Archive May 2011

Is your computing desk well set up? Grant Jacobs May 31


Taking my lead from Steve Caplan’s computer-work related pain, I take a brief look at setting up your computer workstation properly.

When I was a Ph.D. student in England, for a time I suffered chronic pain around the right shoulder blade. After a little reading and some experimentation, I came to believe the cause was a poor set-up for my computer desk.

Having put the computer desk layout right I’ve rarely had this pain again, despite working most of the day on computers–and then some time in the evening too–for years.

There are plenty of websites around describing a good set-up for a computer workstation, like the one below from the Computer Workstation Ergonomics page at the website of the Safety & Health division of The University of Western Australia:

Source: Safety & Health, University of Western Autralia

Source: Safety & Health, University of Western Autralia

If you (or your students, staff, etc.) are going to be working at a desk for any real length of time, I think it’s well worth the effort to set it up properly.

When I look at (biology) students working away at their desks, I have to admit I worry that their computer set-up is less than ideal.[1] Most full-time computer workers (secretaries, programmers, computational biologists, etc.) will–I hope–have been offered appropriate desks, etc., but I still see a lot of ‘make do’ in university departments.

The basics are covered in the graphic and the accompanying article, but I’d like to draw to attention two factors I found particularly relevant for me, one of which isn’t mentioned there.

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Post publication peer review – a new way of doing science? Grant Jacobs May 30


I lead off from Carl Zimmer relating how on-line conversation played a role in ’the arsenic bacteria’ publication as an excuse to muse about post-publication peer review.

Reading Carl Zimmer’s update on the ‘arsenic bacteria’ story in Slate last night, while writing my own update, I encountered again the phrase ‘post publication peer review’:

’Redfield and her colleagues are starting to carry out a new way of doing science, known as post-publication peer review. Rather than leaving the evaluation of new studies to a few anonymous scientists, researchers now debate the merit of papers after they have been published.’

On his blog, Carl introduces his Slate article:

Over at Slate, I look at how the online conversation has changed the way scientists do their work.

Post-publication criticism, in all it’s forms,[1] follows any research publication of note or notoriety. Has done for years, decades. I don’t think there is a lot new there.

I personally suspect ‘the arsenic bacteria’ media story may be better viewed as an example of the media making more (read: better!) use of on-line criticism–blogs and all that, too–than it typically does, rather than a change in how science is done. As I wrote last time on this:

There is nothing new going on in scientists writing on blogs, compared to writing on bionet (or its ilk). There might be something new in journalists tapping into this writing, perhaps-?

More to the point, my reading is that those promoting post-publication peer review mean something slightly different by post-publication peer review.

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Arsenic life – more criticism, formally published Grant Jacobs May 29


Science magazine has lined up eight Technical Comments on-line in advance-of-print release, along with a response to these from the authors, that will stand alongside ’the’ arsenic life paper to be published in in print next week’s edition after a wait of roughly six months. With the exception of the accompanying editorial, these are all open-access.

For those new to the story, the ‘lite’ gloss–i.e., for a non-scientist readership–of this research arguing that a bacteria uses arsenic in place of phosphate in it’s DNAgoes something like this.

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What do you think is the most influential science/technology breakthrough? Grant Jacobs May 24

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IBM has released results from surveys of 1000+ people from different countries, asking what they considered the most important technological ‘breakthroughs’ of the last 100 years were.

One striking feature is the difference in responses from women to men. Women favour health-related developments and men, if anything, point at the internet.

While this might perhaps be what intuitive gossip would suggest anyway, I find it a little startling to see it’s as large a difference as it is in print.

Here’s what New Zealander’s thought (this shows the responses for three different questions; the most influential science/technology breakthroughs is on the left):

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Fairy fly Grant Jacobs May 22


Alison has challenged me to another biological image duel.[1] Here’s my response:

Fairy fly. (Credit: Spike Walker. Source: Wellcome Images.)

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Christchurch earthquake telethon Grant Jacobs May 22

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Running for the next twelve hours is a telethon to raise funds for the Christchurch restoration project.

My readers will already know well that Christchurch, my hometown, has experienced a large earthquake last year (September 4th, magnitude 7.1) and a (large!) number of aftershocks, in particular a magnitude 6.3 event on February 22nd.

You can contribute and watch the event live on-line, at Rise Up Christchurch. Local viewers can watch it on MaoriTV.

There’s interviews of people, views of the central business district which is badly damaged, entertainment.

Some items, among others, being sold (see

  • a pair of Gucci shoes worn and autographed by pop singer Lady Gaga
  • pop singer Katy Perry’s guitar (signed)

For those that know them, ’names’ that will be appearing include in no particular order!:

  • Usher (singer)
  • Rachel Hunter (model, NZer)
  • Anna Paquin (Oscar-winning actress, NZer) will be amongst a crowd of other Kiwi actors and company at Hollywood including: Martin Henderson, Mark Hewlett, Chris Hobbs…
  • Neil Finn (singer, of Crowded House, Split Enz)
  • Manchester United boss Sir Alex Ferguson (football manager)
  • Benji Marshall (rugby league star and Kiwis team captain) with sporting guests in Australia
  • Zane Lowe (radio, in England; NZer)
  • Prince Edward (British Royalty; lived in NZ for a year; from recollection there is apparently 30min of time from Buckingham Palace)
  • Peter Jackson (Oscar-winning movie director, Lord of the Rings, King Kong, Heavenly Creatures, The FrightenersThe Lovely Bones, etc.; NZer; this article suggests he’s made a couple of short films for the event)
  • Sir Ian McKellen (actor, stars in the up-coming The Hobbit)
  • Shane Cameron (boxer) and Candy Lane will take to the dance floor

Update: This long article by Cate Brett offers a perspective from three months on. It looks at the wider picture, for example mentioning the ~20,000 homes with significant damage, the social developments and so on.


I may add more details later today, if I find time.

For those from overseas ‘NZer’ is a common short-hand for New Zealander. Less to type…

My apologies for not linking to or giving credit to all the sources of the information (mostly media reports) as I usually would, as my time is very limited.

Other earthquake-related posts on Code for life:

Christchurch/Lyttelton Feb 22nd 2011 earthquake — questions and answers

Aftershock tweets

6.3 earthquake in Christchurch

Christchurch (Lyttelton) earthquake ground movement captured by satellite imagery

Liquefaction in a barrow

Lyttelton earthquake peak ground acceleration

Magnitude vs. intensity; Chile vs. Haiti

Earthquake, South Island, New Zealand

TEDxChCh – TEDx on the Christchurch earthquake Grant Jacobs May 21


Just a quick note to say that this event is already live streaming and running; click on the video to start the streaming. Captions are available (I’ve yet to test this).

For those not familiar the event, TEDx meetings are independently-organised local counterparts to the famous annual TED lectures held in California, aiming to offer ’ideas worth spreading’.

This meeting is focused on ideas for rebuilding Christchurch (my hometown). The programme is available on-line; click on the speakers’s name for more details of each speaker and their presentation. Each speakers’ page has a space the bottom for comments.

If you can keep up with the crazy pace, you can follow twitter comments on the event using the #TEDxEQChCh hashtag.

As I write they are taking lunch break for one hour; if you’re wondering why you’re not seeing much – there’s the reason. Lunch break is now over and they’re should be on-line.

I had hoped this might be in the evening, hence the lack of advance notice – my apologies.

Hopefully the talks will be presented on-line for later viewing; I’ll want to catch them myself!

(Updated to add more introductory material and update the lunch-break situation.)

Other recent posts on Code for life:

Doggie ERVs

Optogenetics: light on brains

Keeping the serendipity

Expert Witness – new forensic science book

Aftershock tweets

Doggie ERVs Grant Jacobs May 20


Humans and their best friend may share ERVs.[1]

My first thought was ‘is 10,000 years long enough?’


(By James Jun, source: Flickr)

Let me explain.

Firstly: ERVs are endogenous retroviruses.



Our genomes are DNA-based. Retroviruses are viruses with RNA-based genomes that, once they’ve infected a cell, create a DNA copy of their genome that they insert into the genome of their host. That’s us, in the case of human endogenous retroviruses, or HERVs.

Endo = within.

HERVs are found within our genomes. They have become part of us, they’re replicated and passed onto our children along with the rest of our DNA. To be passed on through generations, the virus had to have infected our germ cells sometime in the past.

Almost all ERVs no longer function as viruses because they are only remnants or are repressed.

Dogs have ERVs, too. The authors of the research I’m covering here have called them CfERVs: Canis familiaris ERVs. Canis are the dogs – wolves, coyotes, jackals included. familiaris is the one we know well. *Woof* :-)

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Keeping the serendipity Grant Jacobs May 20


Last tonight I was browsing Occam’s Typewriter, one of my favourite science blogging collectives.[1]

Frank’s article, The challenge of going beyond, leads off from two people independently remarking to him that they thought that electronic journals have resulted the loss of serendipity in their reading. The article and comments are well worth reading; I encourage my readers to head on over if you haven’t already.

Contrary to the people the commented to Frank, I don’t think that electronic journals have changed how I capture serendipitous aspects of my reading all that much. If anything they’ve made it a little easier, if a lot more distracting!

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Optogenetics: light on brains Grant Jacobs May 18


Optogenetics lets researchers directly examine the brain through controlling neurons in the brain by inserting genes for particular photoreceptors, proteins that respond to light, into neurons.

But let Ed Boyden explain it.* He gives an excellent presentation, with great visuals:

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