Archive November 2011

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

No Comments

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.

The Mikovits / XMRV research saga continues Grant Jacobs Nov 23


For those following the XMRV saga, or who simply like intrigue, the latest twist is that lead researcher Judy Mitovits, formerly of the Whittemore Peterson Institute–she was dismissed some time ago–has been arrested for theft of materials from the WPI.

Mikovits proposed that the retrovirus Xenotropic murine leukemia virus-related virus (XMRV) was associated with chronic fatigue syndrome (CFS), in a study published in Science. Other researchers found that they could not confirm Mikovits’ earlier results. Since then a number of studies have indicated the that XMRV observed is contamination of the samples.

Subsequent to this Mikovits was dismissed from the WPI.

More details are emerging, via Trine Tsouderos (@ChicagoScience) in the affidavits accompanying her recent article in the Chicago Tribune. Tsouderos has excerpted some of these on twitter: Read the rest of this entry »

All great stuff – Sunday reading Grant Jacobs Nov 20

No Comments

A subset of the best of a what I’ve run into lately for my readers on lazy grey Sunday.

Stunning photographs – Veering off science for a moment take break to look at the 45 images The Atlantic is showing, taken from this year’s National Geographic photo contest.


One criteria for me, personally, is if the image can tell it’s own story without needing a caption. Taken with the caption, all shown tell great stories.

I’d present a few of these in my post, but the copyright thingy looks off-putting. Those I had a mind to use, with some connection to the natural world as an excuse of keeping this somewhat related to science, where images 3, 8, 17, 24 and 25.

Chase those sources to the ground – I’ve written elsewhere on this blog that wikipedia is best viewed as a started point, from which you then want to verify. xkcd seems to think much the same, illustrating something found in a recent popular science book with this cartoon (xkcd’s rollover text is in the legend):


Not very surprisingly this as left several in the science writing community trying to guess what the book was. (I’m not even going to try.)

Read the rest of this entry »

The software developer’s generalisation dilemma Grant Jacobs Nov 12


xkcd nails it :-

I find when someone's taking the time to the right in the present, they're a perfectionist with no ability to prioritize, whereas when someone took the time to do something right in the past, they're a master artisan of great foresight.

I find when someone's taking the time to the right in the present, they're a perfectionist with no ability to prioritize, whereas when someone took the time to do something right in the past, they're a master artisan of great foresight.

It’s the classic dilemma, isn’t it.

Faced with coding a new bit of functionality, do you write the version that solves only your immediate problem or do you think ahead and try cater for future, more varied, uses too?

Perhaps you want to find that middle ground; lay it out enough that the opportunity for future generalisation is documented well enough and sufficiently in place so that you can move on in peace, having noted the opportunity and laid the tracks for future development without having expended too much effort.

Read the rest of this entry »

What use now is handwriting? Grant Jacobs Nov 11


Reading Cath Ennis’ handwritten blog post–do check it out–I was left thinking: will a later generation not use handwriting at all?


Remember those biology exams with their essays? Or those endless lectures frantically scribbling down notes?

I still record thoughts for most talks using a notebook, but I have to admit my writing is now terrible and I can almost certainly type faster.

Like Cath the quality of my writing has deteriorated as I have gotten older. Like commenters to her post, I can’t write furiously for hours any more. But my typing has–slowly!–improved.

For many–most–things it’d be more practical to type rather than write.

There is the issue of doodles and sketches. They’re useful when taking notes. Not to mention those wayward arrows that you add after the fact, with their long twisty lines wandering around the page connecting one point with another.

Read the rest of this entry »

Our pale blue dot Grant Jacobs Nov 11

1 Comment

I’m a little late for Carl Sagan Day* over in my part of our pale blue dot, but nevertheless let me share a video celebrating it:

YouTube Preview Image

I’ve chosen one of the less viewed of the many videos of this, one with images less focusing on either wars or religion.

An older post of mine has offers a little verbiage and a copy of the image behind this ‘pale blue dot’ story.

Read the rest of this entry »

Rebecca Skloot on writing creative non-fiction Grant Jacobs Nov 09


Rebecca Skloot is author of The Immortal Life of Henrietta Lacks, who this morning presented a twitter interview/presentation on creative non-fiction writing and her book, hosted by Misha Angrist (@MishaAngrist), author of Here is a Human Being (subtitled At the Dawn of Personal Genomics) who blogs at GenomeBoy.

Immortal-life-cover-USABelow I have tried to organise the live discussion into something that I hope is useful to others. This material was gathered and written on-the-fly; the bulk of the material is ‘as delivered’.

As I’ve done previously, the bits in square brackets are my own thoughts added at the time.

The material below is roughly grouped to follow themes with the content of each section in chronological order.

I have run-together some tweets that were multi-part to make this more readable.

Usual disclaimer: any errors introduced are my own!

There is also a ‘chirpified’ version of the twitter chat, thanks to Ruth Seeley (@ruthseeley); this has more content, but then I hope my presentation groups the material in a way that is useful to readers.

The chat opened Misha Angrist pointing at an FAQ on Skloot’s work:

MishaAngrist: @rebeccaskloot FAQ:

Skloot opened by discussing the overall structure of the book, recommending writers read other books to get ideas for overall structure: Read the rest of this entry »

ScienceOnline2012 – only two registration slots to go Grant Jacobs Nov 04


ScienceOnline2011 is the sixth of the annual gatherings of the on-line science communication community at Raleigh, North Carolina.

Even if you have no intention of attending, but are interested in science communication, it’s worth reading the draft programme - the ideas in there should give you plenty to think about. (There is so much in the programme that I’m left wondering how participants are supposed to choose what sessions to attend.)

For those familiar with the on-line science writing community, those who have registered thus far read like a who’s who. having said that, as well as the established names, there are many new ones I’ve yet to run into. Read the rest of this entry »

Trust science, not scientists Grant Jacobs Nov 03


Trust science, not scientists says the title of an article written by virologist Professor Vincent Racanielo.

It’s a great line.

Vincent Racanielo was writing in the context of the continued saga over proposals of a link between the mouse XMRV virus (xenotropic murine leukemia virus-related virus) and chronic fatigue syndrome (CFS). My interest here is not on this particular saga,[1] intriguing as it might be, but on the wider issue of who or what do you trust.

He closes his article writing,

There are many lessons to be learned from XMRV, but an important one is that science progresses not from the work of a single investigator, but from the collective efforts of many laboratories. XMRV reminds us to trust science, not scientists.

One useful way to view new research papers, is as an argument for a case that has yet to be heard by a jury of their peers–the in-house peer-review of the research journal not withstanding.[2]

It’s a cautiousness and a willingness to critique, rather than accept at face value; Science’s community-based sanity filter. Read the rest of this entry »

Teaching bioinformatics at high school Grant Jacobs Nov 01


As many of my readers will be aware, my work area and research interests are in computational biology[1] – the wider field is better known as bioinformatics.

Biology has long been a core subject at high school.

Computer science is now well established too.

Bioinformatics takes computer science and applies it to biological questions. Given that the basic principles are straight-forward and can be allied to basic biology, it seems reasonable that it could be taught at a high school level too.

I can imagine doing this myself, not that I’ll ever be in the position of doing it.

Two articles in PLoS Computational Biology address teaching bioinformatics at high school:

Both are straight-forward reads.

I particularly liked the first in that it tries to pick apart what students were struggling with, or not, and why.

A theme that emerges from this, that resonates with me, is a need for the focus to be on concepts underlying the tools, not the tools per se. Read the rest of this entry »

Network-wide options by YD - Freelance Wordpress Developer