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POT-POURRI: A reading collection for a winter’s evening. Popular science, careers, protein bioinformatics and a little controversy for good measure.

Named for the light-hating demon of the underworld. A kilometre below the earth’s surface a nematode worm (roundworm) lives, feeding on bacterial goo. You really can’t go past Nadia Drake’s article at Nature describing this new finding. It’s stunning stuff. Multi-cellular life from depths.

The career paths of science graduates and post-docs. I’ve previously written several articles about academic careers, and careers outside of academia. A long article, No fixed address, in the Time Higher Education Supplement by Paul Jump starts in demoralising fashion, but further down in the piece offers an interesting range of suggestions and actions institutions have taken. In the same issue, Ann Mroz also adds a few words in her article, Leader: Lab bench needs front bench help. (Bear in mind that local factors can play a role.)

Those looking to be inspired at possibilities of using science qualifications outside of academia may wish to browse Chad Orzel’s second round of interviews of non-academic scientists.

Human echolocation. Do I need to say anything more to encourage you to read Mo’s article on fMRI studies of two blind experts in echolocation? It turns out echolocation involves the visual areas of the brain. This reminds me of how sign language is processed in the language areas of the brain. (I’ve been meaning to present this for well over a year now! Sigh.) As always Mo’s writing is excellent – head on over to his place.

Vaccines. Science communication on-line often encounters the various scare stories over vaccines, especially if you are a biologist. Vaccine scares can have had the effect of lowering the vaccination rate. This is an issue because vaccination frequently depends on high rates of vaccination to be effective. Nature has presented a collection of articles on vaccines. The collection contains an editorial, news, features, and comments, news & views and research. With the exception of the editorial, the articles are open-access.

I was particularly drawn to the comments The real issues in vaccines safety (Roberta Kwok) and Target the fence-sitters (Julie Leask) as these touch on issues familiar with many science bloggers.

Since I saw these, Orac has offered his thoughts on these articles. Like him, I find Julie Leask (from the National Centre for Immunisation Research and Surveillance, University of Sydney) striking a chord. She’s a social scientist specializing in immunization take-up. She gives a great outlay of the patterns and issues and offers three steps governments might take to address vaccination concerns. (Make vaccination accessible; target communication to those where it might make a difference; keep the health professionals on board.)

I have often thought that the clearest and most convincing examples to present to those uncertain about the effectiveness of vaccination programmes are the cases where the programmes have been stopped. She gives two such examples in her story. She also suggests that the audience to target are the ‘fence sitters’, arguing that those with firm ideological commitments are likely entrenched by their ideology. Most bloggers, or science communicators in general, will recognise this.

Force fields. (Not the science-fiction kind…)

I started computational biology studying proteins,* including molecular simulations. It’s nice to close this out with a link to an article I stumbled upon in a complicated way (that I won’t bore you with) aboutthe force fields used in molecular simulations. I, too, have memories of that time when I first ’had the pleasure of’ seeing ’the morass of compromises and shady half-steps in the guts of every force-field.’

The same purist vs. ad-hoc plays out elsewhere in computational biology.

It’s a nice article, although some not familiar with proteins may find it a bit technical.**

XMRV. The state of play grows (very) clear.

Judy A. Mikovits (Whittemore Peterson Institute, WPI) and colleagues have argued that a ‘new’ virus, XMRV, is the cause of chronic fatigue syndrome (or ME) in a paper published in Science. Evidence against this has been mounting for some time. The latest turn in this saga is that senior editors of Science have asked Mikovits to volunteer to retract her paper in the face of further evidence to the contrary.

The authors declined. In response to this Science has issued an Expression of Concern, e.g. ’In this week’s edition of Science Express, we are publishing two Reports that strongly support the growing view that the association between XMRV and CFS described by Lombardi et al. likely reflects contamination of laboratories and research reagents with the virus.’

The WPI’s response (PDF file) has been described by others as in denial. (Some have suggested that the WPI looks to want to sell their wares regardless of the science.) I’m not up to speed with the details of virology, but the claim that ’There has been no attempt to fully replicate this study to date.’ is surprising given one of the two new studies examines patients of the WPI group in depth and finding no XMRV.

This story has been widely covered by others, including at these sources:

Vincent Rananiello at Virology blog covers the paper arguing that the origin of XMRV is recombination in laboratory mice, and inconsistent with it being associated with human disease. This recent paper at PLoS One (also) investigates XMRV as laboratory contamination.

Frequent readers will know that Science is currently also hosting the ‘arsenic life’ controversy.

Updates

June 4th: Add a couple more link and fixed link to WPI’s response.

Footnote

* Both DNA and proteins, actually, as I was studying DNA-binding proteins.

** I have to confess it reminds me of ideas about molecular simulation I had wanted to explore. I once dreamt I’d tackle this in my spare time, as a private hobby project, but I’ve since learnt spare time isn’t something I have much of!


Other articles on Code for life:

Temperature-induced hearing loss

XMRV prompts media thought: ask for the ’state of play’

On alternatives to academic careers and ’letting go’

Immunisation, then and now

Vaccine promotion — the medium matters too