Your bones got a little machine

Well, a New Year is fully in swing, so I thought it would be a good time to cleanup my ‘posts in progress’. There are a bunch of posts that I started last year, for reasons of lack of quality, lack of timeliness or general motivation never made it out the gate.

I generally dislike this kind of ‘meta-blogging’, but this is the easiest way for me to let go of them and move on … here is a list of the posts that could have been, but never were:

• “Open Data in structural biology: share your structure factors and restraints” was a post spurred on by the Chang et al incident and a letter written by Alexander Wlodawer about the importance of sharing ‘raw data’ in structural biology, particularly to allow structures to be independently validated. I’m sure mandatory deposition of structure factors tied to publication will become the norm in the not too distant future. The post became a long essay which really went nowhere except to suggest that maybe there should be more incentive (and even enforcement) for sharing not only raw data, but also source code used to process data too.
• There was the seed of a post on “Patenting“, based around this link to Christopher Soghoians blog “slight paranoia”. I’m not against the patent system, but I’m not all for patenting anything and everything either. If I ever got time to flesh this post out, chances are it would have turned into a dumb Slashdot-style anti-patent rant anyway. No one wants to read that crap, so I canned it. I will say, however, that Christophers post reminds me alot of the situation of being a Postdoc in a fairly pro-patent Institute, and underscores why the incentive to patent often isn’t there at the grass-roots level.
• One potential post started as some scribblings about one of last years new hot topics, “Open notebook science“. I wanted to compare a public/private wiki system I was envisaging with the scheme presented on page 2 of this presentation by Jean-Claude Bradley which shows the continuum between Traditional Lab Notebook (unpublished science), through to Tradational and Open Access Journals and finally through to the Open Lab Notebook (full transparency). The whole thing never materialized.
• Then there was a quick post to highlight an article about a GM crop in Nature Biotechnology. I never got it out in a timely fashion, but essentially the article discussed how the Italian media and politicians were continuing their blanket crusade against all GM crops, while conveniently ignoring the independent academic trails showing that the MON810 corn strain had significantly lower levels of the fungal toxin fumonisin when compared with the non-GM equivalents. This was (and still is) a topical and often emotive issue for Australians, as two states (Victoria and New South Wales) have recently lifted moratoria on commercial release of GM crops. It’s nice to see that sometimes a well tested GM strain is often better for human health than an untested traditional strain that has only had the benefit of genetic modification by crossbreeding and selection rather than the new techniques of molecular biology.
• Another post was my attempt at being funny. “Australian Government department concerned about organisms from space: Quarantine assessment of an asteroid“. Actually, I appreciate that they take this type of thing seriously … I wouldn’t be laughing if we end up with an outbreak of some deadly alien virus or something (still not sure if I’m joking or not ….).

There are also a few beginnings of some posts I can’t quite let go of yet, and they may appear in the future. One, while getting a little dated now, is “Why are the still 1000 uncharacterised yeast genes ?“, discussing a 2007 paper by Lourdes Pena-Castillo and Timothy R. Hughes. Another is “Has structural genomics paid off ?” … this is still pretty fresh and in discussion in the November and December issues of Structure. In fact, these letters to Structure are such a treasure trove of practical and philosophical arguments about structural biology the topic probably warrants multiple posts. Finally, I planned to host the inaugural “Bioinformatics data-munging challenge: 2.0-style“, but never felt I had time to devise and run the challenge properly. We can still come up with some guidelines (aka rules) and try it out if anyone is interested.

It’s not a New Years resolution … but I hope that this year I can produce more short, frequent and high quality posts. We’ll see.

So, I’ve been fiddling with the template of this blog for the last couple of weeks. I think I’ve stabilised on a look that I’m happy enough with … so now it’s time to start posting for real.

Let’s see if I can keep this up (and keep it interesting+useful).