Monthly Archives: October 2008

Reasons to love the Web #999

Every day, I’m amazed by the information ecosystem that we call the WWW and how it has changed forever the way we educate ourselves.

Today’s illustration. I spent part of last weekend strolling through the beautiful rainforest of Brisbane Forest Park, a mere hour’s drive from the city. On the track at Maiala I heard a very bizarre noise, high in the misty canopy. The sound was a blend of fighting cats and crying children, yet strangely musical. It was a new sound to me but the cat-like aspect was a give-away, since I was aware of a species called the green catbird.

Back at home, I consulted the trusty Simpson and Day’s Birds of Australia. It described a sound similar to what I had heard but of course, bird sounds don’t translate to written English very well. So I headed off to the appropriate Wikipedia entry. It’s not one of the more compehensive pages but in the external links includes:

Green Catbird audio recording at Freesound

I played the sound – it was exactly what I had heard. What’s more the page is tagged, geotagged and part of a wonderful resource called the Freesound project – a collaborative database of Creative Commons licensed sounds.

So in the space of a few hours I lifted my spirits in the great outdoors, heard something new, tracked it down on the Web and discovered a bunch of new, interesting related information. That’s the Web at its best; integrating seamlessly with your daily life to enhance what you see around you. When it works, it’s an almost Zen-like experience.

The three phases of MySQL usage

As Mike keeps reminding me, getting your data into database tables is A Good Thing. Like many people, my database of choice is MySQL – largely because it was the first one that I tried and it works for me.

However, I’m far from being an expert MySQL user. In fact, I’ve identified 3 stages in my use of MySQL over the years; see if you recognise yourself in any of them.
Read the rest…

Giant panda genome: mapped or sequenced?

I’m with Ogden Nash who said:

I love the baby giant panda,
I’d welcome one to my veranda

This week, I learned via Keith that Chinese scientists announced the completion of the giant panda genome. An impressive achievement, given that the project was announced in March this year, but what exactly has been completed? Has the genome been sequenced – that is, there are strings of A, C, G and T covering most chromosomes, or mapped – that is, the approximate chromosomal location of most genes determined? The media seem unsure.

And so on. Here’s a Google News search with more hits.

So what has been achieved – sequencing or mapping? If the former, is it really complete (I doubt this) or draft – and if draft, what kind of quality? And where are the data? Nothing in the genome project section of NCBI as yet.

Open Access Day

It’s Open Access Day. Mission: to broaden awareness and understanding of Open Access. Their approach: “synchro-blogging” – an attempt to get as many folks as possible to blog on the given topic at the same time.

So, to answer their questions:

  1. Why does Open Access matter to you?
  2. OA is important for many reasons: go and read this by Jonathan Eisen instead of my rambling. One that stands out for me: it signals a fundamental change in the way that information is conveyed from writers to readers and an admission that the traditional publishing process is obsolete in the internet age. We live in a world where people expect instant, relevant information in the top 20 hits from a Google search and that expectation is transferring to science too. I don’t care how prestigious you think your journal is, or whether you see yourself as some kind of “guardian of knowledge”. I want information, I want it now and if you can’t deliver, I’m going somewhere else (*).

  3. How did you first become aware of it?
  4. I honestly don’t remember, but it was some years ago. I suspect it was around the time that journals such as Nucleic Acids Research and Bioinformatics introduced an OA option for authors. I also remember quite vividly the appearance of BMC on the scene and thinking “now, this is different and exciting”.

  5. Why should scientific and medical research be an open-access resource for the world?
  6. Lots of reasons. (i) The world pays for the research and shouldn’t have to pay again to view the results. (ii) Scientists should be accountable – exactly what are we doing with your tax dollars? (iii) When information is free, many eyes can look at it and many eyes = more ideas than fewer eyes.

  7. What do you do to support Open Access, and what can others do?
  8. Hey, I’m just a postdoc – I don’t get to make influential decisions! That said, five of my last six publications are OA. Where possible, I try to submit to OA journals and I review papers for OA journals. Once in a while, I blog about OA and other “open science” issues.
    What can others do? The same and more. Read blogs that cover OA – starting with Jonathan and Bora. Understand its philosophy. Promote it in public (blogs, wikis, FriendFeed). Make it the norm, not a novelty.

(*) OK, I work in a large, relatively-funded university which subscribes to most journals – so I won’t deny myself a non-OA article on principle. Others are less fortunate.

IgNobels 2008

I mark the passing of the years in a couple of ways. One is natural events: the coral tree flowers in mid-winter, the jacaranda flowers in spring, the comings and goings of Queensland’s bird species.

The other is the annual IgNobel award ceremony. 2008 is a vintage year:

It’s hard to choose a favourite this year. Armadillos and archaeology would have to be up there, but based on the idea that how much you laugh correlates with how much you relate, I’m going with: “You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations”, from the journal Organization Studies.