Monthly Archives: October 2006

Let’s ban wastage

The Stern report on the cost of climate change is causing a bit of a stir. The Guardian features a nice article on rising environmental awareness in the UK. The always-reliable George Monbiot has some practical suggestions. I especially like:

Ban the sale of incandescent lightbulbs, patio heaters, garden floodlights and other wasteful and unnecessary technologies

I’d like to add personalised credit cards to the list. There will come a day when society will have to decide which consumer items are unnecessary in order to conserve materials and energy. I can’t think of a better example for the top of the “first to go” list.
I have to admit that sometimes, it’s a little depressing to live in a country governed by people who consistently place individual wealth ahead of social and environmental concerns. That said, at least my current city is more tuned in.

To Edgy or too edgy?

Rumours of horror upgrades to Ubuntu Edgy 6.10 are rife. Conversely, others report no problems at all.
I’ve not tried it myself but in my experience, the Ubuntu upgrade path is always more problematic than a fresh install. It’s also worth pointing out that 6.06 (Dapper) is the recommended stable release and will be supported and updated for a good while to come. Edgy isn’t named Edgy without reason.
One package that doesn’t impress me is F-Spot. It looks like a great photo management package (features include upload to Flickr, for example) and is supposed to be a highlight of the Edgy release. Unfortunately my version mangles the photo date/time (poor use of libexif I suspect) and the current Bugzilla list is 365. One for the “not yet mature” list, I feel.

Not exactly a giant leap

The next space tourist is understandably excited, which perhaps explains his exaggerated claim:

However, he believes on at least one count his trip may be unique: “I might be the first nerd in space,” he said.

Depending on your definition of “nerd”, I’d suggest that many astronauts fit the description. If we’re equating “nerd” with “computer scientist”, try a Google search for "astronaut biographies computer science". Not surprisingly, a lot of astronauts have a background in computer science/engineering.
Trust a Microsoft employee to claim that copying what went before is an innovation.

More on bees

I got a little worked up writing the last bee post and so neglected to mention the avalanche of “bee science” this week.

First up, the oldest known bee fossil, 100 Mya, preserved in amber. This will be reported in Science tomorrow.

My feed reader contains a subscription to GR In Advance, part of the journal Genome Research. It updates so infrequently that I forget that it’s there, but today 13 new articles appeared – every one a bee.

There’s a new issue of Bioinformatics out too. All methods. No bees.

Firefox 2, Ubuntu 6.06

Rumour has it that users of Ubuntu 6.06 (Dapper) are stuck with Firefox 1.5. I’m not quite ready for Edgy, but the good press convinced me that I am ready for Firefox 2.
This forum thread provides an installation script – “sudo sh” does the trick. Your old installation is backed up and it was hitch-free for me.
First impressions – quick with some nice features. Extensions and themes are now grouped togther as “addons”. There are extensions for most of my updates, save for mozex. Check out the recommended addons (over 1000 available) – my new favourite is the download statusbar. One feature that I really like is that when a browser restart is required, the tabs that you had open are restored. I’m not keen on the new default theme but there are plenty to choose from – Orbit Blue gets my vote just now.
Yeah, it’s a slow day at work.

Plants are organisms too

To continue with the theme “what’s wrong with research science”, there’s an interesting letter in Nature entitled “RNAi Nobel ignores vital groundwork on plants”. Chris pointed out to me at the time that the fundamentals of RNAi were discovered first in plants. If it’s true that a finding is considered a biological oddity in plants (or Archaea, or fungi, or [insert non-model organism here]), but a fundamental discovery in animals, then we work in a very sad and flawed community.

I’m reminded of a recent blog post bemoaning the fact that all you need do to make your research more “worthy” (i.e. fundable) is insert the word “biomedical” – regardless of what you actually achieve.

The curse of amino acid alphabets

So, I’m debugging some Perl that uses weight matrices to score sites in a protein sequence. The matrix is stored as a hash of arrays, with each $row of $weights{‘row’} being a row number and $weights{‘row’}{$row}{$aa} being a weight for amino acid $aa in row $row. I’ve tested a few sequences without incident and moved onto whole genomes, when suddenly the script begins to spew:

Use of uninitialized value in addition (+) at line 819

Read the rest…