Wednesday, January 31, 2007

Creating Maps of Inequalities

Strange looking map, isn't it? Well, it's just a modified map, a population cartogram, where the land area is shown in proportion to population. Except that this is an inequality map. Here, researchers have taken together data showing how many people suffer from a certain disease in a certain land area, and then represent the map proportionately.

This particular figure shows early neonatal mortality, the deaths of infants in their first week after birth. India has the highest neonatal mortality rate in the world (along with Pakistan, Bangladesh and other countries of the subcontinent).

Pretty sad, isn't it?

Like the author says; "You can say it, you can prove it, you can tabulate it, but it is only when you show it that it hits home"

Statistics are hard to remember. Facts are easily forgotten. But pictures remain in the mind for a long time.

This paper in PLoS Medicine that I happened to glance at is fascinating for many reasons. A picture does indeed speak a thousand words.

There are fascinating, and sometimes surprising insights from the six test examples; public spending on health, private spending on health, neonatal mortality, HIV/AIDS prevalance, and the prevalance of malaria.

To me, it was also depressing to be reminded how badly India scored on all of these. These are just raw numbers from the United Nations Human Development report, taken and plotted.

The explosive development in India is wonderful and welcome, but mostly meaningless if the basic indicators of human life remain depressing.

(You can read, or just look at the pictures in, the complete paper, here)

Monday, January 22, 2007

What does it take…….

……to be a pioneering scientist?

Or, more simply put, what separates a truly outstanding scientist from a mediocre one?

Sure, there are clear ways to “quantify the contribution” of a scientist. There are ways to measure citations gathered, or the “impact” on a field, and its easy to identify the pioneers of science. But what made them different from the rest (and particularly the bad scientists)? There are a lot of scientists out there. Most of them are very smart. But only a few of them make the pioneering contributions (and it’s not necessarily the one with the highest IQ).

Over the past few years, I’ve had the opportunity to work with some fantastic scientists, and have met many more at conferences, or listened to their seminars. And though its easy to be blinded by their brilliance or overawed by their accomplishments, there seem to be traits common to most of them, a pattern even. These are just a few of my own observations, which I wanted to write down as a part of my own education.

Organization and memory: Its surprising how many people believe the common caricature of a scientist. Absent minded, confused, part-senile and mixing up incorrect solutions in test-tubes all paint a familiar picture of a “typical” scientist. That picture, surprisingly, is pretty distant from what the best scientists usually are. They may be in a world of their own, and forget the birthday of their spouses, but when it comes to their own research, they are invariably superbly organized, and more importantly have phenomenal memories. My PhD advisor had the ability to remember (what I thought were) obscure research papers from as far back as the 70s and 80s, where someone had suggested something, that was pertinent to my own work. During discussions, he would rock back, think for a moment, and then recall details about the authors, their findings and the implications of their work. And most of the best scientists know exactly what is going on in their labs, and what each person is doing, or should not be doing. There is just about no chance of them ever mixing two incorrect solutions and serendipitously discovering the ability to fly. Doddering old fools they are not.

Focus, passion and perseverance: It’s not surprising, but the best scientists are absolutely passionate about science, and are usually (mildly) obsessed with their research. They think about their work constantly, and it’s hardly surprising when they drop in to the lab on a Sunday, and having thought about some new ideas or possibilities, write you an email (or leave a note) with their suggestions, while you are out playing golf. And if they are out playing golf, it usually results in them coming back the next day with better ideas.

Looking for more: Call it greed if you will. But the best scientists do not appear to be satisfied with the findings that come out of their research groups. If a researcher in the group comes up with a set of findings that are in themselves solid and interesting, and contribute to the field, most scientists are happy to publish that work. But the best scientists always seem to look for more in every finding. If a story suggests something, they will want to find out more about it, and build on it until it is no longer a finding but a breakthrough in the field. Every result is usually accompanied by more, and more penetrating questions. Can this finding lead to something more? Will it have implications in more than the small problem it is addressing? Can something apply not just to heart disease, but cancer and diabetes as well? You get the idea.

A stubborn streak: More often than not, the best scientists come up with a hypothesis (usually based on some facts, and where they think it could lead), which they hold on to longer than most of their students or postdocs. They usually don’t want to let their pet “world changing” idea fall through before they have invested enough time and resources and thoroughly eliminated all reasonable possibilities. Usually, the people doing the grunt work (the students and postdocs) have to live with the frustrations, while the head scientist can sit back and speculate. But invariably, the stubborn streak pays off, with most of the pioneers getting their predictions right. And then they can nostalgically say how it was all hard work. Importantly, the best do not cling on to their ideas if the evidence conclusively shows that their hypothesis is not true, but they don’t accept defeat when presented only with “negative data” (where instead of disproving a theory you only can produce data that doesn’t fully answer the question). However, they usually demand solid proof before they declare their ideas to the world (in contrast to some “shooting star” scientists, who publish a blaze of high profile papers in a desire to rush through with their “findings” without being rigorous enough, often to be proven incorrect).

Vision: Understandably, the best scientists also have a vision. From their data, they make and state the appropriate conclusions, and can also predict where the finding may lead. There are a lot of good scientists out there who can interpret their data well, and come to solid conclusions. But only a few can make the leap from those conclusions to the greater implications the findings have for an entire scientific discipline. The best papers have a discussion where statements are made that prove to be prophetic. My favorite remains the understatement by Watson and Crick in their famous paper in Nature.

“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”


(Many of you have worked with (or are) outstanding scientists. Do share your thoughts and what you’ve learnt).

Thursday, January 18, 2007

Nothing like the sports page, and some great carnivals

For a sports fan, the Dallas Morning News is a great newspaper to read, with excellent coverage of football, basketball, baseball, (ice) hockey and golf. But the sports page also provides a wonderful insight in to Texas life, and unique Texas culture.

There is always some detailed coverage and entertaining articles on the Rodeos. But most interesting are the articles on fishing and hunting.

Yup, they are all on the sports page. Detailed articles on the spawning of bass, and the best time of the day to catch cod, or how the lakes filling up will attract a lot of ducks, so wake up early and head out with your duck-whistles and guns.

This might be the forth largest metropolitan area in the United States, but the outback west and Texas lifestyle remain strong, and everywhere.

And to make up for the limited science blogging on Balancing life, here are links to two great science carnivals.

Tangled bank is up at The Voltage gate, and there’s a new and very interesting carnival in town, called Four stone hearth. It’s a blog carnival on anthropology, the study of humankind from all time. The first edition is up at Aardvarchaeology.


Sunday, January 14, 2007


Indian cinema (across languages) has always loved police “dramas”. So a good part of my staple growing up diet consisted of movies where the hero’s an honest cop, fighting a corrupt system. The solution invariably is rather simple. The cop takes up vigilante justice, and bashes up everyone in sight while squeezing time out to romance a coy heroine and sing a few songs. Only rarely (the exceptional Sehar comes to mind) does Indian cinema even try to make a gritty, down-to-reality police drama.

So it has always been an absolute pleasure for me to watch English cinema where gritty, grey shades of police life are more starkly portrayed. Revisiting Serpico at leisure allowed me to relish the nuanced, very real cinematic version of the story of Frank Serpico, with Al Pacino in one of his earliest roles.

Serpico was an NYPD policeman, and joining the police department was the culmination of a lifetime goal. He first works on the beat, and then becomes an undercover plainclothes policeman working in Brooklyn and the Bronx. At every step in his job, he encounters widespread corruption. The system was elaborate, and each region had its own group of officers who went around collecting bribes or protection money. Serpico did not want any part of the corruption, and stayed away from it. And by refusing to take money, was despised by his fellow officers, who “couldn’t trust him”.

Serpico remains among Sydney Lumet’s best (his Dog day afternoon remains an all time favorite of mine) movies, precisely because he doesn’t try to force the movie in to cinematic drama. He takes his time in letting Serpico’s character develop, showing the gradual progression of an enthusiastic, honest cop in to a scared, confused, jaded and yet uncompromisingly honest veteran. And Pacino’s portrayal of Serpico, for many reasons, remains amongst his finest roles.

Serpico’s development in to a plainclothes cop is almost perfectly carried out by Pacino, and his appearance beautifully describes Serpico’s own anguish, from a clean shaven bright eyed rookie, through a handlebar mustache and finally unkempt long hair and bearded anguish. His encounters with police department corruption starts from the first day, where he doesn’t get the food he is supposed to in the police cafeteria. As he goes on the beat, other cops begin to suspect him of being “strange” or “queer” (with all its connotations), as he refuses to go on the take. The tension is slowly allowed to build, as Pacino superbly portrays the frustrations of being honest, with no where to go. He tries desperately to find ways to report this corruption within the police department, but has no where to go. His reports to the commissioner’s office, and then the mayor’s office has no response. Meanwhile, his frustrations build. The scenes where he comes home to scream at his girlfriend, Laurie, who cannot take the constant complaining from Pacino (who is cracking under the pressure of not being to tell anyone) are fantastic. He shuttles between ranting and sulky silence, and eventually Laurie leaves him. As everyone “busts his chops” (he can’t reveal the truth and alienate the police officers, who not so subtly threaten consequences; he can’t report his problems to anyone, and cannot go outside, to the press), Serpico’s anguish only builds, until he finally goes public, which leads to the well known Knapp commission

This movie reminds us why Al Pacino was such a highly rated actor. There is little of the ranting, screaming or “booyahs” that have come to mark his more recent performances. There is little hamming, even as Pacino becomes Frank Serpico (and the character does not become Al Pacino). Pacino uses his very expressive eyes fantastically in this movie, and doesn’t try to force dialog where there isn’t any need for it. His anguish (as Serpico) is very tangible and you feel the squeeze that’s being applied to him from all sides.

In addition to Serpico himself, the characters around him excel. The acceptance of widespread corruption, and the justification of the corruption by some officers is beautifully portrayed (“we don’t do any thing really bad. We don’t take drug money……the Italians, they’re different, they’re men of honor, so we trust them”) and makes you smile in irony. When an honest man (Serpico) becomes the bad guy (since every one else is dishonest), you almost nod in acceptance. The few other honest cops have no place to go as well, and all deal with the situation differently. The pace of the movie plays a superb role in defining the mood and the feel of the movie.

I was prompted to revisit Serpico after watching Scorcese’s The departed. There’s little in common between the movies, but Leonardo’s excellent portrayal of Billy Costigan, the undercover cop squeezed from all sides, reminded me of Pacino’s intensity as Serpico. Serpico pretty much set the benchmark for movies of this genre, and few have reached the standards set here. Classic is a word too easily used to describe old and successful movies. But Serpico was one of them.

Tuesday, January 09, 2007

Why? For the giant microbes!

Life in basic science research isn’t always easy. The road to becoming an independent scientist is long and hard. It usually takes five years (or more) for a PhD, where you are expected to produce good, solid science and write a few good papers. After that, you don’t just get a job. You disappear in to the wilderness as a post-doctoral researcher, and work insanely hard under a lot of pressure (that’s if you want to make it as an independent scientist of course). If all goes well, and you do manage to do “exciting” and “brilliant” science, you finally get an appointment as an assistant professor, and start to establish your independent career (which involves endless work hours under immense pressure).

All this while, you’ve lived barely above poverty. When you’re still renting a small one-bedroom apartment somewhere, and driving the old used car you managed to buy, your friends from college have bought mansions and earn a hundred thousand a year. Ah, but you have flexible work hours, don’t you? Well, that is true. You work a flexible 70 hours a week.

But why do perfectly intelligent people go down this road? Why sacrifice a perfectly simple software programmer’s job, or an MBA and riches for a life in science? There are many different reasons. Almost all of them involve a passion for science and discovery, and a love for learning. For me, there’s one little thing that drives me most.

The days of actual discovery are few and far between. They are occasional sparks in otherwise hard, unforgiving days. But every once in a while, you do make a discovery, and are sure of it. At that moment, you are the only person in the whole wide world who knows about it. You rejoice and reflect. And then you announce it to the world.

But that one moment when that knowledge is only yours, and you know that you can share that knowledge with the world is absolutely priceless.

(There’s also one purely material reason I love being a scientist. I can buy stuffed toys that look like disease causing microbes, and find them absolutely lovable. Now, isn’t that picture below a beauty? (That’s HIV. There’s more here)

Saturday, January 06, 2007

Superheroes, lame heroes and maniacs

Somehow, on Saturday mornings, I am drawn towards the kids TV programming, on WB, ABC or even the usually hopeless Fox. And most of this comes from a childhood obsession with comics, superheroes and cartoons. Today, I reflexively switched on the telly, to find “The Legion of Superheroes” on WB, and this triggered off a series of memories.

Now, the Legion had its heydays in the 60’s and 70’s, and DC comics went overboard in coming up with the most inane superheroes the mind can fathom. But my introduction to them came through another set of comics, Spectrum comics, that a few (and only a few) of us in India will still remember. In the early/mid eighties (by revealing the fact that I read these comics in the early/mid eighties I’m also revealing that I’m ancient by some blogger standards) our world in India was taken by storm. No, not by Maruti cars, but by Indrajaal and Spectrum comics. Indrajaal (and much later Diamond) published Phantom, Mandrake, Flash Gordon and (most importantly) Bahadur comics (and if you crave for them, you can find them here). But Spectrum comics published some of the old DC classics, Spiderman, many forgettable heroes, and the legion of superheroes. Thanks to a granduncle who was connected with the publishers, I got the whole lot of Indrajaal and Spectrum comics (for free!). And so, I was introduced to the zany world of the Legion.

The legion was a gathering of the ultimate group of superheroes, led by Superboy himself (yup, all the heroes were teenagers, and not the men/women they would grow to become). The legion provided an opportunity for DC to come up with the most stupid powers possible. And by stupid, I mean extraordinarily stupid. Two of my favorites were Bouncing Boy, and Mater-eating lad (I still own the Spectrum comics where these two made their grand appearance). Bouncing Boy had the fantastic power of inflating in to a rubber ball.

Yes. I kid you not. And in the issue where he makes his appearance (which I still proudly own), he’s just a regular kid, Charles Taine (I would later learn that the name was a tribute to Citizen Kane), who drinks a potion thinking it’s pop, and becomes a bouncing rubber ball shooting across the road.

What use can that power be, you ask? As a curious kid, I did too, and then read on. In his debut comic, he had to face a super villain, who conducted electricity, and could shock-freeze anyone he touched. So, the other superlegionnaires would try to grab this fiend, only to be shocked to stillness. But Bouncing Boy, being just a bouncing rubber ball, was immune to electric current, and so knocks down the arch-fiend, and saves the day!

Now, if that isn’t way, waaaaay more stupid than being bitten by a radioactive spider, I don’t know what is. When it comes to bragging rights about superpowers, guess where Bouncing Boy fits? (“You can fart lasers? You suck. I can bounce!”).

Coming back to today’s episode on TV, clearly Bouncing Boy’s inability to do anything useful was on constant display. He does nothing (apart from getting caught by some flying robot spiders), even as the others take on robots and crazed man-animals.

And that brings me to my final crib. Why, oh why, do the creators of comic book superheroes hate science and scientists so much? Almost all super villains have no superpowers, but are just smart, and invent fantastic gadgets (and then decide to rule the world). Or else, the superheroes are a result of a crazy science experiment gone wrong. And the superheroes go in, and smash and destroy every little invention the scientist has come up with. I mean, they could just capture the guy. Why trash the computers? Doesn’t brain win over brawn and tights ever? At least they've stopped coming up with bouncing boy and matter-eating lad. We should all be thankful for small mercies.

Now I can wait impatiently for next saturday, and the next installment of Batman or the legion of superheroes on WB.

Monday, January 01, 2007

Got milk?

I hope you readers have a good 2007.

While at dinner with family over the holidays, I observed a little something. Now, if you take a pack of wild wolves (or gorillas or something else), if they obtain a meal, there is a fight for the tastiest/best morsels of food, and the least desirable food is left for last. If a solitary animal finds food, it too gobbles up the best part of the meal, saving or leaving the less desirable rest.

It probably was the same for the hunter-gatherer humans of old. Find food, eat the best, and leave the rest for later. Probably, as food security increased, humans became less worried about not getting the tastiest morsels, and so were less worried about gobbling food up. Well, I’ve been domesticated to such an extent that I usually save the tastiest portions of the meal for last, so that I can relish it at leisure, savoring the smell and taste, taking in small bites, and allowing it to linger.

I wouldn’t last a day in the wild.

Anyway, coming to probably a more interesting result of natural selection; agriculture and domestication of animals dramatically changed human life, and certain traits have rapidly evolved in humans due to this. One of them is a tolerance for lactose, and the ability to drink milk as an adult. Most mammals drink milk as infants, but are then weaned away from milk. However, many of us drink milk with out any problems as an adult. The reason for this is that lactase phlorizin hydrolase (LPH), the enzyme that breaks down lactose (the major sugar in milk) in to glucose and galactose, is expressed in us as adults. In most mammals, the expression of this enzyme is shut-down or repressed as adults.

But many, many people in the world are lactose intolerant, and cannot handle milk. Lactose intolerance is high among Africans, Native Americans and East Asians. Lots of researchers have tried to find out the genetic reasons for lactose intolerance, and varying degrees of lactose intolerance in populations. The gene that codes for LPH is long known, and researchers surprisingly did not find too many differences or mutations in the coding region of the gene (the part that actually becomes a functional protein) across populations. About four years ago, a group found a single specific mutation (a single nucleotide polymorphism, where a cytosine in the DNA was mutated to a thymine) in a completely different gene, MCM6, in Finnish populations that surprisingly had an effect on the expression of LPH, and therefore lactose tolerance. Since then, it is widely believed that this mutation is what gives Europeans lactose tolerance.

However, this mutation was not as prevalent in southern European or Middle Eastern populations, and very rare in African populations, which were also lactose tolerant. So, could there be other mutations that also cause tolerance to lactose? A group of researchers examined over forty African ethnic groups, and for starters searched in the same general region as the earlier mutation, and found three new variants all of which were associated with lactose tolerance. Additionally, their study also showed different mutations spread across different populations, with more pastoral populations having much stronger lactose tolerance, and a clear positive selection for one of the mutations (that provided lactose tolerance).

This study is a really nice example of convergent evolution . One can imagine a tremendous benefit to humans who acquired lactose tolerance. Once animals were domesticated, the meat was an obvious source of food, but the milk was a ready and highly nutritious (and sustainable) source of food as well. So, it clearly benefits pastoral societies to develop tolerance for milk at adulthood. In order to obtain the same outcome (lactose tolerance) nature came up with different was to achieve it. Different mutations all lead to lactose tolerance.

(This reminds me of my school days, where we had to prove theorems in class, in physics or mathematics. We knew the answer (g=9.8 m/s2), but some of us came up with extremely innovative methods to obtain that solution. Beautiful convergent evolution).

This study is really quite nicely done, and suggests how much variation is likely for what were likely “important” needs under strong natural selection. There’s one large population of people closer to home that I’m betting is going to have a lot of variation for SNPs determining lactose tolerance. South Asians. Dairy products are an essential part of every meal (as ghee, yogurt, milk, and every dessert), and India has more cows and produces more milk than any other country. Given the sheer diversity of populations in India, with differences in dietary habits, I’m very curious to know if a majority of the population carries a single mutation conferring lactose tolerance, or if (just like the country itself) there is tremendous diversity in mutations that provide tolerance.

(Read the original research paper here (Nature Genetics - 39, 31 - 40 (2006) )