Archive September 2010

Nature online digital edition, with 3 month trial Grant Jacobs Sep 23


Today Nature has presented it’s new online digital edition.

There is an introductory blog post by Editor-in-Chief Dr. Campbell, a press release (which discusses wider changes), and some independent commentary from GrrlScientist. Videos are available which present the new changes. (I have to admit the American presenter was a surprise – it’s British publication, so I was anticipating a British presenter.)


I recommend using full-screen mode, click on the icon to the lower left (shown to left). If you are using a laptop, as I currently am, you will probably still find it a challenge to read the text. If you click on the text, it will zoom in. While zoomed-in, moving the mouse will move the page. Clicking the mouse again will return you to viewing the two-page layout.


As you can see the concept, like other digital magazines, is to present the user with the magazine as they might read it physically (via a Flash application).

The Editor-in-Chief’s introductory articles says it comes with a three-month free trial, if you register. Read the rest of this entry »

Career paths, redux – the academic research career is the exception Grant Jacobs Sep 22


Two recent posts from (parts I and II) review a graduate student forum where two university staff members presented their thoughts about career paths. I’d like to use these as an opportunity (well, excuse) to pull together in one post some of things I have previously written on this topic, about science-based careers outside academia.

It’s good to see career paths being discussed with Ph.D. students and the points offered are excellent. I wouldn’t have minded a similar presentation when I was younger.

It is also clear from Sarah Morgan’s account that discussion of careers outside academia took place. Great to hear. I hope this encourages institutions to offer presentations from people outside of the universities.

A point I would like to elaborate below is that these people are not exceptions, but are the rule. It is the academic research career that is the exception.

Read the rest of this entry »

Descent into a boiling volcano crater, and puffing smoke rings Grant Jacobs Sep 21


I’m sure many scientists wish – or dream – they still lived in the Romantic era of science that Richard Holmes’ book The Age of Wonder narrates, when science still involved adventurous journeys to far away places with strange local customs and new natural wonders to record.

At this point geologists, field biologists and others probably would pipe up and say they still do, accepting that the world seems a smaller place now that you can be in any continent from pretty much any city within a day or two.

My own scientific adventures as a computational biologist involve reading, developing software and exploring data. There’s a lot in that for the mind – and seriously, there is – but every now and then you see what someone else does for a living and wonder.

As a kid I read too much Gerald Durrell, Thor Heyerdahl, Joy Adamson, James Herriot, and watched David Attenborough point excitedly at strange creatures in remote jungles. I haunted book exchanges with my pocket money and dreamt of being a wildlife photographer and an explorer.

Geoff Mackley isn’t a scientist but a cameraman who covers natural events whose footage was on New Zealand television news last night. If you missed the video clip of a team member descending into the Marum Volcano on Ambrym Island, Vanuatu, it is also on YouTube:

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This isn’t the first time he has been at this. He has a book’s worth of this sort of thing: In Extreme Danger. A search on YouTube shows there is plenty more from Geoff Mackley on-line to watch.

You know all those old movies that have heavy smokers lazily blowing smoke rings? Dressed to the nines and puffing their life away in grand style?

Here some Mackley footage taken ten years ago shows Mt Etna (Sicily, Italy) puffing a smoke ring with the same lazy insolence:

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Watching his adventures, a small part of me thinks (well, dreams) I chose the wrong career. I get to be stuck to a computer all day, fingers on keyboard. The other part of me reminds me that while I like to get out and about – I have travelled and tramped a little – my adventures would likely be slightly tamer. Just ever so slightly.

I prefer long-haul travel* to adrenaline junkets anyway.


My last few posts have strayed off science (again). I would apologise but it is a needed break from reading too much anti-vaccine and vitamin C nonsense, only to look around to find seemingly dozens of equally disturbing discussions elsewhere.** And, as if that weren’t enough, read of things like promotion of what amounts to using industrial bleach to ’treat’ malaria in Kenya only to later read of NewZealanders encouraging the same ’treatment’ here.

* I’m sure he has done more than his fair share of that, too, and I’ve done a little overseas travel, so I can’t complain too loudly.

** All of this isn’t new to me, but the sheer persistence of it is sometimes appalling.

Other articles on Code for life:

The best places to read (some of the grandest library you’d ever see)

Autism – looking for parent-of-origin effects

Preserving endangered species – of gut microbes

Coiling bacterial DNA

Testing common ancestry to all modern-day life

I’ve had a sex change, am older than I am, but write happily most of the time Grant Jacobs Sep 20


Did the news about my sex change get your attention?

Going around science blogs over the last few days have been another of ’those’ blog text-analysis web services. (The previous one was What famous writer do you write like?).

Go to and enter the URL of your favourite blog, or your own.

Apparently I write with a wide range of ages, but most often like someone much older. I seem to have unexpectedly become bisexual with a slight leaning to female. Less unexpectedly, most of the time my writing is happy and there is an even split between academic and personal.



I’m not alone amongst my fellow sciblings in having developed unexpected mixed gender ’issues’ and not writing writing my age. I won’t spoil the fun and will let people find out for themselves.

Other pokes at fun on Code for life:

Happy (Geeky) Valentine’s Day

Friday’s Factoids and Quirky Quotes

Rex and The Wrong Trousers – uncanny resemblance?

Undiluted humour: If Homeopathy Beats Science (video)

Describe your fantasy institute

Neti pots now validated as sound science?

How to teach elementary science – chicken feet first Grant Jacobs Sep 19


This video explains the approach the van Damme science classes takes to introduce youngsters to science. It has a long introduction, but it’s worth getting through to see the example they use. Chicken feet.

(If you really are in a hurry, start three and a half minutes in the video.)

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Could also think about what they discuss here from the perspective of of how you might present something new to an adult, say in science communication.

The issues aren’t that different. It’s often easier to start with something that people are familiar with, and work from that, rather than ’jump’ to what might otherwise be the most logical starting point in terms of presenting the material once you understood it. (Note the past tense.) Textbooks often take the latter approach, asking that the student ’hold on’ to something until later material connects it with a wider range of things, which then make it useful.

Thinking back to things I’ve written, I’ve been guilty of this. It is tempting (even logical!) when you already know the subject, because that’s how you see it, but it may not be the best way of bringing someone new to it.

Other videos on Code for life:

The iPad: a cat toy?

A booster falls

Basic fluid science on the space station

When Galaxies Collide… and directors quote-mine

A plastic ocean

The Anachronism (full-length short film)

The best places to read Grant Jacobs Sep 19

1 Comment

Most scientists are bibliophiles. Count me in.

During my Ph.D. studies in England  I occasionally read in a small college library, astronomers’ globes at one end, surrounded by solid wooden shelves and leather-bound books. It was a treat to read in a place like that.

I was reminded of this by finding this old blog post showing photo after photo of stunning libraries. Readers have added over 800 comments.

I’ve offered a few images below to provide a glimpse of what is on offer as a teaser, but you really must visit the original post from Curious Expeditions and find your favourites. Some of the Baroque libraries are incredibly ornate. If you can’t get enough of them from there, try a google image search on ‘baroque library’, it’s worth it.

Austrian National Library, Vienna

Austrian National Library, Vienna

Strahov Theological Hall

Strahov Theological Hall

Biblioteca Geral, University of Coimbra, Portugal

Biblioteca Geral, University of Coimbra, Portugal

As you would expect, my student reading digs where much, much more modest than these! – cosy rather than grand, although they seemed impressive at the time. Looking at the photographs, these places are awesome to look at, but I’d rather a place with little corners you can make your own while you work. And seats that aren’t wooden planks! Well, I have to make some excuse.

Before I continue, I think it might be helpful to let overseas readers know that I am in New Zealand at this point. I don’t have access to libraries like those grand old dames. All the same – when I’m not trying to meet a deadline, which seems like most of the time these days – I like reading spots with a view. Looking out on forests, hills and sea has it’s charms too.

Other articles on Code for life:

Science-y reading and open book thread

Making the most of lousy book reviews on Amazon

What is your relationship with your research notebook?

Professors, lost souls with great oratory power?

Rain, sleet, snow, music and science blogs Grant Jacobs Sep 18

1 Comment

I’m sitting here in my armchair next to the ranch-slider, laptop on my knees, as the rain turns to sleet. The cat is buried in my beanbag as she likes to on colder days.

She’s not on the beanbag, she’s in it. As she settles in she wriggles and sinks with the bag folding around her. Someday I swear I’ll be reporting a feline drowning by beanbag. (It’s hilarious watching Aimee trying to get out of the beanbag she’s gotten into. It’s kind-of a floundering swim to the edge, then a flop, although sometimes she manages a vaulted leap out.)

It‘s great afternoon for writing with a cup of hot chocolate, a comfortable chair and a laptop. The attack on the springtime growth in the garden will have to wait.

While some in the science writing world are planning the perfect murder with the nocebo effect*1 another reports he

’Promised a beautiful girl I’d be at the hip secret art party in Liverpool tonight. Instead I’m writing about the sex life of zombies. #FML’

Me? I’d be at the party. I guess that makes me a less-than-dedicated blogger. (Then again, here I am on a Saturday afternoon, um, blogging.)

What is it with the sex life of zombies anyway?

Read the rest of this entry »

Autism – looking for parent-of-origin effects Grant Jacobs Sep 16


Autism is probably one of the best known neurological disorders, in part due to promotion in Hollywood movies such as Rain Man. It is described in the On-line Mendelian Inheritance in Man (OMIM) database as being

‘characterized by a triad of limited or absent verbal communication, a lack of reciprocal social interaction or responsiveness, and restricted, stereotypical, and ritualized patterns of interests and behavior (Bailey et al., 1996; Risch et al., 1999).’

(Source: Wikimedia Commons.)

(Source: Wikimedia Commons.)

Related to autism is autism spectrum disorder, often referred to as ASD, a range of conditions with less severe affects and includes Asperger’s Syndrome.

(The OMIM entry for autism, entry 209850, while intended for researchers, is well worth reading if you want a primer on the genetics of autism. In particular, it gives you an interesting look at the changing views over time.)

The problem

The past few years have seen several genome-wide surveys*1 for possible genetic variations related to autism. The results to date have been mixed.

One suggestion is that the mixed results are because imprinting – an epigenetic process – confuses the analysis.

Consistent with this, some of the features of autism are also found in genetic disorders that have been associated with imprinting, suggesting that maybe this is true for autism too.

Delphine Frabin and her colleagues investigated at if an epigenetic event – parent of origin effects – might have a role in autism.

Read the rest of this entry »

Where will science be in 30 years? Grant Jacobs Sep 15


Over at Discover magazine they are encouraging readers to offer their thoughts on where science will go over the next few decades, seeding it with a list of thoughts from leading lights.



I think we have enough people here to run our own show…

Here’s a few loose thoughts to kick it off. Understandably they’re biased to my own reading. Read the rest of this entry »

Friday “movie” Grant Jacobs Sep 10


Well, documentary, really.

I’m watching Carl Sagan’s telling the story of astronomers Ptolemaeus, Copernicus, Brahe, and company, in particular Johannes Kepler, from the famous Cosmos series he fronted.* Why don’t you join in?

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* An 11 minute excerpt at least: I haven’t time for more!

Other articles on Code for life:

Science, bloggers, activists, and science as “the one true global culture”?

Neurological shorts

Science-y reading and open book thread

Coiling bacterial DNA

Loops to tie a knot in proteins?

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