Archive for the 'Daily titbits' Category

New beginnings…

I have been remiss, once again taking a protracted break from this blog. I was essentially forced, by economic factors beyond my control, into taking quarter of this year off work. I used this time to re-assess, travel, reflect and generally think about myself and my own directions; time I’ve not taken since 1999, which was careless of me. Whether I can consider myself rested enough within three months is neither here nor there, for I am back, or at least I will be back, but in a somewhat modified form.

One of the big problems with maintaining a science blog where I wander through a range of subject matter is that it does rather take my eyes away from my day job, and you only need read a few science blogs to realise the the day job of a jobbing postdoc is rather full of teaching, supervision, research, reading, writing and banging ones head against a wall. Thus, whilst I was increasingly thankful for this distraction in my last research position, I have recently joined a new research team who are doing some interesting and meaningful work; I will be taking the advice of Daniel McArthur of Genetic Future who at Science Online London 2009 said that one way to succeed at both blogging and your day job is to fuse the two. To that end, this is what I will be doing, obviously not giving the game of our own research away, that would be silly, but instead talking about the field in general.

So what field? Well, my new position sees me returning to my roots; I started out in Staphylococcal molecular genetics a decade ago and spent my most formative doctoral training years working in a rather academic aspect of horizontal gene transfer. It was then, and still is (though not for long) a highly under-studied area of research that couldn’t possibly be more important with what we are coming to understand about the nature of antibiotic resistance, evolutionary microbiology and the human microbiome. I am now working in an area that brings together several recurring themes of interest for me: evolution, horizontal gene transfer, bacteria (Staphylococcus aureus to be precise) and antibiotics research, specifically the evolution of bacterial fitness.

This is exciting times for me, and I can’t tell you how many fantastic papers I’ve already discovered from my period of absence in this field; people have been busy, and I intend to talk about it. However, much of what I have to say won’t necessary be in this blog, for I will be moving. This blog will remain of course, as part of my efforts to regale you with edifying titbits.

As for where I will be moving to, well I now have a blog over at the Nature Network, called ‘The Gene Gym‘.

I will not be closing this blog down, it will be a repository for all those science stories and titbits that don’t fit in with my Gene Gym remit.

Thanks for reading.

 

 

A confluence of photography…

My sister and me, outside her place of work (School of Botany, Melbourne University)IN a strange series of events, today the Dutch firm Impossible BV announced that they have released a new B&W polaroid film that will fit traditional Polaroid cameras. This is great news, and they will be following up with standard colour Polaroid film soon.

It was exactly a year ago today that I first heard the news that Polaroid were ceasing producting of Polaroid film, and I set out to both acquire an old Polaroid camera, and stock up on film. I have two packets left, both of which are now out of date (which may yield some interesting results). I’ll be taking them on my travels next month.

After 17 months of research and development, The Impossible Project announced that it succeeded in its task of re-producing a new analog Instant Film for traditional Polaroid cameras. Containing more than 30 newly developed components, Impossible today introduced a new, monochrome Instant Film – the PX 100 and PX 600 Silver Shade – and is therewith saving millions of perfectly functioning Polaroid cameras from becoming obsolete. [pdf - 556 kb]

I’ve had photography on the mind today, having taken the day off to get the beginnings of my photographic portfolio up online (also available via the ‘Gallery’ tab above), and working on a new series of textured images. These images were from a fantastic visit to Skye, also this time last year, where I’d taken a macro shot of some Gabbro rock, incidentally my favourite igneous rock (because I have a favourite igneous rock), to use as a texture. This provides an additional link between the landscape images and the geology of the area. A nice fusion I think.

I will be selling these images at a very reasonable price once I have a convenient PayPal button set up, and have trialled the giclée printing I need for some of them.

Blog update:

This blog has been a little low on posts recently, which is bizarre as I’m staring at 12 browser tabs containing some fantastic papers – I will write some of these up in a research highlights format in the next day or so. Alas, as this is my last week of research work on this contract, I’ve been too busy wrapping things up in the lab.

I will (hopefully) be returning to do some research starting in May, on the evolution of bacterial fitness, but until then I’m also planning a lot of travelling, visiting old friends around Europe: I’ll be off to Czech Rep. (Prague, Karlovy Vary), Germany (Dresden), Iceland (Reykjavik), Belgium (Brussels, Gent, Geel) and Italy (Brescia), before finishing up at my annual Old Boys reunion with University of Wales friends in Snowdonia and on the beaches of Anglesey.

I’ll be posting pictures from the road – most likely on my photoblog over at The Overflow (also available in a tab above).

Hopefully I’ve given you a bit of procrastination fodder, but until I return to my regular science slot, add me to your RSS feed and you’ll see when I periodically resurface from my peripatetic sojourns.

Continue reading ‘A confluence of photography…’

Telling tales…

The following is an excerpt about the current interplay between science and the media, taken from an article in this week’s Nature by Colin Macilwain:

…thanks to the massive growth in public relations and to online media’s insatiable appetite for ‘content’, journalism in science, as in other spheres, has evolved into an ugly machine — called ‘churnalism’ by media-watcher Nick Davies and others. This machine delivers inexpensive and safe content, masquerading as news, to an increasingly underwhelmed public.

The machine prospers because it serves the short-term interests of its participants. Editors get coherent and up-to-date copy. Writers get bylines. Researchers, universities and funding agencies get clips that show that their work has had ‘impact’. And readers get snippets, such as how red or white wine makes you live longer or less long, to chat about at the water-cooler.

None of these groups is benefiting strategically from the arrangement. Science is being misrepresented as a cacophony of sometimes divergent but nonetheless definitive ‘findings’, each warmly accepted by colleagues, on the record, as deeply significant. The public learns nothing about the actual cut and thrust of the scientific process, and as a result is beginning to adopt a weary cynicism that can only rebound on science in the long run.

Continue reading ‘Telling tales…’

Changing your beliefs…

FOLLOWING on from my post yesterday regarding people’s concept, or lack thereof, of evidence, it was suggested that it would be an interesting thought experiment for those of us who are willing to offer criticism on a subject to put ourselves on the receiving end. I think it’s a good idea to find something that each of us holds dear or true, and see if we can challenge ourselves to imagine how we’d feel if someone argued against that view. By understanding this, perhaps we can better approach our means of approaching such as subject with someone for whom such criticism would represent a paradigm shift.

As I managed to shake silly beliefs such as ghosts and ley-lines as a child, the only examples I have as a thinking adult are with particular scientific hypotheses that I’ve subscribed to, but subsequently had to ditch. This is the general method of science, and in my own research there have been any number of hypotheses I’ve formed and subsequently disproved on the basis of new evidence.

However, there have also been explanations for some natural phenomena that pre-date my research career, and to which I subscribed whole-heartedly. One example dates from my time as a first-year undergraduate studying marine biology. I had a particular interest in marine invertebrates and once attended a lecture by Donald Williamson, who was the major proponent of a larval evolution hypothesis, and recently came to light as being accused of ‘fringe science’ and getting a paper in the Proceedings of the National Academy of Sciences (PNAS) under the radar; thus also highlighting the pitfalls of the ‘I’ve got a mate in the club’ attitude to publishing.

Essentially Williamson felt that the immature forms (larvae) of many such invertebrates can be thought of as distinct organisms from the adult form, which are often comprehensively different both physically and physiologically; think caterpillar to butterfly, or blobby polyp jellyfish to its adult ‘medusa’ form.

Williamson felt that these different forms arose through hybridization — the fusing of two genomes (of two distinct organisms), one of which is now expressed early in an animal’s life, and the other late.

You can read an Sci. Am. article about it here.

I have to say, I absolutely LOVED this hypothesis, it was very exciting and I lapped it up with the typical fervour of an undergraduate.

Trouble is, since then it has been rebuked often and has not been substantiated by the experiments that were performed to test the hypothesis. I was quite recalcitrant about such rebukes up until the most recent PNAS rebuke that I’ve just linked to.

You can read rebukes to the Sci. Am. article here.

Changing my view about this hypothesis was hard, and a little embarrassing given I so animatedly communicated it to all my friends until I learnt it didn’t have strong grounding.

This is very true of many areas in which we are not experts, whether you are a scientist or not, and the fact is that we do tend to confer a great deal of trust in some individuals depending on their position. I would add that Donald Williamson was not ‘wrong’ to form this hypothesis at that time; scientific knowledge is by its very nature transitory, but once it has been tested, and alternatives developed, then we should seek to move on.

I could have easily ignored the evidence that Williamson’ hypothesis did not hold up to, and continued telling people an interesting and captivating story about why adult and juvenile forms of invertebrates are so different, but I didn’t. There’s still a part of me that thinks that there may still be something in it, which is why I can relate – to a point – with those people facing their first reality-check with regards some pseudoscience that they’ve hitherto believed in.

Donald Williamson is now retired and still stands by his hypothesis.

I don’t.

Stand up for research…

I’VE had a bit of an axe to grind recently about the government’s proposed policy on requiring such a large proportion of research funding to be allocated on the basis of economic and social impact. The University & College Union (UCU) is curently hosting a petition, signed against the statement that I’ve copied from their site below.

Sign it if you care to.

From the UCU’s website:

The latest proposal by the higher education funding councils is for 25% of the new Research Excellence Framework (REF) to be assessed according to ‘economic and social impact’. As academics, researchers and higher education professionals we believe that it is counter-productive to make funding for the best research conditional on its perceived economic and social benefits.

The REF proposals are founded on a lack of understanding of how knowledge advances. It is often difficult to predict which research will create the greatest practical impact. History shows us that in many instances it is curiosity-driven research that has led to major scientific and cultural advances. If implemented, these proposals risk undermining support for basic research across all disciplines and may well lead to an academic brain drain to countries such as the United States that continue to value fundamental research.

Universities must continue to be spaces in which the spirit of adventure thrives and where researchers enjoy academic freedom to push back the boundaries of knowledge in their disciplines.

We, therefore, call on the UK funding councils to withdraw the current REF proposals and to work with academics and researchers on creating a funding regime which supports and fosters basic research in our universities and colleges rather than discourages it.

[12,007 signatures at 11:43, 16 Nov 2009]

Sign the petition here.

Food for thought…

FINALLY, some lectures that don’t require a trip to London. Some big names are coming all the way up North, way up to the provinces, to give lectures as part of a celebration of 150 years of On the Origin of Species:

24th November 2009

2pm: Dr Gordon Chancellor
Charles Darwin, his life and his science
Dr Gordon Chancellor is from the UK Data Archive at the University of Essex. He is an Associate Editor of darwin-online.org.uk which hosts the largest online resource in the world relating to Charles Darwin.

2.45pm: Professor Steve Jones
Is human evolution over?
Professor Steve Jones is Professor of Genetics at University College London and is one of the best known contemporary popular writers on evolution. He is a television science presenter and writes a science column in the Daily Telegraph.

3.30 – 4pm: Interval

4pm: Professor Sydney Brenner
The Reconstruction of the Past: Reading the Human Genome
Professor Sydney Brenner opened the JIF building in 2007, now known as the Wellcome Trust Brenner building. Sydney was awarded the Nobel Prize for Physiology or Medicine in 2002 for his seminal work on discoveries of organ development and programmed cell death.

4.45pm: Professor Sir Alec Jeffreys
DNA fingerprinting and the turbulent genome
Professor Sir Alec Jeffreys is Royal Society Wolfson Professor at Leicester University. He discovered DNA fingerprinting 25 years ago. Among other important aspects of this method is that it allows identification of people by detecting variations in their genomes and has altered forensic science world wide.

5.30pm: Close

It’s going to be popular. Off to try and get a ticket, otherwise I’ll be sweating it out in a lecture teatre watching a live video feed instead.

Intermission….

Apologies for my absenteeism this week, I have been busy researching some family history for an upcoming post, which I hope to finish soon. If you’re looking for some light Sunday reading however, please consider a selection of my other posts:

Fallacies of logic – how logic is abused to achieve nefarious and intellectually dishonest ends.

Bio-suit – how human do you think you are? An essay about the human microbiome, the zoo of organisms that live on us, and in us – without which we wouldn’t be here.

The strength of great apes – describing the folly of engaging in an arm-wrestle with a Chimpanzee in the pub.

A cure in the toxin – describes the early use of bacterial infection to treat some forms of cancer.

…and finally, a book recommendation, ‘Three cups of tea‘.

Productivity…

Productivity (Copyright Jorge @ phdcomics.com)

THE thing about being a practising scientist working in academia is that when such a practising scientist decides they want to write more about science in general, they remember that academia is a toxic gas that expands to fill all available space.

We might hope for reprieve from standing at the bench, just a small amount of time to get a handle on our writing, a quick moment to imbibe some of the multiple streams of information from emails, journal table of contents, RSS feeds; alas, the moment a window opens, it is filled with responsibility. This may come in the form of the help you promised someone when you next got a chance; or hunting down an expensive enzyme in neighbouring labs, of which you require a mere fraction of a unit for a throw-away experiment; it could be trying to find a journal article with some essential information, rather than one that is actually interesting. Alternatively, you may just sit and stare into space, your brain already so depleted of sugar that you are protocolling on auto-pilot.

Having filled your day with preparations for experiments, and the remaining 5% of it getting to finally do the experiments, you turn your attention to your student, who is working on a completely different project, with its own set of unique and inconvenient problems, and for which you must but don’t have answers.

Having finally left the lab, if you’re lucky, you’ll manage to get home in time to cook some award winningly simple food (credit us with some respect, some of us do cook from scratch), which is invariably eaten in front of the computer while you finally get to sift through the now ridiculously over-burgeoning information stream, which now includes – lucky me – about a million twitter entries and their links.

Ultimately, if you’re not ready to go by 2 am, you have two choices: either spiral into pit of information overload, eyes glazing over as the numerous ideas that pop into your head leave just as fleeting and unformed as they arrived; or sleep.

There are of course some researchers out there who do manage overwhelmingly with both their professional and private pursuits, hell, I even manage it myself sometimes. But right now, I need a week’s worth of sleep.

Posing a postural point…

[ratings]

Back-friendly blogger

[Jim tests out his new Wacom tablet. Joys]

Latest discovery….

Portal (copyright The Onion)

Ground-breaking research, reported by The Onion.