Archive January 2010

Bill & Melinda Gates Foundation: $10B towards vaccines Grant Jacobs Jan 30


Vaccines are a major weapon in the fight against disease. Today the Bill & Melinda Gates have pledged funds for a “decade of vaccines” in poor and developing countries.

(Source: Bill & Melinda Gates Foundation)

Their press release goes on to say

The Gateses said that increased investment in vaccines by governments and the private sector could help developing countries dramatically reduce child mortality by the end of the decade, and they called for others to help fill critical financing gaps in both research funding and childhood immunization programs.

’We must make this the decade of vaccines,’ said Bill Gates. ’Vaccines already save and improve millions of lives in developing countries. Innovation will make it possible to save more children than ever before.’

A video of the full press conference is available to the right of the press release page.

The broader announcement called for a wide range of initiatives including scaling vaccine programs up, laboratory research and clinical trials to create new vaccines, introducing new vaccines for pneumonia and severe diarrhoea among other things, and improving the market and access of vaccines in developing countries.

The initiative is ’in addition to the $4.5 billion that the Gates Foundation has already committed to vaccine research, development and delivery to date across its entire disease portfolio since its inception.’

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Ecuadorian Amazonians see Avatar (in 3-D) Grant Jacobs Jan 30

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What would people who have an history and culture based on living in the forests of the Amazon think of James Cameron’s film, Avatar?

avatar-movie-smllWould they see themselves, their people or history echoed in it?

It’s an intriguing thought.

This short video below (4:03 minutes), produced by Siegmund Thies, follows the journey of a bus-load of Amazonians down from the heavily forested hills to bustling Quito, the capital city of Ecuador, where they watch the film in 3-D. After viewing the movie a few of the Amazonian audience are briefly interviewed.

You can’t help hoping this is a pilot or short for a full documentary.

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Animal babies, long snouts Grant Jacobs Jan 29

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Baby animals are cute. You’ve got to admit it.

Long noses or snouts are striking.

The two videos I bring you today feature animal babies with very long snouts.

In the first video zoologist Marie Magnuson from the Smithsonian National Zoo (USA) introduces a baby anteater. Wait until you see the shots of the baby clinging on to to the rear of it’s mother’s back, or you’ll miss the fun.

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The iPad, Apple’s new tablet and the textbook / reference market Grant Jacobs Jan 28


As almost anyone interested in Apple devices knows, today Apple announced it’s tablet device.

Interest on internet has been high. To give the scale of interest, the Arstechnica website, normally a busy site, was unable to cope with the load. I watched a small portion of the presentation live, via TVNZ’s (Television New Zealand, for those outside New Zealand) live streaming on their technology news website.

Caveat: as “breaking news”, please realise there may be errors and there certainly will be omissions. As someone with a hearing “disability”, I would welcome the day when captions were more widely available, the streaming feed is very difficult to follow, so I’ve written most of this from running around the internet picking up other’s reporting, with all the flaws that come with that!


As expected, they use the 9.7″ screens (the rumour-mill started as Apple essentially bought out large volumes of the small screen, without having a product which used them). It features a style very similar to that of the current iMacs, with the screen itself surrounded by black backing, then a thin brushed aluminium border.

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Singing for science Grant Jacobs Jan 27

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If you’re looking for science songs, especially for young kids, not a bad place to start is The Great Beyond blog. A far as I can tell, this is the latest in the series. They’re up to thirty now! You can always trying searching the blog using ‘song science’, using the search box in the upper-left corner. (I’ll be honest some of them make me squirm, but some aren’t so bad, and the kids’ ones are obviously for kids!)

An earlier post in the series passes on that Jef Poskanzer has posted the entire collection of the 1950s-1960s era Singing Science Records online (for kids).

Below I’ve given a video of one of the songs (below the “fold”), which will be (very) familiar to science bloggers, but perhaps new to some of my non-science readers. The fish featured in it is a model of the Tiktaalik fossil. Neil Shubin, who the song mentions, is one of the discoverers of the fossil. An account of his work on this fossil is given in his excellent book Your Inner Fish (cover to right). The author offers an adapted excerpt  from the book, Fish out of water: Your Inner Fish, that you can read on-line.

Anyway, on to the video for you (and back to work for me!):

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Blog post about blog posts with comments about comments Grant Jacobs Jan 27

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Heads’ up: although the post this points to is hosted on a science-related blog, it has nothing to do with science. This is a deviation from normal service, which will resume when the madness of grant writing ends.

Just a little light relief.

It’s midweek, I’m working, you’re working. Aren’t you? What are you doing reading this blog? What am I doing writing this blog? We’re bored, right?

cc2This blog post, from Coyote Crossing, is an excellent meta-referential post about blog posts, particularly the kind that tries to promote herself by showing off her blogstraps. It is getting entirely more traffic than it deserves owing to the blogstraps it reveals.

Erm, no. Let me take that back. The bit about the blogstraps.

Seriously (I really mean seriously), it’s a fine post introspecting some styles of blogs, with the comment section brilliantly following in tune. It’s great when a “community” effort likes this pans out and everyone joins in so well. (Yes, I’ve added a comment to the ever-going list.)

On another note, this author’s blog got so popular (~2,500 visits/hour), that the hosting company pointed out that they’d bill extra for the excess traffic. Poor sod. Hopefully enough time has passed that their traffic has fallen to more sane levels that aren’t costing them by now. I’d feel guilty writing this post otherwise. It’s not as if I could send many readers their way given how few come my way…

HT: bioephemera.

Popularity does not mean effectiveness or sensibility Grant Jacobs Jan 26


In recent comments to an article I wrote on homeopathy in New Zealand pharmacies, some readers suggested that because the remedies were popular, they must be OK.

Buried Alive - BondesonTo give a little light relief from the weightiness of the topic, let’s illustrate the illogic of using popularity in lieu of demonstration of effectiveness by paradoxially considering the morbid example of mausoleums.

Previously I reviewed Bondeson’s book Buried Alive. (There’s also a video of Monty Python’s “Bring out your dead” skit, if you’re a fan.) If you read the book, you’d learn that mausoleums where once popular in Germany.

These mausoleums were institutions set up throughout Germany to ensure that the dead really were dead by babysitting them for several days.

To their credit at least they kept good records, as German administrations seem to have a reputation to.

After a number of years, they realised that no-one was recovering from death, so the mausoleums themselves died.

From this we get two lessons:

  1. No-one survives death (Good lesson, that!)
  2. Just because something is popular, doesn’t make it effective or sensible

More articles at Code for life:

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

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

Explore ancient science books on-line

(I apologise for the inexcusably short post, but that’s the all time I have tonight…! I will return to the homeopathy articles in time. I have nothing against Germans and there are some fine German scientists and scientific institutions.)

Homeopathic remedies in NZ pharmacies Grant Jacobs Jan 25



Why should pharmacies, which generally promote themselves as sellers of tested and reliable treatments, offer homeopathic remedies?

pharmacy-ancientRecently I wrote about a protest against Boots selling homeopathic remedies in England. A quick inspection of several pharmacies here in Dunedin, New Zealand show they do the same.

One of the products even stated it was a “homeopathic product without approved therapeutic implications (“Sleep Well”, Martin & Pleasance; my emboldening). They’re basically saying their product has no support to be used as therapeutic remedy. So then why is a pharmacy carrying it?

Are pharmacies here guilty of the line of reasoning that if the public is willing to pay for it, give it to them, regardless of if it does them any good or not?

Shouldn’t we expect pharmacies to at least make some effort to limit themselves to goods that have been shown to work?

Perhaps it is time that we insisted that claims made of a remedy can be backed with evidence? (See Time for disclaimers on remedies?, ’alternative’ or not.)

These products are implausible several ways: the amounts of the ingredients, what the treatments claim to do and the way the remedy is taken.

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Reproducible research and computational biology Grant Jacobs Jan 24


A concern raised, which I have some sympathies with, is how to make computational science reproducible.

Modern science is largely grounded on the notion that findings can be repeated independently by others to verify them, or to extend them. In practice this can be easier said that done. You’d think that for computational sciences, like computational biology, it’d be cut and dried. It can be, but a lot of the time it isn’t.

Musical repeat sign

I’d like to point to three things discouraging development of reproducible research in computational biology and suggest that in addition to “open” coding and a suitable legal framework, self-documenting output that can be used as input may help.

To start as I did, read John Timmer‘s article Keeping computers from ending science’s reproducibility and the slides (PDF file) from Victoria Stodden’s talk Intellectual Property Issues in Publishing, Sharing and Blogging Science.

It’s claimed that the term “reproducible research” was proposed by Jon Claerbout (Standford University) to encapsulate the idea that “the ultimate product of research is the paper along with the full computational environment used to produce the results in the paper such as the code, data, etc. necessary for reproduction of the results and building upon the research.” What both Timmer and Stodden write about follows this description and the abstract of the paper that the wikipedia entry points to:

WaveLab is a library of Matlab routines for wavelet analysis, wavelet-packet analysis, cosine-packet analysis and matching pursuit. [...]

WaveLab makes available, in one package, all the code to reproduce all the figures in our published wavelet articles. The interested reader can inspect the source code to see exactly what algorithms were used, how parameters were set in producing our figures, and can then modify the source to produce variations on our results.

WaveLab has been developed, in part, because of exhortations by Jon Claerbout of Stanford that computational scientists should engage in “really reproducible” research.

The full paper is available free on-line, via the abstract. (This is well worth reading if you haven’t already. It’s a light read if you skip lightly over the details of the product in section 4 & 5 and focus on the discussion.)

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Light Sunday reading, viewing and thoughts. Grant Jacobs Jan 24

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A potpourri of bits and bobs for some light Sunday entertainment. (I have several more “serious” posts lined up, but they are held up for a variety of reasons.)

Some time ago I write about silly or humorous scientific research article titles or content: Craziest research paper titles, awards and authors. I’d completely forgotten about the NCBI ROFL blog, which has re-surfaced as occasional posts of Discoblog. If humorous takes on research are your thing, head on over. Their latest effort on this theme is NCBI ROFL: the case of the haunted scrotum. A haunted scrotum? Scary.

Once posted...

Once posted... there forever

The incredibly silly illustration to the right is lifted from one of Isis’ blog articles. The point being that what you write on the internet stays. I’m popping this in as a lighter take on a serious topic. (Yes, this picture is incredibly scientific…) There’s been a lot of discussion about civility around the ScienceOnline2010 crowd. There is a serious point to some of these conversations, which is too heavy for light Sunday reading but a rule of thumb I have is not to write something that you wouldn’t want to your family, close friends, workmates, employers, etc., to read. The people that matter to you, basically. (Also: if you really think an internet alias is untraceable, don’t.)

Those looking for on-line science documentaries, don’t miss these lists: 100 best free science documentaries on-lineand DocumentaryHeaven. Enough to keep you going for days.

Many of you will be bookworms. If you’re looking for new non-fiction books, check out the list of books towards the end of this article, recommended by Susan Orlean’s readers.

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