Archive October 2012

Seeking science reading? Grant Jacobs Oct 31

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…you’ll want to know about the update to

As I write ScienceSeeker pools science writing from 1240 blogs, indexing 163,472 articles.

A key new feature added is searching. Unlike limiting google to searching blogs, searching ScienceSeeker limits your search to those science-related sources that have been approved by the ScienceSeeker editors.

When you first land at ScienceSeeker, you’ll see the recent editor’s picks and below it posts with citations – those that are most likely to be directly covering the research literature. As well as the last few posts on ScienceSeeker, the right-hand side may show a selection of posts of whatever topical theme is running. (Selected posts about ‘super storm’ Sandy are up as I write.)

Clicking on ‘Posts’ from the site menubar (see above) will produce a list of the latest posts on ScienceSeeker, most recent first.

If you click on the date for a post, the (first portion of the) first paragraph will appear immediately under the title, as in the first example immediately above. (Alternatively you can click on the little ‘+’ to the right of the title.) Clicking on the title will take you to the article in a new tab.[1]

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Seeing the wind Grant Jacobs Oct 30


A blend of infographic art and meteorological science,’s wind map is mesmerising. It’s almost hypnotic, you can sit and watch the patterns emerge. (You’ll want to see the ‘live’, dynamic, map, not the still snapshot below.)

Those wanting to see tropical storm Sandy are best to take a peek before the next day’s data is uploaded, although I suspect it’ll be added to the gallery.

On that note, don’t miss the gallery of previous notable days. With more complex wind patterns on display, some of these are more interesting to view than the current map, with it’s one dominant feature.

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Free – short science stories Grant Jacobs Oct 26

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The shortlisted entries for this year’s Manhire Prize* are now available on the Royal Society website as PDF files, free for you to read.

One sciblogger features in the fiction section – Gareth Renowden, author of Hot Topic and, more recently in fiction, The Aviator (The Burning World 1). Well done, Gareth!

The stories for the shortlisted entries are listed on the right-hand side of the page – you may need to scroll to the right to see them. There are both fiction and non-fiction stories.

An anthology of past winners from the past five years of the competition is also available as a free eBook in either PDF, .mobo or epub formats. (Cover shown to left.)

Postscript: I’d like to also give a shout-out for Deborah Blum’s new book, Angel Killer, available on-line for $US2. Deborah has written about writing her book about Albert Fish—“the tale of this serial killer of the 1920s and ’30s, this gifted child kidnapper, this notorious American cannibal”**—at Wired.

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Communicating data clearly Grant Jacobs Oct 25

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Correct and appropriate presentation of graphs matters. It’s worth taking time to consider how to present your data, to convey the information clearly in a way that is readily perceived and accurate.

Not just for scientists, either. Graphs are used ubiquitously, after all.

‘Convincing’, xkcd. Original:

On-line there is some excellent material on presenting data. One example is a handout for a presentation[1] Communicating data clearly by Naomi Robbins, who writes Effective Graphs at Forbes blogs. (Some of us here take down poor science coverage in the media. Among other things Naomi writes, she takes down poor graphs in the media!)

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It’s a small, small world (and three wise monkeys) Grant Jacobs Oct 24


The Annual Nikon Small World competition is one of my favourite events.

Wonderful shots of tiny things you don’t see in daily life. I’ve included a couple of favourites below. Readers should go to the Nikon site to find their own favourites.

First is these three black mastiff bat embryos:

Dorit Hockman, University of Cambridge

But why is there no reference in the citation to the three wise monkeys?!* -

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On Italian earthquakes, scientists and communication Grant Jacobs Oct 23


As you’ll know by now there is an uproar over the sentence handed down to six Italian scientists over communication of earthquake risk.

I’m not doubting that the experts drew fair conclusions from the evidence available at the time; there seems ample commentary on this. It’s not my field and I can only take their word for it. My reading is also limited – I have only so much time.

My impression is that the complaints were over not getting risk information from the scientists (and what they did from a local spokesperson being inaccurate). Leaving aside the ‘crime’ aspects, which seem at best vexed, was communicating directly to the public ever part of the scientists’ brief?

This 2011 background piece in Nature by science writer Stephen Hall is a good starting point for this story. It covers many aspects well and many of the comments that follow are worth pursuing, too.[1] (NewScientist has briefly looked at the earthquake prediction angle.)

Communication to the general public is pointed at as being the key question, for example this passage from Hall’s 2011 Nature piece:

The view from L’Aquila, however, is quite different. Prosecutors and the families of victims alike say that the trial has nothing to do with the ability to predict earthquakes, and everything to do with the failure of government-appointed scientists serving on an advisory panel to adequately evaluate, and then communicate, the potential risk to the local population. The charges, detailed in a 224-page document filed by Picuti, allege that members of the National Commission for Forecasting and Predicting Great Risks, who held a special meeting in L’Aquila the week before the earthquake, provided “incomplete, imprecise, and contradictory information” to a public that had been unnerved by months of persistent, low-level tremors. Picuti says that the commission was more interested in pacifying the local population than in giving clear advice about earthquake preparedness.

“I’m not crazy,” Picuti says. “I know they can’t predict earthquakes. The basis of the charges is not that they didn’t predict the earthquake. As functionaries of the state, they had certain duties imposed by law: to evaluate and characterize the risks that were present in L’Aquila.” Part of that risk assessment, he says, should have included the density of the urban population and the known fragility of many ancient buildings in the city centre. “They were obligated to evaluate the degree of risk given all these factors,” he says, “and they did not.”

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Here’s my number, so call me maybe? Grant Jacobs Oct 22

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Researchers can give their number[1] and maybe that glamorous research journal or laboratory will call them sometime, maybe.

ORCIDs are the thing, here. Open Researcher Contributor IDs.[2] Researchers can tag themselves with a number and use this to identify themselves and their work. You can also use the directories to find others with shared interests.

A common issue is that name can be ambiguous. Another will be for those who change their names. (A ‘tradition’, at least in Western nations, has been for women who have published before getting married to retain their née for the scientific word to maintain a continuity of the record.) Researcher identifiers can help these issues.

A key thing I want to bring up is that, in principle, it might be possible to link ORCID to any work. If made available, scientists who do science communication might be able to ‘tag’ their outreach efforts with their ORCID.

As far as I can make out thus far (See Discursion, below) this appears to be in the hands of registered member organisations, who pay a fee for access, but at least it is one mechanism institutions might use to integrate outreach and other work with research work.

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Those behind charter schools are to be exempt from public scrutiny – ? Grant Jacobs Oct 19


 (A Friday tilt at an aspect of New Zealand’s ‘charter’ schools push – back to my usual fare later.[1])

This from Kate Shuttleworth at the NZ Herald:

The people who set up charter schools will be exempt from public scrutiny and Official Information Act requests under legislation that is being pushed through Parliament […]

Read at face value, this is unsettling.[2]

You’d think the way forward is more openness, not less. Parents would certainly want to know who is behind setting up a school and it’s charter and the wider community surely has a right to know the background behind schools that are being set up in the community.

If meant as avoiding the time that enquiries can involve, I might sympathise – but feel it’s no excuse to duck or avoid the interest. People will want to know and surely it is better to satisfy that interest.

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A vaccine discussion forum Grant Jacobs Oct 17


Introducing the New Zealand Immunisation Advisory Centre (IMAC) forum.

Some time ago while mulling over what science writing (blogging) groups might offer parents with questions about vaccinations, Thoughts on, and for, those trying to choose to vaccinate or not, I came to thinking[1] that in the absence of discussion forums set up by those with expertise in immunisation, a useful compromise might be to ask at science writing groups. It is important that people with relevant expertise be present and that discussions be open.[2]

After I wrote that article I become aware of the New Zealand Immunisation Advisory Centre (IMAC) forum.

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All together now: high-throughput sequence mapping tool compendium Grant Jacobs Oct 16

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Biologists and bioinformatics people interested in high-throughput (HTS) mapping may find this this one-page summary of all currently-available HTS mapping tools useful. The comparison table of the different features of each mapping tools will certainly beat having to dig this information out of the papers or on-line documentation. There’s also a timeline of when the methods first appeared. DNA, RNA, miRNA and bisulphite mappers are listed.

Features noted in the comparison table include: Read the rest of this entry »

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