Archive September 2011

Teaching kids critical thinking Grant Jacobs Sep 25


… through adventures with the Nac Mac Feegles.

Looking at the titles of the blog posts over the weekend, it is as if the world had gone on a rampage of sloppy thinking.


Sometimes it really does feel like that when I read local newspapers or magazines.

Terry Pratchett’s The Wee Free Men is a children’s book that encourages critical thinking.

Tiffany Aching is a hag (witch). Like all true witches she has First Sight and Second Thoughts.

First Sight for seeing things as they are, and not as she might want to them to be.

Second Thoughts for questioning things.

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Factoid and links – Sunday reading Grant Jacobs Sep 25


Yup, it’s time I cleaned up my browser tabs and offered my readers pointers to a small selection of the interesting bits’n’bobs hiding there.

Reading the blurb for an up-coming lecture at the University of Otago, The 1918 influenza epidemic in Polynesia, I read ’The 1918 Influenza pandemic was one of the great mortality events in human history. Somewhere between 2 and 5 percent of the global population died due to this outbreak, […]’

Read about Ph.D. comics to be appearing as a movie.

Staying with the subject of movies for a moment, over at Science Progress Jonathan Moreno reviews the up-coming* movie Contagion, arguing it’s respects the intelligence of the audience and represents science and public health workers.

Science has partially retracted a paper proposing a link between the mouse XMRV virus and chronic fatigue syndrome (CFS). For those new to this, it is something of an on-going saga, one that I first touched on over a year ago now. (Others have been following this for longer.) More on this latest development can be read at Retraction Watch and elsewhere (e.g. at ERV).

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The 24/7 lab: in praise of time out Grant Jacobs Sep 23

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I’m coming late to a meme that has been circling around, starting from a several articles at Nature:

Some further commentary can be found on blogs (this is only a small sample of what is available):

Just for a contrast, I’ll toss in an example that has it’s origins in industry. I sometimes find it useful to compare practices in academia and industry. The pragmatic approach of industry can be revealing.

Let me reminiscence for a moment to set the scene.

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Life sciences want bioinformatics, but not so much e-infrastructure? Grant Jacobs Sep 21


During the Queenstown Molecular Biology satellite meeting on bioinformatics, Jeremy Barker, CEO of Queensland Facility for Advanced Bioinformatics (QFAB), presented the results of a survey of wishes of 165 respondents (to be found on the SP Consulting website).

Here’s a synopsis of the results from the survey ’targeted members of the life-science community’:

  • 47.3% (n = 129) consider that the development of e-infrastructures is a priority in bioinformatics.
  • 75.7% (n = 140) consider new methods and programs important (confusingly, the summary of these results refer to development in bioinformatics resources).
  • 84.6% (n = 149) consider the development of data standards important.
  • 79.2% (n = 144) consider development of bioinformatics initial and continuing education important (given as ‘bioinformatics diffusion knowledge’!).
  • 86.7% (n = 143) consider increasing the quality and number of interactions between developers and users important.

I’m not familiar with the details of how the survey participants were recruited, etc., but I’m not especially surprised by the latter responses. I imagine most people interested in using bioinformatics would rank the latter four as important.

What I think is interesting is the comparative lack of interest in e-infrastructures compared to new developments in research bioinformatics.


Other articles on Code for life:

Developing bioinformatics methods: by who and how

Research project coding v. end-user application coding

New bioinformatics journal — EMBnet.journal

Not Darwin’s tree of life

Literate and test-driven programming (in bioinformatics)

Keeping the serendipity

Journalists, editors and science writers – checking with the source Grant Jacobs Sep 21


A head‘s up to all those interested in science writing or, more widely, editing or journalism: make some time to head over to David Kroll’s blog and read his article Trine Tsouderos on This Week in Virology: When do you fact-check article content with sources? and the especially the extensive commentary in response to it.

The question at hand is checking the facts of an article with the source, in the case of science writing – the scientist. Many established (and notable) science writers have already offered thoughts.

My modest contribution is a passing reference to a passage from Elise Hancock’s ideas into words from page 46. Let me share the full passage with you. She writes that she views science writing as a collaboration of sorts, with scientists presenting material she translates for a wider readership. Moving on to the subject of showing copy she writes,

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I’m a scientist – the film Grant Jacobs Sep 20

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Stephen Curry has released his film, I’m a scientist. An introduction to the film can be found on the website hosting the film. He’s written about the making of the film on his blog, Reciprocal Space. (Do head over, read what he has to say and give him feedback.) There are even trailers!

The film features himself as presenter ’interviewing six scientists who are at different stages of their careers. They were kind enough to share their stories of how they got into science and to talk about why they like doing it and what they think it takes to be a good scientist. Most importantly of all, they reveal their favourite type of cheese.’

(I have to admit when I think of films and cheese together, I think of the Wallace and Gromit movies from Aardman Animations.)

Stephen’s film is, in his own words, ’[…] made with teenage school-children in mind but I hope it will also appeal to other students, teachers and the general public, and maybe even to other scientists.’

Despite this, I think many others will be interested in what these six people have to say. Scientists, too, may find it interesting to compare notes, as it were.

Before I leave you to it, one sound bite. When asked if you need to be a bit of a genius to do science Marcia Philbin replies:

No, I’m not a genius. I’m just somebody who knows what she likes to do and when she’s interested in something works hard at it and I will remain focused, determined, committed and I will keep trying. That’s the key thing. To keep trying.

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Paypal’s massive error, hex and nybbles Grant Jacobs Sep 20


(A little light computing entertainment for general readers.)

Seen recently on an on-line bookseller’s news updates:

Paypal has a global problem where for some customers the ‘$’ in their email confirmation is being replaced by ’24′. For example if you purchase something for $19.99, your paypal email will say you have purchased it for 2499.99.

There is no need to worry however as you have been charged the correct amount. Paypal engineers are working to fix the problem.

Ohhhhh… some people are in for a shock!

Computer geeks–programmers, at least–will instantly spot the problem.

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In the near future: genome sequencing for the masses Grant Jacobs Sep 18


In this short (11 minute) TEDxBoston lecture Dr. Richard Resnick gives the hard sell on widespread genome sequencing.

YouTube Preview Image

A few quick pointers or thoughts from my viewing of it: Read the rest of this entry »

Christchurch rockfall Grant Jacobs Sep 16

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While I slave away, looking forward to the weekend when I might find time to write something (as opposed to pasting up other’s work*), two items on rockfall in, or from, the Port Hills.

The Port Hills lie to the south of the city, forming the northern portion of what locally is known as the Crater Rim – a circular ring of hills around the harbour that are the rim of an extinct volcano.

For me one of the not-foreseen hazards of the earthquakes in the Christchurch area was rockfall. While it might have been a known risk amongst geologists, I am under the impression many Christchurch residents (past and present) were, like me, caught by surprise on hearing reports of rockfall and the damage caused.

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Discussion: ‘Manager-free zone’ call for university Grant Jacobs Sep 13


To provide a space for open discussion I’m bringing you these two letters to the editor from today’s edition of the Otago Daily Times. (The letters they don’t seem to be on their website, and there is only so much space for the ODT to print letters to the editor.)

Mike Hamblyn writes, somewhat tongue-in-cheek:

THERE has been disquiet lately about Otago University having been taken over by the managers. This means academics cannot flourish any more because they’re hog-tied by the strictures of managers who want researchers to tick the right boxes instead of engaging in ’blue skies’ research. So, it would seem academics are an endangered breed. It seems to me then, we need to find some new means of protecting our university at Otago and our academics from the managers. In keeping with the spirit of the times, we should pass some legislation. The legislation would be, in keeping with Dunedin’s reputation as the wildlife capital of New Zealand, predicated on a currently fashionable wildlife or conservation theme. I propose the Protection of Endangered (Otago) Academics Act.

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