Archive February 2010

Book review: The Open Laboratory: The Best Science Writing on Blogs 2009 Grant Jacobs Feb 28


The Open Laboratory offers 50 of the best writing that science blogs gave over 2009.

You know the WWW is the source when the editor is listed by their pseudonym! Scicurious edits, with Blake Stacey as production editor and Bora Zivkovic the series editor.

It’s available for the princely sum of $US 15.50 from Lulu in either book form, or as a download. The PDF version includes links to sources. (Those new to Lulu may want my tips in the footnotes.)

The volume opens with with a poem (Beyond Energy, by Kristopher Hite), a refreshing start that caught me slightly off guard. It’s bookended with another poem: My Personal Genome Project by The Digital Cuttlefish.

Next in line, editor Scicurious’ Preface introduces science blogs, to quote, we scientists and science writers:

do our geeky best to fight ignorance and hype, and to show people just how useful, and cool, science can be

(I’d add that one more thing that people can get from science blogs is to they are ask scientists things and can engage in conversation. More than just seeing science and scientists for what they really are: they can interact with them. It’s something I don’t see enough of.)

She rightfully hopes that this volume can extend the reach of the science blogs further into ’living rooms and offices around the world’ and looking at it, I hope it does.

There’s 50 articles. That’s precisely 31¢ per article, if anyone cares.

Read the rest of this entry »

Advertising campaigns: homeopathy or a sceptical series? Grant Jacobs Feb 26


The atheist bus campaign has me thinking… what if there were a similar campaign against homeopathic remedies? Or an on-going series of advertisements questioning dubious practices of all kinds? Fridays are good for day-dreaming, right?

uk-bus-2NZ Bus seems to have had an attack of tremulous timidity in the face of ’some’ complaints and have withdrawn their initial approval, the advertising campaign is getting plenty of attention as a consequence of their withdrawing approval. (Articles I’ve read don’t have them saying how many complaints were received from, nor from who.)

It strikes me this is strategy where the advertisers more-or-less can’t completely lose. If the advertising company pulls out, the withdrawal only attracts more attention!

Imagine a series of sceptical advertisements, perhaps run along the lines of the Tui beer advertisements? (For those from overseas, this local beer company is famous for it’s marketing campaign featuring a two part advertisement with a short statement on the left-hand side and ’Yeah, right’ on the right-hand side. They’re typically to the point and unsubtle. Think: ’Homeopathic remedies work. Yeah right.’)

Read the rest of this entry »

Best research blogs: get ready for voting; well done Aimee and David Grant Jacobs Feb 26


Research blogging have put up their list of candidates for the Research Blogging Awards, 2010.

research-blogging-awardsIn them are a few familiar names.

misc.ience, one of our own, makes the short-list for the Best Blog — Chemistry, Physics, or Astronomy category. Well done, Aimee!

The Atavism, syndicated here, also makes the Best Lay-Level blog selection (the link points to the stand-alone blog). Well done, David.

They can now add the Research Blogging Finalist icon to there blogs.

Read the rest of this entry »

Post-embargo publication delays: be gone Grant Jacobs Feb 25


Scientific research articles cited in the media should be available at the time embargoes are lifted, not later.

missing-in-actionRecently there was an article I very much wanted to write about in a timely fashion, having seen the news in local media and on Ed Yong’s blog. To my complete frustration, the research paper was unavailable despite the story being widely reported in the media. And not just frustration, either: it seemed wrong.

Others explained it was because PNAS (the prestigious Proceedings of the National Academy of Sciences, USA) has a practice of not releasing the paper for a period after the media embargo.

It seems a number of journals take some time to release the DOIs (Document Object Identifiers) associated with a publication or even the article itself following an embargo on reporting the publication.

As Yong writes in his call to Kill the post-embargo publication window:

This practice punishes scientists who are unable to see, comment on, or discuss work that is outed in the mainstream media, it punishes journalists who are trying to link to original sources, and it punishes readers who are inquisitive and skeptical enough to try to verify the information they read. None of these is acceptable.

I agree.

Read the rest of this entry »

Undiluted humour: If Homeopathy Beats Science Grant Jacobs Feb 24


I know I really shouldn’t… But I can’t help myself.

This video, picked up via undergraduate biology student Michael Hawkins’s blog (which has just been restored to him after considerable fuss) is too good to pass up. Can’t beat British humour.

YouTube Preview Image

The alert will note the signage in the ’hospital’.

In case you’re wondering, it’s taken from the BAFTA award-winning British (BBC 2) comedy sketch show That Mitchell and Webb Look.

More on homeopathy articles on Code for Life:

Homeopathy check-up: Not in the health system, disclaimers on labels

Homeopathic remedies in NZ pharmacies

British homeopathy sceptics group aims for sugar high (with Dawkins video)

Other articles on Code for Life:

Positive encouragement for vaccination

Special edition of Biochemist E-volution: Science and the Media on-line free

Has Andrew Wakefield resigned from Thoughtful House? (Updated)

Map shows New Zealand with lowest death rate on earth in 1856, over 11 in 1000 dying

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

All this talk about 3-D movies and TVs is depressing

Developing bioinformatics methods: by who and how

Homeopathy check-up: Not in the health system, disclaimers on labels Grant Jacobs Feb 23


Today England’s Science and Technology Committee published it’s “Evidence Check 2″ report on Homeopathy.

evidence-check-2-homeopathyOverall, it’s a resounding “no” to homeopathy. The report comes down hard on UK government agencies relationships to homeopathy and recommends stronger transparency in the commercial sector, too.

The report was to look at government policy, particularly the NHS (England’s National Health System) funding and provision of homeopathy and on MHRA licensing of these remedies. (MHRA = Medicines and Healthcare products Regulatory Agency.)

Given the amount of material reviewed, it’s a reasonably compact report, with pages 1-47 covering all most people will want to read.

I’m going to leave aside the science arguments for later articles and deal with only their overall conclusions and their remarks about pharmacies here. I’m condensing, so visit the full documents if you want the original contexts.

Among the recommendations (p43-47) are:

On homeopathy, that:

Homeopathy is not efficacious, i.e., homeopathy does not work beyond the placebo effect

Read the rest of this entry »

Lab lit: for bookworms who like the science to be plausible Grant Jacobs Feb 23


Jenniffer Rohn defines ‘lab lit’ as ’realistic mainstream fiction featuring scientists as central characters’.

Dr. Rohn is the editor of, which, along with articles and other material, hosts the Lab Lit List.

(Source: Lab Lit)

(Source: Lab Lit)

You can read about Dr. Rohn’s experiment with promoting Lab Lit in Waterstones in London. (PDF file.)

The LabLit website aims to support the portrayal and perceptions of ’real laboratory culture’, including the science, scientists and labs, in fiction, the media and across popular culture.

On the list you’ll find a wide range of books, films and TV shows, even plays. If you’re looking for new things to read, this is a good place to poke around.

If you’re thinking that the list is looking a little behind the times, enough lab lit has been published that it’s developed a backlog! They don’t just bung ’em in there, they check them out first, then create synopses. I’m told that they are aiming at an update in 2-3 weeks or thereabouts.

Being a computational biologist or a bioinformaticist, depending on how you want to split hairs, I just had to look to see what books featured someone from my field.

Read the rest of this entry »

Dem pesky birds Grant Jacobs Feb 19

No Comments

The Australian outback has flies. You know the eponymous hand-flick of countries with flies? Locals there apparently call it the ’Australian Salute’.

Whales seem to have flocks of birds and tail flicks.

In this video, I can just imagine the whale cruising along thinking, ’it’s dem pesky birds again!’:

YouTube Preview Image

You got to admit that whale nearly nailed that bird. The bird’s reflexes were pretty quick too. Mind you, if a large black thing rose out of the ocean at you, you’d probably move pretty quickly too…

It’s only 13 seconds of your life, check it out… (You’re not superstitious about the ‘unlucky 13’ are you?)

Yes, posting lighter things on Friday afternoon is a theme around here.


I’m reluctant to “borrow” from the contents of other’s articles, but I pass this one up. Big hat tip to GrrlScentist for posting it! (If you’re a ’local’ on her blog, go over and wish Mr GrrlScientist (Bob O’H) a happy birthday. Or, as they say around there, Happy Birdday.

Other light-hearted articles at Code for life:

Happy (Geeky) Valentine’s Day

Preconceptual science, the dismissal-ness of it all

Animal babies, long snouts

Singing for science

Scientific baking. Great for those lab meetings or kids’ parties

New decade cartoon: Calvin on scientific progress

Has Andrew Wakefield resigned from Thoughtful House? (Updated) Grant Jacobs Feb 18


Andrew Wakefield, whose work has been at the heart of a MMR vaccine ’scare’, has been in the news of late owing to the UK General Medical Council ruling on his 1998 Lancet paper, the retraction of this research paper and more recently the withdrawal of another research paper.

Orac has a blog post tonight querying if this news of his resignation is true. If it’s true, and I want to stress that ’if’, it’s a bit of a bolt out of the blue. At the moment there is no formal announcement on the Thoughtful House website.

Thoughtful House‘s response to the GMC ruling was very much to support Wakefield, so this would be a considerable shift in position. [This web page has now been removed, see update below.]

While still awaiting confirmation Brian Deer, the investigative journalist behind bringing this story to the public eye, has just commented:

Yes, I heard this was coming some days ago.

With this in hand, I would say we should be looking forward to a formal confirmation of this news in the near future. (I trust no-one is silly enough to be posing as Brian Deer!)

Update: [7:30am 19-Feb-2010] While no formal statement of Wakefield resignation has been posted, Thoughtful House has removed their statement responding to the GMC ruling and have removed Wakefield from the list of staff on their website.

Other posts on Wakefield and autism on Code for life:

Another Wakefield paper pulled?

Lancet formally retracts Wakesfield paper

Autistic children and blood mercury levels

A course for all degrees: PHIL 105, Critical Thinking Grant Jacobs Feb 18


Some argue that all students should take courses in basic logic. At Otago University any student, from any degree course, can take ‘Critical Thinking’. If it’s a good course,1 as I suspect it is, they should.

Plato and Aristotle (Source: wikipedia)

Plato and Aristotle (Source: wikipedia)

In an earlier advisory essay I wrote that one thing all students should get out of university is to be self-learners. Another would be critical thinking. It ought to be part of every student’s repertoire.

At Otago University, PHIL 105, Critical Thinking, has the interesting honour of being the only course in the university that can be accredited to any degree course. (I’d be keen to hear readers suggest any others that could perhaps be made available to all degrees,2 or if a similar practice exists in other universities.)

The description of PHIL 105 reads:

This paper aims to educate students in clear thinking and rational argument. Topics covered include: how to sort out good arguments from bad ones; techniques for testing the validity of an argument; common fallacies of argument; and the distinction between science and pseudoscience.

Or, from the prescription:

The ideas of reason, truth and argument. What are the limits of argument? Common fallacies of reasoning. Traditional logic and its limitations. Modern logic. Non-deductive reasoning.

Dr Maclaurin (Head of the department of Philosophy) teaches the course with Associate Professor Heather Dyke.

I imagine it’s a great course to teach. You’d get a chance to dissect and smack down your favourite pieces of illogic! According to Assoc. Prof., interviewed by Mr. Bertram for D-Scene:

’Bullsh*t detection is what we teach.’

Read the rest of this entry »

Network-wide options by YD - Freelance Wordpress Developer