Archive 2011

Clay tablet science Grant Jacobs Dec 31

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Modern day scientists fret about data storage and processing issues.

Their ancient predecessors* probably did too.

Consider this example,

A Saros period contains almost exactly 239 anomalistic months. So every 223 synodic months — or just over 18 years — eclipses don’t just happen at the same time; the characteristics of each eclipse will be similar as well.

The Babylonians […] didn’t understand the theory behind why the pattern worked, instead they learned it from centuries of observations, all carefully noted down on clay tablets […]

(From pages 248-9, Decoding the Heavens by Jo Marchant.**)

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XMRV-CFS, further retraction Grant Jacobs Dec 27


A few days ago I reported that the editors of Science retracted the paper that initially linked the mouse virus XMRV with chronic fatigue syndrome (Lombardi et al.).

While busy attending parties (and recovering in between them!) another paper that forms part of the line of evidence offered to support the idea that XMRV is associated with CFS has been retracted. Since these papers efforts by others failed to reproduce the association and evidence that this was laboratory contamination mounted.

In this case the authors (Lo et al.) have themselves retracted their paper.

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Earthquake at Christchurch Grant Jacobs Dec 23


(This brief report may be updated periodically.)

Geonet reports magnitude 5.8 earthquake at 1:58pm just offshore to the east of Christchurch, at a depth of 8km. This was followed by a magnitude 5.3 and just a few minutes ago (3:18pm) another aftershock that looks to be over magnitude 5. USGS is reporting both larger aftershocks to be magnitude 5.8, reporting both to be at an estimated depth of  just under 5km.


With goods falling of shelves and the general chaos that happens, this will have put a spanner in the works of anyone trying last-minute Christmas shopping in Christchurch.

Those that follow my earthquake report thread will know this is the first event over magnitude 4 in quite a while. Here’s hoping for not too much damage and that everyone is fine. Initial comments from informal sources suggest there is little major damage and no loss of life, with only one injury reported thus far.

Telecom NZ has called for mobile calls to be limited to emergency use.

An initial Police report is available, reporting ’no serious injuries or widespread damage at this stage.’

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XMRF-CFS: full retraction on it’s way Grant Jacobs Dec 23


Earlier in the year saw a partial retraction of a paper in Science, published in 2009, proposing the mouse virus XMRV as a possible cause of CFS (chronic fatigue syndrome).

Today Science has announced this is moving towards a full retraction.

While a small number of advocates are likely to cling to the original claims, this full retraction–I hope–may let the larger CFS patient community have some sort of closure on this issue.

The retraction text appears to still being drafted – see my link to Retraction Watch, below. (Update To be clear: ’It is Science’s opinion that a retraction signed by all the authors is unlikely to be forthcoming. We are therefore editorially retracting the Report.’ – my apologies over this confusion.) In the interim, readers may find early coverage of this new at: Read the rest of this entry »

The Oath – BBC Radio 4 Grant Jacobs Dec 22


Update: BBC seems to think that this programme has ‘rights issues’ and is not for replay later. Disappointing. (I’m trying not to say something less polite…) My apologies to those who have come here thinking there might be something to listen to.

Michael Edmonds recently raised (again*) the issue of an oath for scientists.

BBC Radio 4 has presented today a show ‘The Oath’ on just that.

Details on the programme are on-line on their website; readers are can follow the programme on-line too – click on Listen Live on BBC Radio 4

I’m going to update this post a little later, as this programme is currently running. If you’re around, listen in first!

* ‘Again’, because it’s been raised before – I suspect quite a few times.

Computational biologists at ScienceOnline2012 Grant Jacobs Dec 18

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I’ve compiled a twitter (sub-)list of those with an interest in computational biology who are attending the ScienceOnline2012 event.

The definition of ‘computational biology’ for the purposes of this list is pretty liberal – I’d rather be inclusive and not have anyone feel left out. If you’re attending and would like to be on this list, just let me know. I am not on the list, as it seems you can’t add yourself to your own lists…!

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What a wonderful world Grant Jacobs Dec 09


You don’t want to miss this.

David Attenborough reciting passages from the lyrics of What a Wonderful World to a backdrop of that glorious BBC photography.* Although some might say that this is, in the end, an advertisement it well worth watching for the stunning natural history photography. It’s a montage of some of the best clips I’ve seen.

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Free vector graphics for Mac (and Linux/Windows) Grant Jacobs Dec 08


If you are looking for a cost-free option to draw vector graphics on Mac OS X, consider Inkscape.

While it will not be everyone’s preferred solution–no one application ever is–it is cost-free, very capable and, thus far, stable.

Vector graphics featured early for Macintosh users. Those with longer memories will have experience with MacDraw or MacDraw II.

The key notion is that the image is composed of points, vectors (line segments), curves and other ‘shape’ objects. All of these can be represented as being on a very finely graded grid that can be scaled up or down in size. Areas bounded by lines, curves or shapes can be filled.

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Two half-brains Grant Jacobs Dec 06


Most of us–bar a very few*–have two cerebral hemispheres in our brain. Our two cerebral hemispheres are connected by the corpus callosum, a fibrous tissues estimated to have around 200 million neurons.

In treating some cases of otherwise intractable epilepsy surgery is performed to cut the corpus callosum, leaving the person with what we might think of as two half brains – hence my title. (More accurately two cerebral hemispheres that no longer interact with each other via the corpus callosum.)

There is a lot of study of the consequences of the absence of a corpus callosum for brain function, both in patients of surgery and those that naturally lack a corpus callosum. Today I have been listening to Associate Professor Liz Franz speaking about her work investigating handedness. During her talk she reminded the audience that while with practice we can do different things with each hand simultaneously, when pushed we prefer to do the same thing – like the patting your head while rubbing circles on your stomach thing. (You can see a photo of Liz doing this in the link I gave earlier!)

I’d love to give you a run down on the ins and outs of work involving the corpus callosum, it’s fascinating stuff. Being short on time, I’ll instead bring you the video she showed a brief portion of in her talk. In it Alan Alda, of M*A*S*H fame,** presents in Scientific American Frontiers ten minutes on what they’ve titled the Severed Corpus Callosum. He talks with a patient of the surgery I mentioned and compares their performance on tests for independent cross-hemisphere activities. (Hint: the guy without a corpus callosum does better.)

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The Ghost Map, a TED alternative to election night programming Grant Jacobs Nov 26

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If you’re in New Zealand, you can’t miss that it’s election night.

Some of you might prefer to try watch something else, maybe.

In this TED lecture, A guided tour of the Ghost Map, Steven Johnson gives and excellent presentation of key aspects leading up to and including John Snow’s famous map centred on the Broad Street pump in London. Although about a dark subject–cholera–his talk is laced with black humour. (British, of course.)

I’ll leave you to it.

YouTube Preview Image

There are many articles about this on-line, for example this one from The Victorianist blog. There’s even a blog named after it.

Of course, this isn’t long enough to take all election night. Try the TED website for more.

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