Archive January 2011

Transcribing a gene, free poster Grant Jacobs Jan 30


If you’re looking for a pictorial overview of gene transcription–the process of making a RNA copy of a gene–or just like making up posters to put on your walls, you might like to download this free poster (1.94 Mb PDF) from Nature Reviews Genetics by Vikki Weake and Jerry Workman.


As you can see it’s very large, so I can’t show you more than a small portion in a scale that you can read.

Although intended for scientists, if you are familiar with the basics of transcription this might give some idea of what scientists now think goes on. (There will–of course–be more to add!)

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Egypt has taken itself off the internet (updated 29-Jan) Grant Jacobs Jan 28


Updates are at the bottom of the article and in comments after the article.

Reports on-line are that Egypt has taken itself off the internet, presumably as a request of the government.

Tweets from those in touch with people in Egypt report that both the internet and SMS network have been shut down. If so, there is no texting, email, blogs, twitter, etc., in Egypt. Likewise, no-one from outside Egypt should be able to read internet-based information coming from within the country.

Source Renesys via James Cowie.

Source Renesys via James Cowie.

In an article by James Cowie an accompanying graph (copied to left) shows a ’virtually simultaneous withdrawal of all routes to Egyptian networks in the Internet’s global routing table’ leaving ’no valid paths by which the rest of the world could continue to exchange Internet traffic with Egypt’s service providers.’

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Map of scientific collaborations, worldwide Grant Jacobs Jan 28


A tweet from Jennifer Rohn (@JennyRohn) late last night alerted me to an excellent infographic made by Olivier Beauchesne showing a world map of scientific collaborations. Readers should visit his blog for an explanation of what he’s built and to the zoomable map to browse it.

Below is a portion of the map showing Europe to the centre left and India to the right. I presume the point out to the top-left is Iceland. As for the point near the very top–somewhere up in the Arctic? (Any ideas?)


In broad terms research papers with authors from more than one city/country are plotted as a line between the cities, with the brightness of the lines connecting two cities reflecting the logarithm of the number of collaborations between the pair of cities and the logarithm of the distance between the two cities.

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What’s the weirdest university course you know of? Grant Jacobs Jan 27


(Lighter fare while I’m bogged down with a grant application.)

Today I learnt that former Miss Canada finalist, Mary-Lu Zahalan-Kennedy, has been awarded the world’s first Master’s degree in Beatle-ology. Actually it’s a more formal ‘Beatles, Popular Music and Society’ degree, which every newspaper on the planet will no doubt send up.

So, readers, what’s the weirdest degree courses you know of?*

Here’s a just few, to get you started.

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Update – BMJ Wakefield series continues, fingers pointed at Lancet and Royal Free Grant Jacobs Jan 24


A pointer to further articles by Brian Deer and others, highlighting an excellent comment by a reader of Respectful Insolence and brief thoughts.

The British Medical Journal–better known by it’s acronym, BMJ–continues to offer articles by Brian Deer on the long-running Wakefield saga, accompanied by several opinion pieces and editorials.

In particular Deer’s latest article points fingers at the Royal Free Hospital Medical School and the editorial board of Lancet as Harvey Marcovitch, Associate Editor at BMJ, relates with an edge of understated British humour:

Experience of cases reported to the Committee on Publication Ethics, a body founded by medical journal editors, leads to a conclusion that universities and other funding bodies differ in their response to reports from suspicious editors, reviewers, or readers. Some investigate, some retreat into a Trappist silence, and others are adept at carpet sweeping. Brian Deer’s report in the BMJ this week implies no shortage of shagpile in the Royal Free Hospital Medical School and the Lancet office.7

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ScienceOnline2011 – tweets on blogging, networks and calling bullshit Grant Jacobs Jan 21

No Comments

Below I’ve created several groups of tweets from the second day of the ScienceOnline2011 meeting.


After each group of tweets I’d added a few brief thoughts, which readers are welcome to comment on. I’ve added a few shorter comments in square brackets–emboldened to make them easier to find–immediately after some tweets.

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Capturing bodies – medical imaging data Grant Jacobs Jan 21


This Friday video explores medical imaging data, looking at scans of the human body and what’s involved in capturing them.

We’re increasingly looking at ourselves using ever more sophisticated ways. Peering into the interior of a patient aids doctors in diagnosing ills. One of the better-known would be the various types of body scanners that provide three-dimensional images of the interior of (portions of) a living body.

Exploring the human body using scanners involves considerable technology and large amounts of data. This TEDx* talk explores what’s involved in modern medical imaging.

YouTube Preview Image

The talk itself is excellent, but I wish the video presentation showed more of the slide images as full-screen images, rather than in the background.

* TEDx are the local versions of the famous TED talks.

Other article on Code for life:

Fainting kittens – feline myotonia congenita?

Immunisation, then and now

Fact or fallacy, a survey of immunisation statements in the print media

A History of Surgery on NZ TV (Prime, Sun., 9:35pm)

Reviews & IV vitamin C as treatment for severe pneumonia

Temperature-induced hearing loss

A History of Surgery on NZ TV (Prime, Sun., 9:35pm) Grant Jacobs Jan 20


Introducing New Zealander readers to a free-to-air documentary series that might interest those with science-y tastes.


Science-y documentaries are relatively rare on free-to-air television in New Zealand. With that justification I’d like to give a head’s up to a new documentary series screening on Prime Television, Sundays at 9:35pm, starting this Sunday (January 23rd).

Blood and guts: A History of Surgery is a BBC production accompanied by Richard Hollingham’s book (cover shown to left; click on the cover image to read reviews at Good Reads).

Having not seen it I can’t offer a review myself but remarks found on-line are very favourable. An oft-repeated comment, however, is that viewers who are squeamish about close-ups of surgery may prefer to divert their attention from time to time.

The BioethnicsBytes blog looks at the third episode, Spare Parts, discussing (to no surprise) some of the the ethnical issues of transplants of external limbs or features.

The opening episode (this Sunday) looks at the history of brain surgery, a topic I have read a little about and there are fascinating stories to become acquainted with.

Episodes are: Into The Brain, Bleeding Hearts, Spare Parts, Fixing Faces and Bloody Beginnings.

Let others know what you think of the show. (If you’ve already see it (perhaps you’re an overseas readers), but all means chip in with your thoughts. Try avoid spoilers!)

Other articles on Code for life:

Understanding the brain through controlling it

Positive news

Fact or fallacy, a survey of immunisation statements in the print media

Seeking science-y reading?

Consumer brain-computer interface

Fact or fallacy, a survey of immunisation statements in the print media Grant Jacobs Jan 19


Most of us know anecdotally that print media on occasion present immunisation information incorrectly, but you can’t put a finger on how often and when without hard numbers.

A recent research article examining New Zealand newspapers puts numbers to the errors.

Helen Petousis-Harris led a team surveying the immunisation statements in articles printed in four national New Zealand newspapers over 6 years (2002-2007).

They find that the proportion of unsubstantiated statements about the meningococcal immunisation programme increased with increased public interest and fell again as interest waned.

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Seeking science-y reading? Grant Jacobs Jan 17


Check out

Not standing still, the developers of have tried to improve upon what they offered.

The differing names of the platforms nicely reflect what they offer to the visitor.


Where is organised around the platforms that offer science writing, scienceseeker is organised around the topics., by contrast, is naturally biased to the networks or collectives: single sites that host several writers, like this one.

An early criticisms of was lack of support for independent bloggers.

While the initial cast of blogs on scienceseeker is biased to networks, a registration scheme allows independent bloggers to sign on. Tweets from registering independent blog sites at scienceseeker say the registration process is straight-forward–encourage your favourite blogs to sign up.

Those whose blogs are already listed (like ours’) should ‘claim’ them.*

You can browse blogs by topic (left-hand column) or scroll down the list of posts (most recent at the top). Each article is listed by topic, title, blog site and date. You can subscribe to a RSS field for each subject topic, which I imagine will be popular.

Scienceseeker also has a section for photos (at top, via Flickr) and a twitter stream (right-hand side). There’s also a news blog, including open discussion on further developments and a call for assistance (if you’re a developer).


There are benefits to both schemes. If you’re looking for the last handful of posts from a particular major platforms, scienceblogging will serve you well. (Although some might feel the page has now grown too long for a quick-reference index.)

If you’re seeking something to read, scienceseeker’s topic-based approach should prove better and, as the independents sign on, you’ll cover a wider sphere of writers.

This new effort is on-going. Among other things, topics are per blog site at present, rather than per article. The developers hope that this will change over time; this from their ‘About’ page:

This site is a work in progress. Consider it to be the first step in our effort. Blogs are categorized according to a fixed list of topics. You can see lists of posts from those blogs, but since many bloggers have wide-ranging interests, some of the topics might not quite fit. Ultimately we plan on categorizing not by blog, but by individual post. We hope to have other ways of arranging posts as well: just the best posts, chosen by experts; the most popular posts; posts about particular events.

So head on over and give it a whirl.


If you use twitter and you really want to drown yourself in tweets notifying science-y reading opportunities, follow @SciSeekFeed. (For the less crazy, you can take (RSS) feeds of topic areas rather than the whole caboodle.)

Science bloggers who would like the details displayed on ScienceSeeker revised (or corrected, if that’s the appropriate verb) can use this form.

Those wanting to tweet to ScienceSeeker can send messages to @SciSeeker. (Now manned my @BoraZ, as if he doesn’t already have enough to do!)


* Register an account, login, then go to the Member blogs page to view the alphabetical list of blogs.

Other articles at Code for life:

Science blogging aggregated and streamed

Finding platypus venom

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

How long does it take you to write a science blog post?

Quips from ScienceOnline2011

Who blogs on what, and why

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