Monthly Archives: August 2006

Planet debate rumbles on

Claims by astronomers that they don’t really care about the “is Pluto a planet” question would seem to be untrue, judging by this report on the IAU debate.

“He was cut off when he tried to read his proposal aloud. When more questions were prevented, there was a cry of: ‘If there is democracy, listen to the questions. Let the people speak!'”

The good news is that common sense seems to be prevailing, with a new draft resolution stating the case for eight planets. Now they just have to decide what to call Pluto. Nobody likes “plutons”, least of geologists who use the term already. Via John Hawks, an amusing account of how astronomers failed to recognise this fact:

“Since the term is not in the MS Word or the WordPerfect spell checkers, we thought it was not that common.”

Oh dear.

When what you’re doing is rather relevant

In today’s Australian news, the announcement that the government is to subsidise the breast cancer drug Herceptin, also known as Trastuzumab. The cost of the drug for some 2000 women in Australia comes to around AUD 50 000 – 70 000 a year; read one touching story.
The drug is a monoclonal antibody that binds to a protein known as human epidermal growth factor receptor 2 (HER2), also known as ERBB-2. This protein is a tyrosine kinase cell surface receptor – in cancerous cells it activates a cascade of protein kinases which promote cell division. Blocking the receptor switches off the signal for the cells to grow and divide.

I often struggle to explain to my non-scientist friends and family exactly what it is that I do all day. However, my current project involves the computational prediction of substrates for protein kinases. So now I can tell them that I really am finding cures for cancer.

Dark matter and hobbits

Dark matter exists! In another example of science blogs as news sources, this story quotes Sean from Cosmic Variance. He writes about the discovery in this post. For the hardcore, the paper is now in the astro-ph archive, in multiple formats. When, oh when, will biologists get a preprint archive?

Rather less exciting is the continuing hobbit debate, which is in danger of becoming tedious. The latest round (“pygmies not species”) is now published in PNAS (open access). There’s excellent discussion at John Hawks Anthropology Weblog.

Rejoice, Australian space geeks

NASA has selected two companies to develop its Commercial Orbital Transportation Services (COTS). If all goes well, services like these will supply cargo and perhaps crew to the ISS when the space shuttle is retired in 2010.
The surprise part of the package is the development of a $A 100 million launch site at Woomera, South Australia. Woomera is real outback territory – it fits the image of Australia that you might have if you’ve only seen it in the movies. Back in the 50s and 60s it was a British missile testing range, most famously for the Blue Streak project. I grew up not far from RAF Spadeadam in Cumbria, which was also a Blue Streak test site. More recently, Woomera has gained some notoriety as an immigration detention centre, thankfully now closed.
Could be exciting times ahead for Aussie space fans.

Managing structural genomics data

I recently discovered the website of the TB Structural Genomics Consortium. It’s very nicely designed and cross-referenced, allowing users to navigate the TB genome and rapidly locate information about protein structures.
The reason that I mention it is that the lab where I work is involved with a structural genomics project and they desperately need a way to manage their data. At the moment it’s a bunch of files in the group Wiki, which is clearly inappropriate for structured data of this nature. I’m resisting the urge to code up a MySQL schema and PHP frontend in the hope that someone else has already done so. I wonder if the software that drives the TB website, or other SG sites, is available? There seems to be a market for this kind of application.

YouTube sound fix for Firefox 1.5/Ubuntu 6.06

One day I had sound in YouTube videos, the next I didn’t. Doug’s blog to the rescue. Basically:

sudo apt-get install alsa-oss
edit /etc/firefox/firefoxrc and ensure that you have “FIREFOX_DSP=aoss”
restart all Firefoxes

and you should be right.

I don’t think the Dapper team have quite got the hang of not breaking things that worked previously on system upgrade. My advice is – if you have a Breezy box working perfectly, stick with it. If it’s a new box, Dapper is fine.

Bovine genomics

Genomics often promises us two things – insight into diseases and improvements to agriculture. So the headline "scientists map DNA sequence for bovine animals" caught my eye.

I wonder why the ABC even bothered to post this story. It consists of 5 sentences, with no links to additional information. It claims that a 5-year project is now “finished”. It’s unclear whether we are talking about genetic mapping or genome sequencing – a common source of confusion in this type of article.

Some Googling lead me to this press release from the Baylor College of Medicine. I’m fairly sure that this was the source for the story. What we’re actually talking about is the bovine genome sequencing project. Far from being “finished”, the project has released a new dataset which includes a genetic map, SNP data and the latest sequence assembly. Your starting point is of course at the NCBI. Links from there will lead you to mammalian genome projects. The bovine genome consortium includes contributions from the Genome Sciences Center, Vancouver and CSIRO, Australia.

I find increasingly that piecing together stories via Google News is the best way to get all the information. Individual news sites, excepting the BBC of course, are frequently quite pitiful.