Of pandas and other genomes

So, it's already three weeks after the ostensible end of 23 Things Cambridge, I'm still only two-thirds of the way through the Things, and this is my first blog post for a month. I do still intend to look at a few more of the Things; for one reason or another, Prezi, data visualisation, Creative Commons and QR codes hold particular appeal. But I have always had another reason for starting this blog: if it's not too self-referential, to flag up some of my own science writing and similar activities. And where else for Ursula Small to start than with a bear - although not a particularly little one?

Since 1996 (almost pre-history in Web terms) I have had a regular column in The Biochemist, the membership magazine of the Biochemical Society. This was my first piece of regular science writing, and I will always be grateful to its then editor, Frank Burnet (now emeritus professor of science communication at the University of the West of England) for giving my fledgling second career such a flying start. In my column, The Cyberbiochemist, I aim to explain a topic or issue related in some way to computational biochemistry (or bioinformatics) in a way that is relevant and interesting to bench biochemists. Each issue has a theme, and very often, but not always, my column is related to that overall theme. In October 2011, to celebrate both the centenary of the Society and its opening an office in Beijing, that theme was "Biochemistry in China".

My contribution to this "China issue" was a survey of how bioinformatics has developed in China over the last few decades. And, like so many other technologies, that development has been meteorically upwards. The first Chinese bioinformatics research centre was set up in Beijing in 1996, the year I began my Cyberbiochemist column, but only fifteen years later the country boasts some of the fastest and most sophisticated genome sequencing technology in the world.

China does, however, still see itself as a scientific leader of the so-called Third World. It is the home of genetic sequencing projects and databases for its staple crop, rice, and the iconic giant panda. The panda's Latin name, Ailuropoda melanoleuca, means literally "black-and-white cat-foot" and  its classification within the mammals was unclear until the advent of molecular genetics. Now, however, it is known to fit in the family Ursidae: the true bears.

Chinese molecular genetics, however, has proved itself in more important areas than just in solving a controversy over the naming of bears. A consortium including many Chinese scientists was responsible for sequencing the genome of the virus that caused the outbreak of SARS (severe acute respiratory syndrome) in 2003, and just last year a Chinese-led consortium rapidly analysed the genome of the exact bacterial strain that caused a deadly outbreak of food poisoning (remember the killer cucumber stories?) If, God forbid (and as only one example), avian influenza were to mutate into a highly infectious strain, I predict that Chinese scientists will play a crucial role in analysing and eventually controlling it.

You can read the whole article here (freely accessible). I would love to post the gorgeous photo of a seven-month-old panda cub that the editors used there, but it's not Creative Commons. And that, as I've said already, is for another post and another time.

Thing 5: Screenshots

For quite a few years, I've been using a rather old, cut-down, non-licensed (cut-down because it's non-licensed) version of Corel Paint Shop Pro to take screen shots. This has worked fine, but it's occurred to me from time to time that it would be good to find a completely open source equivalent. I was therefore very pleased to come (eventually) to Thing 5, and find LightShot recommended there.

I found it easy enough to install as an add-on to Firefox although I do have to confess that I wasted a good thirty seconds looking in the wrong part of the screen for the purple feather.

And so, I now have a new toy. What to do with it? Well, I could do with livening up my blog with an image or two. An image, perhaps, of a little bear... Googling "little bear", however, proved embarrassing. A whole page of primary-school cartoon images, all copyright. "Bear cub" was rather more promising:

A whole screenfull of little bears

But wait. I'm no wildlife photographer, and each one of those cute images is almost certainly copyrighted to someone who is. What I want - no, what I need - is an image that is firmly in the public domain. Wikimedia Commons has a few, labelled, in a most un-primary-school-like manner, as "Category: Ursidae (juvenile)".


The one I like is one up a tree. No author name is given, and it is licensed under a Creative Commons Attribution Share Alike 3.0 Unported license and a GNU Free Documentation License. You can see the result on the left-hand side of my top page. I think it looks OK; if anyone reading this and who knows more about copyright (and copyleft) than I do suggests that I take it down, I will.

The constellation Ursa minor (Creative Commons image by BorgQueen)

Had I stuck to my first degree subject of Physics, I might well have landed up with an image like this one

First Post...

Welcome to my blog.

And three questions for my first post. Firstly the two posed by Thing 2. What do I hope to get out of 23 Things Cambridge version 2.0 - and why am I doing it at all, as I'm not even a librarian? And secondly, what is my experience of Web 2.0 so far? But also thirdly - why Ursula Small?

I owe my interest in this course to my husband, Aidan Baker, Haddon Librarian and poet, who blogs at Blurtmetry. Aidan has said often enough that the original Cam23 was the best thing that his 2010 had to offer, and that has been enough to intrigue me.

I have been using a handful of Web 2.0 tools since possibly before the term was invented, but in a rather amateur fashion: some, such as RSS feeds, I've simply ignored (giving the poor excuse of lack of time) and others, such as Linked In and Aidan's favourite, Twitter, I feel I don't get as much out of as I could. I will post my experience of the various "things" so far in my next post. I hope that I will be allowed to dip in and out of 2011's "extra things" as my very mixed levels of prior experience suggest.

But my main reason for tackling this now is that it gives me an excuse to get up a personal blog, and learn about blogging while doing so. From time to time, the Association of British Science Writers (of which I am an associate member) discusses the thorny issue of whether a science writer needs to have a blog. "Suck it and see" has been the usual answer. Will I keep blogging after Cam23 2.0 is done and dusted? Time will tell.

And why Ursula Small? Since long before we got engaged, Aidan's affectionate nickname for me has been "Little Bear". I first thought of Ursula Small as a pseudonym that I could use if I ever took to writing fiction. But I don't realistically think that I ever will, and when, earlier this year, I mentioned it to a friend who does write fiction, she said it was too good to forget...

Oh, and while on the subject of pseudonyms, I answer to "Clare Baker" just as readily, but not when I'm working.