IgNobels 2008

I mark the passing of the years in a couple of ways. One is natural events: the coral tree flowers in mid-winter, the jacaranda flowers in spring, the comings and goings of Queensland’s bird species.

The other is the annual IgNobel award ceremony. 2008 is a vintage year:

It’s hard to choose a favourite this year. Armadillos and archaeology would have to be up there, but based on the idea that how much you laugh correlates with how much you relate, I’m going with: “You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations”, from the journal Organization Studies.

But just before I go…

…I have to mention Carl Zimmer’s post on the quest to find English words in human protein sequences.

This game has been around as long as sequence databases have existed. I have a vague memory of a letter from the early 1990s (possibly in Trends in Biochemical Sciences Nature) in which the authors reported the results of comparing SwissProt with the Oxford English Dictionary. As I recall, the longest word that they found was ENSILISTS – meaning people who practice the art of making silage.

Anyway – here’s a quick and easy way to tackle the problem using EMBOSS and some Linux command line trickery.
Read the rest…

What’s in a (gene) name?

I’ve posted before on standard names (or lack thereof) for genes and proteins and in particular, the whacky names of which biologists are so fond. Hopefully they now realise that in the age of bioinformatics – where we have to find stuff easily – descriptions such as ken and barbie, scott of the antarctic or glass-bottom boat are, um, unhelpful to say the least.

So hot on the heels of my “man, you can publish anything in bioinformatics these days” post comes:

Seringhaus, M. et al. (2008).
Uncovering trends in gene naming.
Genome Biology 9:401 Abstract | DOI 10.1186/gb-2008-9-1-401

We take stock of current genetic nomenclature and attempt to organize strange and notable gene names. We categorize, for instance, those that involve a naming system transferred from another context (for example, Pavlov’s dogs). We hope this analysis provides clues to better steer gene naming in the future.

It’s actually a fun and informative read.

See also: FlyNome, Clever Drosophila gene names and Sonic Hedgehog Sounded Funny, at First. From the latter source: “It’s a cute name when you have stupid flies and you call it a ‘turnip,’ ” Dr. Doe said. “When it’s linked to development in humans, it’s not so cute any more.”

All kinds of bioinformatics

If you haven’t already, go and read Mike’s amusing and pertinent post, World of Bioinformatics Quest: Character generation. Which one are you?

I often think that in academic research at least, there are 3 types of bioinformatics:

  1. Bioinformatics that provides insight into biological systems
    The ideal case being that you make a computational prediction which is then confirmed experimentally. Requires close collaboration between you and wet lab colleagues. By far the rarest category.
  2. Bioinformatics that provides insight into biological data
    An example might be a statistical analysis of the PDB to identify factors common to protein chains that interact. Often useful and may overlap with type (1) in the best cases.
  3. Bioinformatics that develops an algorithm or statistical procedure, but provides no insight into biology whatsoever
    By far the commonest category and the most prevalent in the bioinformatics literature. Normally takes the form: (a) amass some variables, (b) build a SVM, (c) run 10-fold cross-validation, (d) report sensitivity, specificity, accuracy etc. etc. Leading to the imminent death of bioinformatics as a respected research discipline. Largely responsible for the divide between bioinformaticians and bench scientists.

When web servers go bad

WoLF PSORT – prediction of eukaryotic protein subcellular location:

System error
error: Couldn’t close object file /var/web/wolfpsort/data/obj/results/fVQe44b65212dbf34d83ff0e21d0f855acb.html: No space left on device

Oh dear. You know, this post could be number 1 in an occasional series.

Friday light relief

One of my RSS feeds comes from Improbable Research, the source of many an Ig Nobel award. Yesterday’s item is a real treat:

Recurrent Clostridium difficile colitis: case series involving 18 patients treated with donor stool administered via a nasogastric tube.
Johannes Aas, Charles E. Gessert, and Johan S. Bakken.
Clinical Infectious Diseases, vol. 36, March 2003, pp. 585.
Improbable summary | PDF

Improbable feed

Yes, it is every bit as unpleasant as the title suggests.

Ig Nobels 2007

Can it really be Ig Nobel time again?

Details of the 2007 ceremony are not yet up at the official site; also check these news sites:

Good to see an Australian contribution:

Literature – Glenda Browne of Blue Mountains, Australia, for her study of the word “the”, and how it can flummox those trying to put things into alphabetical order.