Archive April 2010

Science walks into a bar Grant Jacobs Apr 30


Brian Malow is a science comedian.

Yeah, you read that right. This is the guy who on being asked why be came a science comedian replied ’I used to be an astronomer, but I got stuck in the day shift.’

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The jokes are a little geeky. If you don’t get any of them, don’t be too timid to ask.

Perhaps it’s a measure of my geeky-ness that I get all of them?

Now, if only I could work one out starting with ’Brian Malow walks into a bar…’

Other ’entertainment’ posts on Code for Life:

Scientists’ other lives

Wellcome diversions

When Galaxies Collide… and directors quote-mine

New internet meme: google suggestions for scientists

Undiluted humour: If Homeopathy Beats Science

Happy (Geeky) Valentine’s Day

Your thoughts on the future of bioinformatics in New Zealand Grant Jacobs Apr 28

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I’d like to invite you to share your thoughts on the future of bioinformatics in NZ over the next few years.

On the 3rd of May be a one-day meeting ’Where will New Zealand Bioinformatics be in 2013?’ will be held at the University of Auckland. As the title suggests, this is to be a future-looking event, discussing what is needed in the (short-term) future.

A wide range of topics are being discussed, including GRID computing, which I (tried to!) open a discussion on.

I have started to write a longer post offering some of my own thoughts, but in the meantime, I would like to invite people to look at the schedule for the meeting, then speak up and share what they see as important for the short-term future of bioinformatics.

For those that won’t be attending the meeting, I will do what I can to present your views. (Bear in mind that as I am not a speaker, my opportunities may be limited.)

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National research collaborative services, open discussion Grant Jacobs Apr 27


National and international collaborative computer networks offer different styles of data and computing interactions. I’m curious to hear people’s opinions on these. Below I offer some local links and invite discussion.

Australia’s has opened an their Australian Research Collaboration Service (arcs) and eResearch Australasia websites.

The latter, eResearch Australasia, is a meeting sponsored by the DSIIR aimed at:

  • A catalyst for innovation and collaboration, by bringing together researchers, practitioners, and educators from diverse disciplines;
  • A forum to support the development, enhancement, and harmonisation of national, regional, and discipline-specific eResearch infrastructures and services;
  • A showcase for innovative science and research enabled through these technologies and services.

KAREN is offering support for KAREN core members to attend. (I’m not a member; core membership is big bucks!)


(Graphics credits: Marie-Agnès Messan, Andrè-Pierre Olivier)

The former is an ~A$100 million initiative to provide collaborative services to the Australian research community.

New Zealand has a GRID computing initiative, BestGRID. One example of use of this is the now long-established biomirror node accessible via the KAREN network.

The GridCafé website has good explanations of the basics for those not familiar with GRID computing, complete with fun graphics. It’s worth seeing just to look at the presentation, design and how they try make the topic friendlier.

The essence of the thing is that grids share more than just data; they share computer power. (Cloud computing is a similar concept.)

Rather than try tie these bits together, I’m going to invite you to explore them if you aren’t familiar with them, let whatever comes stew in your mind, and invite discussion.

(Graphics credits: Marie-Agnès Messan, Andrè-Pierre Olivier)

(Graphics credits: Marie-Agnès Messan, Andrè-Pierre Olivier)

Great stuff? Too much infrastructure? Disconnected from the typical researcher? Privacy or ethical issues? (Data sharing and access by others raises these…) Is there something you think is needed?

Share your thoughts in the comments.

(Graphics credits: Marie-Agnès Messan, Andrè-Pierre Olivier)

Other articles in Code for life:

Wellcome diversions

National Library of New Zealand Web Harvest 2010

Alliances of pharmacists & GPs; opportunities to pressure for removal of useless “remedies”?

iPads for the disabled

A plastic ocean

The Anachronism (full-length short film) Grant Jacobs Apr 26

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A high-quality version of an award-winning short film The Anachronism is available for free viewing. (The film also has a Facebook page.)

When I viewed the film, I found it worked best to use full-screen viewing. (Move your mouse over the video and press the button to the lower right that shows four arrows pointing to the corners of it’s icon.)

The forest & shoreline scenes are apparently shot near Vancouver, Canada. (On Vancouver Island?)

I’ll leave you to your thoughts on the film.

Other videos on Code for life:

The iPad: a cat toy?

When Galaxies Collide… and directors quote-mine

Singing for science

Undiluted humour: If Homeopathy Beats Science

Ecuadorian Amazonians see Avatar (in 3-D)

Pharmacists to say that homeopathy does not work? Grant Jacobs Apr 25


Previously I have written that in my opinion homeopathy has no place in pharmacies. In a recent comment on his blog, Stephen Curry pointed to a BBC News article reporting that the governing body of pharmacists in Northern Ireland has

proposed that patients be told that homeopathic products do not work, other than having a placebo effect

A copy of the draft proposed to form the consultation guidelines for pharmacists in Northern Ireland is available on-line (PDF file, 5 pages including title page).

The opening paragraph notes that given an obligation to provide patients with scientific accurate advice,

the only advice a pharmacist could reasonably give about such products is that they are placebos

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Scientists’ other lives Grant Jacobs Apr 24


Nova‘s series The Secret Life of Scientists exposes the lives of scientists.

There is this stereotype that scientists are well, nerdy.

(Originally sourced from, 22nd Sept. 2009.)

(Originally sourced from, 22nd Sept. 2009.)

Not geeky or dweeby. Nerdy. For the  confused, there is a Venn diagram.

Your ideas on what is what may vary. Most definitions of ‘geeky’ I’ve seen on the WWW are more positive with the ’obsession’ angle, describing it as people that are into new things, curious, pushing the boundaries. I like that.

What are scientists like in their own time?

Movies usually have us as being nerdy there too.

Full-time nerds.


Nova’s The Secret Life of Scientists series pops the lid on scientists’s lives, featuring a cast of scientists in both their work and non-work lives.

The series has recently been nominated for a Webby award. GrrlScientist has a blog post encouraging people to vote for Best Documentary Series in the Weeby’s, featuring a promotional video.

If you search YouTube for ’the secret life of scientists’ you’ll see that they have posted many short ~2 minute ‘10 questions’ interviews of scientists presented on the series there.

There’s virologist and beauty pageant queen, Erika Ebbel:

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A leech researcher and foodie (’The Leech man’, Mark Siddall):

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View the sun using the cross image fader Grant Jacobs Apr 22

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Kristian Larsen’s clever cross image fader lets you see regions of different temperatures on the sun on the WWW by moving a slider.



Sciblogs latest video shows some of the first images from astronomers’ latest ’toy’, the Hinode satellite. (Geeks can check out Nasa’s ’lite’ take on it’s technical specifications.)

The satellite has several telescopes. The opening frames of the video showing the sun in red, green, blue then yellow are from the Extreme ultraviolet Imaging Telescope, or EIT for short.


(Source: wikipedia.)

Light can be thought of as repeated waves, like ripples on a pond. The wavelength of light is the length from the top of one wave to the top of the next wave.

Each colour in the video represents light from a different wavelength in the extreme ultraviolet.

Ultraviolet light have shorter wavelengths than visible light, what you and I see with our eyes. The shortest light we can see is perceived as a deep purple.

)”](Source: wikipedia [cropped from original])

(Source: wikipedia [cropped from original

The EIT records light at four different wavelengths: 304, 171, 195 and 284 Ã…ngströms (or Ã…). An Ã…ngström is one ten-millionth of a millimetre, or 10-10 of a metre. (The scale in the graphic above is in metres. One Ã…ngströms is a 10-10 of a metre. 100 Ã…ngströms is 10-8 metres, which you can see in the left extreme of the UV region.)

(Screen capture of Larsen’s cross-image fader of sun images. Source: Nasa.)

(Screen capture of Larsen’s cross-image fader of sun images. Source: Nasa.)

These different measurements are used to determine which regions surrounding the sun are at several different temperatures: 60,000 – 80,000, 1, 1.5 and 2 million degrees Kelvin, respectively for each wavelength of 304, 171, 195 and 284 Ã…ngströms. They’ve coloured the regions detected red, blue, green then yellow, respectively. (A degree Kelvin is temperature measured with zero set at absolute zero, or -273.15ËšC. The scale is named after Lord Kelvin.)

Kristian Larsen, an applied physics engineer from Denmark, developed a web application to show the latest images from the Hinode satellite using a slider (show to right) that fades the images from one wavelength into the next, so that you can easily compare them.

Try it out.

As you move the slider, the text below will tell you what you are seeing.


I’m not an astronomer; I’m just offering a few steps towards breaking down the jargon.

More posts on Code for life:

Wellcome diversions

iPads for the disabled

A plastic ocean

Aww, crap.

You can change the ideas, but not the data

Wellcome diversions Grant Jacobs Apr 21


Looking for intriguing short stories of medicine, modern and old, to browse a while?

Sickle (in front, orange) and normal red blood cell. Sickle cell anaemia is a genetically-inherited trait that affects red blood cells that provided resistance to malaria. (Source Wellcome Images, available under Creative Commons licence.)

Sickle (in front, orange) and normal red blood cell. Sickle cell anaemia is a genetically-inherited trait that affects red blood cells but provides resistance to malaria. (Source: Wellcome Images, available under Creative Commons licence.)

Check out the Wellcome Collection.

Billed as ’a free destination for the incurably curious’, it presents a collection of excellent photographs and accompanying stories.

Under different sections (Life, Genes & You, Mind and Body, Sickness & Health, Time & Place, Science & Art, Education), a panel of images link to stories, videos and audio tracks. Click on images to see larger copies of them.

There is a recording of Florence of Nightingale, speaking from 1890, transcribed from a wax cylinder original.

Fans of the TV series Bones, might enjoy a video describing how bones are examined, including how to determine the age and sex of skeletons.

Freelance science writer, editor and broadcaster Georgina Ferry gives a brief history of X-ray crystallography. Ferry is also the author of Max Perutz and the Secret of Life, that I hope to review. (When I can find time to read it…!)

In a room filled with skulls of the famous, the phrenologist Gall examines Pitt the Younger and Gustavus IV, the King of Sweden, both currently plagued by Napoléon. Coloured etching, 1806. (Source: Wellcome Images, available under Creative Commons licence.)

In a room filled with skulls of the famous, the phrenologist Gall examines Pitt the Younger and Gustavus IV, the King of Sweden, both currently plagued by Napoléon. Coloured etching, 1806. (Source: Wellcome Images, available under Creative Commons licence.)

The Wellcome Trust also has a medical library, including the Wellcome Images collection, that the Wellcome Collection website draws on.

Happy browsing!

(Share your favourite finds in the comments.)

Other articles at Code for life:

iPads for the disabled

A plastic ocean

Molecular biology in museums

137 years of Popular Science back issues, free

Positive encouragement for vaccination

iPads for the disabled Grant Jacobs Apr 19


The touch interface of the iPad opens opportunities for affordable assistive devices for some disabled people.

In a funny way it’s appropriate following my recent posting of a video of a cat interacting with their owner’s iPad. If a cat can interact with the device, so could some disabled children. In the video below, a 2.5 year-old tries the iPad for the first time.

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Young children find the interface natural, which is being exploited by companies producing interactive ’books’ and teaching aids for young children.

I’m showing you this video because of a comment by sarahcooley to a blog post hosting the video:

This is amazing! When my mother first saw the iPad she immediately thought of my youngest brother who is developmentally disabled. She said “I wish people would create software for kids like Philip who are smart, but their fine motor skills are not the best, a touch screen would be perfect”

I wanted to thank you for sharing this video because it really demonstrates the power of the device and how simple it is to use!

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Bloggers, journalists, same difference? Grant Jacobs Apr 17


A debate on ‘Science in the Media’ was recently held at City University in London. Fiona Fox, director of the British Science Media Centre was one of the speakers, as were science writer and blogger Ed Yong,  Natasha Loder, science and technology correspondent from The Economist, and pharmaceutical correspondent of the Financial Times, Andrew Jack.

This apparently morphed into a bloggers v. journalists debate. Reports are this shift centred around Fiona Fox saying ’ignore the mass media at your peril. Blogs are good but they are not journalism’ in response to Ed Yong expressing enthusiasm for the developments in blogging efforts.

I wasn’t at the event; I’m reading about it from a great distance, long after it happened through the words of others. So I can’t very well comment on the event. I can still opine about the general issue of bloggers v. journalists!

Fiona Fox has since written on the BBC College of Journalism website, arguing that Blogs are not real journalism. There she repeats her thought that blogs lack crucial objectivity.

There are a number of responses to this around the WWW, listed in the references. While I have read these, and encourage interested readers to read them too, I’m going to try write from my own thoughts.



First the obvious: Blogs themselves are a media, a means of delivering content. Journalism is an approach to delivering content, in particular content about news events.

One is a technology, the other a practice. (Martin at LayScience has since expressed a similar view.)

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