Archive for August, 2011

Thesis word cloud…

I haven’t decided yet if this is a good thing or a gross under-representation of what it’s like to write a thesis. Sixty-nine thousand plus words,  seven chapters, two hundred and forty nine pages, eighty-nine figures, thirteen tables, and a brain aneurism summarised into a word cloudThesis

But the idea for this came to me when a while back I was congratulating a friend of mine on completing her thesis. She mentioned to me that her favourite word in it was “vitiate” (to impair or weaken the effectiveness of). Odd, I thought to myself. To be quite specific in that way. Then I thought to myself what is my favourite word from my thesis. After coming up blank the first time, the second time I thought of my favourtie word that wasn’t in my thesis. Mainly because my examiner thought it was funny I described certain effects of RNAi “abhorent” (causing repugnance; detestable; loathsome) instead of “aberrant” (departing from the right, normal, or usual course). For a lot of the experiments that didn’t work, I stand by my original phrasing.

Despite not coming up with a favourite word from my thesis, I do have a favourite sentence — mine spans the last two pages, after appendix, references and all:

“ma voix est faible…”

“…et même, un peu profane.”

Origin of the Haitian cholera…

The Haitian earthquake of last year seems such a long time ago, and yet its effects are long lasting. On Tuesday, January 12, 2010 at 21:53:10 UTC a 7.0 magnitude earthquake struck Haiti at a depth of 8.1 miles. The epicenter was located 15 miles away from Port-Au-Prince. The quake, at the time, killed 200 000 people, and displaced 2 million more. Aid, both public and private, entered the country, as well as many aid workers and emergency respondents. Only 10 short months after the quake, cholera broke out.

In January of this year, more than 93 000 persons have been affected by the outbreak, and more than 2100 have died. By the 7th July, 386 429 cases, including 5 885 deaths have been reported. In the wake of the cholera outbreak, tensions rose, as the exact origin of the outbreak was questioned. Early indications pointed to the bacterium had been introduced by Nepalese soldiers taking part in the United Nations Stabilization Mission in Haiti (MINUSTAH). An obviously delicate issue, one that promised to embarrass a few within the aid community, it would be important to pinpoint the exact origin of the Haitian cholera epidemic.

A study from earlier this year concluded that “the Haitian epidemic is probably the result of the introduction, through human activity, of a V. cholerae strain from a distant geographic source.” Serogroups of different V. cholerae strains, based on the structure of an outer-membrane O antigen and biotypes on the basis of a variety of biochemical and micro-biologic tests, allow ease of classification.

By using real-time DNA sequencing and comparing the genome sequences of two Haitian V. cholerae isolates and three additional V. cholerae clinical isolates from other regions of the world, they were able to determine the probable origin. “The V. cholerae strain responsible for the expanding cholera epidemic in Haiti is nearly identical to so-called variant seventh-pandemic El Tor O1 strains (the most important human pathogen in the last century) that are predominant in South Asia, including Bangladesh.”

A new study also adds weight to the conclusion that the outbreak originated foreignly. The authors of the study testing to characterize 24 recent V. cholerae isolates from Nepal and evaluate the suggested epidemiological link with the Haitian outbreak.

The Haitian cholera outbreak highlights how rapidly infectious diseases might be transmitted globally through international travel — a concept which is nothing new in this day and age. And points out that efforts to understand disease outbreak should take a global rather than local view.

And with this week being world water week, the link between access to clean safe water and health should be at the front of everyone’s mind.

Public health officials use advanced molecular tools along with standard epidemiological analyses to quickly determine the sources of outbreaks. As with SARS and swine flu epidemics that came before, the speed in which full genome sequences are obtained is accelerating at an unprecedented rate — and how bioinformatic knowledge can rapidly be turned into public health efforts.

World Cities…

And the next capital of the world is…? London!

Distorting science…

Another reason why traditional media can no longer be trusted to communicate science…

Science, Art, and the cliché…

The Guardian has an interesting piece up on the intersection between Art and Science. These types of collaborations garner a lot of column inches. The Wellcome Trust funds many projects along the same lines.

As interesting as the piece is, especially the one on speech, it all felt slightly odd. Trite and tame for some reason. Until I read John Hawks Weblog and understood why. The sense I got was that it was all very forced. A one way street. In none of the cases is the art used to better the science. Art simply takes the science and runs wild with it.

Which led me to think, instead of trying to marry two worlds, how about looking for the art in science. Primo Levi, writer of the greatest piece of science literature out there (The Periodic Table), beautifully found the art in his science — chemistry. Never had chemistry seemed more poetic, and for no other reason than because chemistry is poetic. The human experience told through the elements, or the elements explained through the human experience. I’m sure there are many more examples of art within science.

What had I twaught…

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