Saturday, April 17, 2010

Road Warriors

Icelandic ash produces chaos in air travel. So it is time for the road warriors to have some enforced adventure (see the link on this blog's title).

I am reminded of a few adventures myself. That time in 1977, the express train from New Delhi gets stranded in Bengal-Bihar border due to some problem on the track. We wait for some four hours, walking around the train in the middle of nowhere. The track seems beyond salvage any time soon. An engine is apparently en route from the direction we have just come so our train can be hauled back to the previous junction in Bihar. So it is a choice between getting stranded in Bihar versus finding our own way to Calcutta. My friend and I jump ship. We walk along the railway track about five miles to the next town, catch a bus that travels along bumpy way through glacial moraines of Bihar and then the coal fields to a rail junction after some six hours. It is night by that time. We wait until the next passenger train rattles into the platform in the middle of night, its coal engine hissing. We set off, to arrive in Burdwan at the crack of dawn. Sweet tea and jhal muri along the way. What fun.

Thursday, April 15, 2010

The Power of Sequencing

Back in 1992 I was in a conference where someone famously powerful was proposing to sequence the genome of the model organism with which I used to study my favorite questions in research. Sitting in the dark hall I quickly made a back-of-the-envelope calculation: how long would it take to discover the function of an unknown gene, known only by its sequence, given the rate of gene function discovery for the first organism's DNA ever sequenced completely (the lambda virus) in 1979. The answer was several hundred centuries. So at the end of the talk, I announced the result of my calculation, and asked why not spend the money, millions of dollars, on simple investigator-initiated research that asks straight questions and gets straight answers. There was silence in the hall, and I felt smug and smart. Until the last talk in the conference, which announced the discovery of microarrays, for parallel measurement of RNA transcripts made from hundreds (at that time) of genes. Quite uncomfortably, I realized my mistake--the vice of linear extrapolation. That changed my mind.

So today I read and discussed a paper published this last January, which reported the successful identification of a gene that appears to harbor the causative mutations for Miller Syndrome (Google it, if you don't know it), a particularly debilitating rare and inherited disease that severely affects the lives of some children. The methods that the researchers used, based on sequencing nearly the entire protein-coding gene set of the patients, were unimaginable back in 1992--it would have been considered a science fiction dream in popular forums and would have been derided as madness in scientific company. But it is a reality today. What surprise will the next month bring?
[Update, April 16: Here is a link to an editorial on this paper published in today's Nature Genetics:]

Tuesday, April 13, 2010

They say it is the cruelest month

Today is the Bengali New Years day. It is not held on every April 13, because it goes by the lunar calendar. Vagaries of celestial bodies mean that my mother, who passed away on April 15 morning last year, on the Bengali New Year's day, has two more days to live as it were in the year since her passage. This year it was Winko's turn, but he just missed the New Year's day. He perhaps could have made it but it was better for his own sake that he didn't. I also wish that mother suffered fewer days the agony that she endured last. I miss Winko's silent paws as he paced behind me, up and down the room, as I am given to do often, and he so followed. A shadow. Funny. I miss my mother's distant look on the empty balcony, waiting for April nor'wester to break against the sky. Winko's paws, strangely soft, as soft as mother's hands on my forehead a distant memory. Kisses that I would disown when grown were to be sought again from a mouth with a hanging tongue. Selfless devotion? Yes, that. Dog and mother. That is why this pain in April.