History repeating

“The morality of U.S. conduct of the war was a major political issue both in the United States and abroad. First, there was the question whether a proxy war…without a clear and decisive path to victory was worth fighting and worth the casualties sustained both by the combatants and by civilians. Second, there was the question whether a guerrilla war in which the enemy was often indistinguishable from civilians could be fought at all without unacceptable casualties among innocent civilians. Last, there was the question whether young, inexperienced U.S. soldiers — many of them involuntary conscripts — could reasonably be expected to engage in such guerrilla warfare without succumbing to stress and resorting to acts of wanton brutality. Fighting a mostly invisible enemy mixed in the civilian population — an enemy that did not obey the conventional rules of warfare — and suffering injuries and deaths from booby traps and attacks by soldiers who pretended to be civilians could not help but lead to the kind of fear and hatred that would compromise morals.”

Sound familiar? Now read the source.

Google Books PDFs

Google Books now offer PDF downloads of public domain books. A quick search for “bioinformatics” limited to full view books throws up 128 titles, though not much in the way of useful bioinformatics texts so far as I could see. Still, worth bearing the service in mind.

SOAP services

SOAP (the network access protocol) is something that I’ve heard a lot about, but never really investigated very much. Today I was searching for standalone software to predict subcellular localisation of proteins. I didn’t find much, so I began to wonder if there were any decent APIs or tools to access a network service. That’s what led me to SubLoc: a server/client suite for protein subcellular location based on SOAP. It works pretty well and the developers provide sample clients in Perl, Python, Java, Ruby and C, plus binary executables for Linux and if you must, Windows, all at this page. The Linux version worked fine for me.
One thing that’s put me off this type of service in the past is the requirement for the server to be up and for the process to occur in seconds, rather than hours. I was impressed with this though and inspired to investigate further. I gather that SOAP is not the fastest game in town, but if you’d like to comment on your favourite SOAP service(s) or SOAP alternatives, go for it.

Ozone “hole” appears stable

BBC Science News reports that the ozone layer over the Antarctic seems to be on the road to recovery.
It’s not all good news though. Ozone depletion has stabilised, but it will take decades for a full recovery. The report also states that CFC replacements contribute to global warming, without going into any detail on this aspect.
There’s a nice discussion over at Asymptotia, which points out that once in a while, humans can get it right. The problem was identified, the solution was devised and for once, the world got together and acted for the common good.

Ancient atmospheres

Back in the 1970s when NASA launched the Viking probes to Mars in search of life, James Lovelock suggested that the Martian atmosphere (and that of Venus, Earth’s evil twin) told a story when compared with Earth. Our nitrogen-oxygen atmosphere is unusual and owes its existence to the biological activity of microbes and plants. Our neighbours have atmospheres of predominantly carbon dioxide and their chemical nature suggests that little if anything biological is going on there.
It’s commonly believed that before about 2.4 billion years ago, Earth’s atmosphere was free of oxygen. There’s a lot of evidence for this, including the absence of oxidised compounds in ancient rocks. There’s considerable debate about the exact composition of the early atmosphere – in particular, how “reducing” it was – that is, what were the levels of hydrogen-rich molecules such as methane and ammonia. This is important for understanding prebiotic chemistry and the emergence of the first things that we would call living organisms. Most biologists are familiar to some degree with the famous, if misleading, Urey-Miller experiment.

An interesting paper in Nature last week examines sulphur isotopes in 2.8 billion year-old sediments from Western Australia. They expected to see evidence for UV-induced photochemical reactions, due to the assumed absence of an oxygen-derived ozone layer at that time – but they didn’t. So was the atmosphere actually oxic when the rocks formed, or is something else going on? It’s a complex problem that illustrates how we often have to rely on assumptions and models and struggle to reconcile them when the data doesn’t fit.

Planet defined – now there are eight

The votes are in and the community has spoken – Pluto is not a planet. Clifford explains all at his new blog, Asymptotia. At the end of the day, it looks like the IAU have a pretty good democratic process in place.
There was much wailing on our local radio station this morning – textbooks to be rewritten! Confusion in high school science class! How will the kids digest this new and confusing information? I suspect that they’ll take it in their stride. It’s not difficult – eight, not nine. That’s science – it’s not static, ideas change with new information. Science teachers should see this as a great opportunity to discuss the nature of science, but I suppose most school science is more concerned with rote learning of facts just like “how many planets”.

Points mean prizes

Maths genius declines top prize. The prize in question is the Fields Medal. The research in question concerns the Poincaré conjecture, which is all about how to define a sphere, topologically. “He has a different psychological make up, which makes him see life differently”, says one mathematician of the reclusive genius. Is that a nice way of saying he’s a bit nuts?

Here in Australia, the self-proclaimed “Oscars of Australian science” – the Eureka prizes – have been announced.