[This post was restored from a WayBackWhen archive. It was originally posted to a blog called ‘The Gene Gym” that began life on the Nature Network in 2010, and then moved to Spekrum’s SciLogs platform. Unfortunately many of the original images have not survived the import]
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 in this very modern Scandinavian country. Sure enough, in a mere 20 minutes I am delivered to Stockholm central station and can make my bid for the open air; yet emerging into a fog of -9C air was probably rather more fresh than I’d anticipated. Stockholm is seasonably festooned with lights, which twinkle in the crystalline cold and cast their light on streets paved with a compaction of snow, sand and salt, giving the consistency of gingerbread dough.
Continue reading “Capturing Stockholm…” →
On why a move to Open-Access publishing is a blessing, and a younger generation of scholars have little understanding of just how locked away knowledge used to be.
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 course, this fog of solipsism would evaporate upon arriving to find your photocopier being used by another person. You would then resign yourself to waiting, staring indignantly at the interloper.
Continue reading “Locked out…” →
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 those of the patients or doctors. You can see a video of Ben discussing this here.
The problem of publication bias in the scientific and medical literature is that positive results get published, and negative results – or those from studies attempting to replicate previous studies – by and large, don’t. There are several problems with this, and with which I’ve had practical experience:
Continue reading “On publishing negative results…” →
Welcome to The Gene Gym on SciLogs.com.
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 [shit] (comprising a cross-section of a healthy gut microflora), prior to departing on an exotic holiday, or undergoing antibiotic treatment. The premise was that any insult or injury arising from catching a bout of traveller’s Delhi-Belly, or depletion of the gut flora from chemotherapy, could be abated by having your original gut flora restored from your earlier banked sample. The service would naturally be called, the ‘Shit Bank’. Continue reading “The ‘faecal’ bank…” →
Text books commonly state that in the natural environment antibiotics are a means by which bacteria (and yeasts) reduce competition for resources, by creating a ‘zone of inhibition’ around themselves—kind of like unleashing a smelly fart to stop people sitting too closely. However, antibiotics can also be seen as part a more complex system of cell to cell communication/signalling in microbial communities, in fact, they can also be food. When used at the concentrations we employ therapeutically, they can either stop bacterial growth, or kill outright. Just because they can have this effect, doesn’t mean that this is what they evolved to do—’antibiotic’ is simply the name we give to the few (of many) small organic molecules produced by bacteria that happen to have an effect on a particular group of bacteria against which it (along with many other molecules) was screened.
Continue reading “Bugs & drugs…” →