Archive March 2011

Tsunami forecast animation & warning systems Grant Jacobs Mar 14

1 Comment

Short videos & articles on tsunami and earthquake warning systems.

This video provided by NOAA* shows a one-minute animation of forecast results** for the tsunami from the March 11th Honshu M=9.0 earthquake:

YouTube Preview Image

Animations like this prove to be a regular feature from this source, with animations like the one above for most of the major earthquakes that have induced tsunami in recent years.

NOAA hosts a great deal of other instructive videos on a wide range of topics. On the current topic, examples include a video explaining the tsunami detection and warning system:

Read the rest of this entry »

Make it a brainy week Grant Jacobs Mar 13


NEW ZEALAND EVENTS: Introducing the ‘Brain Week’ and ‘Brain Day’ events being held throughout New Zealand this coming week.

These are for everyone: come along.

Events are being held in Queenstown, Gisborne, New Plymouth, Whangarei, Napier Hamilton, Palmerston North, Pukekohe, Tauranga, Invercargill, Wellington, Dunedin and various locations in Auckland (East, West, North Shore and Central).


Different towns have events on different days, with Saturday being Brain Day, with a series of events in the major centres. The first event is to be held in Queenstown at 10am on Monday. Please note that the Christchurch and Rangiora events have been cancelled owing to the earthquake. A full list of the events can be found on the Brain Week website.

I have to admit the Auckland Brain Day programme (PDF file) looks particularly impressive. It includes our very own Fabiana Kukbe hosting a workshop teaching people How to build your own brain.

Dunedin (where I live) will host four lectures with on-going displays outside on the Saturday, at the Castle lecture theatre complex (in the middle of the campus, south of the clock tower building).

Read the rest of this entry »

Mapping connections in the brain Grant Jacobs Mar 12


This short ’for the masses’ video from the scientific journal Nature gives a ‘lite’ introduction to work aimed at mapping small portions of the human brain from the visual cortex, summarising two papers recently published in the journal.

You can view this as a small-scale pilot program to look at the issues involved in a larger-scale mapping of neuronal connections in the brain, by examining first a well-studied system like the visual cortex.

As the narrator explains, one of the key things about this work isn’t just working out what is connected with what, but getting some idea of what the connected neurons do. The mapping work and the functional work complement each other to create a bigger picture than each on their own.

YouTube Preview Image

Unfortunately for those who’d like to read further both research papers are not open-access, so those without access to university library are a bit stuck there.

(On a personal note, as a computational biologist, I’d have to admit the thought of ’playing’ with some of the datasets that underlie the colourful representations shown in the video appeals!)

Update Credit where it’s due: this is the work of Charlotte Stoddart. I apologise for not including this earlier as a personal credit was not listed on the original; I’ve since seen her credited elsewhere.

Recent videos and lighter articles on Code for Life:

Weekend shorts (including Japan earthquake links)

Printing a human kidney

Sinclair ZX envy

Liquefaction in a barrow

Russell Doolittle on Life before Bioinformatics

Weekend shorts (including Japan earthquake links) Grant Jacobs Mar 12


A collection of links and comments on articles and discussions elsewhere that might interest my readers. I hope there is something here for everyone.

This post has been overtaken by the massive earthquake in Japan last evening, hitting with over 1000 times the force of the Feb. 22nd Christchurch earthquake. An early collection of images can be seen on the LA Time website (who also brought an excellent photo collection for the Feb. 22nd Christchurch earthquake); another can be found at the Boston Globe. The tsunami is clearly a major disaster, and has breached whatever tsunami walls were present. Japanese rescue workers assisting at Christchurch are travelling back to Japan to assist.

For New Zealand, Civil Defence statements on television are that the tsunami will hopefully only have an impact in upper Northland and mainly on boaties (e.g. strong currents). Advice is to stay away from beaches and rivers near coastlines, not to go swimming (etc.) and not to go sightseeing. The full advisory is available at the Civil Defence website.

ScienceInsider explains that the event was larger than was expected to occur. (‘And Japan’s latest national seismic risk map gave a 99% chance of a magnitude-7.5 or greater quake occurring in that area in the next 30 years, Geller says.’) John Horgan writing at Scientific American offers a few words on earthquake prediction and warning.

My thoughts and best wishes for all those in Japan.

The remainder of this post was written prior to the Japan earthquake.

Drawing the map of life - cover

The Human Genome Project celebrated it’s tenth anniversary a little while ago. Michael Morgan’s review of the Victor McElheny’s book, Drawing the Map of Life, has itself a potted history of the early stages of the project, one well worth reading. (I admit to a slight vested interest: I was a student at the institute that John Sulston worked at, at the time.)

Still on the subject of genomes, Emily Willingham writes about her and her partner’s experience of personal genomics.

Discussions You could try an interactive involvement and encourage those uncertain about Ken Ring’s earthquake ‘predictions’ to look more closely at his claims on his Facebook page. (Be warned, though, that this Facebook group has an element of a ‘fan’ scene with a few individuals thinking it their job to muscle out those who offer constructive criticism or point to sources of information.)

Read the rest of this entry »

Printing a human kidney Grant Jacobs Mar 11

No Comments

FRIDAY VIDEO: Speaking at TED surgeon Anthony Atala presents early work on ‘printing’ a kidney and other regenerative medicine.

The basic idea is to use a 3-D printer working with living cells to create an organ, for example a kidney. (Do remember that most of the work talked about is about prototypes, looking to the future.)

His talk presents regenerative medicine, work trying to replace organs through bioengineering. Among other things he introduces a replacement heart valve under development and introduces a patient who received an engineered bladder ten years ago.

There’s new technology he presents that they aim to–his words from his talk–‘print right on the patient’ to treat surface wounds. Rather than use grafts, they hope to directly print the replacement tissue onto the patient.

Read the rest of this entry »

Christchurch (Lyttelton) earthquake ground movement captured by satellite imagery Grant Jacobs Mar 08


This imagery from the Japanese Alos spacecraft data captures the movement of the earth towards or away from the satellite:

Source: COMET website -

Source: COMET website -

(Click on the image to see a huge copy of it; in some browsers you may have to click on the image to enlarge it to it’s full size.)

I’m using this ‘bright shiny thing’ to encourage readers to read an excellent article* on the BBC website describing this and other data on the recent earthquake. The article has extensive input from Dr John Elliott from the Centre for the Observation and Modelling of Earthquakes and Tectonics (Comet) at Oxford University, UK.

Further imagery and background for both the February 22nd, 2011, magnitude 6.3 and the September 4th, 2010, magnitude 7.1 earthquake is also available at the ALOS website.

(* In lieu of me writing tonight. I’ve other work to do. Honest!)

Other articles on Code for Life:

6.3 earthquake in Christchurch

Liquefaction in a barrow

Lyttelton earthquake peak ground acceleration

Sinclair ZX envy

Retrospective–The mythology of bioinformatics

Sinclair ZX envy Grant Jacobs Mar 08


Last week was the 30th anniversary of the Sinclair ZX-81. I missed it.

Am I that old? Yeah, unfortunately I am. Sigh.

(Source: Wikimedia Commons.)

(Source: Wikimedia Commons.)

My first sight of one of these things was as at school. Some other kid–I can’t remember who now–brought one to class and was showing it to everyone.

I coveted that thing.

Read the rest of this entry »

Ken Ring’s predictions – what happens on March 20th doesn’t matter Grant Jacobs Mar 07


Some ‘scientific commonsense’ to clarify a few misunderstandings that seem to have arisen since John Campbell’s interview with astrologer Ken Ring.

(If you came here looking for my ’continuously updated’ comments on the 2011 earthquakes the aftershocks go here – older comments are appended to this post.)

I am writing this in response to commentary I have seen since John Campbell’s interview of astrologer Ken Ring and the articles by my colleagues. It’s now very late in the act I know, but I hope these clarifications might still be of help for a few readers and provide a (partial) round-up of sorts.

We’ll see what happens on March 20th

On a number of forums I’m seen people writing ‘wait for March 20th’ or the like as if this were the arbiter of if Ken Ring is right or not.

What happens on March 20th will not determine if his method works.

What matters is if the ‘predictions’ are meaningful and if he is able to reliably predict earthquakes.

You can test if Ken Ring’s ‘predictions’ are not worthy of the word prediction before March 20th by comparing them with what you’d get by ‘dumb luck’ using the typical rate earthquakes occur.

Read the rest of this entry »

Life BBC documentary (2009) Prime 8:45pm Grant Jacobs Mar 06

No Comments

A quick heads’ up for New Zealand readers that the big budget BBC documentary series Life narrated by the formidable and excellent David Attenborough is screening on Prime TV at 8:45pm. Rating 9.3 (out of ten) by IMDb, reviews say that the photography is superb.

Tonight is the second of ten episodes, featuring amphibians and reptiles. Apparently the opening sequence features a Komodo dragon. While I’ve never seen one (despite having years ago planned to travel the Indonesia Island extensively) I have had the experience of getting out of the water from swimming in the tropics to be faced with and approximately 5-foot long lizard. It was big enough to make me pause for thought ’no, that is not a Komodo dragon…’

Enjoy it – I’ll probably be busy programming!

(Updated to add tags and make title clearer.)

High tides and earthquakes – an interview Grant Jacobs Mar 05


High tides and earthquakes: an interview with a scientist.

Ken Ring is an astrologer who is causing some fuss in some circles in New Zealand for having promoting the idea that he ’predicted’ the recent February 22nd event near Christchurch, for ’predicting’ an earthquake for Christchurch on March 20th and for being the subject of an interview on prime-time television.

Fellow science blogger Ken Perrot has posted an interview with media commentator Russell Brown on Radio Radio Wammo. Below is a recording of an interview on the same station with scientist Elizabeth Cochran who was an author of a study correlating large (“king”) tides and earthquakes.

Read the rest of this entry »

Network-wide options by YD - Freelance Wordpress Developer