Thursday, December 27, 2007

Recycling woes

I try hard to minimize my carbon footprint (according to the calculator, my footprint is 5.5 tonnes, compared to the US average of 20 tonnes per person, pat pat). The years in Seattle ensured that recycling would always be on my mind, and that city is a wonderful example of what is possible, where there is a constant effort to maximize recycling and reduce waste and consumption.

Anyway, after having moved to Dallas, my efforts to conserve and recycle have run into a number of challenges, and plenty of amusing incidents.

Most of Dallas city itself still doesn't recycle (though there is some recycling in Dallas suburbs). Which means if you want to recycle, you need to collect whatever you can at home, and then drop it off at the nearest recycling center. Luckily for me, I managed to find a recycling center just a couple of miles from home, and started collecting and sorting trash out at home (into the usual, paper, plastic, glass and cans). The problem though lies in taking that trash in a timely manner to the recycling center. More often than not, I end up with a small mountain of recyclable trash, which eventually makes entry into the laundry room impossible. Loading all of that into the car ends up being quite an ordeal. But it’s also led to some embarrassing situations.

On one occasion there I was, standing by the apartment elevator, with two large trash bags and two smaller bags full of cans and bottles, and on my way down, the inevitable happened. One of the bags ripped open and there were cans rolling all over the corridor. As I was chasing down one of the fugitive cans, one of my neighbors stepped forward to help, and with a twinkle in his eye asked me if I was collecting trash for a reason. Perhaps I wanted to sell them on eBay!

On another occasion I had so much trash that the trunk of our little car wouldn’t close (damn those humongous plastic milk containers). As I huffed and puffed under the warm Texas sun, another neighbor who was driving out in his truck took one look at me and said “that’s why you need a truck”, smiled and drove off. On a third occasion, I almost made it to the car intact, when I tripped on the curb by the parking lot and splattered cans and bottles across the lot. But I soldier on.

Grocery stores sometimes provide even more entertainment. I was used to taking a shopping bag to stores in Seattle. Anyway, most stores there give a choice between paper and plastic bags, and also have drop-off points for store plastic bags. But only a few stores in Dallas have drop off points, and none (at least the affordable ones) offer paper bags. So, we try to take shopping baskets with us when we shop, or try to minimize plastic bags. Often when I say I don’t want a bag, the store attendants shrug incredulously but sometimes ask ”no bags?”, as if to ask if we plan to teleport the groceries. But today, when I said we’d like to put stuff in our own shopping basket, the cashier looked at them for the first time and said “Oh sorry, I thought they were your laundry baskets”, and burst out laughing. Clearly, there couldn’t be a funnier sight in town.

The hardest part of living in Dallas though is that the city is not built for people who like to walk. The pavements are bad, most people in their cars don’t notice pedestrians, and pedestrians are a rarity in most streets (bicycles are an even rarer species). I’ve often wanted to walk the 3 miles to work (on days when the weather is reasonable), but the streets aren’t particularly safe after dark, there isn’t any one else walking (except some homeless people), and at every third intersection the pavement disappears into the street.

Living the green life in Dallas sure is challenging. It’s almost as if every possible obstacle has been placed in your way, and it just might be easier for me to train and run next year’s city marathon.

But what’s life, if it isn’t challenging.

Wednesday, December 19, 2007

Newsmaker of the year: Rajendra Pachauri

Nature has announced its newsmaker of the year. It is Rajendra “Pachy” Pachauri.

For those of you who ask “Rajendra who?”, he’s the chair of the Intergovernmental Panel on Climate Change, and the director of The Energy and Resources Institute (formerly Tata Energy and Resources Institute). The IPCC shared this years Nobel peach…uh…peace prize with the Goracle.

His profile in Nature is both entertaining and inspiring (particularly for Indian scientists, who should read the bit about his work ethic). From a slightly controversial selection, to being called a “feet dragger” or worse, Pachauri systematically overcame all critics and helped the IPCC forge ahead with its findings and getting global leaders to agree on something.

“On his way to collect his own medal, Gore stopped to shake Pachauri warmly by the hand. Patchy and Al, as they call each other, get along famously. It is all a far cry from the situation in 2002, when Pachauri beat Gore's favoured candidate to run the IPCC in a bitterly fought contest. Immediately afterwards, Gore lambasted Pachauri in the pages of The New York Times as the “let's drag our feet candidate”, a patsy put in place to weaken the IPCC as one of various “acts of sabotage” by the new Bush administration. Pachauri had fought back with a letter of his own to the Times . “In a 1991 speech, Mr Gore [referred] to my 'commitment', 'vision' and 'dedication' … Will the real Al Gore please stand up?”

You can read the entire profile here, on the Nature website. It is an excellent article to read.

(And if Nature decides this is subscription only, and you want to read it, send me an email and I’ll send you a pdf)

Monday, December 17, 2007

If this story sounds familiar.... many of you, it will probably be because you’ve seen or experienced something exactly like this.

Here’s the story, and you just might be able to replace the situation and the people without changing a single incident.

The wife goes down to her alma mater for the graduation ceremony of some of her friends. Now, graduation ceremonies are a rather grand celebratory affair, especially when someone is getting the doctoral “hood”. Two of her friends were being hooded, and so she was given the job of being their official photographer and cheerleader.

Like almost everyone else, she was at the auditorium early, and quietly seated herself at the back, where there was seating. When it was close to the time her friend was going to be hooded, she quietly went up (going unobtrusively from the side), found a corner where she could stand without disturbing anyone to take a picture, and got her camera out. The American couple who were seated besides her (likely waiting for their son or daughter to graduate) saw her, and asked if she’d like to come to their spot in order to get a better picture. Everything was as it should be, joyous and celebratory.

And then these two Indian students walked, or should I say, swaggered into the front aisle without a care in the world. While every one was perfectly well behaved, these two behaved as if they ruled the world. They walked right up, obstructing as many views as humanly possible, all while talking happily. One guy whips out a camera, and stands akimbo right in the middle of the stage taking a picture. They decide to stand right there and turn back and wave or call out to their friend (who was walking up on stage). You know…..the “hey, look here, we’re here” kind of voice that was hardly congratulatory. While this was going on, and everyone else in the hall was getting pissed off, one of their cell phones rang (with a suitably colorful ringtone). Instead of switching the damn thing off, he turns back, grins and says “sorry, bad timing” and continues, incredibly, to click pictures without shutting off that phone, even as some of the audience looked at him in disbelief. This, right after a clear message from the organizers requesting the audience to shut off their cellphones. Now, to top things, after clicking the pictures he wanted, he proceeds to whip out his (still ringing) phone and yell “do minute me phone karna, main thoda busy hoon” (call me after two minutes, I’m a little busy right now). Two minutes later, almost on cue, the phone rings again! This time, an American gentleman sitting in front couldn’t take it any more, and asks this guy to take it outside, which he reluctantly does, talking away on his phone as he’s leaving the hall.

Meanwhile, my wife gets ready to quietly take her friend’s picture. Just as she’s about to take a short video, this same guy and his friend walk right back in, and stand right in front of her (as her friend is hooded), shutting off her view. She now has a delightful video of the back and head of this guy for posterity, with some of his running Hindi commentary to boot.

And this was hardly the only incident of the day, but a single sample from many such. Here’s yet another one. In the aisle behind where she and her friends were seated were yet another group of Indian students, talking away as if they owned this world (while all others in the audience were quietly seated, listening to the names being read out, and clapping politely). The all important topic of the discussion of this group of loudmouths was cameras. The conversation goes thus:

“Hey, check out my camera phone, it’s got 1 megapixel resolution”

“That’s nothing, mine’s got 3 megapixels. Shut up and smile.”

Few more loud words exchanged in a few Indian languages.

Click. Click. What fun.

The wife was understandably furious with all of this, and was talking to her friends at the end of the day (two of them were European, the other Canadian). Since she had initiated the discussion, the others said they didn’t want to say this in her presence, but in numerous public places (from places on campus to airports or restaurants) they had all experienced some extremely boorish or downright rude behavior from Indians. Most times they were too stunned to respond (I’ll avoid details here).

This is hardly surprising to most of us. Anyone who has gone to a movie hall screening an Indian movie, or an Indian concert, must have experienced this and much more. Cell phones ring constantly. Kids run berserk, yelling at the top of their voices as their parents let them be, oblivious to the disturbed crowd around them. Conversations continue in loud voices (talking is bad enough, but if you have to, whisper). People stand up and obstruct everyone’s view of the stage/screen, without a care in the world, and certainly don’t put in any effort to get out of the way. Others answer loudly ringing cell phones and engage in long, loud conversations within earshot of everyone else. Still others don’t bother to stand in line, but walk right up to the front of the counter without even acknowledging the existence of others in line, or jostle for space using painfully bony elbows. An endless list.

I’ve been reluctant to admit it (or usually have been defensive about it when some non-Indian friends bring it up), but I think, after viewing a rather large sample size, I’m compelled to say that we’re a country of rude, inconsiderate boors. And unfortunately, most of us haven’t even heard of the saying “when in Rome, do as the Romans do”, and don’t behave as well as most American audiences would.

And it doesn’t matter who you are or what you do or how much money you have.

It NEVER hurts to be polite and considerate.

Saturday, December 08, 2007

Ethics, plagiarism, eTBLAST and déjà vu

(It has been an eventful week, with moving apartments and lots of boxes to pack and unpack, but there are some interesting blog posts stored in my mind, and they’ll be up as soon as I get typing)

Abi and other Indian researchers have written extensively about a couple of cases of plagiarism in research from India over the past year or so. There have been two major recent examples of what can only be called blatant and unacceptable cases of plagiarism, which have rightfully been panned by Abi and many others.

But here’s the thing which perhaps hasn’t been discussed enough. Sure, there have been a few researchers who resort to plagiarism or make dubious ethical decisions to steal research or duplicate their own work and present it as different work. But at a larger scale, within the broader education system, there is no understanding or even recognition that this is a problem, nor is there any effort to educate all students about ethics, plagiarism and the importance of citing one’s sources.

The simple concept of citing references should start at a very early stage, in junior school or middle school. I recall numerous science, history and geography projects that we did starting late in junior school. The charts and reports were always something I looked forward doing, and for projects in my 9th and 10th grade, I spent many wonderful hours in the library of the Indian Institute of World culture, looking up their terrific collection of history books. Thankfully, we had been told to cite our references by our history teacher, and I meticulously made a list of all my references and added that to a bibliography. But I remember many more examples from school and even college where students would come up with reports without a single reference, or in other cases copy large sections of text from textbooks or other sources, verbatim. They were never once told that they were wrong, and that was unacceptable. In one instance, for a social studies class project, a teacher proudly announced to the class that one such project was “outstanding” and “beautifully written” (a comment more pertinent to this student’s elegant artwork and layout, but nothing about the content). This project was copied out faithfully from a textbook, which wasn’t even cited in the non-existent reference/bibliography section. In stark contrast, when I moved to the States some years ago, I was pleasantly surprised when I found that most school kids here were required to cite their sources in their class projects and essays. The lackadaisical approach towards ethics in research often continues through college in India, and the student learns of citing resources or ethical issues only when he/she is a graduate student, or in some cases never at all. I’ve hardly been surprised to find some international students here in the States (this malady isn’t restricted to India, but may be widespread across parts of Asia or Africa) who aren’t exactly sure what is acceptable and what is not. There is an urgent need to educate educators in India, and make an ethics and plagiarism course a serious part of the curriculum at least in the freshman/sophomore years of college. (And when I say serious, I mean that if a person “flunks” this course, that person should not be allowed to progress to the next year in college).

Blogging on Peer-Reviewed Research
That said, here’s an interesting second part of this post. A month or so ago, Dr. Harold “Skip” Garner, a researcher here, talked about some of his latest research. He, amongst other things, is a bioinformaticist, and his group came up with the eTBLAST resource. Now, most of us researchers are used to searching for other researchers’ work using databases such as PubMed and SciFinder. What these do is allow us to find research publications or resources typically by topic or author. But eTBLAST is a more sophisticated tool since it is capable of searching large sections of text. So, let us say you put in an entire summary of a research paper, and you want to find more research similar to this entire topic, eTBLAST in its results section spits out a list of researchers/authors who have worked on topics similar to what you have queried, with a listing of the details of the work/publications (if it isn’t all clear to you, give it a try here). This allows the user to do a number of things. It allows the user to identify leading researchers in a certain area, or identify the most appropriate journals for a particular type of research. It is popular now with journal editors or grant funding agencies to identify appropriate reviewers for papers or grants. In short, if used well, this can be an extremely powerful tool for bibliographical data mining.

Skip and his team built eTBLAST primarily for this purpose, but found that eTBLAST had a potentially very useful “side effect”. It turns out that his tool was extremely good at finding duplicate citations.

Yup, this tool is extremely useful in finding published work which are very close replicates of already existing published work.

Skip and his team used a sample of about 60000 citations that they drew from Medline, and used eTBLAST to analyze them. What they found were a couple of dozen cases of citations with no shared authors, i.e. cases which were very likely to have been completely plagiarized. Some of the examples Skip gave were hilarious, with one particular example that had me in splits. There was this researcher in England (and I couldn’t help but thinking that his name seemed suspiciously of subcontinental or middle-eastern origin) who had published a paper, and then decided that this paper was so good that he would publish the entire thing again, practically verbatim, in a different journal. What’s more, not satisfied by this he published this paper yet again, an incredible third time, without changing much more than a few numbers, in a third journal! He must think his work is so good that it need to be published the same way three times. In addition to these examples, there were many hundreds of cases where the same author had published “very similar work” in different journals, without having bothered to change the text, title or references too much.

The utility of eTBLAST was incredibly apparent in this live demonstration that Skip put together. I’m just hoping that along with an increasing awareness of ethics in research, there will be more such tools that not only help research and bibliographical mining, but also can be used effectively to find and expose these “researchers”.

The details of using eTBLAST to find duplicate citations have now been described in an excellent publication in Bioinformatics. Here’s the link to the research paper from Skip’s group in Bioinformatics, titled Déjà vu – A Study of Duplicate Citations in Medline. This second link is to the aptly titled Déjà vu database, a “repository of duplicate citations” from numerous databases.

Wednesday, November 28, 2007

Desserts and places

I’ve been on a constant eating binge since Diwali, a couple of weeks ago (and that’s a reason for not blogging much. Honestly). This thanksgiving was spent consuming unimaginably large quantities of food, with tons of sweets and desserts thrown in. And somewhere over the past few weeks, we drove by the little Czech town of West, Texas, and gorged on their famous kolache (which were rather good, I must add) (note: kolache itself is a plural word, so “kolaches” would be incorrect, though people popularly use kolaches as a plural for kolac). That, and a visit to one of the large Indian sweet stores here somehow led to a discussion on Indian sweets, and places in India that were famous for their sweets.

The insatiable sweet and dessert gourmand in me was delighted with the travels through Indian dessert land.

As far as Mysore pak goes, the name automatically and correctly suggests Mysore as the origin, and there are terrific Mysore paks to be had there, but I would argue that they can be just as good in Bangalore, or in Coimbatore’s Sri Krishna sweets. But there’s another uniquely Kannadiga sweet called Chiroti, flakey, layered and ideally eaten soaked in almond-milk. Bangalore and Mysore rule for this.

When it came to the delicious, milky peda, we were evenly split on our verdict. I’m partial to the tiny, dark Dharwad pedas that melt in the mouth, but the strong claim to supremacy from Mathura’s pedas could not be easily brushed aside.

Some sweets are almost synonymous with towns or cities in India. Apart from the just mentioned Mysore pak, there are the super-saccharine pethas from Agra (which I never really fancied). The little town of Tirunelvelli in Tamil Nadu is probably best known for its unique halva, quite different from the more common types of halva (such as those made out of semolina or carrots) found across India. Laddus (ladoos) are perhaps the most popular sweet across India. While I don’t particularly fancy them, the laddus from Tirupathi have made it to song and legend. On the other hand, a trip to Uttar Pradesh just to sample my favorite mothichur laddos there is long overdue. Some day I hope to complete a UP-laddu pilgrimage, starting at Haridwar, and steadily working my way across UP, through Muzafarnagar, Lucknow and finally to Kanpur’s Thaggu ke laddu.

While still in UP, I’ve been told by authoritative sources that the best gulab jamuns in the world are to be found in a little Podunk town in UP called Orai. In fact, as far as I can tell, this is the only claim to fame of this town, at least according to the omniscient wikipedia.

Sweet sojourns in India cannot be complete without indulging in Bengali sweets. There are two things that remain etched in my memory from numerous childhood visits to Calcutta (Kolkata); incredibly slow trams, and absolutely delicious varieties of Sandesh. And if you want to really go off the beaten Indian dessert track, go to Hyderabad and eat the absolutely sublime double ka meetha.

For some classic Indian sweets, we were hard pressed to say if some places were better known for them than others. I’ve had terrific jalebis in many places, as well as their South Indian counterparts, jangris, and cannot think of any place that can stake a claim on them. There are special types of kheer that each region claims to make better than others. And while the best Shrikhand I’ve had was in Pune, I’m sure a good chunk of Maharashtra and Gujarat will claim to make better Shrikhand.

I’m many of you guys have favorite desserts not just from India, but from across the world (a Florentine colleague told me Fritelle di riso was to die for, so I made it a point to eat some when I visited Florence some years ago).

Go ahead, educate me so that we can plan our next dream holiday accordingly.

Wednesday, November 21, 2007

Animate this!

It almost seems unreal, but the first presentation I saw that was done completely on PowerPoint was only about seven years ago. Before that, almost all talks I heard used a combination of overheads (with the old fashioned transparency on an overhead projector, sometimes with a few impromptu scribbles along the way) and slides (and an old fashioned slide projector). But we were mesmerized by the power of the PowerPoint dark magic and the neat little graphic animations. At the time my unequivocal opinion was that PowerPoint was the most advanced and sophisticated tool ever created to enable effective presentations.

Of course, like most things, perspectives change over time.

While I haven’t quite classified PowerPoint presentations as the great evil, I’m slowly coming around to the point that PowerPoint, in most hands, can do more to damage talks than to enhance them. It has taken time, but by closely observing the really good speakers and their presentations and trying to learn from them, I’ve put together some thoughts on the pitfalls of PowerPoint, and what needs to be done or avoided in giving good thoughts (putting them to practice seems to be a completely different ball game though).

Perhaps because of the ease of making slides due to PowerPoint, many of us have forgotten what talks are all about. There is an auditory component in talks, and there is the visual component. Striking a balance between the two is essential. But what PowerPoint seduces us to do is to go overboard on the visual component. This means it is easy to overload the slide with data or words or to throw in too many bells and whistles. I remember a couple of occasions when I (shamefully) “winged” through some journal club style presentations, because I thought I could easily create some slides with a lot of verbal and visual content which I could use as a crutch to work through the talk. This ability to put a lot on the slide can easily allow laziness to creep in, and by not planning through the talk well enough, one becomes too reliant on what is on those slides. Almost always, the talk suffers, since you haven’t done enough homework on the content, or have put in so much information on the slides that the audience zones out due to a visual overload.

The second thing PowerPoint does (which sometimes takes a while to undo) is make you create slides that dictate the content of the talk. Instead of planning a careful outline of the talk, and systematically outlining the flow of the talk in your head, one might easily succumb to the temptation of making slides on the go. Traditionally, one would sit down and carefully outline all parts of the talk (usually on paper or a document), but the very ease of making and deleting slides might make you avoid that. Interestingly, PowerPoint does have an “outline” option which most of us don’t use but probably should.

Sometimes, when you make a really neat presentation with plenty of nice bells and whistles or cool pictures, you are tempted to use it no matter what, and end up recycling too many slides regardless of the audience. This goes back to the previous point of not planning through your talk well enough, which goes back to the ease of making slides (or reusing old slides) on the go. Sure, a lot of this comes from laziness, but hey, aren’t we all lazy?

Powerpoint also seems to take away the dynamic nature of talks. Talks are very personal, and the nature of the speaker really dictates the quality of the talks. But if the audience is forced to stare only at a large white screen and visually overloaded PowerPoint slides, the dynamism of the speaker and the interactions of the speaker with the audience are often lost. Also, if the speaker has this “eureka” moment during a talk, or thinks of something connected to his/her talk; it is really hard to incorporate that into the talk easily, since the slides dictate the content of the talk. Unfortunately, most lecture halls have lost the overhead projector, screen and transparency (which can so easily and effectively be used to illustrate a point or a tangential thought during a presentation). It’s a pity, since some of the very best talks I’ve attended were by speakers who almost completely used transparencies (with some writing and illustrations thrown in during the talk) while presenting their own thoughts very clearly in their words. The big screen with the PowerPoint slides also sometimes tempts the speaker (I’m certainly guilty of this) to hide behind the slides, as opposed to stepping up and making the talk his or hers, using the slides only to illustrate the point.

So essentially the effort has to be made by the speaker to use PowerPoint effectively to communicate with the audience, and that fact should never be forgotten. This starts with making a good outline of the presentation, and using dynamic headings on the slide (making statements, instead of stating detailed facts in the titles). Illustrations with fewer words whenever possible make life much easier for an audience (a picture does speak a thousand words, usually without putting the audience to sleep). But finally, the presentation must be made personal and about you. Every conscious effort needs to be made to avoid making the presentation glossy-generic (which PowerPoint almost automatically does). Presentations should be about standing and delivering, and avoiding the crutch of slides whenever it can be avoided. And every possible effort should be made to avoid slipping into slide mediocrity, and forgetting the fact that presentations are about the speaker communicating with an audience.

Have a good thanksgiving all, and pitch in with your opinions about the evil magic slide maker TM.

Thursday, November 15, 2007

Mirror neurons, phantom limbs and the Capgras delusion

I first heard about phantom limbs in a journal club some three years ago. I don’t know any amputees or people who have lost their limbs, so when I heard that a very large percentage of amputees experienced “phantom limbs” I was more than surprised. If a limb is amputated, it is gone, finis. But apparently many amputees can still feel their amputated limb moving. What is more, this is accompanied often by excruciating pain which they cannot control. Even more bizarre is the Capgras delusion, which is something practically taken out of Bollywood movies, except it is imaginary. Here, the person with Capgras delusion absolutely believes that some acquaintance (a friend or family member, say) has been replaced by an identical looking impostor. To the delusional patient, the impostor looks the same, sounds the same, feels the same, but is an impostor!

V. Ramachandran, at the center for brain and cognition at UCSD is one of the pioneer researchers of these phenomena. Almost more importantly, he is an engaging, eloquent and charismatic speaker. Not long ago, he gave a talk at TED, which is more than well worth your time.

Take 20 minutes off whatever you are doing, and enjoy the talk. (If the video doesn't work from the browser, you can view and download it here).

Monday, November 05, 2007

Where’s the science section?

A small, unexpected windfall in the form of a gift card made us go down to the nearest Barnes & Nobles bookstore for some bookshopping. It has been a while since I visited a large bookstore. While in Seattle, I’d always walk down to any one of the half dozen used bookstores all around campus, and delight in browsing through their collections amidst the irresistible aroma of old books. But once I moved to Dallas even that became a novelty, since there aren’t too many used bookstores around in these parts. Anyway, I do most of my bookshopping online, thanks to the wonderful choice of Amazon,, Abebooks and the likes. Essentially, it had been years since I had last stepped into a large bookstore like Barnes & Nobles.

So a good hour or more was spent browsing through the collections at Barnes & Nobles. There were impressive fiction and non-fiction sections and aisle after aisle of the latest bestsellers. There was an excellent section on history, from US through world history, and there were also excellent collections of books on travel and places. The religion section was, not unexpectedly, massive. There were three full aisles for bibles alone, and four or five more aisles for all sorts of books on religion (mostly Christianity). Clearly, the demand for such fiction knows no bounds here.

But I was looking for the science section. So I searched and I searched, and finally found it. There it was, one single shelf, tucked in between “oversize books” and “atlases”, with a tiny collection of books, most of which were on astronomy (stargazing, actually). I couldn’t believe that was it, so looked around some more, and finally found two more shelves, one with books on physics, and another shelf with books on chemistry and biology combined. In the biology section was a pitifully small collection of books, a couple on Darwin, three of Richard Dawkins’ books, and Michael Behe’s “Edge of Evolution”, which should rightly have been in the speculative fiction section and not in the science/biology section.

That was it. A whole massive bookstore with a gazillion books, and three small shelves devoted to all of science. If that isn’t disappointing, tell me what is.

I managed to pick up Bill Bryson’s “A short history of nearly everything”, which has been on my reading list for two years now, as well as a nice book (with superb pictures) on lost cities (great metropolises of the past that lie in ruin today) as what claims to be “the 30 best drinking games from around the world”, and all of this left me reasonably satisfied.

But talk about slender pickings! Sticking to Amazon might just seem better. I wonder if the store collections are similar across the country, or if different regions have slightly different collections, reflecting the demand and tastes of local readers?

Sunday, October 28, 2007

Walking with dinosaurs

When I moved to Texas, I did so with trepidation. I was used to the welcoming, green outdoors of the Pacific Northwest, and spending many summer weekends enjoying the crisp air of the North Cascades or the Olympic rainforest, walking on soft pine needles. So the extreme harshness of the Texas climate, which rarely says “come out and play” didn’t appeal too much to me.

That said though, I found that Texas has a range of natural terrains and wildlife, from complete, arid desert to rolling hills with rivers and lush forests. And what’s more, some of them are surprisingly close to the Dallas-Fortworth urban sprawl. A week ago, we spent a day in one of these often overlooked jewels just a stones throw from Dallas, the Dinosaur valley state park, where some of the world’s finest collections of dinosaur fossils, prints and tracks had been discovered.

When we reached the park, the tiny visitor center disappointed me, but only for a moment. The little display room was surprisingly superbly informative. I knew that a long time ago, the region that is now the gulf coast was part of the ocean. But I didn’t realize that what is today Dallas (and hundreds of miles from the coast) was once part of a large, shallow sea, or lagoon. Now fossils usually are hard to find, and it is even harder to find prints or tracks left behind millions of years ago. The tracks found in this park were mostly made about 150 million years ago, in the Cretaceous era. The majority of the tracks found here belong to two different types of dinosaurs, three-toed meat eating theropods called Acrocanthosaurus, and huge prints of giant sauropod herbivores called Pleurocoelus. Interestingly, outside the park visitor center are life-size sculptures of the more celluloid friendly Tyrannosaurus rex and the giant brontosaurus. A serendipitous combination of soil and rock compositions of the region and climate allowed the prints of the dinosaurs to be preserved. Limestone, sandstone and mudstone gradually deposited in the region, where the theropods and sauropods perhaps migrated through, or came for food or prey. They left their prints on this limey mud, which was gently covered up by different sediment. Millions of years later, the Plauxy river (a tributary of the Brazos) flowed by, and slowly disloged some of the other sediment, revealing the dinosaur tracks for all of us to see, while other tracks were found later, by human excavation.

The visitor center nicely explained how these tracks were formed, how they were discovered, and also outlined the various timelines as well as a description of the formation of continents from pangea through gondwana to present times. In addition, the visitor center described the geology of the region, and the types of fossils found in the region, including those of ancient marine life. All of this should be a part of all school curricula in geography and natural history, but unfortunately, I don’t think much of this is taught anymore. At least, some of the visitors there (particularly the kids) seemed surprised to read this. It seems like a huge amount of irreparable damage has been done by the Flintstones, misinformative Hollywood movies and persuasive religious brainwashing.

The “fall” weather was perfect for the park, since after a long summer the river was just a gentle stream. Most of the dinosaur tracks were found along the river, and the shallow water meant that we could see the prints beautifully through the slightly muddy water (though I don’t know how good my photography skills are in that shot). The water in the rivers deepest point was at best waist high, so it meant the setting was perfect for splashing about in, or standing perfectly still to watch curious tadpoles nibble your toes. Along the bank of the river, you can look at both the sauropod and theropod tracks, as well as a few points where the tail drag of a sauropod has been preserved. While looking at a print in a photograph hardly inspires awe, staring at a real footprint many times the size of my oversized, ugly feet was more than sufficient to put things in perspective. I’m pretty glad humans weren’t around when the dinosaurs were. I’ve seen elephant dung, and if these beasts produced ten times that amount in a single sitting, I don’t even want to imagine how the Cretaceous era must have smelt. Of course, there’s also the possibility of mistaking a little hole in the soil as a dinosaur track. But the little pamphlets at eh visitor center explain how to distinguish them, and once you see the real tracks, it is easy to distinguish them from natural erosion, with the clear absence of any distinct features. There’s some nice hiking to be done in the park as well, and if you’re lucky you might catch a glimpse of some of the endemic birds of this region as you walk on trails along the river or on the little wooded limestone hills. I also stumbled upon some gorgeous lizards along the trail that were so well camouflaged amongst the rocks that I would never have spotted them had they not been startled and run for their lives.

Last and certainly the least, being in Texas, it was hardly surprising that a few miles before the state park itself there was a little “creation evidence museum”. Here's a picture of it, that little building no bigger than a little barn, without a single car in the vast parking lot. I’m sure the devil came by one night and planted the fossils and prints all over the park, along with traces of marine creatures, not to mention the limestone soil itself, to fool us all into thinking this region was underwater centuries ago.

Thursday, October 18, 2007

Book review: Textures of time: Writing History in South India

(Apologies for being a bit irregular on the posts. Work has been rather busy the past week, but things are back to normal now)

As an avid amateur historian, reading about the history of kingdoms and cultures (and their influences on religion) has been a long standing hobby of mine. So my interest was more than piqued when I obtained a copy of Textures of time: Writing history in South India 1600-1800.

The main focus of the book is rather novel. It has been postulated often, by numerous historians, that India did not have a tradition of recording and preserving history. It has been said that history in India is a mixture of fact, legend, myth and popular belief. The Arab polymath, Al-Biruni, observed way back in the 10th century that “the Hindus did not pay much attention to the historical order of things.”

A substantial section of historians conclude that a historiographical tradition came to India with the Europeans coming and establishing themselves in India. It was they who brought with them the dry, “factual” style of recording history. This assertion usually crumbles under the mountain of historiographical literature the Delhi sultans, and subsequently the Mughals and their feudal nobles left behind. But two questions immediately raise themselves; the first being that perhaps the Indian historiographical traditions were borrowed from the well developed Persian and Turkish systems of recording history, and two, what about South India? Did the literary traditions of South India not have a historiographical tradition at all, but only had facts blended into stories and myths.

The authors of this book, Velcheru Narayana Rao, David Shulman and Sanjay Subrahmanyam, decide to investigate this assertion, and also see if they could bridge the somewhat artificial divide between “Hindu” and “Muslim” writing, by digging into a vast collection of resources from the 16th to the 18th century. They draw on primarily Telugu sources, along with a collection of Tamizh, Sanskrit, Marathi, Kannada and other sources of the time. Using an approach where the authors combine story-telling (of events from those times) with a systematic and rigorous analysis of those works, the authors steadily set about disproving that hypothesis.

For their material, the authors draw upon various court writings by scribes in the courts of various rulers; the songs and works of ballads and poets of the times, folk epics, as well as prose narratives of the time. Early on in the book, the authors point out that any choice of genre for writing history isn’t a constant, but has changed over time, as the society changes its preferred literary style. So, over time, a historical work ends up becoming a “literary work”. In the course of the book, as they explore four major historical incidents between the 16th and 18th century, based in what is today Andhra Pradesh and Northern Tamil Nadu, the authors subtly but elegantly point out that any history is invariantly written in the dominant literary genre of a particular community at that particular time (something that is quite intuitive, yet overlooked). For example, if puraana is the dominant literary form of the time, history would be written in puraana style, or kaavya style when kaavya is the dominant literary style. Obviously, this means that in any style, you will find both history and literature, and the trick is in distinguishing the two. But there are definite textual markers, syntax and expression styles, metrical devices and other indicators that distinguish literature from history. It is these that the authors try to distinguish and point out through the book.

The key question is how can they distinguish historical work from non-historical texts. The authors say that the answer lies in adopting a new way of reading the text. The “texture” of historical writing is substantially different from literature, though the style used may be the same. Part of the reason that this difference has been lost is because, to modern historians, the context has often been lost. In any story, the relation between the teller of the tale and the audience is of paramount importance. But if their connection is displaced, confusion is but inevitable. Literary traditions are easily broken, particularly when the audience for that text is “fragile”.

In this book, the authors explore stories which many of us would consider lesser-known, yet were well known (at least in South India) at the time. The major incidents explored in this book were recorded by numerous writers of the time (or even a little later) in the karanam style. Karanams were primarily accountants or court scribes of the time, and the authors describe their collective style of writing as the “karanam” style. Karanam scribes had been well established all across Telugu lands for centuries, and there exists a vast mountain of their recordings, from before the time of the Vijayanagara empire, and their traditions continued to evolve and develop long after Vijayanagara had fallen.

The authors start with the battle of Bobbili (which took place in 1757), of which detailed recordings and folk ballads were composed in Telugu. It essentially was a battle between two small-time warrior velama kings (who were both technically under the rule of the Nizam of Hyderabad). One of them decides to usurp the lands of the other (the “valiant” ruler of Bobbili, Pedda Bobbili Raju), and does so using the help of a confused, clueless French general, Bussey. The beauty of this tale is that it had distinct chronicles written by various sides; the admirers of the Bobbili Raju, or the rival treacherous king of Vijayanagaram (later Vizianagaram, and not to be confused with the earlier Vijayanagara empire).

In all these chronicles, while the characters may be described in different hues, and the valor or cowardice of one character might be exaggerated or diminished, the major facts of the story remain remarkably consistent. What’s more, the “dry, historical” recordings of a few English of French sources who were present match exquisitely with the facts in the Telugu sources. Similarly, later the authors explore the tale of the Desingu raja, in Senji, in the Arcot region of (present) Tamil Nadu. This minor chief rose up agains his lord, the Nawab of Arcot. Here too diverse sources, from karanams to folk singers, to Jaswant Rai, who chronicled history for the Nawab of Arcot, have remarkably consistent details. Jaswant Rai was a munshi, the north Indian equivalent of a karanam, who chronicled the life of the then Nawab of Arcot (who fought the king of Senji fort). As the authors take us through these (in themselves fascinating) tales, they consistently point out aspects of the narrative that shift from fact to fiction and to eulogy. The distinctions are subtle, but clearly consistent and significant.

By the end of the book, you are certainly convinced that there was a historiographical tradition in South India, which was very mature long before the establishment of European presence in India. However, like most academic books, this one too left me with many thoughts.

One question that immediately comes up is that a main intention of this book was to show a substantial and well developed histographical tradition in South India that was thriving before the establishment of European colonial rule in India. So, would the earlier literary and historical traditions of the preceding South Indian empires (Vijayanagara, the Kakatiyas, the Pallavas, Cholas, Chalukyas etc) not be a better choice of material to show this? Those sources distinctly preceded the arrival of the Europeans, and were possibly less influenced by Mughal, Persian or Turkish histographical traditions as well. A related but obvious question would be to ask how well developed the historiographical traditions of those times were in South India. Could Al-biruni have been right, and did even the karanam style develop after the Mughals came to India? How different was the style of recording history in the 8th century versus the 16th?

A particularly interesting question would be to ask if there were similarities in the style of writing of Indian muslim writers (who went beyond the traditional Persian style of historiography) and other Hindu writers (of the karanam tradition). How much did each influence the other’s style? Was there an effort made by writers of each style to remain true to their chosen literary styles, or was there a strong influence of each style, and co-evolution? After all, by the 16th century, at least the northern parts of South India were strongly under the influence of the Mughals or the Dakkani sultans etc.

Of course, as the old saying goes, “history is written by the victors.” Even the most hardened skeptic will agree to some truth in that saying. The authors perhaps expect only South Asian historians to read this book, and therefore much of the book remains only of academic interest for the hardcore historian. But their engaging writing style, and admirable choice of thoroughly entertaining ballads and stories with which to make their points, actually makes the book rather readable. Through their systematic and nuanced analysis the authors go a long way in demolishing the idea that there was no concept of recording history in South India.

(Crossposted from Desicritics)

Thursday, October 04, 2007

Gaping dorks in vendor shows

All major campuses around the country have major product/vendor shows every few months. Here companies big and small, from Invitrogen and Sigma to little-unknown-biotech all have their tables and flyers and product displays of the latest and best in lab technology.

But what's hilarious is that most of us scientists are such loser dorks that what attracts us most to the displays aren't super-efficient pipette displays, but bouncy stress relieving squeeze balls, fluorescent orange pens, permanent markers that have caps and tips on both ends, and the lure of the odd T-shirt. We're like kids in a candy store.

That, and the attraction of free food. Nothing can bring together a bunch of graduate students and postdocs better than tables filled with donuts, cookies, bagels or more.

There I was, bright and early this morning, lining up to collect my supply of utterly useless items, and gawk at freebies. I ended up with about a dozen pens, a floaty for eppendorf tubes, a weird box to keep "suff" in, and a T-shirt (yes! I will advertise anything for free).

And then there was the highlight of my day. I got the most fascinating freebie of them all, a ball point pen that has a transparent liquid gel at the other end, filled with little floating balls, and a little on-off switch that turns on an led that changes colors.

Life couldn't be better.

Friday, September 28, 2007

The value of failure

It is an interesting life being a postdoc. One big difference from being a graduate student is that you do start to look at life in science a little differently. Contrary to what many people accuse me of having, life as a postdoc isn’t all fun and games, and there are plenty of stresses to cope with. Sure, you have a PhD and aren’t worried about graduation, but there are plenty of other things to worry about. The postdoc time is supposed to be that transition towards a “real job”, and while it used to be a road taken only for people interested in a future in academia, it no longer is so. The past two decades have seen a surge in science spending and growth in departments across universities, but more recent numbers are depressing. While the numbers of postdocs have increased many fold, the number of faculty positions haven’t. So, there are far fewer jobs that a postdoc has to compete for in universities. This leaves industry and startups (small biotech companies) as options for many of us.

Which brings us to the point of this post. Now, particularly in these ultra competitive times, a postdoc requires a substantial amount of high profile work in order to get that coveted faculty appointment. “High profile” can mean a couple of things; the first is work in an extremely “hot” field of research. Something like stem cells (and if you can throw in some more hot topics there, like micro RNA expression regulating ubiquitination that in turn controls histone methylases, all of which controls cell fate, then you are golden). But these areas are obviously ultracompetitive, and often become “hot” when the field has matured a little bit. So, if you enter it at the top of the wave, you are most likely to have to compete with too many people in the field, and may not be able to carve out a successful academic career. However, working in “hot” fields do sometimes give the postdoc the (illusionary) security of believing that even if her work isn’t pathbreaking, a couple of solid publications and mastering of some techniques will be sufficient to land a job in industry.

But there is a second road some postdocs choose to take (and I like to think of myself as one of them), to work on extremely challenging projects that ask questions that aren’t in the mainstream. In this case, all the experimental tools needed may not exist (or may exist but will have to be adapted from something else), but more importantly, the “field” itself does not really exist. The hope is that the hypothesis turns out to be correct, and you will make a discovery that will open up new areas of science. Perhaps this could be described as vertical as opposed to horizontal or incremental research. The problem lies in the possibility that the hypothesis could be completely wrong. Sometimes even if the hypothesis doesn’t hold up, the findings are modest and incremental enough to be publishable. Other times, it is all or nothing, and you could be left with absolutely nothing.

It is sometimes interesting to see how things work in industry. Sometimes with (say) startup companies, the people starting it up have a good idea(s), are extremely competent and take up significant challenges, but for various reasons the company does not take off, and eventually folds. Failure to make the company take off isn’t necessarily viewed negatively. Many people have failed in their attempts to start up companies, but are still highly valued by the industry for their experience and knowledge (of the process of building a company). They remain eminently employable and sometimes also desirable.

Unfortunately, I think life in academia may be a less rewarding for similar situations. Sometimes postdocs (or principal investigators) work incredibly hard on a potentially breakthrough hypothesis for years, only for the results to be unremarkable, or even go against the hypothesis (that could have resulted in a major breakthrough). Usually, you can predict that the person is in store for more hard times in the future, since the lack of any substantial publications means that there’s no chance of being offered a faculty position (or perhaps being denied tenure for a young investigator). It is also unlikely that this person would easily find an industry job, since jobs are relatively few, and industry itself has no clear metrics to measure you by (unlike failing in a biotech startup venture). The way things are set up presently, it is hard to impress someone by showing that you disproved a hypothesis. Most of the postdocs who decide to go down this road are pretty smart, technically competent, and think they can handle hard projects, hope they have some vision (in addition to the vision of their bosses), and are usually aware of the risks. But they are willing to spend the 3-4 years trying. If they fail, then they spend two more years doing something “safe”, which they usually are quite successful in doing, and so manage to get a job in industry after a painfully long postdoc.

So, just using this comparison with industry, can there be any ways to measure the value of a postdoc who has worked on some extremely risky projects which have failed? Is a postdoc who has worked on some extremely challenging projects (which haven’t worked) more or less valuable than a postdoc who has managed a couple of publications, but done so using well established methods and a well established system? Can risk takers become valuable in academia? After all, they’re extremely valuable to investigators who need postdocs willing to go after the most challenging ideas the investigator has, but how can that value carry over to the job market?

Wednesday, September 26, 2007

Sleep, the final frontier

Sleep is something (most of us) spend a third of our lives doing, though we hardly give it a second thought. Yet sleep is absolutely essential for all vertebrates, and if an animal is completely deprived of sleep, it will die. Rats that are sleep deprived die in a matter of days, and in the past, when it was still possible to do crazy human experiments, humans have been kept awake for as long as 72 hours, within which time they would descend into psychosis. The few human sleepless anomalies who exist remain with numerous mental and metabolic problems, and the reason why they remain alive are unanswered (warning: do not try to avoid sleeping completely for days on end in order to discover that you are a natural anomaly. You WILL die).

One of the most fascinating questions that still remains somewhat unanswered is “why did sleep evolve in animals”? Now, single celled organisms (like bacteria or yeast) don’t sleep. They continue to grow, and constantly divide at a certain rate. More interestingly, our own cells, when isolated and grown independently in culture, don’t “sleep”, but continue to divide and grow constantly. Sleep itself is a complex phenomenon with distinct physiological, neurological and psychological features. Evolutionarily, one could reason that it could even be advantageous for an animal to evolve to avoid sleeping completely. This would give that animal twice the amount of time needed to forage for food, or reproduce (compared to other competitors), and could even be considered a huge survival advantage. But that has not happened, suggesting that the evolutionary need for sleep is far greater than any benefit a lack of sleep could allow.

Sleep remains essential for all animals, and there remain a number of reasons why that could be so. One reason is that as organisms became more complex (and evolved into multicellular organisms from single celled ones), the need to adapt to a day-night cycle on earth became stronger. This is what’s known as the circadian clock. Much progress has been made in understanding the molecular mechanisms of the circadian clocks, and identifying master-regulators of this clock (like the clock, period and BMAL genes). The subsequent consequences on the cell cycle and metabolism are slowly being unraveled. Yet, the circadian clock does not answer the need for sleep (though understanding the clock allows us to understand many aspects of basic metabolism and growth), since some single cellular organisms that don’t “sleep”, like cyanobacteria, exhibit a robust circadian clock.

Other researchers look at sleep and the circadian clock itself from a metabolic perspective, and from the basic metabolic needs of the body. During sleep, some dramatic processes occur, starting with the basic metabolism of the animal, which shifts from catabolism (or breakdown of molecules, and the release of energy) to anabolism (the active consumption of energy, and subsequent growth and building). So, sleep is in some ways the opposite of a “resting state”, as energy is being consumed, in order to let the body grow or build or recover.

All these details are slowly being unraveled. Yet understanding the very fundamental question of “why we sleep, and how sleep evolved” remains one of the great unanswered questions of science. In a recent post, I described Dan Koshland’s concept of discovery; Charge, challenge and chance. Understanding the fundamental need for sleep, and the evolutionary reasons for it will remain one of the great science questions which will perhaps be answered by “charge”, or “challenge”.

Wednesday, September 19, 2007

Oh what a good time for miracles

I had spent a lifetime thinking the wonderfully superstitious and gullible folks back home in India held a monopoly on natural “miracles” in these modern times. What with people drinking sewage filled seawater that had turned sweet or wasting perfectly good and nutritious milk on Ganesha idols which lapped the milk up (and that is just a select sampling of wonderful “miracles” to pick from).

But nooooooooo, I couldn’t be more wrong. There are no geographical boundaries for gullible folks searching for that next miracle to happen, so that they can reinforce their irrationality and allow their ability to think to atrophy. I discovered that the land of free thinkers, the United States, has a long and proud tradition of miracles as well. In fact there is a veritable cornucopia of miracles here, happening all the time. From the virgin Mary on tortillas to the NunBun in Nashville, there’s a fine collection of miracles all around.

So I was hardly surprised when I read today’s Dallas Morning News, which proudly reported the story of the holy “weeping tree”, which is loaded with “supernatural ice”. Here’s the deal; an old woman dies, and is buried. Soon, a tree that belonged to her starts to collect yellowish-white froth, and bits of liquid started accumulating under the tree.

Family members said they noticed the yellow-tinted froth and the puddles of liquid around the trunk a day after they buried the 92-year-old matriarch…The tree has been "weeping" ever since, they say.

Here’s more; “her daughter, Mary Lou Sanders, said. "Where it's coming from, I do not know. It is something I cannot explain."

Sure, you can’t explain it, therefore it must be a bonafide miracle. And so the faithful flock towards it, in docile submission and hope for more miracles, like restoring the health of a wheelchair ridden child.

If it wasn't true, it would be so funny.

They kneel before it and pray. They stand, patiently extending their open palms or clutching Styrofoam cups with hopes of getting some of the "holy water" drops.

I’m sure that holy water tasted good. After all, it has a wonderfully miraculous source.

Insect spit.

Yup, bonafide insect drool produced by the infamous spittle bug. Or, to quote the Dallas morning news article:

“Not likely, say insect and tree experts who viewed photographs of the substance. They said the "miracle ice" is probably nothing more than a spittlebug nest.” link

Oh well, at least they weren’t drinking sea water. Not much seems to have changed since the dark ages, or so it seems.

(I might as well point towards a guest essay I had written for The Scian, titled The joy of questioning, for those of you who missed reading it earlier. It’s my futile effort to resist the relentless forces of ignorance).

Saturday, September 15, 2007

Charge, challenge, and chance

A few weeks ago, a giant in the world of science passed away. Daniel Koshland left behind a legacy in science. Daniel Koshland left his mark on many aspects of science. As a pioneering enzymologist, he proposed the “induced fit” model of protein-ligand interactions, which now forms one of the foundations of enzymology and most protein-ligand interaction studies. He also had a number of other outstanding discoveries in a long career as a pioneering biochemist, which won him many awards and honors.

In addition, he was perhaps the best known editor of the premier scientific journal Science, which he transformed from “a good journal” to one of the highest impact journals out there. Most scientists strive to publish their best work in Cell, Science or Nature.

Of course, I never knew Dr. Koshland, but my present boss did, and he had the greatest respect and regard for him. He once told us about one of his own major scientific breakthroughs in the late eighties/early nineties, which he had sent to Science and which the reviewers had rejected (the findings seemed too speculative and out of the mainstream for the time). Dan, who was the editor then, overruled the reviewers, published the paper anyway, and the reported findings were proven to be absolutely right, and my boss went on to do many wonderful things in his scientific life.

Anyway, just a couple of weeks before he died, he wrote a perspective in Science called The Cha-Cha-Cha Theory of Scientific Discovery (subscription may be required). In this, he insightfully categorizes scientific discoveries into three groups; charge, challenge and chance, that he calls the “cha-cha-cha” theory. He describes “charge” discoveries as those where the discovery itself is obvious (the movement of stars and gravity, the laws of heredity, causes of heart attacks), but the way to solve to problem, or describe how it happens, is not clear. Everyone has seen it, but the discovery is in thinking of something no one else has thought about. Challenge is where there is a slow accumulation of facts or concepts that don’t quite fit with the existing scientific ideas of the time. The classic example of this would be quantum mechanics, which went beyond classical Newtonian mechanics. Finally, chance discoveries are those that the “prepared mind” encounters. The classic examples here are X-rays or Penicillin.

This succinct group pretty much describes how almost all major discoveries are made. I thought this was a tremendous little article particularly for young scientists. From these examples, it is obvious that waiting around for chance discoveries is unlikely to lead to a great career in science. For that you need to be at the right place at the right time, and most times are not those times. But “charge” could define a majority of everyday science. Even for small findings, the scientist takes charge and attempts to find a solution to an already existing problem (however small it might be). So, the key is to keep working on problems that exist, and to constantly work towards new solutions or explanations for them. Along the way, there may be times when solutions to “challenge” problems might arise.

So far, some of my most enriching moments in science have come from reading or listening to thinkers like Koshland, who help put things in perspective, while simultaneously inspiring scores of scientists around them.

Some further reading/resources:
The nine lives of Daniel E. Koshland (Randy Schekman, subscription may be required).
Interviews with Daniel Koshland (audio).
Lasker award.
A retrospective of Koshland’s life in Science magazine.

Sunday, September 09, 2007

Mendel's garden at Balancing life

Welcome to the September 10, 2007 edition of Mendel's garden, and apologies for the late posting. Mendel's garden #18, hosted here at Balancing life. Mendel's garden is a blog carnival devoted to genetics, featuring some of the best science blogging focused on genetics, from the past month.

Speaking of Mendel, one of the "founding fathers" of modern genetics, too many people think Mendel was just a simple monk pottering about in his garden, where he accidentally observed the inheritance of traits in peas, from which the laws of inheritance (classical Mendelian genetics) were formed. Little could be farther from the truth. Mendel was a very well trained scientist, and systematically applied statistical methods (more typical of the physical science then) to biology. After his schooling (gymnasium) he went on to study for two years at the Philosophical Institute in Olmutz, as preparation for University. Since he was too poor to go on to University, he joined the monastry of St. Thomas in Brunn, and the abbot, an enlightened man who wanted to create an intellectual center at Brunn, strongly supported Mendel's research and education. He even sent Mendel to the University of Vienna to study for two years, where Mendel studied as much physics, statistics, probability, chemistry and biology as he could. His subsequent work with peas, which laid the foundations for the understanding of how attributes of parents are inherited by their offspring, took over seven years of meticulous research.

Anyway, that was a little aside. One with the carnival!

Larry Moran has an excellent post titled Identity of the Product of Mendel's Green Cotyledon Gene posted at Sandwalk.

Hsien-Hsien Lei, PhD takes some time off to visit the Wellcome collection exhibits, and writes about Genomes at the Wellcome Collection at Eye on DNA. This looks like a must see exhibit, if you are in the neighborhood.


I had a running joke with some of my friends in grad school (who used to study the wnt signaling pathway) that wnts were responsible for everything. Chris Patil now writes A hazy shade of Wnt over at Ouroboros.

Evolutionary genetics

CAD writes about Evolutionary Solutions to the Hairy Back Problem posted at VWXYNot?, mostly describing primarily evolutionary genetics, with a touch of development and gene expression! This post summarizes recent research that explicity links multiple microevolutionary changes to a novel morphology in the larvae of a Drosophila species."

Luigi Guarino has a few posts on iron, and writes a little more on iron at Agricultural Biodiversity Weblog> at the Agricultural Biodiversity Weblog, saying, "We've had a couple of posts on the human genetics of iron metabolism and the role of agricultural biodiversity in fighting iron malnutrition"

RPM has an excellent post titled "Promoting Intelligence" over at evolgen, describing promoter differences between humans and chimps which reveal that brain genes and nutrition genes may have changes in expression.

Gene expression

Eric Michael Johnson has a well written post called Shamanic Visions of Selective Sweep at The Primate Diaries where he discusses the evolution of schizophrenia and the nature of contingency.

Fun stuff

Sandra Porter has a little DNA puzzle for us to solve over at Discovering Biology in a Digital World, and it should be quick, enjoyable and entertaining for most biochemists to figure out.

More fun stuff

Andrew Fox has some DNA you can wear! posted at Sexy Secularist!, blogging about a jewelry maker who is fashioning custom Double Helix bracelets with messages spelled out in genetic code.

GrrlScientist says why Pretty Boys Have All the Chicks at Living the Scientific Life. She says "Everyone is familiar with sexual dichromatism in birds; you know, the gorgeous, colorful male who is paired with the drab female or two. It has been observed in birds that, when males and females differ dramatically in appearance, the females are preferentially mating with a few "pretty boys"; those that have elaborate plumage colors or ornamentation. As a direct result of female breeding preferences, these "pretty boys" sire more offspring than those males with less colorful plumage, thus driving the evolution of sexual dichromatism in the population. This behavior concurrently drives evolution of a polygynous breeding system in the population. But what about those birds that are monogamous yet still show strong sexual dichromatism? How did they get to be that way?"

Finally, in case you need some good reading material, and are looking for good general science history, I have a review of John Gribbin's "The Scientists", which I quite enjoyed reading.

That concludes this edition. Apologies if I missed any submissions, but do send that post over to the next Mendel's garden next month. Submit your blog article to the next edition of Mendel's garden using our carnival submission form. Past posts and future hosts can be found on our blog carnival index page.
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Wednesday, September 05, 2007

Some entertaining mind control

(This blog certainly has been neglected over the past week, and has been crying for some attention. So, even while weekdays leave little time for active blogging, here’s a little post saying I’m alive).

Most of the time, the SciFi channel on TV kills the mind with some awful movies or Star Trek reruns. But every once in a while there’s something really enjoyable. On top of that group must be Mind control with Derren Brown. In case you haven’t heard of Derren Brown, he’s a “psychological illusionist”, doing stage hypnosis and that kind of stuff. And he’s also a terrific entertainer, who sometimes reveals some secrets, just to keep all of us really intrigued, and wondering how he does it.

I particularly enjoyed a show where he had different groups of people in rooms, and asked them all to draw out an outline of their hands, and put a personal item in an envelope. He then went on to give them all detailed typed up accounts of their lives, and their inner desires. They all swore that the statements were 90% accurate, and most of them thought he had psychic abilities. He then showed them their typed documents. ALL of them were the same!

Anyway, for your entertainment, here are two videos of him, one of them where he plays chess with 9 opponents simultaneously (a bunch of British Grandmasters, International masters and FIDE masters), coming out on top, and a second one with the inimitable Stephen Fry.

Terrific entertainment, and while I don’t know how he does it all, he certainly keeps us lapping it up.

Saturday, September 01, 2007

What's with the accent?

Every once in a while, I switch off from NPR and tune into one of the Indian radio stations that you can catch here in Dallas. Just so that I can pretend to be up to date with the latest music in Bollywood, or listen to oldies (or occasionally even catch some Tamil songs that they air on weekends).

Anyway, while I have no complaint with the content, here's something that doesn't cease to puzzle and annoy me. What's with the language of the RJ's and hosts on these shows? I perfectly understand hosts speaking in English with an American twang. We're in America, and many of the hosts were raised here, so that's fine with me. I can also tolerate some hosts who speak English naturally with an Indian accent, but try to put on an American drawl (usually failing miserably, resulting in something that is neither here nor there, but mostly unintentionally funny). That's fine too, you're trying to assimilate or whatever.

But what I really, really cannot stand is hosts who try to speak Hindi (or Tamil or Telugu or whatever else) with a ridiculous anglicized accent, and a terrible vocabulary. What's the deal there? Why murder a language which you obviously are a native speaker of, by putting on a terrible accent, and killing all semblance of grammar, just to sound "cool"? If we're having a show in Hindi (or another language), why can't that show be in Hindi (or what ever language), with a reasonable diction and without an overuse of English?

I'm almost tempted to call some of those shows and tell the hosts what I think.

Or maybe I'll just go back to listening to NPR, and my cds and mp3s with Indian music on them. I'm probably just a fusspot, that's all.


Wednesday, August 29, 2007

Tangled bank #87

Welcome to another edition of the Tangled Bank, the blog carnival broadly about the natural sciences. My original idea was to get creative, and trace the history of logic while threading through another edition of the Tangled Bank. But these are busy days, so we’ll keep it short and sweet (and please excuse any typos or errors, this was put together rather quickly).

Here goes.

Critters everywhere:
Starting with archer fish, Andre at Biocurious writes about animals that intuitively know and use very advanced concepts in physics, but then, can they write equations? And I had absolutely no idea that those garden destroying squirrels were immune to rattle snake poisons. Read all about that, infrared body temperatures and tail flagging over at Grrlscientist’s. She also has another post on the deadly Marburg hemorrhagic disease, which is incurable and is transmitted by a virus. Apparently the the source of this virus is a fruit bat. At the Invasive Species Weblog, Jennifer writes about the common periwinkle snail, which we first thought was an invasive species, then were told that it has been in North America for 8000 years, and now it is back to being an invasive species. And what’s a “tangled bank” without mention of the Galapagos islands and the fabled finches? Mike of 10,000 birds writes about the unique birds of the Galapagos. That island has such an amazing concentration of diversity, it even has four endemic mockingbirds (and there’s just one in all of the rest of North America).

Pure, unadulterated science:
Veo Claramente has an excellent post on the damage response framework of microbial pathogenesis. That’s some very good science writing on a fascinating topic. At the wonderful world of Archaeozology there is a post on the diversity and origins of cattle. If you ever wondered how and when the wild, cud-chewing bovine was domesticated, here is your answer. In some more excellent science writing, Aaron at Synapostasy has a three part mini-review on the evolution of X and Y chromosomes, so here are links to Part I, Part II and Part III. At, Joe, writing about evolution and cancer, neatly summarizes a review on DNA check points, tumors and the loss of apoptosis. And over at Ouroboros, there is an interesting post on delayed aging via increased Arf and p53, discussing if tumor suppressor genes are beneficial or detrimental with respect to ageing and lifespan.

Religion and science:
There’s surprisingly little about religion and science this week. But there’s still some good stuff. At the Primate Diaries, Eric lucidly explains The feeling of what happens: Science, faith and Nature’s error. He also has an excellent post on sexual equality, double standards and social scale.

Odds and ends:
Andrew the Sexy Secularist is making a sales pitch for some rather nice looking jewelry. Except that these are DNA double-helix bracelets! Go buy some.

Its midnight, and you can’t go to sleep? Do you look at those early sleepers and early risers with utter disbelief? Don’t worry, you aren’t an unnatural freak. You fall into the group Paddy K calls the B-team, and your tribe is large.

Sharp brains links to a number of research articles on “Computer based cognitive training (or “brain fitness”), and some of the links are fascinating. Also worth reading are the ten habits of highly effective brains. I’m going to practice positive, future oriented thoughts everyday, starting now.

From Omnome comes the story of an inventor who claims to have invented injectable heat generating nanoparticles which will cure tumors. Omnome doesn’t think a cure for cancer is going to come from here. Finally, from my own blog, here’s a little bit of history, on standing on the shoulders of Giants.

That’s it for this edition of the Tangled Bank. The next edition will be in two weeks, at The behavioral ecology blog.

Monday, August 27, 2007

Book review: The scientists

I have to start off by admitting that it had been quite a while since I read any book that was over 500 pages long, with the words neatly typed in a small font size. The Harry Potters don’t count, and their pleasing illustrations and tween-friendly, reassuringly large, bold font and plenty of action make them rather easy to read. But when I saw the exquisite cover of John Gribbin’s The Scientists: A History of Science Told Through the Lives of Its Greatest Inventors I knew it was a book I had to read.

Gribbin, of course, is a formidable science writer, and his In search of Schrodinger’s Cat once taught me more about quantum physics than high school and college did together (admittedly, even after reading the book, I still knew next to nothing about quantum physics). So, when I noticed that he was the author, I expected The Scientists to be creative as well as highly readable. This book sets out to do much more than describe the history and facts behind one (or even a group) of discoveries. The book attempts to describe the past 500 odd years of scientific discovery, starting during the later part of the European renaissance, where a burst of human creativity eventually laid the foundations of the modern scientific method, and progresses to the present times of frenetic scientific activity and discovery by the minute.

Any book that sets off to describe 500 years of discovery takes the risk of being excessively descriptive or tedious, burying the reader in scientific fact or jargon. Constantly talking about great discoveries can effortlessly kill any interest the reader has in science, a fact neatly attested by my own high-school science text books (which were well meaning, but failed to capture our attention). But Gribbin beautifully weaves a tapestry of the stories of the discoverers, the scientists themselves, and through these stories brings out the great scientific discoveries that ushered in the modern world of science. Everyone likes reading stories about people, their lives, their problems, their inspirations, their animosities and their transgressions. But a purely historical account of the great scientists of the past, without describing their discoveries, is meaningless. Gribbon manages to perfectly balance both aspects, and walks through the lives of the scientists who shaped modern science, while beautifully describing (in considerable detail) their contributions not just to that aspect of science, but to scientific thinking and future discoveries as well.

The first chapters of the book are aptly titled Renaissance men and The last of the mystics, starting with the likes of Copernicus, Bruno, William Harvey and moving quickly to Tycho Brahe and Kepler. It is both fascinating and incredible to read about the times in Europe then, in a world deeply clouded by superstition, and where religion (in Europe it was the Catholic Church) had a vice-like grip on all knowledge. The earliest scientists weren’t really called “scientists”, and most of them did quite a bit to ruffle the feathers of those in authority, particularly the church, for which many of them suffered. It is equally interesting to read about their lives, and how many of them were themselves deeply influenced by the church (or were clergymen themselves). While here, Gribbin describes Galileo as the “first scientist”. While describing these early giants, Gribbon subtly but surely brings out the concept of the Scientific method, which was slowly beginning to develop and starting to leave an imprint. In the first few chapters, Gribbon devotes much of the space to a description of the times and the lives of these pioneers, rather than their discoveries alone. This allows him to elegantly establish a historical context from where the modern scientific schools of thought were allowed to emerge from.

It also allows Gribbon to steadily build the pace of the book. The fascinating stories of these scientists draw the reader deep into the book, and allows the reader to paint a picture of these people and their times (the only annoying thing is that I keep picturizing Pope Urban VIII with a bald head, sunken jaws and gleaming schrew-like eyes, while Galileo describes his Dialogue Concerning the Two Chief World Systems, and I just can’t get that out of my head). By the third chapter you are engrossed in the book, and are ready to jump into the world of the “founding fathers”, Descartes, Huygens, Boyle and the subsequent “Newtonian revolution” (while Newton was undoubtedly a giant amongst giants, it is without doubt that numerous pioneers like Halley and Hooke played almost as significant a role in ushering the scientific “revolution”). Gribbon also points out that the “scientific revolution” didn’t really happen the way we think “revolutions” happen (giant rumbles and the falling of the Bastille), but slowly churned and grew, with each generation of scientists building upon the work of the preceding one. And from the era of Newton, there was no looking back for the world of science.

After Newton, the face of science changed for ever. The foundations laid by astronomy and classical physics (culminating in the Principia allowed scientists (or “gentlemen scientists”, as they were in those days) to start thinking of simple laws by which the universe worked. The steady discoveries of astronomy and geology meant that geologists and biologists would have to confront the fact that the earth was far older than traditional Biblical interpretations, something that would have substantial ramifications on society. By the time Gribbon finally describes Charles Darwin and his life, he has already described the prior foundations that helped Darwin formulate his theory of natural selection; the substantial work on understanding the age of the earth, the work of Charles Lyell, the earlier work of Hooke and Leeuwenhoeke in describing biological cells (and their similarities), the superb work of Carolus Linneaus (who classified organisms based on similarity, breaking them down from species all the way to phylum and kingdom), and finally the brilliant work of Alfred Wallace, who independently proposed a theory of natural selection, which prompted Darwin to complete and publish his own (more well developed) theory. Given this complete historical context, we understand how it was but inevitable that Darwin (or someone else like Wallace) would naturally have to put all the pieces together.

As the book nears modern times, the pace dramatically starts to increase. After all, by the late 19th century, science was poised to explode. It was the end of the amateur gentleman scientist, and the beginning of the professional scientist. The fields of chemistry, physics and biology started to become distinct. And then with the discovery of radioactivity and the beginnings of quantum physics, the world of science pretty much changed for ever. The chapters describing the work of the likes of Thomson, Rutherford, Plank, Pauli, Heisenberg, Schrodinger and the innumerable contributions of Albert Einstein, all move along at a frenzied pace. There are now too many characters around, and Gribbin can no longer linger on the lives of one or two alone. Yet he manages to squeeze in little anecdotes or stories that keep us, the reader, lapping it all up. Nuggets, like Rutherford being greatly amused when awarded the Nobel prize for Chemistry (since at the time the atom was under the purview of chemistry), since Rutherford thought of himself as a physicist and didn’t think too much of chemists, or the story of the Curies, and Marie Curie’s notebooks are to this date still so radioactive that they are kept behind a leaden safe (both Marie and Pierre Curie suffered seriously due to radiation, something they didn’t know about then. So they literally died because of their science). Near the very end, we reach the spectacular discoveries of genetics, DNA, the genetic code and finally, the realm of outer space.

I can only describe this book as a superb effort. It is one of those books that appeals at different levels. A reader can open any chapter and read it independently, enjoying the stories in them. The writing is tight and vividly descriptive, and is simultaneously written for scientists, amateur scientists, science aficionados, historians and everyone who likes a good yarn. The book serves as an outstanding reference for the past 500 years of western scientific thought. There are some books we never buy (but sometimes “borrow”), others we buy just to read once and then forget. But some books are keepers, which we keep going back to again and again, discovering or relishing a new nugget each time we dig into it. This is one of those books.

Thursday, August 23, 2007

The joy of questioning

Selva, who publishes and blogs as the Scientific Indian on scienceblogs had asked me to write a guest essay for his publication, TheScian.

My essay, titled "The joy of questioning" is now online on TheScian. What's more, Selva has taken the effort to make an audiocast out of it, with some snazzy background music to boot.

Quite flattering.

Read or hear the essay here.

Tuesday, August 21, 2007

A history of Indian mathematics

As many readers of this blog know, I’m fascinated by the history of discovery. While you certainly can be a good scientist without a knowledge of the history of discovery, there is much to learn from not just what is known, but also how it was discovered. Usually the stories behind discoveries are almost as fascinating as the discoveries themselves. Additionally, reading about the stories behind the discoveries also sometimes are humbling experiences; and makes you realize how much work might have gone into some findings, or how much some other discoveries was based on a collective work many individuals preceding the discoverer.

Additionally, reading about the history of discovery also makes you realize that knowledge or discovery was never restricted to one group or place alone, but different civilizations at different times had bursts of creativity, resulting in important discoveries. From there you can begin to understand how some societies progressed more rapidly than others. For example, Jared Diamond in his Guns, germs and steel uses this knowledge to understand how western societies managed to reach their current level of domination.

Anyway, coming to this post, I have always been a little disappointed in the way Indian history was taught to us in our schools. This is particularly true about the history of discovery (in science and mathematics) in India. There was the old colonial school of thought (which some people still have) that the foundation of all knowledge came from the west (starting with Egypt, Greece and Rome). Yet any historian knows that in the ancient world, there were thriving civilizations in Persia, India and China, and more importantly, there was not just trade, but well established and vibrant exchange of ideas and practices across these regions. This automatically suggests that there must have been some good ideas and discoveries in all these regions, in order for them all to be advanced (for the time) societies. There’s also the opposite (and rather amusing) view that comes from an excessively Indian nationalistic prism, which more or less states that all knowledge that exists in the world was discovered in India first (come on, tell me you’ve heard this one). Again, given the evidence (about vibrant civilizations in contact with each other across Europe and Asia), this isn’t likely to be true either. That said, there was nothing worthwhile that was ever taught to us about Indian science and mathematics.

As I read more about Indian mathematics in particular, I was fascinated by how rich the field was, and how much it has contributed to the field of mathematics in general. Some contributions are quite well known; and many of us are aware of the modern numeral system and the use of zero, first developed in India. This number system was later adopted (and improved) by the Arabs and Persians, from whom it reached Europe, and is now called the Hindu-Arabic numeral system. Some other contributions, like the development of the decimal system are also well known.

Anyway, here is a fantastic article by J.J. O’Connor and E.F. Robertson, on the excellent Mac tutor, on the history of Indian mathematics. This briefly mentions contributions like the numeral system, but also describes (or links to more articles about) major contributions and discoveries in algebra, trigonometry (including an independent discovery of the Pythagoras theorem at about the same time as Pythagoras), quadratic equations, the invention of the “Taylor” series, the value of pi, and much more, all of which makes absolutely fascinating reading.

I found it well worth my time to read more about it here (Indian mathematics, The sulbasutras, Indian numerals). Fascinating.