Archive June 2011

Independent top-tier open-access biomedical and life sciences journal Grant Jacobs Jun 30


Over at Occam’s Typewriter[1] Frank has written introducing an initiative by The Wellcome Trust, the Max Planck Society and the Howard Hughes Medical Institute to launch a new top-tier open access journal for biomedical and life sciences research.

Frank has most of the news, so I won’t repeat it, but to add that there is a lot to like about this initiative. Here’s a quick bullet-point list of points and thought gathered from Frank’s article and the Wellcome News press release and some of the commentary Frank’s article links to:

  • To open in northern hemisphere summer, 2012.
  • Edited by leading actively-working research scientists
  • Only one round of revisions – reduce need for modifications or additional experiments.
  • On-line only – opportunity to explore/exploit new formats and tools to present content.
  • No author charges.
  • No page limits. (But limited supplementary figures.)
  • Frank notes that the reviewers’ comments will be published anonymously and they are considering paying reviewers.
  • Open access: ’the entire content will be freely available for all to read, to reproduce and for unrestricted use.’
  • [own thought] Directly funded by research funders. In a sense research funding already funds journals, just via a chain of hands: research grant, levy to library, then library to publisher; also direct publication costs are taken from research grants. Here three of the bigger funders are directly putting funds into the publication for wider benefit. Intuitively feels good – at first glance, anyway.

Frank’s article has a links and quote to number of responses to this announcement, e.g. how this model is to be made sustainable. In particular, Declan Butler, from Nature, has a lot to say (see also the comments that follow his opinion piece).

On the mix of no author charges and open access: what not to like? I imagine this alone would attract submissions, and with it competition amongst submitters. It will particularly appeal to those outside academic institutions or institutions with limited budgets.

Read the rest of this entry »

Christchurch earthquake, buildings and acceleration maps Grant Jacobs Jun 29


Just released by the Royal Society of New Zealand today (June 29th, 2011) is an information paper The Canterbury Earthquakes: Answers to critical questions about buildings (PDF file, 718kb).

It’s well worth reading – not just for those in Christchurch, but anyone in earthquake-prone areas in New Zealand or elsewhere, or the merely curious.

This work presents questions and answers in a joint effort by ’the Royal Society of New Zealand, the Institution of Professional Engineers New Zealand, the Structural Engineering Society New Zealand, the New Zealand Geotechnical Society and the New Zealand Society for Earthquake Engineering, who have co-ordinated science and engineering expertise from across New Zealand.’

(Update: Take-home points at end of this post.)

In addition to talking about buildings they have presented the peak horizontal and vertical ground acceleration recordings for the February 22nd and June 13th events onto maps (shown below).

Read the rest of this entry »

Follow the World Conference of Science Journalists on-line Grant Jacobs Jun 27


For those interested in science communication, a quick heads’ up: the World Conference of Science Journalists, moved from Cairo to Doha, Qatar, starts ’today’. (Where they are, that is!) Details of how to follow the event on-line can be found on a page at the US National Association of Science Writers.

Update: looks as if videos will be coming under the WCSJ2011 YouTube account. There are no presentations up (yet), but there are some interviews. I’d include one below as a taster, but the WordPress blog editor doesn’t seem to want to embed these, so you’ll have to make the trek over there yourself!

Other articles in Code for life:

Follow arsenic life science ’live’

Media thought: Ask what is known, not the expert’s opinion

To link or not to link: mainstream media and no links at all

Of use of the active voice by scientists

XMRV prompts media thought: ask for the ’state of play’

Three kinds of knowledge about science and journalism

Scientists can’t write?

Follow arsenic life science “live” Grant Jacobs Jun 26


Try following a research project on-line.

Professor Rosie Redfield’s (UBC, Vancouver, Canada) on-line criticism of Felicia Wolfe-Simon’s proposal that a particular species of bacteria utilising arsenic in place of phosphate in it’s DNA backbone featured in early criticism of this work.

Having obtained samples of the bacteria, Prof. Redfield is live blogging her research on GFAJ-1. The articles are a little geeky–it is research, after all–but I’d encourage my non-scientist readers to try their hand at following the story as it evolves, as it gives you a feel for a research project.*

So far there is:

Read the rest of this entry »

Christchurch earthquake land damage background Grant Jacobs Jun 24

1 Comment

Before starting, I should apologise to readers for bringing so little of late, being swamped with work…[1]

The latest news on the Christchurch earthquake has been the announcement of a relief package for some of the worst affected suburbs in Christchurch from the September 4th, 2010, February 22nd, 2011, June 13th, 2011 (and other aftershocks) target an initial ‘red zone’ (large PDF map) of properties with badly damaged land, rather than damaged buildings as such.

Here I’ve gathered a few background items available on-line that might interest readers. (I’m not a geologist; I’m offering this loose collection of a video, brochure and a presentation (summary report) of the survey work in lieu of something more substantial from a geologist in the meantime.)

Read the rest of this entry »

Some thoughts on book reviews (and the cat’s progress) Grant Jacobs Jun 19


A quiet evening rumination mulling the need for reviewers to recommend who the book would suit and other things.[1] There’s also the cat’s progress while writing. Nothing to do with science, I’m afraid: just consider that these thoughts also apply to reviewing books with science themes.

Wine. Check.

Cat in basket on desk. Sort-of check.

She’s tried the basket but is preferring to sit next to the computer. Wants to take over my lap but seems very content to perch right next to and looking down over my keyboard, watching my fingers work the keys. The sort of thing that enthrals a cat.


I ruminate about everything. Sometimes I think it almost defines me.[2]

Originally had thought to name this blog Random Ruminations; if I let myself go it probably would be. (It’d be awful; don’t encourage me.)

A couple of review copies of books sit on the little cabinet next to my bed. There are plenty more besides on my shelves that I’d share my thoughts with you on – if I had time. I wish could invent extra hours or warp time. Don’t we all?

Aimee–my cat–is now trying investigate the inside of my vest by carefully stretching a paw out across me into it.[3] I suspect she’s attracted to the zip of the inside pocket. She likes to flick the slider handles. When she was younger her waving her paw around my crutch puzzled me until I realised she was after the my trouser zipper. Shiny things that move.

I’ve never studied how to review a book. Maybe I have in English at high school, but I’ve forgotten it. There are plenty of articles with suggestions and of course anyone who read books much has read plenty of book reviews.

So what makes a good book review?

Read the rest of this entry »

Early life (and trilobite eyes) Grant Jacobs Jun 18


A brief diversion on trilobite eyes for everyone and a quick head’s up for New Zealanders on a couple of events related to the science of early life.

This Sunday sees the start of the David Attenborough narrated BBC two-episode series First Life. Rated 8.5 out of 10 by reviewers at IMDB, the promotional material promises the BBC’s stunning photography from all over the world. Catch it on Prime TV Sunday at 8:30pm.


Explore the series website, too. Beyond a synopsis of the series, there’s short trailer video (see below or on their website), photos, and information about making the series.

I’m not a palaeontologist–I know very little about fossils–but the fossil shown in the trailer (see to left) with it’s impressive raised spines and conical structures might be an Erbenochile genus of trilobite. As Attenborough says in the trailer, those raised conical things are compound eyes.

Read the rest of this entry »

Mac OS X Time Machine backups – a need for versions Grant Jacobs Jun 17

1 Comment

Apple’s new Versions feature in their up-coming Mac OS X Lion. (For general readers, not hard-core geeks!)

Some time ago I wrote about backups under Mac OS X. One of the limitations I mentioned was that Time Machine drops intermediate versions:

4.2.1 The backup loses finer increments over time


Apple’s newest version of it’s operating system, Mac OS X ‘Lion’ has a new feature called Versions that for users with more modest needs may help address this.

Apple has a blurb on Versions right near the bottom of their page summarising what they claim are over 250 new features in OS X Lion.

Basically put, one solution to the loss of intermediate files in Time Machine backups is to create copies of a project (with different filenames) that represent old versions of the project you want to hang on to.

One way to implement this solution is to use existing version control software. For those will more modest needs it looks as if Apple’s Versions may do the trick.

Read the rest of this entry »

The Vulcan Laser Grant Jacobs Jun 16

1 Comment

For a bit of light relief and as a follow-on of sorts from Aimee Whitcroft’s recent post Dr Evil’s fondest wish may yet come true (you can’t miss a post with title like that, surely), I bring you this video from the Backstage Science series of a tour around one of the world’s most intense lasers, the Vulcan Laser:

YouTube Preview Image

Other articles on Code for life:

“Knowledge is merely opinion.” Storm – in cartoon and words

Ernest Rutherford’s gold foil experiment

Literate and test-driven programming (in bioinformatics)

The Christchurch / Lyttelton earthquake aftershocks news thread

The Roots of Bioinformatics in Theoretical Biology

Why (some) people don’t trust science Grant Jacobs Jun 14


A commenter, John, wrote in another thread–which is really about another topic entirely–offered this (quoted in full):

I think the bigger question is, why don’t people trust science anymore?


1. It’s been wrong before (asbestos, 245-T, etc)

2. Potential corruption (by funders, politicians, government departments, etc. AFTER the scientists release it)

3. Public’s lack of time to research evidence, so decide based on perceptions (easily swayed)

4. ‘The man’ — science is cold, establishment, authoritarian.

New Agers present a much more attractive image — peace and love. True they don’t do rigorous tests, but then they don’t make as many ’scientifically proven’ promises the way science does. Little wonder they earn more trust.

Maybe science is antiquated and out of alignment with how society thinks now? Many other industries are having to adapt to survive — music, journalism, museums, etc. Has science made any radical, fundamental changes to try to gain the public’s trust?

I’d like to offer some very quick starter thoughts. I haven’t had time to think this through (work to do), but I hope this might seed useful discussion. Free-form rumination rather than an essay, if you will.

I’d suggest it’s not science itself that is ‘wrong’, but that the interface that science has with the public that might benefit from change.

Read the rest of this entry »

Network-wide options by YD - Freelance Wordpress Developer