Archive October 2010

Writing tip – avoid promoting particular booksellers… Grant Jacobs Oct 31


… by linking to a neutral intermediary, such as OpenLibrary or GoodReads, rather than a bookseller.

I often write about books. Something to do with enjoying reading!


Some readers might have noticed that when I link to a book, I almost always the link to OpenLibrary.

While reading many blogs I found most people linked to one particular very well-known US-based international on-line bookseller. In doing this they were effectively promoting that company over alternatives, driving potential clients to them.

It struck me as conflicting with the notion of not promoting particular companies when writing neutrally.

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Fainting kittens – feline myotonia congenita? Grant Jacobs Oct 29


Going all over the internet is this bitter-sweet video:

YouTube Preview Image

Below is some of what a quick sweep of reading teaches me about myotonia congenita. (This is hardly a definitive survey of this disorder! Share what you know, I’m learning too.)

Myotonia congenita, or congenital myotonia is a skeletal muscle-locking disorder. In affected individuals, when the muscles contract, they do not immediately relax again: for a short period the affected muscles stiffen. If the individuals are standing up, they’ll fall over, as the kittens in the video do.

Startle reflexes can cause sudden muscle contraction, hence startles can induce falling in these individuals.

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Friday tabs Grant Jacobs Oct 29


Not the bar kind.

As has become customary for me, on Friday I try clean up browser tabs I’ve left open holding an interesting article. It’s my end-of-the-week clean-up and blog links for readers.

Gott pocket map of universe (small) 300px

The scale of the universe (Those not interested in astronomy or the scale of things may wish to skip to the next section.)

Chris McDowall posted this morning several videos showing the scale of things. I toyed with posting one of those videos a while back myself, and did post a link to an infographic showing the scale of intracellular life.

They’re great to view, but I personally find that presentations that zoom to show scale, impressive as they are, don’t really convey to me good impression of the scale of anything that’s more than a couple of ‘zoom steps’ apart.

I prefer a series of static pictures with explanation, like those in Ethan Siegel’s excellent recent presentation on the scale of the unobservable universe.

A comparison uses Voyager 2. A twitter feed currently reports that Voyager 2 is a smidgen over 13 hours of light-travel time from earth. Our observable universe is ~93 billion light years across, roughly 93 * 365 * 24 = 814680 billion hours of light-time travel. That’s 62667.7 billions times further than it’s travelled so far.

Voyager 2 is travelling at ~150,000 km/h and been at it 33 years. At it’s current rate, it’d take over 2 million billion years to travel the width of observable universe.

Read Siegel’s article for more on the unobservable universe. It’s lot bigger.

My favourite presentations of the scale of universe, which leave out all the small things that the videos Chris presents show, are variations on Gott et al’s pocket map of the universe (big PDF file) from their research paper. I’ve shown a smaller copy to the left.

You need to have a handle on log-scale graphs, though. Each major step on the graph is covers ten times the distance the previous one did. Start at the bottom and mentally inflate each segment ten times the height (= distance) of the one before it.

Bring Back Babbage The name Babbage will be familiar to those with a computing background. Jennifer Ouellette at Cocktail Party Physics alerts us to that there are fresh plans to raise funds to finally build Babbage’s Analytical Engine, giving a brief history of the machine’s design. There’s more at the computer history website. (I’ve a copy of Doron Swade’s excellent book on the Difference Engine on my shelves, describing his work to build the Difference Engine. This proposed Analytical Engine project has obvious parallels.)

China guns for large-scale genome sequencing Steve Hsu posted a short article reporting a claim that the Beijing Genomics Institute (BGI) will soon have the capacity to sequence 1000 human genomes a day. Given their labour costs are likely to be lower than in other centres, they could be a major force in this area. Even if you debate the numbers, they’re clearly putting a big effort in.

What did you do for geek cred? I’m going to steal a line from Alice Bell’s exploration of geekery and geek cred. (Some of the comments there are worth reading, too.) So… what did you do for geek cred? Go on, tell us!

Other recent articles on Code for life:

Paul Nurse on ‘anti-science doubters’ and the blogosphere

Another one bits the dust: Goodbye Walkman

Vaccine promotion – the medium matters too

One thousand genomes deep Grant Jacobs Oct 28

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I’d like to write about today’s paper* from the 1000 genomes project, but I have a tax return to file first. In the meantime a quatrain and a haiku:

There’s no forsaking what you are

No existential leap

As witnessed here in DNA and code

A thousand genomes deep

We’re all mutants

you and I, all broken codes

for humanity

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Vaccine promotion – the medium matters too Grant Jacobs Oct 28


While some of the writers here are gearing up for Vaccine Awareness Week, Esther Taunton from Taranaki Daily News reports that the low up-take of the government-funded human papillomavirus (HPV) immunisation programme is being laid at the feet of lack of engagement with social media in the program.

They argue that without a presence in the social media popular with the age-group that they were targeting, the kids were receiving too much of a cautionary (or even misleading) message.

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Open Laboratory submissions close in a month Grant Jacobs Oct 26


A quick head’s up: Open Laboratory submissions close in a month. Readers are encouraged to nominate articles.

Submit to open lab 2010

Open Laboratory collates 52 blog articles each year into book form, in both electronic and print formats.

Entries are nominated (by anyone including the author), then judged, with 52 chosen for publication. The full instructions for nomination have useful guidelines, including:

  • Bear in mind it will be a printed book, in black and white. The articles must easily translate into print form! (The selected articles are edited, but an article won’t get selected if it looks too much work to convert into suitable form for print.)
  • Without wanting to discourage submissions, try not over-submit: copious dross will most likely just annoy the judges! (And perhaps put them off your favourite writers.)
  • The target audience should be a lay audience. Even if excellent, if it’s too geeky it’s unlikely to make the cut.

Current nominations are periodically listed at A Blog Around the Clock.

The final date a blog post can be written for inclusion is the 1st December 2010, so you have a little over a month to go.

(My thanks to a reader who nominated one of my articles. It needs a solid once-over of editing, if you ask me, but I’m grateful for the nomination!)

Other articles on Code for life:

Another one bits the dust: Goodbye Walkman

Manhire Prize for Creative Science Writing shortlist free to read

Paul Nurse on ‘anti-science doubters’ and the blogosphere

Finding platypus venom

Career paths, redux – the academic research career is the exception

Autism – looking for parent-of-origin effects

Another one bits the dust: Goodbye Walkman Grant Jacobs Oct 25


As you get older iconic brands of your youth die.

In the way that an older generation must lament the loss of the steam locomotives and Studebakers, more recent times have seen farewell to Kodachrome and the floppy disk.

Sony Walkman

It’s the Walkman’s turn.

Like millions of other kids I had a Walkman. A Sony, the real thing -not a knock-off.

It was only a little bigger than the hearing aid I had as a kid. A little wider, a little longer, and about twice as thick.

The sounds came not the world around me, but music I could take with me anyplace.

A portable bubble of sound I could enclose myself in.

Until the batteries ran out.

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Paul Nurse on ‘anti-science doubters’ and the blogosphere Grant Jacobs Oct 25


Paul Nurse remarks that the WWW and blogging have given anti-science views a disproportionate impact on policy. I idle away part of my Labour Day holiday ruminating the thought.

The closing three paragraphs of an article in the Guardian on Paul Nurse, Nobel Laureate and now president of the Royal Society of London, reveal an interest in the activities of the blogosphere and how science is perceived by society:

Before he takes up his new jobs, Nurse will spend a few weeks finishing off a documentary for the BBC science series Horizon on the subject of trust in science.

“I think it is clear that the rise of the blogosphere and the internet has allowed a very small group of vociferous anti-science doubters to have a disproportionate impact on policy issues,” he says.

For his part, Nurse — “as ever the old socialist”, as Hunt puts it — is clear about the solution: engagement with the public, a mantra that he is likely to repeat throughout his Royal Society presidency. As he says: “Scientists have to earn their licence to operate and that means getting out there to talk to people and explain what we do.”

People expressing anti-science views on the internet isn’t new, but perhaps their impact on a wider range of readers and policy is.

As a Ph.D. student I used to follow a number of newsgroups, mostly on bionet. Good sound science there. But other newsgroups were less conventional.

Oh, you little devil. (Source: Living Internet)

Oh, you little devil. ASCII email signature art. (Source: Living Internet)

This was before the WWW became the dominant thing it is today, with all correspondence being by email.

No web pages with comment forms.

Email addresses were openly displayed in the newsgroups and weren’t the privacy screens they can be today.

There wasn’t the tendency to anonymous posting as there is today, either. More the trend – to my memory – was posting with email signatures openly giving people’s details.

Email signatures were sometimes works of art – literally. For a while I had a spider – scrolling down the page, it ’fell’ dangling on it’s silk thread. I’ve no idea what my Ph.D. supervisor thought of it.

The newsgroup section for ‘anti-science doubters’ was .alt – literally the ‘alternative’ section. Various versions of it still exist. Things seemed very alternative in there to my student-day self.

I once timidly ventured in there. Being rather naïve then, it felt at that time as if I were Craig Schwartz in an alternative take of Being John Malkovich,[1] where I’d fallen into the brain of someone with a cognitive disorder, perhaps a schizophrenic. (Nothing against schizophrenics: I’ve the upmost respect for those who struggle with mental health issues, I just mean that back then this was a leap into a very different, unsettling, mindset.) Read the rest of this entry »

Manhire Prize for Creative Science Writing shortlist free to read Grant Jacobs Oct 21

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The shortlisted submissions for the Royal Society of New Zealand’s Manhire Prize for Creative Science Writing for 2010 are now available on-line. Congratulations to all short-listed writers.

The entries are available as PDF files to download. Share your favourites in the comments. Have happy reading!

(As an aside I had wanted very much to enter myself, especially as neuroscience is an area I love to follow, but work commitments meant I didn’t have time put towards an entry. Next year maybe…)

Other articles at Code for life:

Book sales, frumpy readers, and mental rotation of book titles

I remember because my DNA was methylated

Deleting a gene can turn an ovary into a testis in adult mammals

GMOs and the plants we eat: neither are ’natural’

The inheritance of face recognition (should you blame your parents if you can’t recognise faces?)

Monkey business, or is my uncle also my Dad?

Mac OS X dreams Grant Jacobs Oct 21


First I must apologise to regular readers for the writing hiatus. I’m being buried in work. It’s late at night here and following the mood I am writing lazily off the top of my head.

Today is one of ‘those’ Mac event days. I’ve read of so many over the years, I’m now fairly blasé about them in some ways, but stepping back a bit they’re fun excuses to offer what you’d wish to see in the new version of Mac OS X and chance to gossip.


Of the few lists of ideas I’ve read, most are pretty scatter-brained. This one from MacWorld at least seems to have it’s head screwed on. (Mostly.)

I’m not going to speculate myself, as much of the speculation centres around stuff I’m not familiar with. I’ve never used iOS, but people are talking about stuff being added to Mac OS X from there. Haven’t clue what that might mean. There’s talk of cloud computing features, but I see that as a little further down the track. I personally wonder at the choice of ‘3-D’ Apple in the logo used. A 3-D Finder? Hmm… others can speculate on that.

With a mere hours before the event, few will see my feeble ’requests’ before the event itself. Most New Zealanders will read it after the event, which no doubt will leave me looking the poorer for it. I’m going to further make myself look a mug by focusing almost entirely on the desktop aspects, rather than devices, networking, cloud computing, etc.

So, I encourage people to offer what they would like to have seen in Mac OS X that was not shown in the event! (C’mon surely this is an original twist to this? Besides this way I stand a better chance of getting something right…, erm, wrong. Whatever.)

On my wish-list is:

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