Archive August 2011

Mutating a line Grant Jacobs Aug 30

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(For [younger] readers to view and science communicators to admire or critique.)

This short video has an engaging and very clever way of illustrating some basic aspects of evolution – using a simple line:

YouTube Preview Image

It’s a great starting point, I just wish it were extended to include selection and so on. Also, while it presents an analogy, it doesn’t then go on to relate the analogy to genome sequences, tying it to how things happen ‘in real life’. Extending the analogy or making it more closely fit reality would require that a lot more people get involved and more generations used, so fair enough perhaps.

I’d offer my thoughts on how to extend this but I’m all out of time this morning so I’ll invite you, readers,  to offer your ideas. (Briefly I had the idea of selecting for blocking objects travelling horizontally across and vertically downards.)

Other articles on Code for life:

Not Darwin’s tree of life

Doggie ERVs

Abbie Smith on vaccines, your immune system and viruses

Haemophilia – towards a cure using genetic engineering

World report on disability

Local events: science story telling, non-academic careers, doctors and evidence Grant Jacobs Aug 27


A few dates for the diary for locals. (Or those who happen to be in town at the time!)

Regular readers will know that I have several times written about careers after the Ph.D. outside academia, particular to point out that these careers are not the ‘alternative’ as working outside of academia after completing a Ph.D. is the rule, not the exception.

ScienceTeller2011As one of the events making up Graduate Research Month, the Careers Development Centre is presenting Options After a PhD Other Than in the Academic World at 2pm on Monday August 29th. This workshop is for PhD candidates who want to explore the world of employment beyond academia. The venue is the Hocken Seminar Room (on Anzac Ave, next to Unipol). Speakers are listed on the talk description.

The University of Otago hosts the Centre for Science Communication, a small department dedicated to science communication. November 15-19th will see them host the inaugural ScienceTellers event. An introduction to the event can also be found on the University of Otago website (many additional presenters beyond those listed on this page can be found in the programme).

Submissions for presentations, films, etc., remain open until October 1st. Registration is, of course, still open. Early bird registration (with cheaper fees) closes October 1st.

Read the rest of this entry »

Steve Jobs stands down as CEO of Apple Computer Grant Jacobs Aug 25


Breaking news is that Steve Jobs, CEO and co-founder of Apple Computer, has resigned his post.

Press reports are citing his resignation letter,

To the Apple Board of Directors and the Apple Community:

I have always said if there ever came a day when I could no longer meet my duties and expectations as Apple’s CEO, I would be the first to let you know. Unfortunately, that day has come.

I hereby resign as CEO of Apple. I would like to serve, if the Board sees fit, as Chairman of the Board, director and Apple employee.

As far as my successor goes, I strongly recommend that we execute our succession plan and name Tim Cook as CEO of Apple.

I believe Apple’s brightest and most innovative days are ahead of it. And I look forward to watching and contributing to its success in a new role.

I have made some of the best friends of my life at Apple, and I thank you all for the many years of being able to work alongside you.


Steve Jobs, diagnosed and treated for pancreatic cancer in 2004 has been on medical leave since January. Reports are that he will continue to be involved in product design (this is perhaps the ‘new role’ he refers to in his resignation letter).

Further reports and commentary can be found at at the Wall Street Journal and  ArsTechnica.

Readers are welcome to share there thoughts.

(Updated to add links below.)

Other articles on Code for life:

Mac OS X dreams

Mac OS X — quickly inspecting the contents of a file

Haemophilia — towards a cure using genetic engineering

Finding platypus venom

Developing bioinformatics methods: by who and how

Research project coding v. end-user application coding

Not Darwin’s tree of life Grant Jacobs Aug 24


In January 2009, Ian Sample, a science correspondent writing for the Guardian opened an article writing,

Charles Darwin’s “tree of life”, which shows how species are related through evolutionary history, is wrong and needs to be replaced, according to leading scientists.

The great naturalist first sketched how species might evolve along branches of an imaginary tree in 1837, an idea that quickly came to symbolise the theory of evolution by natural selection.

In response to claims like these New Zealand evolutionary biologist, Professor David Penny, has written an article in PLoS Biology tackling ’a strong urban myth that Charles Darwin introduced and/or advocated a ’Tree of Life’ for the classification of living organisms.’

Read the rest of this entry »

How did you learn to critique the scientific literature? Grant Jacobs Aug 22


Larry Moran writing on his blog, Sandwalk, started a post* with these remarks about teaching students critical reading of the scientific literature,

I teach a course called “Scientific Controversies and Misconceptions.” (You won’t be surprised to learn that one of the main topics is evolution vs. creationism.) The most difficult part of the course is teaching students to be skeptical about the scientific literature. The reason why this is difficult is because the main focus is evidence based reasoning and science is an important way to gather reliable evidence. […]

I haven’t figured out a way to teach students to read the scientific literature with the same skeptical perspective as those of us who have been doing it for decades. It seems as though this is a skill that must be learned through experience and can’t be taught.

I feel a little uneasy at his second paragraph. You’d like to think that this process can be learnt by more that just osmosis or trial-and-error. (I do anyway.)

A part of how I learnt this as a student was through small-group literature-based classes in the final-year of my BSc(Hons).  The groups consisted of a series of meetings. At the end of each meeting we were set a small number of papers to read and draw our own conclusions. At the next meeting the class would discuss what conclusions we had drawn, aided by the staff member. These classes had from a handful to a dozen students. Read the rest of this entry »

Mac OS X – quickly inspecting the contents of a file Grant Jacobs Aug 19


You’re scrolling down a list of files, trying to remember their contents. You did give most files a name that reflects the contents of the file, but a few leave you stumped.

Rather than open the file to find out what’s in it you can just select the file, then press the space bar.

OS X will present a quick preview of the first page of the file.


To close the preview, type command-W. You can browse the contents of most files by scrolling through them.

If you leave the quick view up and ‘touch’ (single click) another file, it’s contents will be presented in the quick view window that is open.

Tap the bottom bar and it’ll zoom for full-screen viewing. Click on Esc to return to the Finder view.

(Updated to add blog post tags & final line of text.)

Other articles in Code for life:

Before installing Mac OS X Lion

Safari v. Opera

WWW database servers on Mac OS X 10.6.x, part I: Installing MySQL (3 parts)

Sinclair ZX envy

Web browsers: poser tips for Safari users

Corrections and clarifications Grant Jacobs Aug 19

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Should all media have a Corrections and Clarifications page on their websites?

My previous article followed Peter Griffin’s lead on a kerfuffle over a local Broadcasting Standard Authority (BSA) ruling on an error in a television news popular science item.

Should the BSA to ask/encourage broadcasters to have corrigenda pages on their websites–less formally, ‘we goofed’ pages–that they would be encouraged to self-report errors on? (Linked from their top home page, lest the page be ‘buried’.)

Some (if not most) newspapers have a Corrections & Clarifications column* for a similar purpose. We could debate what fraction of errors are in fact self-corrected! – but it’s the principle of the thing and a mechanism for reporting errors that I’m after here. If newspapers can do this, why not television companies? Read the rest of this entry »

Science reporting – accuracy does not matter? Grant Jacobs Aug 17


I’m joining Peter Griffin in voicing surprise and dismay at the New Zealand Broadcasting Standards Authority (BSA) response to a complaint over a factual error–acknowledged by the broadcaster as wrong–as immaterial in reporting a science item. Peter has the full story; I’m not going to repeat it here. Readers will also want to read media commentator Brian Edward’s article and the comments in response to it.

What I’d like to do is quickly look at the BSA ruling, which I find instructive.

The news item reported a 10 year-old Canadian girl’s discovery of a supernova approximately 240 million light years away as being only 240 light years away. The BSA notes that TVNZ accepted their error but also rejected it as unimportant in the context of the story,

Furthermore, we consider that Mr McDonald’s complaint was dealt with adequately and appropriately by the broadcaster, which accepted that the figure was incorrect, but explained that it was not material to the item.

The key point is that the broadcaster rejects it as not important, arguing that they were presenting a general human interest event – but even there they describe it terms of a science achievement: ’[…] the item, which focused on the discovery of the supernova by a 10-year-old girl.’

The broadcaster’s response feels a little disingenuous to me. Their story features an achievement but they have, in part, inaccurately represented the achievement. (One thing that would be useful is some idea of how difficult, or not, it is to observe an event that far away using modest amateur equipment.)

A bigger problem is lurking – general standards of reporting science news, and what is acceptable.

Further down in the BSA ruling this line complains that Mr McDonald is ‘asking for too much’ -

Mr McDonald wishes to apply standards of scientific or mathematical accuracy where these are not required.

Let me see if I understand this.

The broadcaster reports a science event, but wishes to not be held to the standards expected of a science event? More fully, when their error is pointed out, they argue that inaccuracy is ‘immaterial’, and the BSA supports this?

If you are to report on a science event, the basic facts have to be accurate, surely? Isn’t that part of the territory? Read the rest of this entry »

Who are you? Grant Jacobs Aug 16

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Head on over to Richard Grant’s blog to describe your (exciting!) work life ’in haiku, limerick form or rhyming couplets.’

His post is a response to receiving a CV in exceptionally brief form – a haiku; you can read about that there, too.

My own feeble contribution (mangled by late-night typos) was:

There are codes for life,
in those letters that my code
builds some sense of life.

(As a computational biologist a fair amount of my time is spent writing computer code; there’s also oblique to other ‘codes for life’. I did write a longer version, based in part on my explanation of the name of this blog (Code for life) in my About page (in the banner, above) but I don’t think you need to see more of my poor poetry!)

I’m sure my readers could do better; head on over and give it your best.

New bioinformatics journal – EMBnet.journal Grant Jacobs Aug 15

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Bioinformatics researchers, managers and consultants may like to know that the long-running EMBnet news has expanded to become a peer-reviewed journal, EMBnet.journal.

The first issue is now out and has a focus on next generation sequencing data analysis.

Readers can download the individual papers or the whole issue. RSS tracking is available. (The first issue is numbered issues 17(1), as it follows on from EMBnet news.) Upcoming issues include 

  • Metagenomics, Metatranscriptomics and Biodiversity
  • Networks and Connectomics
  • Pharmacogenomics

EMBnet.journal is to be an ’international, Open Access, peer-reviewed journal whose primary goal is to provide biomedical scientists with practical information to help’ with practical information to help: Read the rest of this entry »

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