The Great Australian Internet Blackout WordPress Plugin

Normally I stick to posts about science and technology on this blog. Like most Australians, I vote in elections, try to remain informed, but otherwise stay away from getting involved in politics. However, occasionally certain things become important enough issues that they need to be advertised more widely.

As you may know, the Australian Federal Government is attempting to censor the Internet within Australia by forcing ISPs to block a list of websites. This proposed internet filter will not be optional; it will effect all Australians, and the blocklist will compiled by a small group of people. The list of blocked sites will remain secret, so the Australian public will find it difficult to determine if this power is being abused. It will not prevent the spread of illegal material, which is typically shared via peer-to-peer networks that will not be blocked by the internet filter. If it is not already self evident why this approach to internet censorship is both an ineffective, a waste of resources and a potential threat to the freedom of information flow required for a healthy democracy, you can read more at the Great Australian Internet Blackout site and the Electronic Frontiers Australia site.

The Great Australian Internet Blackout is a combined online and offline demonstration against this imposed online censorship. For one week – January 25-29th – Aussie websites will “black out” to inform an even wider audience about the threat of imposed censorship.

This is what it looks like right now. I'm guessing that on January 25th something exciting will appear inside that popup box !

This is what it looks like right now. I'm guessing that on January 25th something exciting (or educational) will appear inside that popup box !

Continue reading

2009 – the posts that never made it

So, people tell me 2009 ended recently. Apparently there were fireworks and stuff. This blog as seen very little action during 2009, despite my various good intentions for a blog ‘reboot’ (ala Pawel).

Like many of my online friends, I blame FriendFeed. I find commenting on a FriendFeed post a much more productive way of having a conversation around some new development sweeping the web than writing a dedicated blog post. Still, despite this being my “year of FriendFeed”, I started writing a few blog posts / articles / essays this year which never made it out of the Drafts folder. There is a positive side to unpublished drafts – they serve to nicely organize some thoughts, even if they are ultimately never shared. Anyhow, it’s time to clean them out and move on – and as part of that process – here are the highlights of my posts that never were.

Continue reading

That Science Blog Meme Thing Going Around

Something broke out of the picket-fence surrounding Nature Networks Blogs. I’ve never participated in a blog meme … but this one appealed to me simply because I liked the questions. I haven’t read anyone else’s answers yet, to avoid biasing my own.

1. What is your blog about?

I often ask myself this question. Being a scientist, I always feel like it should be about science, and the various biological systems I work with. I reality, it is about programming, bioinformatics, the web with the tiniest bit of structural biology thrown in. I used to blog about Linux related things occasionally, but I split that off into another blog (which gets 10 times more traffic :)).

Continue reading

Migration from Blogger to WordPress

Blogger has served me well for the last two years or so. When I started with Blogger, I’d never really blogged before, and decided that it was a good way to get going quickly. I avoided the free blog hosting on because it wouldn’t allow enough customization of the templates. Today I’ve completed migration of this blog from Blogger to the WordPress software … read on for the “how” and “why”.

New URL is:

Feed url is via FeedBurner at:

(Don’t read on if you don’t like meta-discussion about blogging software …. I personally have become pretty bored with this type of post, but it has to be done once after changing URLs etc. The blogger who “Blogs about blogging” is akin to those hip-hop artists who only ever sing about hip-hop … sort of like eating your own … yeck !).

Continue reading

Posts that didn’t make it in 2007

Well, a New Year is fully in swing, so I thought it would be a good time to cleanup my ‘posts in progress’. There are a bunch of posts that I started last year, for reasons of lack of quality, lack of timeliness or general motivation never made it out the gate.

I generally dislike this kind of ‘meta-blogging’, but this is the easiest way for me to let go of them and move on … here is a list of the posts that could have been, but never were:

  • Open Data in structural biology: share your structure factors and restraints” was a post spurred on by the Chang et al incident and a letter written by Alexander Wlodawer about the importance of sharing ‘raw data’ in structural biology, particularly to allow structures to be independently validated. I’m sure mandatory deposition of structure factors tied to publication will become the norm in the not too distant future. The post became a long essay which really went nowhere except to suggest that maybe there should be more incentive (and even enforcement) for sharing not only raw data, but also source code used to process data too.
  • There was the seed of a post on “Patenting“, based around this link to Christopher Soghoians blog “slight paranoia”. I’m not against the patent system, but I’m not all for patenting anything and everything either. If I ever got time to flesh this post out, chances are it would have turned into a dumb Slashdot-style anti-patent rant anyway. No one wants to read that crap, so I canned it. I will say, however, that Christophers post reminds me alot of the situation of being a Postdoc in a fairly pro-patent Institute, and underscores why the incentive to patent often isn’t there at the grass-roots level.
  • One potential post started as some scribblings about one of last years new hot topics, “Open notebook science“. I wanted to compare a public/private wiki system I was envisaging with the scheme presented on page 2 of this presentation by Jean-Claude Bradley which shows the continuum between Traditional Lab Notebook (unpublished science), through to Tradational and Open Access Journals and finally through to the Open Lab Notebook (full transparency). The whole thing never materialized.
  • Then there was a quick post to highlight an article about a GM crop in Nature Biotechnology. I never got it out in a timely fashion, but essentially the article discussed how the Italian media and politicians were continuing their blanket crusade against all GM crops, while conveniently ignoring the independent academic trails showing that the MON810 corn strain had significantly lower levels of the fungal toxin fumonisin when compared with the non-GM equivalents. This was (and still is) a topical and often emotive issue for Australians, as two states (Victoria and New South Wales) have recently lifted moratoria on commercial release of GM crops. It’s nice to see that sometimes a well tested GM strain is often better for human health than an untested traditional strain that has only had the benefit of genetic modification by crossbreeding and selection rather than the new techniques of molecular biology.
  • Another post was my attempt at being funny. “Australian Government department concerned about organisms from space: Quarantine assessment of an asteroid“. Actually, I appreciate that they take this type of thing seriously … I wouldn’t be laughing if we end up with an outbreak of some deadly alien virus or something (still not sure if I’m joking or not ….).

There are also a few beginnings of some posts I can’t quite let go of yet, and they may appear in the future. One, while getting a little dated now, is “Why are the still 1000 uncharacterised yeast genes ?“, discussing a 2007 paper by Lourdes Pena-Castillo and Timothy R. Hughes. Another is “Has structural genomics paid off ?” … this is still pretty fresh and in discussion in the November and December issues of Structure. In fact, these letters to Structure are such a treasure trove of practical and philosophical arguments about structural biology the topic probably warrants multiple posts. Finally, I planned to host the inaugural “Bioinformatics data-munging challenge: 2.0-style“, but never felt I had time to devise and run the challenge properly. We can still come up with some guidelines (aka rules) and try it out if anyone is interested.

It’s not a New Years resolution … but I hope that this year I can produce more short, frequent and high quality posts. We’ll see.