Field notes and the promise of science…

Posted 10 December 2012 by Jim Caryl

Live blogging was a new experience for me; the aim being to sit through a lecture/dialogue, digest the information, write a coherent and constructive blog post and then publish before (or while) heading to next discussion. Despite some thorough research prep ahead of the first day, and reading plenty of live-blogging advice about battery power and staying hydrated, I managed to arrive in the auditorium totally dehydrated, and proceed to deplete my macbook battery in 90 mins. Thus, my first post... Read more

Capturing Stockholm…

Posted 9 December 2012 by Jim Caryl

It's amazing how far you can travel internationally before smelling fresh non-air conditioned air. I arrived at Arlanda airport - 50 km North of Stockholm - in the late afternoon, and was immediately siphoned into the familiar human corral of border security that is facsimiled the world over. The fastest route from the airport to the city centre is via the Arlanda Express, a name that evokes a surety of function that I'm willing to accept as a factual statement... Read more

An interview with Kerstin Lindblad-Toh, comparative genomicist…

Posted 8 December 2012 by Jim Caryl

An important means by which we try to understand the human genome is, oddly enough, by looking at the genomes of other mammals. The aim is to identify areas of evolutionary constraint, regions of the genome that we all share (both coding and non-coding) and are thus likely to be important for all of these species. These regions have not only assisted with the identification and assignment of genes on the human genome, but they also provide important information about disease... Read more

A Nobel weekend in Stockholm…

Posted 6 December 2012 by Jim Caryl

On Saturday morning I'll be rising at a hideously early hour to board the first of two flights that will (eventually) bear me on my merry way to Stockholm. I was lucky enough to be invited to be part of the blog team covering the Nobel Week Dialogue 2012, a new annual conference that will form part of the week of events leading up to the Nobel Prizes. I'm a big fan of conferences, I've lost count of the number... Read more

Locked out…

Posted 10 November 2012 by Jim Caryl

When I was an undergraduate you couldn't get a journal article online, about the most you could hope for was a table of contents (ToC). Getting access to scientific articles meant a visit to the library with a photocopy card and a great deal of patience. 'Bagging' a photocopier was an artform in itself - I think everyone thought they knew of a secret, hidden photocopier on an upper level of the library, one that you felt you owned. Of... Read more

My published negative result…

Posted 11 October 2012 by Jim Caryl

IMAGINE your excitement as a budding young researcher taking on your first piece of research as part of an undergraduate summer studentship; you're working on a gene that makes a type of medically important bacteria resistant to a key group of antibiotics, the tetracyclines. The gene in question is described in a peer-reviewed specialist journal, but no-one is quite sure how the gene works. If we're to understand and address the problem of antibiotic resistance, one of the many things we... Read more

On publishing negative results…

Posted 4 October 2012 by Jim Caryl

IN the last week Ben Goldacre’s ire has been felt, and rightly so, because what the Ire of Goldacre has been pointing at is a systematic bias in the publication of science and medical information. Ben’s focus relates to the way in which big pharmaceutical companies manipulate an overwhelmingly positive academic publication record, accusing them of selectively burying the results of negative trial data and publishing only the positive trial data. This serves the interests of pharmaceutical companies, but not... Read more

The ‘faecal’ bank…

Posted 26 July 2012 by Jim Caryl

Welcome to The Gene Gym on I'm going to take great license to wander around numerous areas that overlap, nudge, cajole and nestle up against the main theme of my blog, which is of course bug and drugs. So firstly, a brain dump: A colleague and I once – rather drunkenly – planned a letter to The Lancet [a popular medical journal] in which we describe a means by which one might ‘bank’ a sample of ones faecal matter... Read more

Re-awakening enemy sleepers…

Posted 29 August 2011 by Jim Caryl

The idea of an enemy sleeper agent is a central plot device in many a spy novel or movie, and certainly the idea of going to ground behind enemy lines is not unheard of in many theatres of conflict. The idea in all cases is to remain undetected until re-activated to cause harm behind enemy defences. The trick to identifying if there are latent sleepers operating is to try and re-activate them and get them to reveal themselves. Cue any... Read more

Where I am quoted not quite correctly….

Posted 1 August 2011 by Jim Caryl

I was recently called by an editor at NewScientist asking for some background on the field of fitness in bacteria, and particularly the issue of multi-resistant bacteria persisting in the environment (or clinic) in the absence of antibiotic selection. The reason for the question arose due to the upcoming publishing of an interesting paper in PLoS Genetics: Silva RF, Mendonça SCM, Carvalho LM, Reis AM, Gordo I, et al. 2011 Pervasive Sign Epistasis between Conjugative Plasmids and Drug-Resistance Chromosomal Mutations.... Read more