Science communication

Scientists are specialists…

…at making their incredibly interesting work sound utterly boring: Jargon and scientists’ love for their own prose tending to weave dense, impenetrable sentences.. like.. this… one.

Luckily, I was able to attend an excellent Science Communication course hosted by the UK Medical Research Council last week. Ably hosted by Michael Regnier the short course aimed to cover just the basics – fundamentals of communication like how to tell compelling stories by creating narratives and building on them to hold readers. The course was brilliant – we all got a lot from it, especially since we have to continually remind ourselves that yes, our research is interesting to other people, and yes, they can understand it and even come up with good ideas if the basic problem’s explained clearly enough.

There were no icebreaking activities or crappy mnemonics at all, just some really good wider discussions about the wider role of science – and scientists – in society. As part of the exercise, we had to write a short jargon-free summary of part of our research. Here’s mine: as per brief, it’s intended for an ‘intelligent, yet uninformed’ reader – a twelve year-old, say. It’s actually a good audience to pitch for general writing, as most of us forget everything learnt at GCSE as soon as possible…

Speed-trap vaccines:

Training the body to fight off AIDS using pieces of the virus that causes it.

How do you catch a speeding bullet? Despite billions of dollars spent over nearly three decades of research, scientists have so far failed to find a vaccine that prevents new infections of the deadly HIV virus, which causes AIDS.

Part of the problem is that, like Wyle E. Coyote trying to trap the Road Runner, the virus mutates so rapidly that our bodies’ defences are continually playing catch-up, only able to successfully neutralise a small percentage of old viruses while new ones evade detection. This is because the surface of the virus is covered with a shifting ‘cloak’ of special sugar molecules that is able to change shape in successive generations of virus.

Vaccines against other diseases, like polio or measles, work by showing our bodies’ defences a ‘sneak preview’ of the disease, normally chopped-up or dead pieces of the germs that cause it. The surface cloak the HIV virus uses frustrates vaccine design because pieces of one HIV virus may look dissimilar to another. This means a sneak preview of even a handful of HIV viruses fails to brief the body to protect against all potential HIV infections.

New research turns this problem around. By using computers to examine which parts of the virus’ surface cloak show the least variation, scientists are trying to design synthetic peptides – small chemical molecules based on the virus’ own structure – that effectively brief the body’s defences on only those parts of the virus that change at the slowest rate.

The researchers hope that the body’s defences will be primed to trap the virus as it mutates through certain predetermined surface cloak combinations amongst the many shapes that are possible. So, unlike that crafty coyote, they may eventually be able to head their prey off at the pass.

In fact, although most of us are loath to deign to express our opinions anywhere outside of the peer-reviewed media, I think there’s a very strong case to be made here for professionals’ continual public engagement, whatever your technical speciality – be that science, medicine, policy, law, engineering or whatever.

After all (in brain-cell-count terms) we pretty much peak in intelligence around the middle or end of our second decade. So if that hypothetical ‘intelligent twelve year-old’ doesn’t get your explanation, maybe your understanding’s at fault – not theirs.

Erith adventure

For Her birthday we went on a little ride to Erith and back.

The weather was shit, and we ended up next to a poo factory on the Thames. 25 miles of rain + getting very lost on the Thames Path near the Dome (roadwurksss etc) was lame, but for Her first experience of winter touring, it wasn’t so bad. Plus, the Poo Factory man was a laugh.


View Thames poo tour in a larger map

More later…

Befi-BaTS v0.1.1 alpha release

Long-overdue update for beta version of Befi-BaTS.

Software: Befi-BaTS

Author: Joe Parker

Version: 0.1.1 beta (download here)

Release notes: Befi-BaTS v0.1 beta drops support for hard polytomies (tree nodes with > 2 daughters), now throwing a HardPolytomyException to the error stack when these are parsed. This is because of potential bugs when dealing with topology + distance measures (NTI/NRI) of polytomies. These bugs will be fixed in a future release. The current version 0.1.1 improves #NEXUS input file parsing.

Befi-BaTS: Befi-BaTS uses two established statistics (the Association Index, AI (Wang et al., 2001), and Fitch parsimony score, PS) as well as a third statistic (maximum exclusive single-state clade size, MC) introduced by us in the BaTS citation, where the merits of each of these are discussed. Befi-BaTS 0.1.1 includes additional statistics that include branch length as well as tree topology. What sets Befi-BaTS aside from previous methods, however, is that we incorporate uncertainty arising from phylogenetic error into the analysis through a Bayesian framework. While other many other methods obtain a null distribution for significance testing through tip character randomization, they rely on a single tree upon which phylogeny-trait association is measured for any observed or expected set of tip characters.

Numerology!

Yeah, I’m not talking about the famous Lemmings level, unfortunately (anyone know a good Flash implement of that btw?), but the tendency for certain dates to be kickass.

By kickass, I mean:

Kickass (n) (cic-aze). A sequence of date and time digits of spurious yet substantial numerological significance.

A great one happened a few weeks ago, on the 10th October, better known to you and me as:

10/10/2010

Or, if you get really anal and look at the time as well:

10/10/10 10:10:10

I think I’ve always collected these most excellent dates since I noticed 6/7/89 as a kid. Obviously 09:09 on 9/9/89 was a date of seminal excitement to me (not shared by my junior-school teacher, unfortunately), and at the same time on 9/9/99 I went completely wild. 01:01 on 1/1/2001 sadly passed me by as I was busy drunkenly drying my bricklike mobile phone off with a hairdryer, having fallen into a pool soon after midnight.

Being born on the 11th December, I’m particularly looking forward to a quarter-past two on my birthday in 2013, and both 11/11/11 11:11:11 and 2012/3/4 05:06:07 should be special too, as will 3/14/15 09:26 (using US dates) and 2/7/18 02:08. I’ll probably end up missing 22/2/2222 2:22 though…

Why?

Being ever-so-slightly OCD, I am more excited by these numbers than is possibly healthy, but from experience most people have a bit of a soft spot for these dates, the study of which is known as numerology, and is especially popular in China, apparently. Whole organizations have based mass-action days around them.

Without wanting to cod-psychoanalyze too deeply (I’ll save that for the pub) I wonder if the (fairly) modern obsession with significant date combinations has anything to do with our need to mark the passing of time in a relentlessly-changing world. ‘Never mind that you can’t even remember what you had for tea yesterday,’ this argument runs, ‘at least you had that tea on a date of cosmic significance.’

The fact that said dates are measured from the (arbitrarily-defined) birthday of a largely fictionalized individual in Judea 2000+ solar orbits ago is immaterial. Perhaps this need to mark the passing of significant chunks of our life is primal; we’re not so different from our Stonehenge-building, mushroom-eating proto-hippie ancestors after all…

About this new site

As you can see, I’m running a new site now. Some content will be loaded pretty soon (old blogs, lyrics, music, software etc) but the design I want to do is pretty complicated, especially as the client-side stuff, so I want to wireframe it first somewhere else offline. Might get it done in a couple of months, so look out for a bit redesign after Christmas!

This is partly an ego trip, but mainly because I’m pissed off with Facebook / Myspace and all their popularity contests and formulaic box-filling shit, and want to get back to the good old Netscape days of the 1990s, when a personal website really was just that, and you could put whatever you liked up, however you wanted to.

I’ve installed plugins for Twitter and Soundcloud, and will get flickr in there too soon. Also, for commenting, I’ve activated the really-pretty-cool DisQus engine, so that those of you on social networking sites that want to comment, can.

In the meantime I’m going to slowly let the Facebook and Myspace accounts die. Just as a little piece of me dies every time I login to those damn things.

1,313: A Sotones Sampler

STCD037'1,313: A Sotones Sampler' - Artwork by Billy Mather IllustrationReleased 04/11/2010

CD | MP3 | Spotify

Buy now: iTunes | Amazon | All stores

‘1,313: A Sotones Sampler’ is the second Sotones Records compilation, featuring some of the best music from across the south coast, spanning indie rock to dubstep, folk to electronica. Featuring smash singles by Moulettes, Moneytree, Haunted Stereo, Peter Lyons and Fresh Legs, as well as new works by artists including rude_NHS, nato, Ann The Arc and Jeffisalive. Artwork by Billy Mather (billymather.co.uk)

Tracklisting:

  1. Moulettes / Horses For Hearses / Horses For Hearses EP (Licensed from B.alling The Jack)
  2. Fresh Legs / Julian / Julian EP – Deluxe
  3. Moneytree / Medicineland / The Great Indoors Part III
  4. Haunted Stereo / Lock The Doors / On A Pin/Lock The Doors
  5. Anja McCloskey / Newton / Turn – Turn – Turn
  6. Jackie Paper / All The Wine / What’s Wrong With Broken Glass
  7. Peter Lyons / Old Friends / Old Friends
  8. Jeffisalive / Sunlight’s Yellow Dress / Sunlight’s Yellow Dress
  9. rude_NHS / Roy Orbital / Roy Orbital
  10. JayEtAl / Feather / Where No City Lights
  11. nato / Missing Song / Eating Clouds
  12. Ann The Arc / Buttercup (Single) / Buttercup (Single)
  13. The Beaux Hardts / Hey, Who Turned Up The Gravity? / Leisure (B-Sides & Rarities Special Edition).
  14. Lonely Joe Parker / Brooklyn / What’s Wrong With Broken Glass
  15. Bobby Wade & Cristof Certic (4TK De Nada Demo) / Tax For Sure / Double Barreled

Buy Now direct from Sotones.co.uk