szostak or Greider started working on these organisms, there was no “application” for their research. At the time, telomeres weren’t known to cause any disease, nor could any “product” be made from studying them. The work was done in tetrahymena and yeast, and there was no “utility” in studying them. But the researchers followed their noses, pursuing questions in basic biology. Now their discoveries might play key roles in developing new therapeutics for cancer, ageing or hereditary diseases. When chromosomes shorten too much (and the telomeres shorten beyond a point), the cell stops dividing and goes into senescence. Normal cells don’t divide too much, so don’t need too much telomerase activity. Yet cancer cells divide incessantly. But they still preserve their telomeres, and don’t go into senescence. It has now been observed that cancer cells have high telomerase activity, and people now believe cancer can be treated by removing telomerases from cancer cells (and thus forcing the cells to go into senescence). There is a ton of work being done now to develop therapeutics against cancer targeting telomerases. Yet when this process was being studied, none of this was apparent.

The chemistry Nobels have gone to Venki Ramakrishnan, Tom Steitz and Ada Yonath for their pioneering work revealing the structures of yet another of the fundamental enabling units of life, the ribosome. This prize also recognizes the third act by which the process of how DNA encodes the units of life is completed. All three discoveries were seen at the level of the chemical atom using the same technique, called X-ray crystallography. Something that can only be described as an atomic photographic snapshot of biological molecules can be obtained using this technique. In the first Nobel Prize awarded way back when to Watson and Crick, X-ray crystallography revealed the famous double helical structure of DNA, which showed how DNA could be easily copied and replicated. Crick was later able to devise the triplet code, which allowed us to understand how DNA, with just combinations of four nucleic acids, could encode all the information for proteins, the building blocks of all life. This DNA was faithfully copied out to another form of nucleic acid, called (messenger) RNA. mRNA is made by a complex of proteins which form the RNA polymerase units, and the precise molecular details of this process were also largely revealed by X-ray crystallography. This work was recognized in the 2006 Nobel to Roger Kornberg. But there remains the third step, the extremely complex process by which this RNA is made into the actual functional units, the proteins of the cell. This work is done by the massive RNA-protein complex within the cell, called the ribosome. Primarily using X-ray crystallography (with other structural and biophysical methods) Ramakrishnan, Steitz and Yonath revealed the structures of the ribosome, first with different sub-units of the complex, and later with the structures of the entire complex itself. The Nobel website has a good, simple summary of the process here. It is a pity that only three Nobel prizes are awarded at a time for a discovery, because Harry Noller has made just as many pioneering contributions to ribosome structure and function. It is too bad that he missed out (and it must have been a close call between Ramakrishnan and Noller).

Most of the work on ribosomes was also done on the most obscure of organisms, mostly microbes that live in harsh environments, like Geobacillus stearothermophilus or Haloarcula marismortui (which lives in the Dead Sea) or Thermus thermophilus. Much of the basic mechanisms of ribosome function are conserved right from bacteria through eukaryotes (of which humans are also a part of). Yet, there are also many differences between bacteria and eukaryotes (and the microbial yeast, a eukaryote, has ribosomes more similar to humans than to bacteria, a fellow microbe). Yonath, Steitz and Ramakrishnan soon had structures of ribosomes with various antibiotics bound to them, showing how these antibiotics could block the ribosome and hence kill bacteria. Their work now gives us a fantastic snapshot to ribosome function, and provides a platform for chemists to come in and make new antibiotics against harmful bacteria.

All in all, the prizes have gone to recipients without any major surprises, and their work has tremendous impact, and is a celebration of research in basic, fundamental biology.

I’ll leave you with this video of the ribosome from Tom Steitz’s lab. I never thought the ribosome looked like a death star, but with the music playing I see it in a different light.

Tuesday, September 15, 2009

Book review: The missing manual – Living Green

(Posted on Desicritics)

Over the past few years “sustainable living” has suddenly grown in importance in the more developed and affluent countries of the world, and most people are at least curious about it. Yet it isn’t always easy for people to know if their lifestyles are green or not. An easily readable yet comprehensive and enjoyable resource for green living would be of great value to everyone, from the die hard eco-warrior to the gently curious citizen. Nancy Conner’s Living Green is just that much required reference to fill that void.

A well written book that can be read as a serious reference or a quick pointer for specific questions, this book (from O’reilly’s missing manual series) addresses most questions anyone could have about living green, and what all it involves. Living green isn’t just about replacing a few light bulbs or occasionally bicycling to work, but is about a comprehensive lifestyle change where the consequences of all our actions are considered from an earth perspective. The book also does well in suggesting that we do have choices, and by living green we do not have to abandon all the comforts we have become accustomed to.

This book is organized in chapters that deal with changes we can make in our homes, all the way through green business and getting involved towards sustaining a greener planet. If you are just starting with small changes in your life, and want to see what little things you can easily do around the house, the first section addresses these questions. You will easily be surprised by the number of toxins you are exposed to routinely, from harsh detergents to cleaners and solutions commonly used in bathrooms or kitchens. Importantly, the book provides low cost, simple alternatives that are far less harmful to our own health as well as the health of the planet. Taking just one example, it was most useful to hear that the ultimate all purpose natural cleaner is white vinegar and boric acid powder, which can be used to scour sinks, clean bathtubs, wipe countertops and clean floors. With a few modifications, it can also be used as a garden pesticide. The book then builds towards reducing unnecessary consumption (going for quality over inexpensive quantity is an easy first step), and reusing and recycling. It then goes a level higher, and provides outstanding resources and ideas towards building houses that are green as well as energy saving, talking about everything from simple design solutions to LEED certification for buildings.

The next section talks about a complete lifestyle change, from raising a green family (ever thought about how many landfills a baby’s diapers could fill up?), green eating and cooking, raising kids who are sensitive towards the environment, through responsible shopping, and another big cause of pollution to the earth, daily transportation. The book provides a handy reminder of the different transportation options (from walking and biking to car pooling) to the costs of air travel or hotel stay, and how easy it can be to offset these effects for little or no extra cost. There are excellent resources for example on hotels or automobiles that take their environmental costs seriously, and are trying hard to improve energy efficiency and environmental stewardship. So, given a choice between two hotels or two cars of similar quality, this book makes it easy to choose the one that does a better job in protecting the environment.

The final section goes in depth into green business, and how it is possible to actually make a profit or create substantial savings by actually being green. Much of it is just simple improvements in efficiency. Using less paper or office recycling programs are low cost efforts that result in big “green” savings. There are significant energy savings offices can obtain by simply allowing more natural light in, or opening windows (as opposed to cranking up the air conditioners all the time). There are choices that can be made for the source of energy (and the differences between renewable and non-renewable energy choices, as well as how one can buy and use more renewable energy resources). Finally, the book goes into different ways by which one can be involved, from activism to socially responsible investing.

There is little doubt that the book is comprehensive, and provides information to someone curious about green living at every level. Yet, there are some caveats or limitations in this book.

For one, it is certainly true that many people have tried various eco-friendly/green choices around the house, and it just didn’t “work as well” as the regular choice. This book, while providing excellent choices for green options around the house, does not acknowledge that there can be some limitations with green products. From my own personal example, we’ve tried just about every single green dishwashing solution out there. But none of them work as well as conventional dishwashing gels (which do have phosphates in them) while cleaning dishes that have been used for spicy, sometimes greasy, and often heavily cooked Indian or Thai food, though they do work satisfactorily for more standard “American” cooking. So, after much trial and error, we had to go back to conventional dishwasher detergents, after experimenting with a dozen natural ones that claimed to be just as “hard on dirt” but gentle on the environment. On the other hand, many other green products work satisfactorily (green laundry detergent with a little bit of hydrogen peroxide added to it works fine for lightly soiled clothes, but perhaps not as well for the rare, heavily soiled garment). Future editions of the book would do well to acknowledge some limitations of green products, and perhaps compare the two, saying where the green product is perfectly adequate, but where it might fall short. Acknowledging some limitations of green products is not necessarily a weakness, and makes it easier for the average person to make better choices while stepping towards green living.

Then, there is an extensive (and overall good) chapter on food, which oversimplifies the “organic is good” mantra, unequivocally casting all fertilizers, pesticides and genetically modified food as the great evil. However, the argument is far from that simple, since it is a very complex area that is grey and not black or white. Yes, pesticides can be harmful, and overuse of fertilizers has ruined land. But it is also true that careful and controlled use of fertilizer (along with suitable crop rotation and mixed cropping) can yield more food (at no nutritional disadvantage) than simple organic mono-cropping alone. Nor are all genetically modified foods dangerous. It remains a fact that every single food crop we eat today has been modified, over years of crossing and creating “hybrids”, except that the methods used have been different. There certainly are issues with proprietary seeds and over aggressive patents, but casting all genetically modified food as bad is simplistic at best and false at worst. There is no doubt that sustainable (including organic) food practices are excellent for the earth, but by avoiding nuance, this book might put away some people who aren’t blindly gung ho yet about everything green.

The book has been written from the perspective of a person living green. So, perhaps, the tone does not fully reach out to people across the aisle. Living in Texas has taught me that direct confrontation (about lifestyle) rarely works. In a place where say people often leave their lawn sprinklers on during three hour thunderstorms, or where cities still don’t have recycling programs (and where one has to collect and cart recyclables to a recycling center oneself), finding middle ground is a starting first step. Perhaps this book can do more to address that.

However, overall the book is superbly written, and provides a single stop for the reader to find out anything about living green. A more than useful manual, it should be the book of choice should one want any reference towards green living. It is a worthy addition to any household, and lets you start making those small steps towards green living.

Living Green: the missing manual

Friday, August 14, 2009

The bat and the moth, and the ant and the butterfly

What better way to resume blogging after a break than with a couple of fascinating stories from the natural world, about predator and prey, defensive arms races and survival cues?
Bats invoke a variety of emotions from people, ranging from disgust and (unfounded) fear to “they’re cool”. At least the Batman sometimes did some good in helping kids get rid of their fear or paranoia of bats. But while bats might look like silly rats with wings, they are indeed supremely efficient hunting machines. While some bats eat fruit, a majority of them hunt flying insects in the dark, and eat vast quantities of moths, locusts, flies, mosquitoes and any other bug that flies. In order to do this efficiently in the dark, they have a fabulously developed system of “echolocation”, a better sonar system than most battleships. This is great for the bat, and allows them to locate flying insects with pin-point accuracy. But what about the insects? Obviously, they have a pressing need to survive and need to escape bats. Therefore many insects have evolved remarkable ways to evade their hunters.

Some insects have developed evasive flying maneuvers, others just taste bad and the bats learn to avoid them, while others yet have evolved a neuronal auditory system that can detect the bat sonar frequency and allow them to escape. So there is this constant fight between bat and insect in evolving better sonar or ways to evade it. But, taking a cue from standard defense technology, do any insects actually jam or disrupt bat sonar? It appears that a certain species of tiger moth can do precisely this.

The tiger moth is a perfectly edible snack for the echolocating bat. But some tiger moths emit specific ultrasonic clicks in the presence of attacking bats. These clicks could potentially serve as a warning sound, or perhaps be used to startle bats (thus giving the moth time to escape), or perhaps affect the bat sonar. A group of researchers decided to investigate this phenomenon in a tiger moth species called B. trigona, and used an ingenious test to determine what role these ultrasonic clicks were playing. They pitted moths against bats in a closed chamber and precisely observed what the bats did. If the click was a warning sound (for say a poisonous or distasteful insect), the bat would at first attack the insect, but drop it or spit it out, and then learn to avoid the insect. If it was a startling sound, the bat would at first be startled, but would learn to avoid it. If the click was indeed a sonar jamming sound, the bats would continue to be confused by the clicking over time. In their experiments, the researchers used a bunch of juvenile or adult bats and presented them with either the clicking moths, or other moths of the same size that didn’t click, or just a different type of edible, non-clicking moth. What they found was fascinating. The bats indeed did eat the clicking moths. However, the bats were 400% more likely to eat a non-clicking moth than the clicking B. trigona. But what if these clicking moths just tasted worse? To make sure that this wasn’t the case, the researchers disrupted the clicking mechanisms of these moths, and then let them out with the bats. This time, the bats hunted them down as well as the other non-clicking moths. It became very apparent that the moths used the clicking sound in order to disrupt the bat sonar.

As far as the moths go, the evolutionary race for survival is pretty simple. Out in the wild, they don’t need to develop a fantastic sonar jamming device to completely disrupt the bat sonar. All they need to do to get a huge survival edge is to be able to disrupt the bat echolocator just a little bit (but more than any other insect around), so that they can get away and the other insect gets eaten. To do this, they only needed to develop a simple tymbal structure, and this structure is now widespread amongst some tiger moth species. And by doing that, they haven’t evolved to escape all bats, but have just enough to gain that much needed survival edge over other bat prey.

(Original reference: Corcoran, A., Barber, J., & Conner, W. (2009). Tiger Moth Jams Bat Sonar Science, 325 (5938), 325-327 DOI: 10.1126/science.1174096)


This next story is just as fascinating, though more incomplete and raising more questions. Plants obviously are under constant risk of being eaten by some herbivore or the other. So some plants have a very effective defense strategy. They secrete sugars onto their stem or leaves so that they can attract ants. These ants then stay on the plant, and serve as a nice, natural defense against other plant eating insects or animals. Butterflies, on the other hand, are insects that plants share a love-hate relationship with. On one hand, the butterfly pollinates the flowers, allowing the transfer of genetic material from one plant to the other, thus enabling reproduction. On the other hand, butterflies lay their eggs on plant leaves and the caterpillars then devour the leaves. And for the butterfly itself, the last place it wants to lay eggs on is a leaf full of predatory ants which would eat up the eggs or caterpillars.

But can a butterfly, a mere non-thinking insect, know not to lay eggs on leaves with ants? The answer, surprisingly, is yes. In this little paper in The American Naturalist, some researchers devised ingenious experiments to see if butterflies would distinguish between leaves that had ants, or didn’t have ants on them, in order to decide which leaves to lay their eggs on. In their experiment, the researchers took dead specimens of three species of ants, two of which were predatory (and would eat the eggs/caterpillars) and one of which was a bug of a similar size and shape, but a harmless herbivores. Then, they pinned these ants on different leaves, and let the butterflies decide where they laid their eggs. What they saw was surprising, to say the least. The butterflies not only avoided the leaves with the predatory ants, but also didn’t mind laying eggs on the leaves which had the harmless bug on them. So it wasn’t as if the butterfly was just laying eggs on leaves with no ants on them, but actually seemed to know that laying eggs on leaves with the herbivorous bug wouldn’t hurt their eggs and so ignored the innocuous bug. Clearly, it appears that butterflies can use visual clues and decide where to lay their eggs.

What is particularly fascinating to me though is not the fact that butterflies can distinguish between predatory and non-predatory ants, but the fact that they know how to do so without any prior “training”. After all, butterflies are far away from animals or birds which care for their young and potentially teach them about predators or food. Butterflies aren’t even social insects, to have groups to collectively “learn” from. So what is the internal wiring they are born with that tells them some ants are dangerous, while others aren’t? What neuronal and signaling pathways do visual cues of predatory ants activate, while those of innocuous bugs do not? And how does that happen? Do other things, like smell, also influence the butterflies? There is a whole world of questions out there, waiting to be answered.

Original reference: Sendoya, S., Freitas, A., & Oliveira, P. (2009). Egg‐Laying Butterflies Distinguish Predaceous Ants by Sight The American Naturalist, 174 (1), 134-140 DOI: 10.1086/599302)

Friday, July 03, 2009

Graduate junction

I recently found out about yet another "social network", with a difference. For all the readers of this blog who might be graduate students or post docs, here's a new resource for you.

The graduate junction is a networking resource for early stage researchers, who might be doing their masters, Ph.D. or post doctoral research work in Mount Doom (or whatever else you call your research group). It seems to be a nice, focused resource, with sharing of resources,a good discussion forum, indexing by category of your research, a database of conferences around the world, useful resources (particularly useful writing resources), some fun (a crossword), and much more.

If you are a young researcher still working on your thesis or a postdoctoral fellowship, you might find this useful. It is still work in evolution, but I think it does serve a specific need, and there aren't too many resources for young researchers out there. So go check it out.

Tuesday, June 23, 2009

Iran on my mind

I've been trying to follow all the incredible happenings in Iran right now on blogs and twitter, with all those protests, rallies and much more. These are chilling times in Iran, and though I don't think anything will change there, I'm sincerely hoping it does. Good luck to all of them.

Meanwhile, since Iran is on my mind, I couldn't help but remembering my old room mate. So, its time to revisit an old post of mine about my friend and Iranophile Brian.

I wonder what he's upto now, and hope he is well. Where ever he is, he must be following Iran closely, wearing green, and hoping his friends there are safe. And if he cares to know, I've taken great care of his movie collection, and enjoyed watching all those movies.

Saturday, June 06, 2009

A peace corps for India?

One of the most remarkable organizations in America that is rarely talked about is the Peace corps. Many of my friends have actually never heard of it. But it has perhaps done more for America’s image abroad, in some of the poorest, most underdeveloped regions of the world, than most other organizations or groups. So what is the Peace Corps? Reading from their website, the organization has volunteers who “…..serve in 74 countries in Africa, Asia, the Caribbean, Central and South America, Europe, and the Middle East. Collaborating with local community members, Volunteers work in areas like education, youth outreach and community development, the environment, and information technology.” Effectively, they are agents of change, education and empowerment in distant parts of the globe, and a part of America’s tremendous soft power. I don’t know if JFK actually visualized the impact the Peace Corps would have around the world, but in my opinion, forming the Corps was one of his greatest and most lasting achievements.

I’ve been fortunate to hear about the work the Peace Corps does from friends who have served in the Corps. So, these are the kinds of things the Corps volunteers do. One friend, immediately after graduating college, joined the Peace Corps and went off to Tanzania. There she lived in a medium sized village, and taught the local school kids Chemistry and English, and also found time to make some great friends, learn about Tanzanian culture, share her ideas of American culture with Tanzanians, climb Kilimanjaro, and meet her (now) husband who was another Corps volunteer teaching science and something else to some other kids in Tanzania. After two years and a fabulous experience, she came back to do her PhD in the molecular biosciences. Another friend worked in my former lab as an undergraduate, and once she graduated joined the Corps and headed out to Gautemala to work with village communities, on health, natural resource management and other issues. The way the program works is simple. It recruits mostly from fresh college graduates (or sometimes even current students, who are allowed and even encouraged to take “a year off”). These kids then express their areas of interest, and the region of the world they’d like to go to. And then, they are sent there (almost on a “paid” work/vacation), and work there for a year, or two, or more. What, you might ask, do they get out of it apart from the experience? Isn’t the experience itself everything? No, they get much more, including tangible benefits that help their own careers. They get college credit, a big boost if they want to come back and join masters or PhD programs, they learn new languages, student loan deferments, and also become a part of a network that now has thousands of successful people in all walks of life. They are extremely valuable to corporations who would love to have people with these diverse experiences. The learning is also a two way process, and they learn a tremendous lot while, at a ridiculously low cost, act as informal ambassadors of the United States in places where people have only fuzzy ideas on what the country is about. More often than not, all parties (the Corps volunteers as well as the communities they work with) benefit and learn a lot from this.

So where am I going with this? Well, the concept of “volunteerism” on a larger scale in India is still nascent, and it is rare to find people, especially young people, volunteering for too many community activities. Their lives are understandably busy, with getting through school, and then getting admission into a program in college that will lead to a “good job” (engineering, medicine or the like), and then getting on with lives. And then, every now and then, there will be some story in the media wondering why the educated youth never go and serve in rural, deprived areas, and why much of the country remains underdeveloped. It is well known that few (if any) college graduates in India would even consider starting up enterprises or serving in rural, remote and/or underdeveloped areas. The government, it its typical heavy-handed approach, has occasionally mandated things like requiring medical students to serve for a year in rural areas (where doctors are much needed). Most of these efforts have flopped miserably. One big reason why these schemes don’t work is because they are coercive, and the student perceives little or no benefit from this. So this is where I think the government could spend a small amount, set up something like the Peace Corps, and gain a huge return on that investment.

Here’s how it could work. The organization can provide streamlined avenues for freshly graduated college students to go and stay/work in some rural/underdeveloped area of their choice, in a subject of their choice. This could range from working with government schools (with poor teachers, often absent), to rural health centers, to the forest or agriculture departments and so on. This provides an avenue for students of different backgrounds to work in. This can come with “official” recognition (say from the education department or the science and technology department), and a significant stipend (I’m thinking of something like rupees eight thousand/$150 per month), as well as options for local accommodation (there is no shortage of government places to stay across the country). As additional, significant incentives, the experience of the students can be considered credit to apply for masters/MBA/MD programs, with the provision of educational/college scholarships for these kids if they decide to continue their education at the end of their fellowship term. In particular, if this program can give significant credit to doctors for admission to specialization/MD programs (say a 20% bonus on their entrance tests or direct admission into certain specialties), this can serve as a serious incentive for doctors to serve in rural health centers. For students who work on engineering projects, projects in agriculture, environment, social issues, water issues and so on, thy could similarly get credit for education. Undoubtedly, this work experience would be very valuable indeed to corporations looking to recruit individuals with diverse experiences, as well as to business schools for their MBA students. In addition, it is possible that students who do take this up realize that there are tremendous economic possibilities in rural India, and perhaps they might themselves then go on to start their own organizations that work in these areas.

Of course, most of this has been about incentives for students to join such a program. The reason the government should/could do this is because it is the only entity that has its reach in every corner of the country, and the authority/ability to implement such a program. But the potential problem is that even if the government does this, it might do this in a typical heavy-handed, bureaucratic, top-down approach, and that will fail. So what they need to do is to support the concept, but leave the complete implementation and execution to a board with people who are good at putting grassroots organizations together, and promise never to interfere in that work. All they should do is provide unconditional grants. Given how Indian governments work, with their maai baap attitude, this is bordering on fantasy. But such a concept can work (and has worked, remarkably well, with the Peace Corps). So now, does any one have the drive and will and reach to put this together and get the government to do something like this?

Friday, May 29, 2009

How gardening helps scientists

(Sorry for a long absence. Numerous reasons have kept me away from the blog, but now it should be back to weekly essays on Balancing life).

Arabidopsis thaliana is a distinctively unremarkable plant. It is small, scraggy, has few leaves and very modest flowers. It has no dietary value, nor does it look particularly pretty on a bouquet. It is possible that even goats don’t care much for it.

Yet the plant has served mankind over the past few dozen years like no other. It is the chosen plant genetic model for hundreds of researchers around the world, who take advantage of its short lifespan, relatively easy growth, adaptability and small size and do wonderful research. It also has one of the smallest genomes any plant has, and research from Arabidopsis has not only revealed much of the working mechanisms in plants (of profound use in agriculture and whatnot) but also in general biology. Many findings from Arabidopsis has applied to all living cells, from bacteria to mammals.

But when I say “model plant organism of choice”, I don’t mean it is as easy to do experiments with Arabidopsis as it is say with fruit flies or yeast or bacteria. It is much harder, and graduate students pursuing their PhD with Arabidopsis on average have to work 6-7 years before they’ve done enough to get that PhD.

So I was stunned when a Chinese colleague of mine told me about his friend and old university mate. His friend had worked with Arabidopsis for his PhD, and had produced a prodigious amount of work, finishing his PhD in a mere three years. This was a record almost unheard off in the Arabidopsis community. My friend was just as surprised when his friend told him this story. So he asked his friend what the secret to his success was.

His friend grinned and said “Most researchers are pretty smart and know a lot about biochemistry or genetics or development, but they don’t know plants. I’m smart and I know plants. I’m from a family of peasant farmers, and my family used to grow vegetables back in China. I know more about growing and caring for plants than the rest of my lab put together. They spend their time learning how to grow the plants, and I spent all my time just designing and doing experiments.”

Now you tell me there isn’t value in rustic wisdom.


That said, there’s something more in this story. I’ve met lots of Chinese researchers who have come from very humble backgrounds. Many of them grew up in rural areas, and were from families of farmers. But they all got to go to school, and those who shone academically got scholarships to study in top colleges in Beijing or Shanghai or other cities. While there is much that I don’t like about China (particularly politically), I think they’ve done very well in educating a massive population. India and China had similar class conscious, massively illiterate populations some 50 years ago, and China has done far better in educating its people, and giving more chances to the “underprivileged”. Many of my Indian friends here in the US are researchers. But they all come from urban, middle class, “white collar” backgrounds. I don’t know a peasant yet who has done a PhD in an elite institution, or pursued a career in research. Some food for thought, this.

Sunday, March 29, 2009

Urban wetlands

In a fairly recent post, I had mentioned how many of Bangalore’s lakes are being killed. But nature is extremely resilient, and given the slightest chance it will bounce back. And some of Bangalore’s lakes are wonderful examples of urban wetlands that are priceless treasures.

I’d recently visited the Hulimavu lake, a fairly large lake just half a kilometre from Bannerghatta road, one of the busiest roads in the city. This road is filled with apartment complexes and office blocks, with traffic that usually moves at 5 miles an hour on good days. Not surprisingly, this lake is under severe stress. There is plenty of legal and illegal construction all around the lake, and much of the lakebed has been encroached. Many of the other construction sites nearby use the lake as a convenient dumping ground for excavated earth. Along one channel, untreated sewage is slowly being discharged into the lake. A whole lot of people seem to use parts of the lakebed like a public toilet. And there are roads running all around the lake, on what clearly was the lake’s spillover bed. As is sadly the case in most Indian cities, the local residents are either unaware or unable or unwilling to do anything about this.

In spite of this, there remains an incredible diversity of life in and around the lake. We decided to take our binoculars and see what birds still inhabit the lake. I was more than pleasantly surprised at what we saw. There were plenty of brown pariah kites, and a few magnificient copper and white brahminy kites (and we were also able to follow a couple of them to their nest, on a nearby eucalyptus tree). There were also plenty of cattle and little egrets all around the lake. In addition, we saw a couple of grey herons in statuesque stillness, waiting for their next fish or frog to swim by, and a good number of moorhen pottering around the wetland. In the lake itself there were a good number of Eurasian coots swimming around, as well as a few snake-necked darters out hunting. These were just the confirmed sightings in a span of about 15 minutes of standing by the lake with Salim Ali’s indispensible handbook, which makes it more than likely that many more waterfowl inhabit the lake.

Urban wetland management unfortunately is not much of a concept in most of India. Yet this lake is just one example of the kind of diversity and richness of life in lakes around the city. It is also a fine example of a lake that could easily be made into a city nature park. To do that, only a little needs to be done to protect the wetland. Obviously, preventing encroachment around the lake would be a priority, as would be stopping the flow of untreated sewage that is choking the lake would be an obvious other step. In addition, the usual mismanagement of “lake development” that most city authorities eagerly embrace should be avoided. Usually, the city decides to build a big “garden” around lakes, which means manicured lawns, paved paths, lots of flowers and trees that don’t usually grow in wetlands, and a complete destruction of the wetland around lakes. This usually ends up slowly killing the lake. Most of these birds live and nest amidst the reeds that grow in lake wetlands, nurturing a rich ecosystem that supports frogs, breeding fish, small reptiles and small insects. Unfortunately, “beautifying” or “developing” lakes by building parks only breeds mosquitoes (by killing off fish and dragonflies that eat them, and breed in the reeds). The Yediyur lake in Jayanagar was a thriving lake that was killed off by just this effort of “development”. First came some lawns, and then there were motor boats and motor scooters, and now it is just a little swamp that breeds mosquitoes.

Instead, if the city could declare some of the lakes of Bangalore protected wetlands, and then spend a pittance on preserving the wetlands, we would be left with wonderful city parks where children and adults alike could spend evenings or weekends observing a diversity of birdlife and plant life (in addition to perhaps small amounts of regulated recreational fishing). It would be a chance to educate and enrich our own lives, and reconnect with nature in the heart of a stressful urban environment. A fond memory of mine is the environment around Lake Washington, in Seattle, right by the magnificent Husky Stadium. The wetlands around the lake are now carefully protected, and there is a beautiful little nature trail, with a description of the flora and fauna around the lake, as well as the importance of wetlands for human survival. People relax here now on weekends, paddle in little canoes, or walk around the unpaved nature trails, or spend lazy sunday afternoons trying to fish (with a permit). Yet this wasn’t always so, and the lake and wetland had nearly been killed in the sixties, and a massive restoration effort of over twenty years revived it. Here, we have wonderful living lakes in the midst of a massive metropolis. Do we need to sacrifice them in the name of “development”, or can we learn to live with them, and allow them to make our lives so much better?

Thursday, March 05, 2009

A scientific temper

Jawaharlal Nehru, for all his numerous follies, strongly believed in two wonderful concepts; freedom of speech, and a concept he had coined, a nation with a “scientific temper”. That term, a “scientific temper” is a wonderfully succinct way to describe a broad concept. By speaking of a nation with a “scientific temper”, he wanted to speak of the people of a nation who would be able to think independently, understand and practice the scientific method in their daily lives, analyse and not take statements at their face value, and avoid simplistic reasoning. Of course, it has been easier said than done to create that atmosphere in a nation where superstition, religion, rumor, myth and innumerable beliefs abound. Interestingly, I was reminded of the concept of a “scientific temper” by an unlikely source.

One of the pioneering biochemists, science advocates and science policy advisors of our time, Bruce Alberts talked about this concept in a talk of his recently. While talking about science policy, research and much more, he also talked a bit about some of his efforts with City Science, an effort to improve science education in schools in San Francisco, which he hoped would not just improve science education, but would get kids to think about everything. Now, this effort isn’t just about getting kids to learn their science books better, but it is about bringing about a fundamental change in their way of thinking, enabling them to question, analyse and reason better in all aspects of their everyday lives, making the scientific method a part of it. He used a simple example of just one of the types of lessons that the kids learnt which illustrated the concept beautifully. I thought it would be just the kind of story to share on this blog.

This was a lesson for five year old kids in kindergarden, showing how this concept can be inculcated in kids very early in life. A bunch of five year olds were allowed to run around and play in their schoolyards wearing clean white socks. When they returned, each kid was told to collect all the little black and brown bits of dirt, grass, seeds and whatever else from their socks. The kids were then asked to sort out the dirt, separating the seeds from the dirt. At this age of course, the kids knew that seeds were something plants grew from, but couldn’t easily tell seeds from just regular, largish specks of dirt. But they were allowed to come up with their own ideas of what would be a seed and what would be dirt, and they created their own little piles of “seed” or “dirt”. Now, at this stage, you would think the teacher would just come in and correct the kids. But no, the exercise was taken further. First, the kids were asked to look at their seeds and dirt under a 5$ “microscope”, where they could get a clear idea of the shape and dimensions of their dirt or seeds. Then they could draw out the different patterns they saw, making their own guesses for dirt or seed from this, and perhaps intuitively looking for a regular pattern into which all seeds could fall into. Finally, in order to prove their hypothesis, the kids were asked to plant their “seeds” or “dirt” in seed free earth, keeping a record of what they planted, with a small drawing of what each speck planted looked like. If their separation was correct, the dirt would never grow into grass or a plant, but a majority of the seeds would grow in a few days into grass or sprouting plants. Then, the kids could see for themselves which specks were dirt, and which were seeds. So, with this fun little experiment, the kids were introduced to the concept of forming a hypothesis, and then testing the hypothesis. They could easily have just been shown seeds, and dirt, and told which was what, ending the lesson. But by allowing them to go through this process, it enabled them to understand that just an idea, however appealing it might sound, wasn’t necessarily true. It inculcated the idea of the “testability” of a hypothesis, and the concept that a statement that couldn’t be verified or tested wouldn’t fall under the scientific domain. It also showed them something about “falsifiability”, the fact that if something convincingly failed the test (say all pieces of dirt classified as “seed” not growing into plants) could suggest then that the idea could be false. Of course, this didn’t go into the limits of falsifiability and suchlike, but this is pretty good for five year olds isn’t it?

The broader idea here is that by doing this early in a child’s life, it would enable the child to understand the scientific method better, better enable the child to question simplistic statements or “theories” (thereby differentiating scientific theories from popular “theories”), and would help the child grow up into someone more rational and someone less likely to be swayed purely by emotion or passion.

So, coming back to Nehru’s scientific temper, I think these are the type of initiatives that we need, starting with kids at a very young age. There certainly are small efforts here and there, by wonderful NGOs or other organizations, but most of the efforts are few and far between. With education in India itself, most of the effort (or argument) appears to be for better colleges or research institutes or more IITs, but the biggest hole lies in our schools. It is a white elephant no one wants to touch. But only when that hole is plugged will terms like a nation with a scientific temper mean anything.

Monday, February 23, 2009

Only a memory

The first time I heard about “urban planning” was from some friends at the School of Architecture and Planning in Chennai, when I was still in college. That was what some of them were planning to study when they went to the US for their masters degrees. I wondered aloud if that was something ever practiced in India, and was greeted with a unanimous laugh, and a witty quip about urban non-planning. Anyway, now that I’ve visited Bangalore after nearly four years, I can only nod in agreement. That the city has changed rapidly over the past ten years, there is no doubt. But the callousness and utter mismanagement of what should have been good urban planning has only left me deeply saddened.

The mismanagement has been at every level, resulting in the chaos that is now almost descriptive of the city. The city has, expectedly, grown rapidly. Unfortunately, it has grown with common-sense defying haphazardness, and has massively misused or mismanaged resources. The most important resource completely mismanaged has been water. There has understandably been a proliferation of new layouts, and an explosion of apartment complexes. Interestingly, some of the biggest growth has come in areas like HSR layout and Whitefield. These areas are apparently close to major technology centers, hence the growth. However, while the apartments have come up, promising ultra-luxurious living, the single most important thing you need for survival has been overlooked. Water. These areas have precious little of it. These areas have the lowest water table in the entire region, and try as you will, it is hard to strike any ground water here even at depths of 300 feet. Which then makes one wonder why or how such large residential complexes have been sanctioned in these areas. Typically, residents here shell out in the range of rupees five thousand every month for just their water needs, provided in part by tankers supplying water, and in part by depleting the little ground water that is left. How exactly this is sustainable eludes me. The presence of consecutive weak, apathetic governments in the states hasn’t helped. I cannot but help comparing the city to Chennai, which also had acute water problems. Years ago, they started enforcing rainwater harvesting, made it mandatory, and actually enforced the rule. The water situation in Chennai dramatically improved over the years. In stark contrast, the city of Bangalore “recommended” rainwater harvesting at least in large apartment complexes years ago. This was poorly implemented, with only a fraction of the larger complexes setting up rainwater harvesting systems (which don’t really cost much), and fewer actually utilizing them. In some belated form of realization, the city now plans to enforce a rule they passed four years ago.

Given the fact that Bangalore lies in a dry region, one would imagine that the administration would at least want to preserve the few sources of water around the city. Yet, instead of making the few lakes that still remain into city or state parks, they are now viewed as prime sources of real estate for buildings. Here’s how the system apparently works. There is plenty of construction happening all around town. There is obviously a lot of earth that construction digs up. Obviously, the easiest way to get rid of that earth is to take it to the nearest lake and dump it in there. If you visit some lakes like the Gottigere, Hulimavu or even Madiwala lakes (to name just three), you’ll see this happening all around them. Soon, a few acres of lake will disappear, and then in a year or two, the local authorities (or a local politician) will announce the creation of a new layout in that very former lake bed. The next thing you know, there will be a new “ultra-luxury American style” condominium complex coming right up. If this scheme doesn’t work, there’s an easier one. Just build a small temple in that reclaimed lakebed. Illegal or not, within a few months, crowds will start thronging to the temple, thereby forcing the temple to expand. Before you know what’s happening, a few acres of former wetland would have disappeared, all in the name of god.

A third strategy seems to be to cut off all sources of water for the lake, by allowing construction (residential and commercial, there isn’t much of a difference between the two) on all sides of the lake, up to the very lakebed itself. In a few years, all rainwater that should have fed the lake won’t make it there anymore, and then you’ll have a few feet a year of new construction land.

Finally, the greedy administrators in collusion with the land mafia seem to have another trump card to acquire lake land for buildings. Bring up the bogey of development. Clearly, if you want an “international” city, the best places to build a new technology park with an associated residential layout have to be on a reclaimed lakebed. And anyone who raises an objection to this is naturally anti-development.

The city (that once apparently had over 300 lakes in it) is being ruined by masterful mismanagement. For all the glitzy technology complexes with gleaming glass facades, a city can’t live without water. It remains unfortunate that the residents of the city don’t care too much about the issue, but when faced with water shortages clamor to the government to get more water from the Cauvery (miles away, passing through Mysore), potentially stroking inter-state disputes. To top the utterly callous mismanagement of water, the proliferation of residential and commercial buildings has been random, haphazard and mostly unregulated. A number of buildings have exceeded the number of floors they are legally allowed (on the specified area), or have come up without any parking space, or else commercial complexes have come up in ostensibly residential neighborhoods.

What is now left is a city that is monstrously large, and in utter chaos. Any changes the administration would now want to make can only be cosmetic. In comparison, Delhi and Chennai have also grown, but the authorities have at least managed to maintain a semblance of logic in this growth, resulting in cities which are, if not admirable, at least functional. Bangalore used to be one of the most attractive cities in India, because of the lovely climate, tree-lined avenues, quiet, organized suburbs and a cosmopolitan population. Now only the cosmopolitan population remains, under immense regional chauvinistic pressure. I think I can safely say that the city of my growing years can only be a memory.

Wednesday, January 28, 2009

Muddling through chaos

For the past few weeks, I've been getting used to the chaos that is India. Our return to the US has been temporarily delayed, but we hope that issue is taken care of soon enough. Till then though, I'm having as much fun here as possible, while shuttling between Bangalore and Chennai. It has been a few years since I last visited India, and all I can say is that years of pathetic administration continue to run down Bangalore. Chennai, while also bursting in its seams, seems to have better order within the madness. Exchange the bus drivers and climate of Bangalore with Chennai, and you end up with a city that wins hands down over Bangalore. It is amazing how quickly weak administrations can ruin something that is good.


While I try to get back to regular blogging (with perhaps some observations from India) here's a story I'll leave you with.

I happened to sit in an autorickshaw in Chennai that was being driven by an extremely chatty driver. Never someone to resist conversation, I probed him on with questions, which he was only too happy to answer. Now, there are thousands of autorickshaws in Chennai ferrying passengers across town, and fleecing them without ever bothering to turn on that meter. I usually consider them to be rogues and thieves. But there are stories behind their lives as well. Only some of the autodrivers actually own the auto that they drive, with most of them renting the auto from auto owners for a large sum. The ones that do own their own autos though don't have it easy. This driver was particularly happy that day because he had just finished paying the entire cost for the auto, and was now an independent auto owner. To prove it, he showed me his freshly minted receipt of payment.

So I asked him how he could afford to buy me an auto, and he told me his tale. He used to be a vegetable seller (as proof we whizzed past some vegetable vendors, he yahooed them, and then told me that was his brother-in-law and family, who still continued the family trade), and then decided to buy an auto. He first wanted a bank loan, so opened a savings account in the bank. He had some 5000 rupees in it, and thought that was good enough to get a loan. But the bank wanted collateral (or at least a minimum savings balance of rupees 60000). So he said goodbye to the bank, and found a money lender, who willingly gave him the money (with the auto itself taken as collateral). Now this poor guy has to pay some ridiculous amount as interest. He didn't know the exact percentage, but said that his total loan was about rupees 120000, and he would have to pay around rupees 175000 back to the money lender, over a period of some 5 years. That was his scratchpad calculation, though if he didn't pay that up in 5 years, even that sum would skyrocket.

No wonder, he said with a smile, that he would never ever put that meter, but charge me whatever he thought I could pay (which, apparently, was quite a bit). I wonder though, can't there be any better way for someone like him to raise capital to buy an auto? I understand the banks have a need for collateral, but if money lenders can lend the money (and I'm sure they are more careful with their money than banks are), can't banks do it? Economic gurus, what ideas do you have?

That said, auto drivers in Chennai remain thieves, and I curse them all with a lifetime of indigestion for their dishonesty.