Archive November 2012

Whole genome sequencing for serious vaccine complaints? Grant Jacobs Nov 30

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While I work on longer pieces, a stray thought: how far away are we from genome screening for (court) inquiries about ‘vaccine damage’ so that those with genetic causes might be resolved promptly?

A number of countries maintain databases of reports of possible adverse reactions to medications. For possible vaccine reactions, in New Zealand we have the CARM database[1]; in the USA there is VAERS.

In the USA claims for ‘vaccine damage’ can be filed to the National Vaccine Injury Compensation Program.

I imagine these proceedings can take considerable time and cost. What fraction of the alleged cases of ‘vaccine damage’ are in fact rare genetic defects? How many of these case are in effect a cohort of sorts of rare disorders like mitochondrial defect conditions, heart disorders, seizure disorders (e.g. Dravet syndrome) – with genetic causes? Will it be pragmatic soon to routinely screen these cases for genetic conditions?

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Sea stars and mosaics Grant Jacobs Nov 29

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At first you wonder if this sea star is real. It looks more like a kid’s geometric doodle from a distracted afternoon at school than an animal.[1]

Click on image for source; Creative Commons Attribution-Noncommercial-Share Alike 3.0 license

The World Asteriodea Database indicates Iconaster longimanus was first described in 1859. (The photo above was taken by Dieter in the Philippines in February 2007.)

(Source: Wikimeda, pubic domain.)

Among the later descriptions in the Asteriodea Database entries are ones from the famous HMS Challenger voyage.

To most today the name Challenger recalls the space shuttle that horrifically broke up little over a minute into it’s flight and brought a temporary halt to the shuttle program. The shuttle Challenger was named after the HMS Challenger, whose voyage was a grand British scientific survey of it’s day.[2]

Unlike the short life of the ill-fated space-farer, HMS Challenger’s voyage spanned over several years, 1872-1876 and travelled the world.

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Brain drain and gain (brain flow) in 16 nations Grant Jacobs Nov 26


From the National Bureau of Economic Research come results of a web-based survey of 17,182 corresponding authors in 16 countries from four fields during 2011:[1]

The abstract goes on to say:

Switzerland has the largest percent of immigrant scientists working in country (56.7); Canada, and Australia trail by nine or more percent; the U.S. and Sweden by approximately eighteen percent. India has the lowest (0.8), followed closely by Italy and Japan. The most likely reason to come to a country for postdoctoral study or work is professional. Our survey methodology also allows us to study emigration patterns of individuals who were living in one of the 16 countries at age 18. Again, considerable variation exists by country. India heads the list with three in eight of those living in country when they were 18 out of country in 2011. The country with the lowest diaspora is Japan. Return rates also vary by country, with emigrants from Spain being most likely to return and those from India being least like to return. Regardless of country, the most likely reason respondents report for returning to one’s home country is family or personal.

My own attention was drawn to those countries that had both a low frequency of acquisition of overseas researchers and low a low frequency of ‘exporting’ their own researchers. IEEE Spectrum magazine had a similar thought: ‘Japan is the most insular country surveyed, exchanging relatively little scientific talent with the rest of the world.
’[2] Brazil and Spain also strike me has having low percentage ‘brain flows’.

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Did you get a feel for what the grant-application process and lifestyle involved as a PhD student? Grant Jacobs Nov 22


Do you think Ph.D. students should?

One thing I’ve written about in the past is what is taught to Ph.D. students. Perhaps more accurately, elements of what might be taught to them. (I would say what should be taught to them, but your opinion may differ.)

Ph.D. training ought to prepare the student for future positions in research science. I’ve previously touched on how we teach students how to write scientific papers, for example. Ph.D. training might also prepare students for the wider range of positions that science Ph.D.s in practice take up—the research career as the follow-on from a Ph.D. occurs less often than work outside of academia.

Recently I have been talking amongst others about grant applications.

Were you taught about the grant application process as a student? How did you learn what grant funding and the soft-funded lifestyle might involve?

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Dear journalists and editors, (again) Grant Jacobs Nov 14


Some time ago I wrote to you over your advocating unsound treatments in reporting fund-raising efforts.

I now find myself writing again on much the same issue, this time regards your advocating unsound services. The issues are so similar I find myself drawing on my earlier words.

Please, when you decide to ‘advocate’ for a service, check that it is sound.

Articles about services offering hope of treating illness no doubt sell copy, but with that comes responsibility.

These articles, with their details of how to contact the service provider at the bottom, effectively advocate the service to the reader.

Sure, you could argue whether the treatment is sound is for the reader to judge before giving them their money – but wouldn’t that be newspapers shirking their moral responsibilities?

If you put down details of the service in the article you’re effectively putting your weight behind it.

Editors, like most people, will be aware that articles in the press carry some weight of creditability, rightly or wrongly. There will be an expectation among many that the media has checked ‘the facts’.[1]

It seems to me either that this checking should done, and done properly, or the advocacy dropped.

My brief missive here follows from an article espousing the services of an iridologist published yesterday in the New Zealand Herald that was brought to my attention by my colleagues.[2]

Even the briefest of background research would have revealed that iridology is nonsense. Quaint, well-meaning nonsense, perhaps, but nonsense nevertheless.

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Is a PhD enough to teach at school? Grant Jacobs Nov 02


Radio NZ writes,

The group advising the Government on how to set up charter schools wants people who have no teaching qualifications to be given official teacher registration.

The Charter School Working Group says expertise, rather than a teaching qualification, should also be enough to gain registration.

Chairperson Catherine Isaac says this may include PhDs or degrees in science, engineering or languages. “They may be people with music, arts, trades qualifications who would make great teachers,” she says.

More details are in a NZ Herald article,

While we await full details on the idea, what are readers’ thoughts?

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