Saturday, 29 September 2012

Good-bye, polar bears :o(

For the past couple of years, I have been using this image of a polar bear riding a small iceberg to illustrate climate change in the talk I give to a local(ish) school about studying biological sciences at University - it's just one of the important areas to which biological sciences graduates can contribute. Sadly, according to a Guardian article earlier this week, it is an image that might go out of date sooner than I thought.

The title of the article says it all, really: "Arctic expert predicts final collapse of sea ice within four years".

As the expert in question (Prof Peter Wadhams of Cambridge University) is quoted to suggest in the article, surely it is time to start throwing everything at this problem, including the kitchen sink of geoengineering. With a catastrophe of this magnitude so close, it is hard to see how such attempts could possibly make things worse.

Thursday, 27 September 2012

Google Sea View

The Google Maps Street View Collections are pretty cool (and just plain pretty!) and well worth an explore whenever you have a few moments to kill. (Armchair tourism at its best.) The new Ocean Collection is particularly impressive because you can wander around underwater! As reported in the Guardian Science Section "Google Maps' virtual diving brings the Great Barrier Reef into view":
Millions of people will be able to take a virtual dive on the Great Barrier Reef via Google Maps on Wednesday as part of a pioneering underwater scientific expedition.

The Catlin Seaview Survey will allow internet users to share the discoveries of scientists who are using new technology to study the composition and health of the Great Barrier Reef.
I like!

Wednesday, 26 September 2012

Amazing photos In Focus at The Atlantic

This Sri Lankan bovid "adorned with frogs" is just one of the 50 photos selected by Alan Taylor for The Atlantic from entries for the National Geographic Photo Contest 2012:
"Once again, National Geographic is holding its annual photo contest, with the deadline for submissions coming up on November 30. Beginning on September 1, the society started gathering and presenting galleries of submissions, encouraging readers to vote for them as well. National Geographic was kind enough to let me choose among its entries from 2012 for display here on In Focus. Gathered below are 50 images from the three categories of People, Places, and Nature, with captions written by the individual photographers."
Definitely worth a look!

h/t WEIT.

Saturday, 15 September 2012

Apocalyptically loving Slash

When I bought my MacBook and received an iTunes voucher with it, I am not ashamed to say that the first thing I bought with it was the most recent offering from that most excellent of British rockers, Slash. I've previously endorsed Ain't Life Grand from when he was part of Slash's Snakepit and, I must admit, I am a general fan of his. Not everything that came out of the Snakepit, or Velvet Revolver (or Guns 'n' Roses for that matter) is fantastic but every album I own has some gems on it.

Apocalyptic Love raises the bar and has now solidly cemented itself as one of my favourite albums - certainly of the year and probably of all time. It's a grower too, which is always a good sign. If you like Slash at his best, go buy it! Now!

Friday, 14 September 2012

University of Southampton builds world's first Raspberry Pi supercomputer

It's a bit of a busy time of year, so blogging is on the back burner for a bit (and I'm accumulating half-written posts for later!) but this was just so weird and fun that I had to write a quick post. If you haven't heard of a raspberry pi computer before, you can find out all about them here. Basically, they are a very small, very cheap ($25) "credit-card sized computer that plugs into your TV and a keyboard".



According to the FAQ:
It’s a capable little PC which can be used for many of the things that your desktop PC does, like spreadsheets, word-processing and games. It also plays high-definition video. We want to see it being used by kids all over the world to learn programming.
Well, Prof Simon Cox (and colleagues) of the University of Southampton decided to go one better and used a bunch of them to teach his kid how to build a supercomputer! You can read about it on the Computational Modelling Group website.



What can it do? Well, according to Prof Cox:
“The first test we ran – well obviously we calculated Pi on the Raspberry Pi using MPI, which is a well-known first test for any new supercomputer.”
I suspect it can do a bit more than that: the 64 processor system has 1Tb of memory! Not bad for £2500 (plus switches and, possibly, lego).

Tuesday, 11 September 2012

Surely it's time to have more disabled presenters on TV?

So, the Paralympics has drawn to a close and, apart from the occasional annoying advert break, Channel 4 have done a pretty good job. The Channel 4 broadcasting team have been particularly good, I thought, with a good mix of familiar faces and less familiar disabled presenters.

For me, Alex Brooker and Danny Crates were particularly good - the former for general entertainment on The Last Leg and the latter for his boundless enthusiasm during the track and field events. (I really liked the American dude in the wheelchair too but I can't find his name on the Channel 4 site and my memory for names is shocking! [Update: I have committed the cardinal sin. His name is Jeff Adams and he is Canadian. Sorry Jeff!])

I thought Jimmy Carr made a very honest and inciteful comment during his appearance on The Last Leg. He said something to the effect that it had taken him two or three days of watching the games before he really saw past the disabilities and just the sport. I felt something a bit similar with the presenters too. I don't see that many disabled people in day to day life and so at first I found my attention drawn to Danny's missing arm, or Alex Brooker's "hand issues" but, after a couple of days, all I saw was really great presenters making entertaining TV.

There's been a lot of talk about how to carry forward the momentum from these Paralympics and part of the solution seems quite simple to me: put more disabled people on TV. Not because they're disabled - because they're great TV presenters. If Claire Balding, Jonathan Edwards and Iwan Thomas can co-present sport for disabled athletes, then there's no reason why Danny Crates and Ade Adepitan cannot co-present sport for able-bodied athletes. And The Last Leg team of Adam Hill, Alex Brooker and Josh Widdicombe are welcome on my screen any time!

Monday, 10 September 2012

Five Minutes with Ben Goldacre

After yesterday's post about an interview with Richard Dawkins, author of two of my favourite books - The Selfish Gene and The God Delusion - it seemed appropriate to post today about an interview with the author of another of my
"must read" books, Bad Science.

A bit shorter than the Dawkins interview, Five Minutes with Ben Goldacre is a quick-fire tour of:
"bad science", dealing with critics, the importance of randomised trials, whether God exists and Twitter.
I particularly liked Ben's description of himself as an "apatheist". Due to my background, I have quite an interest in religion and think quite a lot about my atheism (although I don't quite consider myself as a "New Atheist") but I think it is always useful (for strident atheists and religious types alike) to remember that there are people out there who really don't care and don't consider it to be that important.

Ben's real passion is clearly science and how to do it properly - particularly in relation to medicine - and I really cannot recommend Bad Science highly enough. Although bordering on ranting at times (but always in "righteous anger"!), the early chapters in particular provide an excellent and accessible introduction to why science - and proper use of statistics - is so important. It is the number one book I recommend to my first year tutees studying Biomedical Sciences, as well as A-level students at Open Days.

Ben now goes beyond being a sterling advocate of evidence-based medicine, however, and also has some interesting ideas regarding "evidence-based policy" and how randomised trials can be applied to government policy. My reading list is quite long at the moment (particularly with the recent ENCODE release) but I think I will be adding his Cabinet Office paper: Test, Learn, Adapt: Developing Public Policy with Randomised Controlled Trials.

The whole Five minutes with series is really good and Matthew Stadlen is an excellent interviewer. I am surprised by the breadth of topics they manage to cover in five minutes without it actually feeling superficial. I guess there is often something to be said for "cutting to the chase".

I only recently discovered the series (thanks to my lovely wife) but another notable episode is that with my most recently discovered heroine in Five Minutes with Caitlin Moran. There's a whole host of others, though, and I look forward to working my way through (most of) the list! (Another BBC triumph!)

Sunday, 9 September 2012

The Life Scientific of Richard Dawkins

Richard Dawkins is one of my personal heroes. Although I do not always agree with everything he says, I usually agree with most of it and he has been a source of inspiration at many points in my life. Reading his classic book on gene-centric evolution, The Selfish Gene, was like having a light switched on. I was fascinated in evolution and genetics before then - I was in the first year of a degree in Genetics at the time - but suddenly it all just made sense. It's still a book I recommend.

Another one of my favourite books of all time is The God Delusion. It sums up the position of a rational agnostic atheist incredibly well. A lot of people argue against it, and vilify Dawkins because of it, but I have never actually seen a good argument against what he writes. (Usually, people are arguing against something that he didn't write. I sometimes wonder whether any of the anti-Dawkins crowd have actually read anything by him.)

If you are one of those people - or a fan, like me - then I strongly recommend downloading this week's episode of The Life Scientific and listening to his half hour interview with presenter Jim Al-Khalili. I am always impressed about how calm and rational he is, and not at all strident as his detractors proclaim in ignorance. This is a man who clearly loves nature - the magic of reality - and loves science - the "poetry of reality". Another great BBC podcast.

Thursday, 6 September 2012

ENCODE: highlighting the best and worst of science in the modern world

A massive ENCODE publication release was made yesterday, including 30 papers, an iPad App (downloaded and looking good) and a Virtual Machine full of data. I'm not going to give my opinions on the findings here because, frankly, there's too much to digest. Instead, I recommend reading Ed Yong's summary and the thoughts of Ewan Birney. [Image pinched from Ed Yong.]

ENCODE is an amazing example of what humanity can achieve it is puts time, effort and resources into a coordinated scientific endeavour - and also a reminder (should we need one) of how much more there is to learn about our genome. My mind is blown just thinking about reading all the papers and trying to make sense of them. (I wish I could clear my diary for a few days but deadlines loom!)

ENCODE is also a stark reminder of what it means to do science in the 21st Century world of bloggers, tweeter and general bitchers who just like to take quotes and soundbites out of context and then moan about them. The ability of some folk to digest 30 data-dense papers in a few hours (or minutes) and then have an informed opinion about them - and why they are wrong - is astounding.

So, my second recommendation is this: ignore the hype and all the nonsense flying around about what Ewan Birney meant by "functional" (he explains if you bother to read) and what this means for "junk" DNA. (Probably not much - I am sure it still exists, there just might be quite a lot more functional bits and long-range interactions than we thought - but let's let science and investigation answer that one.) Ignore all this and read the papers (if you're a scientist or committed lay person) or wait for the dust to settle for some reasoned, rational responses (if you are lacking the time/capacity/inclination to tackle 30 papers plus extras). Concentrate on the content and not the language. (I suspect a lot of it comes down to your definition of "junk" and "functional". I don't think I would choose the definitions that they have but, as the authors, it is their prerogative to define their terms and the serious reader's responsibility to make sense of the articles in that context.)

It's going to be years before we make sense of all this new data and work out how much of it is important. Years of wonderful, real science, not soundbites and speculations. As any ground-breaking study is likely to do, ENCODE has raised far more questions than answers - what (if anything) are all these DNA elements doing? Get excited by those questions and start thinking about how we can answer them. Keep your mind open to the possibilities and don't just shoot them down because they make you - or your future discourse with Creationists - uncomfortable.

So, could Ed and Ewan been more careful about the "80% functional" quote? Yes. Should they have been? I'm not so sure. Creationists are having a field day with it but so what? Whatever the finding, Creationists will try to twist it to their goals. That's one of their defining characteristics. If we change how we do or report science to pander to that particular bunch of deluded crackpots, we hand them victory. (Ewan explains his choice and, whether you agree or not, it was his choice to make. Our choice, is how we interpret the quote and whether we bother to find out what he actually meant before slagging it off.)

As a final footnote, I had the pleasure of meeting Ewan Birney once at a conference in Hinxton and the man is phenomenal. As with all great scientists, he is not going to be 100% right 100% of the time but ignore or scoff at him at your peril.

Tuesday, 4 September 2012

Putting Greenwich at the centre of the World

If, whilst watching the Equestrian events at Greenwich Park, you wonder how Greenwich got to be home to the Prime Meridian Line - and thereby determine both world time and world longitude - you could do much worse than Episode 91 of A History of the World in 100 Objects, which features the ship's chronometer from HMS Beagle.

It represents technological advancement that didn't get a mention in the opening ceremonies but was arguably much more important than putting men on the moon (as Steve Jones did argue) or robots on Mars. (As undeniably cool as those things are!)

I've been slowly working my way through the episodes of this great series over the past few months - there are a lot of them! - and was particularly pleased to listen to this one yesterday as Darwin and Deep Time both get a mention. (I'd just been updating the MapTime Organic Evolution TimeLine and Keywords.)

So, if you are in London and looking to kill some time between events, download the podcast (or read the transcript) and then visit the British Museum!

Monday, 3 September 2012

Olympic Highlights VI: Lighting the Cauldron

I'm ashamed to say that I was still stuck in cynicism when the Olympic torch was going round the country, so I didn't really pay it much attention. Looking back, I am not really sure why this was. I suspect that it was a combination of not really enjoying the last two Olympics that much and the standard negative press coverage of everything that went wrong in the build-up without really stressing all the good bits. (I wish the media would cheer up sometimes!)

Despite this, we probably would have gone and seen it come through Southampton had it not been raining so hard at the time that we decided to give it a miss. (Although fantastic in the Paralympic Opening Ceremony, watching a collection of umbrellas is not so fun in real life.) Instead, my only real exposure was the torch relay bunting. (After the Royal Wedding, Jubilee and Torch Relay, I am now thinking that we should always have some form of bunting up. It's so cheery!)

By the time David Beckham arrived at the Olympic park with the flame and passed it on to Olympic legend, Sir Steve Redgrave, however, I was well and truly on board. Literally passing the torch to nominated youths as part of the "Inspire a Generation" theme was a really nice touch, I thought.

I enjoyed most of the Opening Ceremony but, for me, the real star of the whole show was the Cauldron. Indeed, as the memory of the event fades, this sense just increases. Like many, I had been slightly confused by the copper "petals" the different countries had been bringing in but when it all became clear and each one was lit, it began to make sense. There was still a slight hesitation in my house - there should be a single flame but then as the individual arms raised and the cauldron assembled, it was a thing of really beauty. (And pretty impressive engineering!)

In general, I enjoyed the Paralympic Opening Ceremony more and the cauldron was just as beautiful the second time. This time it was more like a favourite song that a band saves for the end of the show. We all knew it was coming but wondered when and how it would be delivered. The arrival of the torch into the stadium was perhaps more impressive than the Olympic ceremony - a Royal Marine flying in by zip wire from the tower next to the stadium. Having Britain's first paralympic gold medal winner light the cauldron was very different from the Olympic ceremony but equally special in its own way. As with much of the ceremony, I was impressed.

Both Opening ceremonies had elements celebrating British contributions to science and technology and I think that the Olympic cauldron captured that element perfectly. Well done to Thomas Heatherwick and all involved with making "Betty"!