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 15: Linked In

Oh dear. I'm going to have to stop counting Cam 23.0 in weeks - I'm already over a month behind, and at this rate it may be Christmas before I finish. I hope that no one's going to throw me out of the party on Thursday...

But I have finally come to Linked In - getting on for a month after its fellow "Week 8" Thing, Facebook. I have had an account on Linked In for well over four years - much longer than my Facebook account, and, in fact, so long that I can't remember when I joined. But I've come to blog about it, rather than skipping to a less familiar Thing (or even Extra Thing) because I have finally got round to updating my profile with such relative basics as a photo and a link to my Twitter account. Perhaps this post should have been named "Procrastination".

When the 2010 version of 23 Things reached social networking sites, Aidan mentioned my observation that, of the three communities I consider myself at least a part-time member of, biotech professionals choose Linked In but science communicators and educationalists congregate on Twitter. I still have little idea why. To my eye, Linked In seems more slick and professional than Twitter (let alone Facebook), less inconsequential, but also, perhaps, a teeny bit duller. It is strictly a site for professional business, with most of the updates appearing on a Linked In timeline being new connections and job changes. And I have used it for a small number of pieces of real professional business. At one end of the scale, a comment on a Linked In group led me to be invited to give a careers talk - not big money or even little money, only expenses and canapes, but something I find rather fun. At the other, I spotted a contract as the in-house science writer for an immunology company, and was almost appointed only to part amicably after realising that the required commitment of a day a week in Oxford was just too much for me

If anyone were to ask my advice on how to get to grips with Linked In - and looking at my profile this is still rather unlikely - I would recommend a guy called Will Kintish. He is a small, unassuming ex-accountant, and one of the best networkers and trainers I have ever come across. His workshops can be fairly expensive (it is possible to find subsidised ones, and I was fortunate enough to attend one such earlier this year) but the combination of entertainment with useful, and memorable, networking tips may be well worth a substantial investment. And he is an evangelist for the value of social networking ("not just for kids") and for Linked In in particular. Check out his Linked In website - it's well worth a visit. I would suggest that you start with the four-minute video.


But I imagine that librarianship has more in common with communication and education than with biotech, but I may be wrong. If this hunch is correct, and my hunch about the three communities is correct (and these combine into a pretty big IF) then I would guess Twitter to be many librarians' network of choice. Is this true for you?

Week 8, Thing 14: Facebook (and a race)

What can I say about Facebook, that hasn't already been said?

I have had an account there for about 3 1/2 years. I joined it well over a year before Twitter and I still use both more or less equally, but for different purposes. Facebook is very definitely my family-and-friends network. So, my CV (which ought to be online by now, but isn't, so I can't point to it here) gives my account details for Twitter and LinkedIn, but not for Facebook. And I post work-related stuff there rarely, and only when I reckon that it might be of general interest to at least some people who have no part in the biomedical, higher education or science communication communities.

Aidan, whose interest in Facebook has dwindled as his enthusiasm for Twitter has grown, posted in July 2010 that Facebook offers "play versions of things that thrive better in a full-sized version elsewhere". I can see the point of that, very clearly, but I can also see the point of play versions.

Take photography. I have one Facebook friend who is an enthusiastic and very able wildlife photographer. The majority of his photos of beasts have their home on his Flickr photostream; Facebook is where he keeps photos of his own wedding. Another keen photographer who is currently using the 365 Project to record a photo a day for a year, nevertheless mounts casual snaps taken at parties on Facebook. My own photography is very much of the "casual snap" variety, and I want my family and friends to see it; Facebook will do.

And sometimes Facebook does rather better than that. Does anyone else with accounts on both run "Facebook-Twitter races", just for fun? The idea is to pose the same query to both sites and see which comes up with the answer first. Today, I had just such a query. I'm going to a conference in Barcelona in September and find that I have a spare morning - no more - between arrival and the start of proceedings. I've never been to Barcelona before; what will I be able to see in that limited time? I posted the question on Facebook and Twitter, and waited. Facebook won hands down, with half a dozen useful suggestions within a few hours; my tweet sank without trace. Why? Well, perhaps because my Twitter network is still rather small, and quite a few of my followers are institutions. Perhaps because they had serious things on their minds (#Libya has been dominating my Twitter feed all day). Or perhaps because (so far) relatively few of my followers are librarians. Any ideas?

Week 7, Thing 12: Bookmarking tools (Delicious)

I start this post with a confession. I had a Delicious account before, once.

The least part-time, and longest-lived, of my several part-time jobs is as a lecturer at Birkbeck College, where I teach on an Internet based distance learning MSc course in structural biology. (You don't need to know anything about structural biology to understand this post - essentially it involves the techniques that are used to discover the three-dimensional structures of proteins and other molecules and to understand how these relate to their biological function.)

A random(-ish) protein structure
This one's myoglobin, found in red blood cells, and the first protein structure to be solved.
In 1958.

Back in 2007, I was awarded a small grant from London University's Centre for Distance Education to explore introducing various Web 2.0 based tools into that course. Some of the tools I tried worked very well. I still maintain the course blog, which manages a rather higher hit rate than this one. But Delicious... no. I set up an account, shared it with the students, and asked them to save bookmarks of structural biology research sites they liked (there are lots to choose from... like this one...) But I don't think a single link was saved. Maybe I should have set it as an assessed exercise.

Maybe, also, I should have set up my own Delicious account before I started using it in teaching. At that time, I couldn't think of anything I, personally, would want to do with delicious (or any other social bookmarking tool) that I couldn't do with my browser's memory and Google. I'm still not quite sure. Two things, however, have encouraged me to give this another go. The first, obviously enough, is this course. The second is reading David Weinberger's excellent book Everything is Miscellaneous, or "the power of the new digital disorder". Published in 2007, this book says nothing about Facebook or Twitter at all, but it allots five index entries, some multi-page, to the power of Delicious. The site's creator, Joshua Schachter, is quoted there as describing it as an "amplification system for your memory of websites".

So, four years and (at least) one change of ownership for Delicious later, I now have an account again. And, so far, about a dozen bookmarks with associated tags. My user name is the same as my Twitter username: Clare_Sansom.

A few bookmarks

I'm still not sure exactly what I will come to use Delicious for, or how much use it will be to me in my professional life, but I'm finding it rather fun to explore.

Pre-Reflection: Catching Up

I seem to have got way behind with Cam 23 already - here we are in Week 6, and here I am still climbing out of the foothills of Week 3. But, fortunately, I have a fair amount of experience of the Things that we have covered since then. So I have decided just to write about my experiences with these. I'd be interested to know if they ring any bells with others.

Week Four was Doodle, to fix appointments, and Google Calendar, to keep track of them once fixed. I have been using both these for a couple of years now, and I am pretty well pleased with both. Like Aidan (as he explains in a post from June 2010) the first online calendar I used was the late and, initially, bitterly lamented Mosuki. When Mosuki closed down in April last year I chose Google reluctantly, because "everyone else" had already done so (starting with my brother-in-law). Since then, however, I have come to appreciate Google Calendar's many virtues, even when compared to my memories of Mosuki. Besides the fact that each calendar has its colour, and the site's very ubiquity [yes, I know, the same excuse I use for staying with Windows when I could move to Linux or save up for a Mac] I particularly value the fact that, when a calendar is viewed a month at a time, each day's entries appear chronologically.

Aidan pointed this out last year, but let me explain why that matters so much to me. Ever since I was a raw post-doc (when men were real men and disks were 5.25" wide) I have printed out monthly schedules to go on my (later our) and on my parents' kitchen walls. These started off in Microsoft Outlook, which worked quite well. When I tried to migrate to Mosuki, however, I found that each day's items appeared in the order they were posted, which led to oddities such as the train home from a meeting appearing before the meeting itself. Google Calendar's order is more logical, and that alone has made it more useful.

I've been using Doodle for a couple of years, too. The only similar tool I've tried is Meet-o-matic, which does much the same thing. I greatly prefer Doodle, mostly because it lets me see others' responses before posting. Whether you are trying to arrange a meeting (when participants will congregate towards the most popular slots) or to fill spaces on a rota (when the reverse applies), making people post blind feels very second best.

I did say that, if I came across a week where I knew the Things well, I would jump straight in to the Extra Thing. In Week 4, however, the Extra Thing was the Cambridge Libraries Widget, and I can't think what I, as a non-Cambridge non-librarian, might use it for. ["So what are you doing on this course, impostor!?" The explanation is here]

Onwards to Week 5, and we come first to Google Docs, which I have used to share documents with myself (on different computers), with family, and with external collaborators on a couple of professional projects. (The most recent of these has been a project to review and catalogue open educational resources for bioscience, which I might blog about separately some time.) This tool is now a near-invaluable part of my professional life, but I've only used it for the standard docs, spreadsheets and presentations so far. I'm thinking of an excuse to try out creating a form.

I've not tried PushNote and EndNote yet, so I'll leave them - along with my reflections on the course so far - for a separate post. But at least I've caught up a bit...

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

Things 4 & 3: Twitter, and RSS Feeds

Coming rather late in the week to Things 3 and 4, I have decided to blog about them in one post. And as I know considerably more of Twitter than I do of RSS feeds, I have decided to write about them in the wrong order. I do hope that I'm not breaking any rules...

So, Thing 4: Twitter. I have had a personal Twitter account since October 2009 - I started it on my birthday, no less - and I have been using it fairly enthusiastically since. Aidan would almost certainly concur with the comment made by the author of the Thing 4 post that Twitter is his favourite Thing. I wouldn't go that far, but I do find it fun, somewhat addictive, and occasionally very useful. I tweet mainly to publicise events I'm involved with, post quirky pieces of news, and respond one-to-one (or one-to-many, depending on how many followers we have in common) to others' tweets.

I have sometimes felt slightly jealous of Aidan, who has so clearly found a community of interested and interesting librarians in his corner of the Twitterverse. (I am following, and being followed by, a few of them myself, and I hope to add some more during this course.) My rather more eclectic professional life makes that difficult to replicate, however. I am at least a semi-detached member of three professional communities: science journalists, teachers in higher education, and molecular biologists / biotechnologists. It has been interesting to see that while the journalists and the educationalists frequent Twitter, the biotech people congregate in Linked In. I may speculate more about possible reasons for this when we come to Thing 15...

When I was still a very raw Twitter newbie, less than three months into my Twitter account, I had the temerity to write about it in a regular column in The Biochemist, the trade magazine of the UK's Biochemical Society (and so more or less analogous to Library & Information Update). This piece, entitled Tweeting Biochemistry and now rather out of date (with references to ministers in the previous government), urges biochemists to try it out, explains how the Society encourages delegates to its conferences to publicise them on Twitter, and gives a few hints and tips culled from articles I'd found useful. Very much later, I came across a blog post from Dorothy Bishop, a psychologist at Oxford: A gentle guide to Twitter for the apprehensive academic. It's the piece I wish I could have written myself.

You can find me on Twitter as @Clare_Sansom. And I intend, when I figure out how, to add my latest tweets to a sidebar on this blog. Does anyone have instructions for this to hand?

And now, Thing 3: RSS Feeds. I have to confess that I have found it difficult to see much use for these, and until this week I'd not installed any on the iGoogle page that I've been using intermittently as my home page for several years. I think my main reluctance has been the risk of information overload. With my portfolio career, and with my academic discipline being such a fast-moving one, I could literally spend all day reading relevant blogs, and I have had an enormous problem deciding which feeds to subscribe to. For now, I have come to this exercise as librarian manque. Besides the cam23 blog, and (of course) Aidan's, I am now following some in the information arena that seem to be of wider interest. So far, I particularly recommend the excellent Phil Bradley's weblog, and, for following the all-important campaign to save the public library (to think that this should even be necessary!), Voices for the Library.

Maybe one day I will get the bit between my teeth and add 150 molecular biology blogs and newsfeeds. But will I ever read them if I do?

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.