Monthly Archives: November 2006

A day off

Ah, cricket. Loved by those who grow up where it’s played and an utter mystery to everyone else.

I spent yesterday at Brisbane’s Gabba, a modern day amphitheatre, enjoying day 3 of the first Ashes test. It wasn’t the most compelling game – Australia’s dominance reminded me of a cat toying with an injured baby bird and the “fun police” have cracked down on water melon helmets, trumpets, beach balls and Mexican waves. However, if you’re visiting Australia and get the chance to see cricket or AFL at a major venue, I recommend that you do. It’s always good fun, relaxing in the sun with a beer, chatting with your mates, watching the crowd dynamics and the game. And it’s a great way to put work aside and wind down for a few hours.

More on those CNVs

The human CNV study in Nature is highlighted in the science media this week. Researchers seem surprised at the amount of variation observed. “It would seem the assumption that the DNA of any two humans is 99.9% similar in content and identity no longer holds”, observes the article. I’m not sure that we ever held that assumption.

Should we be so surprised? I think it’s worth remembering that any genome sequence is really a consensus based on a small sub-population. Perhaps this idea that individuals are almost genetically identical stems from there. I seem to recall from high school biology that genomes get shuffled during meiosis. In a sense, doesn’t every cell also have its own genome, reflecting its own environmental history?

Nature round-up

Some articles of interest for November 23rd.

The web as journal

Pedro presents a very nice study in which he creates a “virtual journal” using Connotea tags and analyses citations. It demonstrates that we can analyse the quality of scientific content in ways other than the traditional emphasis on impact factors and citations for single journals.

The traditional approach to assessing research “worth” and use of that approach in funding decisions is probably the aspect of academic research that I hate the most. We are all forced to pretend that we believe in a lie perpetuated by grant agencies and publishing companies – and living a lie is not what scientists are about. Let’s hope that the Web continues to provide new and challenging ways of providing content until even stodgy science traditionalists are forced to take notice.

Unknown authenticity

Culture travels slowly to our shores, so only after watching Unknown White Male last night did I discover that the rest of the world has been discussing it for over a year. For those not in the know, it’s a documentary about a man who suffers an extreme case of retrograde amnesia. Effectively, his entire life prior to the memory loss is erased, forcing him to rediscover everything that he once knew.

I enjoyed it – but as the film progressed, I sensed more and more that something wasn’t quite right. Apparently I’m not alone in my suspicions. So on the basis that one day, truth will out, I’m going with the “it’s fake” crowd. How about you?

Phylogenetic debate

In a previous life as an “archaeal genome biologist”, I spent a lot of time explaining to people why Archaea are distinct from Bacteria and Eukarya. One day, I happened across a long, detailed review paper entitled: The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. It briefly sowed seeds of doubt in my mind as to how distinct Archaea really are, until I realised that much of the analysis centred on cell membrane structure – which in my humble opinion, is not very sensible.

I’m not a phylogeneticist, nor am I wedded to any one classification scheme, but I think there are good arguments for the current three domain system. Others disagree; if that excites you, go read the discussion at evolgen and keep an eye on Sandwalk, Larry Moran’s new blog.