Monthly Archives: December 2006

Vacation

It’s likely to be quiet round here until January 8th or so. Yes, I’m done for the year. Off to Sydney tomorrow for a couple of weeks in the lovely resort of Bundeena. There’ll be nothing to do but walk in the Royal National Park, swim, look after a couple of puppies and generally chill. There may be internet access, but who cares.

Happy holidays to you all, see you on the other side.

Lights out

Next March, WWF Australia are organising Earth Hour. If all goes to plan, Sydney homes and businesses will switch off the lights for one hour, the city will fade to black and we’ll get an interesting snapshot of energy consumption.

It’s an interesting idea and a good publicity stunt. What I’d really like to see though, are some incentives and/or legislation to make energy conservation in cities the norm, not a one-off event. Do we really need all those office buildings and shop fronts illuminated throughout the night?

A genome dear to me

There are a huge number of ongoing and completed genome sequencing projects now. The NCBI Entrez database lists 1447, 1289 and 75 sequence records for Eukarya, Bacteria and Archaea, respectively, as of today.
With so many – why are any of them special? One answer is that individual projects mean a lot to the people who work on them. So I give you one of my favourites – Paracoccus denitrificans PD1222, genome closed as of two days ago.

Back in my wet-lab days, PD1222 and its close relatives formed the basis of my Ph.D. research. They were less data-intensive days; like most projects at that time, mine consisted of cloning and sequencing a single gene, doing some mutagenesis and a few biochemical assays. Here we are, not so many years later, with the complete genome. Now that’s progress.

“Joys” of web programming

The last couple of weeks have taught me that I’m not a natural web coder. For one thing, my grasp of PHP/javascript is really pitiful. It goes deeper than that, though. I’m a command-line script guy. I like to write clean code with short, discrete subroutines, type “program_name file_name”, sit back with a coffee and wait for a CSV file to pop out.

In a web application, you write an awful lot of code – most of which either (a) checks user input for errors or (b) makes things look pretty. The underlying algorithm is only a small part of it. On top of that, you have to imagine what users might want to do – unlike a set of linear procedures, they might want to go back, or forward, or jump in the middle. So you need a picture of the whole working site in your mind. For some reason, good coding practice goes out the window when I write web code. I forget to declare variables, or include checks for missing values. I copy/paste the same code with different variables multiple times, instead of writing functions. In short, I find it hard.

That said, I have a mostly-working web application which should see the light of day in the new year, so stay tuned.

No worries mate

In a sure candidate for an IgNobel prize, research indicates that Australians are less prone than Europeans to heart attacks induced by watching sport. This ground-breaking work is reported in the Christmas special section of the Medical Journal of Australia.

One of their datasets is the nail-biting 2005 AFL Grand Final, won at the death by the Sydney Swans. I wonder if they included a “fan factor” – the population at large may have been relaxed, but I know several people who repeatedly came close to cardiac arrest over the finals series that year. And we still can’t speak of the 2006 final.

The WWW stole my brain

Some elements in the media would have you believe that we’ve become passive receptacles for information, to the extent that information providers are responsible for our actions.

Various news outlets are running a ridiculous story, suggesting that online mapping services contributed to the death of a journalist in Oregon. The driver:

“…may never have made that fateful wrong turn if he hadn’t used the internet to look up directions for his journey, US media reports suggest.”

There’s so much wrong with this simplistic analysis, it’s hard to know where to begin. Another quote sums it up:

“…the cyber-savvy family may have plucked the route…from an online mapping service, unaware of the elements”

No map – online or otherwise – provides contextual information. A road on a map is just a line – it tells you nothing about the state of the road now. As for unaware of the elements – it’s winter in the Oregon wilderness. How unaware can a person be? You don’t use Google Maps to tell you whether it’s winter; you use a weather service. Or look out the window.

I think what we have here is an unfortunate case of someone who assumed that they would not break down or become lost and so failed to take a few sensible precautions, such as checking the conditions, carrying sufficient food, supplies and appropriate clothing. It’s a tragic accident – let’s not inflate it into another “the internet is the root of all evil” story.

Is there hype on Mars?

The recently-demised Mars Global Surveyor has left us a legacy – evidence for flowing water today on Mars. Here’s the NASA press release and a BBC Science News story. The findings will be reported in Science tomorrow.

Let’s not get too excited. Planetary photogeology is a very interpretive science. Interpretations have been wrong before and always seem to split scientists into “for” and “against” – in this case the water versus CO2 camps. On the other hand, the possibility of subterranean water is very exciting. I’ve always had a sneaking admiration for Gilbert Levin, the Viking mission scientist who maintains that the Viking lander has already found evidence of microbial life. One of his arguments is that surface water is quite possible based on temperature/pressure measurements from Viking. It would be fun if the evidence finally brought NASA around to his position after all these years.

update – Science abstract, also reports present-day impact craters.