Monthly Archives: September 2006

Brazen quotes

Don’t you love it when governments have been in power for so long that they start to think that they can say anything – anything at all – and get away with it? Sometimes I wonder if their minds enter some sort of alternate state which allows them to believe that obvious falsehoods are in fact true. Here’s an example from our education minister, discussing the relationship between falling student numbers and higher fees:

“There is no evidence that cost plays a significant role in the decision to attend university.”

What? Did I really read that sentence? Yes I did. Does anyone record these quotes for posterity on a website somewhere? If not, I may have to start doing so myself.

Much ado or heads in the sand?

I sincerely hope that rumours of revenge attacks on stingrays are untrue. What’s interesting about this is the Australian media coverage. The ABC have buried the story to the extent that I’ve not yet found it. The SMH article leads in with assurances from a biologist that the incidents are unrelated. It’s almost as if the media are attempting to convince themselves and us that noone could be so stupid.

Frankenstein protein

There was a very interesting paper in Science last week. It describes a process in a class of immune cell called CD8+ T-lymphocytes, in which two peptides are spliced together in the reverse order to that predicted from gene sequence. The reaction is believed to be a transpeptidation catalysed by the 20S proteasome and the process may be a way of generating additional antigen diversity.

New Scientist covered the story under the headline “Frankenstein protein defies biology textbooks”, telling us that “it has always been believed that the structure of a protein is fixed by the DNA template that encodes it”. I think this is a case of slight over-dramatisation and besides, is not really true. We’ve known about inteins, or “protein introns”, for many years now. It strikes me once again that many researchers and writers lack awareness of many biological processes because they continually neglect the Archaea.

Friday snippets

NASA to proceed with shuttle launch despite objections. The objections come from the company that manufactures a misbehaving fuel cell. Does this sound familiar? What odds on another accident due to schedule pressure before ISS is completed?

Here in Queensland, tomorrow is state election day.

one of the most curious points is that many people are dissatisfied with both parties

Most curious? Surely least curious. Can you think of a single government who are in power because people like them, rather than because people think that they’re less rubbish than the opposition?

Finally, it’s a dangerous week to be a famous Australian. In the past 10 days we’ve lost Steve Irwin, Peter Brock, Don Chipp and Colin Thiele. Overseas readers probably know at least one of those.

Forgotten rovers

With Pluto not being a planet, SMART-1 crashing into the moon and the latest shuttle mission gearing up, don’t forget about these little guys. Originally guaranteed for 90 days, Spirit and Opportunity have notched up around 950 and 930 Martian sols, respectively and are still going strong. In that time, they’ve travelled between just seven to nine kilometres! Opportunity is now just 200 metres or so from Victoria Crater, a deep, wide crater with at least 30-40 m of exposed bedrock to examine. The rock was spotted by another forgotten craft – Mars Global Surveyor, now the oldest active craft at Mars with 3284 days (9 years on September 12) in orbit.

Using Perl from PHP

I know, mixing and matching is messy. Here’s my problem though – I’m currently working on a project that requires both standalone code (Perl/Bioperl) and a web interface. Now, I could just convert my Perl to CGI for the web – but I want to work within a CMS framework that uses PHP. I don’t especially want to rewrite the Perl as PHP and in some cases I can’t, because the Bioperl functions are not available in PHP. Leaving me no choice but to access my Perl from PHP. How?

Enter the PHP Perl extension. It requires PHP 5.0.0 or higher. On my Ubuntu system, I installed libapache2-mod-php5, php5-cgi and some other useful php5 modules (php5-gd, php5-xsl, php5-mysql). You also need libperl-dev and php5-dev, which supplies the commands phpize and php-config. Download the extension from this link, unpack and follow the instructions in the README. Enable “” in /etc/php5/apache2/php.ini, restart Apache and you’re set. You can now access Perl code and variables from within PHP5.

Stating the obvious

More lazy technology journalism. Here’s how I picture the scene. Major news event results in overloaded news websites. Technology editor wonders how this can be prevented. Technology journalist calls a local IT expert. The IT expert says “um well, a bigger computer would help.”

And that’s more or less what the editor runs with. I wonder how “big” they imagine hardware needs to be. Size of a house? A small city? Poor, lazy, worthless journalism, again.

Has bioinformatics increased the pace of drug discovery?

Last week, I gave a postgraduate seminar in bioinformatics. Rather pleasingly, there was a lot of discussion afterwards and one of the students asked whether bioinformatics had increased the pace of drug discovery.

I’m sure that it has helped – if nothing else, you would think that computational methods and databases have reduced the number of compounds that we have to screen for activity. I realised though that I have no firm data or numbers that can answer the question “is the turnaround time for getting drugs onto the market shorter because of bioinformatics?” My suspicion would be that the speed and amount of development has not increased as markedly as we might have hoped. Any experts in the field care to comment on this?