Friday, 30 December 2011

The Oar House revisited: still fantastic

One of the good things about having relatives in Dublin is that I get to go back from time to time for visits. As my in-laws live there, this includes Christmas - approx. every other Christmas, as it happens. (Not through planning, as such, but it just seems to work out this way.)

Christmas away from home seems to feature even more tasty food and drink than Christmas at home. This year, we rounded things off with a lunchtime visit to The Oar House in Howth on the way to the airport. I've posted about The Oar House before, four years ago. It was one of my favourites then and it still is.

The only problem with The Oar House is choosing what to have, as everything is so good! Fortunately, they have a solution for this too: a delicious and versatile tapas menu that can be ordered as a starter, scaled up for a main course or, as we did, shared among a few of us.

In addition to the must-haves - smokies and prawns of some variety (we had Prawns Pil Pil) - we had the calamari and a trio of dishes from the specials menu. Two of these had a decidedly Mexican theme - grilled prawn nachos and salmon tostadas. Tasty! The third was something that I would not normally order but was very glad that we did: crab claws. These were the biggest and most delicious crab claws that I have ever tasted, in yummy garlicky goodness. Amazing stuff.

Perhaps most exciting of all, whilst visiting The Oar House website for images, I discovered that they have a recipes section. Yummy! Watch this space for more on that. (When I feel brave enough to cook fish.)

Sunday, 25 December 2011

Santa's reached Germany!

Thanks to Google and NORAD teaming up, I have been tracking Santa's progress this year. He's reached Germany now, so time for bed soon, I think!

Update...



Of course, the actual NORAD Santa Tracker website was even better. You can even watch videos of Santa visiting various major cities and landmarks. Good to see some of the US defence budget being spent on stuff for the good of mankind.

Thursday, 22 December 2011

Beyond Busted: Charlie Simpson and the fantastic Fightstar

My most recent big musical discovery is that of Fightstar Fightstar, a British rock band whose most famous member is probably Charlie Simpson, formerly of Busted.

I must confess that I don't really know a lot about Busted. My one real experience of them is hearing them sound-check, or possibly rehearse, Year 3000 prior to a gig in Dublin. What I heard was not pretty but this may have been more to do with me being outside the stadium (Lansdowne Road, as it was then,) and/or the fact that they hadn't got their sound set up than a reflection on their talent. Either way, the sound-bite combined with my natural distrust of teen "Pop punk", meant that I have avoided them ever since. This makes the discovery of the sublime Fightstar all the more surprising, as the lead member is none other than Charlie Simpson, formerly of Busted.

I can't really compare Fightstar to Busted but I suspect that the sound is very different, as Fightstar kick out proper rock tunes with heavy guitar and the occasional screeching rock scream, in addition to the more melodic singing that dominates. I find it hard to pigeon-hole bands into genres and so I am not really sure to what sub-category of rock Fightstar belong. (Wikipedia editors have opted for "alternative" or "Post-hardcore", whatever that means.) I would probably just say "Rock" or "Modern Rock", for this is no Bon Jovi either.

It was probably a short customer review on EMusic that made me take the step of having a listen. To paraphrase, it said something along the lines of:
if you like Rock music, you will like this.
I would have to agree 100%. I think that wherever you sit on the rock spectrum, Fightstar offer something. If, like me, you sit somewhere in the middle and enjoy music and influences in all directions from Pop/Rock to Metal, you will love them. The two albums that I have are the later One Day Son, This Will All Be Yours (2007) and Be Human (2009) and, if recommending just one, I would be hard-pushed to choose. (Probably "One Day Son, This Will All Be Yours", especially as you pick up a two-disc version for a bargain on Play.com!) They're both currently available from Emusic, if you want a bargain.

The other factor that made me try them, quite surprisingly, was listening to Young Pilgrim, the more recent solo album of Charlie Simpson. This is a very different beast, and is proper singer-songwriter acoustic pop rock along the lines of Jack Johnson. It's good stuff, though, and definitely marks Charlie Simpson out as an accomplished musician and singer. For me, this was important, as I find that I cannot look beyond bad singing, however good the music is. (The Wildhearts are the possible exception but their singing is not too bad and their tunes are very good!)

Monday, 19 December 2011

When snowmen go bad (Christmas graffiti)

Our walk to work takes us through Southampton Common, which features a pedestrian underpass that is a popular spot for the local graffiti artists - and many of these guys are artists, not just vandals who want to tag their turf. The fruits of their labours are not always to my taste but this one, snapped a couple of weeks ago but happily not yet sprayed over, is one of my favourites.

Sunday, 18 December 2011

The Cabbages of Doom: Kindle Edition out now!

My fictional folly is complete (for now) and The Cabbages of Doom is now available in a Kindle Edition too.

I thought it was going to be priced at £1.49 for the UK market but there seems to have been a glitch somewhere. I did find it a bit odd that the cheapest UK price allowed was lower than the USD or EUR prices. Oh well. If the extra 22p puts you off, the PDF and ePub versions are still only £1.44.

Over Christmas, I shall hopefully blog the full e-publishing experience. It's been interesting and I am sure I could do it better next time! (Content aside, that is.)

BBC Planet Earth/Blue Planet - Deep ocean creatures

Thanks go to the Why Evolution is True website for highlighting this video. Amazing footage of some weird and wonderful critters. (Planet Earth and Blue Planet are separate series, for those (like Michael at WEIT) wondering.)

The Cabbages of Doom, PDF version and free sample now available!

I am happy to report that a PDF edition of The Cabbages of Doom is now available along with a free sample chapter (PDF). Try before you (maybe) buy!

Thursday, 15 December 2011

Polar bear dimwits should cut Attenborough (& BBC) some slack

Yesterday, I read something in the "i" that made me angry. For anyone who has missed it, presumably by misfortune of not having access to BBC, Frozen Planet is an amazing series, with spectacular footage and Sir David Attenborough at his narrative best. But, it seems, not everything on the show was quite as it appeared. Some of the polar bear footage of mother and newborn cubs was shot in a zoo.

No, this is not what made me angry. It seems that, for some strange reason, this revelation - revealed by the BBC themselves on their website - has cause furores in some circles, with cries of deceit. The Arts Editor of "i", David Lister, sticks in his own oar, saying: "An explanation on the website is simple trickery. The explanation for a television programme must be made within that television programme." The only insight provided here is that David Lister is a man with a very poor sense of perspective. Apparently, "i" stands for "idiocy" or "ignorance".

The show features a "Freeze Frame" section at the end, where they show some of the behind-the-scenes action getting the footage. For anyone paying any attention, it is blindingly obvious that the footage of animals is sometimes used out of context to aid the narrative. It would not be anywhere near as interesting otherwise. But this is not deceit, or "simple trickery", it's just good film-making. Don't tell David Lister, but some of the action used time-lapse photography - the sun didn't really speed up and circle the Earth in a few seconds.

Seriously, folks! Anyone who takes umbrage at this and thinks it should have been somehow made obvious in the program has missed the point of nature documentaries big time and doesn't deserve the genius of Attenborough and the BBC wildlife units. Ridiculous.

PS. More great polar bear stuff from the BBC here.

Sunday, 11 December 2011

The Cabbages of Doom has an ISBN!

The blogging has been light of late to due excessive busyness. One of the contributing factors to this has been the e-publication of The Cabbages of Doom through Lulu. I think the book itself will take a bit of time to filter through the system but it has an ISBN number now and everything!
I've also worked on a bit of cover art for the new edition. It's not a masterpiece but is certainly better than the previous, blank cover.
The story itself is essentially unchanged, but I have modified the text here and there, both to correct a few typos and remove a few bits that might not go down so well with a more general audience. (Or made me cringe at my ten-years-younger self!) There was also some reformatting for e-Readers to be done. Overall, though, I am happy.

It will be on sale for the princely sum of £1.44, which works out at 16p a chapter (or about 3p per 1000 words). Should you buy it and hate it, let me know and I will donate the portion that goes to me to a charity of your choice. If, on the other hand, you think it's a bargain, please make a donation to Cancer Research UK or the World Wildlife Fund. (I'm not endorsed by either, in case it's not obvious!)

Monday, 5 December 2011

Playmobil goes recursive

During a spot of Christmas* shopping, I came across this gem from Playmobil - it's a Playmobil Playmobil delivery truck! My only regret is that the lorry does not come with little boxes of Playmobil Playmobil delivery trucks itself: that would be truly recursive! (A bit of a missed opportunity in my book!)

[*On my iPhone, my big thumbs typed "Christmad" at first. Seems somehow appropriate when town reaches peak busyness!]

Sunday, 4 December 2011

Carcassonne: still the best board game in the world

Today, we cracked out Carcassonne for the first time this festive season.

For anyone not familiar with Carcassonne, it's a tile-laying strategy game in which you build up roads and cities and score points for having more of your men (or "meeple") associated with them when they are completed. In my opinion, it has the perfect balance of strategy and luck. The tiles are drawn at random, and so a lot can hinge on getting the right one at the right time. At the same time, however, there are clearly strategic moves to be made. Playing with more then two players can even lead to some interesting cooperative behaviour - and occasional back-stabbing - as temporary alliances form over shared goals. You can obviously sabotage other people's strategies too (a favourite move of mine is to hijack other people's cities) but I don't leave a game of Carcassonne feeling as picked on as after a game of "Settler's of Catan". I also think that the length of the game is just right. "Puerto Rico" is another great game by the the same people (I think) but I always end a game feeling like it was over one or two turns too soon.

Today, we had a bit of a rare occurrence: a finished game without any holes in the middle! When you lay tiles, roads have to match road, cities match cities and fields match fields, so clearly if you get a hole where a specific tile needs to go, you will not always come across it. Normally we play with "The River" expansion, whereas today we just used the basic starting tile, so that might have contributed to the tightness of the layout. Anyway, the end result was quite pleasing, if such things please you. (They please me!)

I'm obviously not going to go through the rules here. (See the Carcassonne Wikipedia entry for a summary. In reading this entry, I just learnt that they have changed the rules for farmers and fields, plus there's now an iOS Carcassonne App, which I will have to check out!) Suffice it to say that if you like board games - or someone you know does - and you are short of Christmas present ideas, you can do a lot worse than getting a copy of Carcassone.

If you already have Carcassonne, I can recommend a couple of the expansions, which are particularly good: Inns and Cathedrals and Traders and Builders.

HTML ASCII code

For those of you, like me, who have to write posts in HTML from time to time, a good reference of HTML coded for special ASCII characters is invaluable. The best I have found so far, is on the website of Ed Lazor (www.edlazorvfx.com). No frills, no fuss, just lots of useful HTML codes. (Although he did neglect the interrobang, "‽" - ‽.)

Hoorah for NAR!

I have a bit of a soft-spot for Nucleic Acids Research. This is partly because one of my colleagues is one of the Senior Executive Editors, and the Editorial Manager is at the desk next to mine. It is also partly because they have been kind enough to publish five of my papers, which is more than any other journal. This week, however, it is mainly because I have just received my "thank you for reviewing" present of The Oxford Book of Modern Science Writing from Oxford University Press, an anthology of extracts from other scientists that Richard Dawkins has chosen, along with a brief introductory spiel to each one by the man himself.

Reviewing for journals is typically a bit of a thankless task and so I really like that NAR reward their reviewers with a small gift voucher for their parent publisher. It's the little things in life that often make the difference, so well done NAR!

As for the book itself... I have only read one extract so far and I enjoyed it. I'll review the book properly once I have read a bit more. Given that, until 2008, Dawkins held the Simonyi Professorship for the Public Understanding of Science at Oxford, I expect that I am in for a treat.

Thursday, 1 December 2011

Festive feline folly

It's almost December, so it's time to get the Christmas decorations ready. Arthur has kicked things off for us this year. (Not by choice, obviously!)

In the background, you can just see Mia lurking. She really wasn't sure what to make of Arthur's new attire. I'm not sure if it was the look or all the jingly bells. (Later, thanks to my wife's persistence in these matters, she got to try it out for herself.)

Monday, 28 November 2011

iPlan: geeky gadget fun with energy efficiency

Some time ago, I signed up to the "iPlan" scheme of Southern Electric. It was not the cheapest tariff available but the idea is that you can monitor - and therefore reduce - your energy usage, and this appealed to me on several levels. Unfortunately, my iPlan energy monitor never turned up, so I emailed them a week or so ago and they sent out a new one, which arrived on Friday. Yesterday, I cracked it open and had a play.

The device itself is an "Onzo smart energy kit" and consists of two parts: a sensor that clamps on to a cable, and a wireless receiver for monitoring usage.


As the instructions implied, it's was dead easy to set up and start monitoring power usage.

Of course, setting everything up when the washing machine and dishwasher are on and consuming nearly 2,500W is probably not the most reassuring way to start energy monitoring!

It needs to collect data for a week or so before the proper assessment kicks in but it's still interesting to see what effect turning stuff on or off makes. The kettle, for example, wacks a couple of kilowatts onto the reading (not surprisingly), though not for too long. The wireless monitor is great and can be stuck in any room, making such things easy - you can pop it next to the device about to be switched on and watch what happens. I love it!

Our baseline at the moment seems to be around 15-40 watts, although there is a lot of fluctuation. I look forward to testing out a few urban myths over the current weeks, such as the old question of how much power does a TV use on standby versus on? I've already had a bit of a shock about the kitchen lights, so I think this could work as an energy saving device - I'm off now to switch off some lights!

Great and Small, Climb and Hide

Today, we got the cat's a present of a new scratching post, as the old one was looking a bit ropey. We got them a "climb and hide" post from Great and Small, as it looked fun and they're worth it. I think Arthur likes it! As I was write this, he is now sitting on top and Mia has gone inside instead - as a black cat in a dark hole, however, she's not quite so photogenic.

My favourite thing about this photo, though, is that it looks like Arthur has climbed into some kind of strange suit in the style of Wallace and Gromit's "Wrong Trousers"!

Saturday, 26 November 2011

It's a chunky mug day!

There are very few things in life that are as consistently pleasing and comforting as a good cup of tea. As the seasons change, the nights begin drawing in and the mornings start feeling more chill, it is time to break out the big guns for tea delivery. One of my favourite mugs is this one, which was a souvenir from skiing in Breckenridge.


Somehow, it feels too chunky during the summer months but now that it's getting darker and colder, the chunkiness is somehow extra comforting. Unfortunately, I cannot read the name on the bottom to give due credit to its maker, but here it is, in case your deciphering skills are better than mine!

Friday, 25 November 2011

Another Marlborough classic

Being a wine-drinker of limited knowledge, I have a fairly crude but effective way of sourcing new wines. When I am in the supermarket, I keep an eye out for half-price bottles of a variety I like (usally Rioja, New World Sauvignon Blanc, or some kind of Shiraz/Merlot/Cabernet Sauvignon affair) that usually costs around £10. Experience has told me that this price range seems to match the (lack of) sophistication of my palate plus the lack of extravagance of my wallet. (I'm prepared to risk a fiver on untested wine but not much more!)

Occasionally, this tactic goes a bit wrong and I bring home something rather bland, or too sweet, destined for a risotto or casserole dish of some kind. Sometimes, though, it reaps welcome rewards. One of the latter is the Sauvignon Blanc from Glenridge Point. This is a crisp, zesty and fruity wine with all the new world features that I love from New Zealand Sauvignons. I will happily add it to my exisiting go-to Sauvignon Blanc from Marlborough: Oyster Bay and Villa Maria. If you are a fan of such things... head to Sainsburys whilst it's still on offer!

Wednesday, 23 November 2011

TimeTreeHD: an App 2.5 billion years in the making

I feel that one of of my weaknesses is a poor memory for facts and figures. Although I tend to learn principles and concepts pretty well, I can easily start to doubt arbitrary pieces of information. This is particularly true when the information itself is subject to change; am I thinking of the new number, or the old one?

One such situation is the age of divergence of different species. As a lecturer of evolutionary biology, this can be a bit embarrassing and awkward. Fortunately, this is not something that I need to worry about (too much) any more, thanks to the TimeTreeHD App for my iPad. Want to know when a cat and a squirrel last shared a common ancestor? (And who wouldn't?!) Simple!



It's 95.2 million years ago (Mya), plus or minus. Probably plus - the "expert opinion" is 97.4Mya. At first, it gives you the mean estimate but down the timeline on the left all the different estimates are marked. The estimates themselves come from all pairwise estimates (in the TimeTree database) featuring species from each side of the tree; cat versus squirrel, for example, includes cow (closer to cat) and mouse (closer to squirrel). Tapping for details allows you to drill down further into different age estimates and see the source publications. Sorted! Well done, TimeTree.Org! (NB. The website might be even better!)

Tuesday, 22 November 2011

Where do new proteins come from?

As part of my second year lectures on protein evolution, I cover (albeit far too briefly) the topic of where new proteins come from. The most common answer to this question, is "other proteins". Gene duplication is common and happens at a variety of levels, from individual domains (independent folding units of proteins) to full length proteins, multiple proteins (on larger chromosomal stretches) to whole genome duplication, in which every single gene is duplicated.

Duplication is so important because it generates a copy that can remain essentially unchanged, performing the ancestral function, and a copy that is free to accumulate mutations. Often - usually - these mutations will ultimately disable one of the copies, generating what are known as "pseudogenes", the easily identified relics of past mutational dead ends. Occasionally, however, a new function will arise, such as the binding of a new enzyme substrate, the the reception of a different wavelength of light, and both copies will be retained. 

This is fascinating stuff in itself (and I may post more on it later) but it is not what I want to talk about here. Important as they are, duplications rely on something - an existing protein-coding gene - being there to be duplicated. Where do these proteins come from in the first place? Are all modern proteins just duplicated and edited versions of a suite of ancestral proteins? Does this mean that supporters of Intelligent Design community are right and that some kind of intelligent intervention is necessary to increase the repertoire of proteins that are available?

Well, no. Far from being a statistical improbable event unlikely to ever occur, the "de novo" creation of new proteins from non-coding DNA seems to be a reasonably common event. In an article just published in PLoS Genetics, for example, "De Novo Origin of Human Protein-Coding Genes" (PLoS Genet 7(11): e1002379), Wu, Irwin & Zhang describe sixty such proteins that appear to have arisen in the human lineage since we shared a common ancestor with chimps. 

This and other work in the area is nicely summarised in the same issue by Guerzoni & McLysaght in a two page article that is well worth the read, "De Novo Origins of Human Genes" (PLoS Genet 7(11): e1002381). The Wu paper itself builds on earlier work from the McLysaght lab, and they include a nice summary of the type of evidence the work looks for (see the paper for details):



It is important to bear in mind that not all of the sixty novel protein-coding genes might be "true positive" results in the strictest sense. As Guerzoni & McLysaght point out:
"The operational definition of a de novo gene used by Wu et al. means that there may be an ORF (and thus potentially a protein-coding gene) in the chimpanzee genome that is up to 80% of the length of the human gene (for about a third of the genes the chimpanzee ORF is at least 50% of the length of the human gene). This is a more lenient criterion than employed by other studies, and this may partly explain the comparatively high number of de novo genes identified. Some of these cases may be human-specific extensions of pre-existing genes, rather than entirely de novo genes—an interesting, but distinct, phenomenon."
Nevertheless, this is still the creation of de novo protein sequence, just not whole genes. Indeed, if one were to relax the criteria, how much more might this happen within proteins? Domains are frequently linked by disordered regions and also have a tendency to be flanked by intron/exon boundaries, making it quite plausible for extra exons to be picked up along their evolutionary journey. In some ways, therefore, this sixty is likely to be an underestimate. 

There are other issues with identification process itself that make real estimates difficult. For robustness, authors limit themselves to stretches of DNA that are present in both humans and chimps, to rule out the loss of an ancestral protein, rather than the gain of a human-specific one. Insertions and deletions ("indels") are quite common and actually account for most of the difference (in absolute genetic terms) between humans and chimps:
"It is now common knowledge human and chimpanzee DNA differ by only 1% (more accurately, they differ in 1%of alignable regions of genome, with a further 3% divergence due to lineage- specific indels)."
It is quite possible, therefore, that a few extra protein sequences have arisen in non-coding human-lineage DNA that was deleted in the chimp lineage. The other limiting factor - and probably one that has a greater impact - is that of protein annotation. Discovery relies on proteins that are annotated as such in the human genome. The problem here is that such annotations are normally made using conservation of proteins from other organisms - something that is, by definition, lacking for lineage-specific proteins. This issue is not insurmountable and there are sources of evidence that are used but it is still likely to result in underestimation.

An important caveat remains, however. Although we have some examples of de novo proteins that appear to have function, for the majority of them we have no idea what they do, if indeed they do anything at all. A more interesting question opens up of when do you define translated DNA as a protein? Leaky transcription and translation almost certainly happens (although I have no idea how much) and so we might be detecting stuff that is really there but only rarely. Alternatively, it might be consistently transcribed and translated but have no function whatsoever - a neutral mutation that has drifted randomly to high frequency but may have no long-term future.

These questions and issues are unlikely to be resolved soon. For now, we just know that de novo creation of proteins is more common than we used to think and is likely to be a substantial source of raw material on which natural selection (and random drift) can act to evolve new functions. What the ultimate fate of these proteins tends to be, only time will tell.

Sunday, 20 November 2011

It's a Small World (with Nikon)

Whilst doing some email house-keeping today, I came across a link I sent to myself over a month ago for an In Focus article (Nikon Small World 2011) about Nikon's Small World Photomicrography Competition. This has some amazing images and is well worth a look.

The reason I think I emailed this link to my work account was probably this photo of a giant waterflea (Leptodora kindtii), which is one of my favourites (kudos, Wim van Egmond!):



I have to lecture on Eyes and Vision next semester, and therefore keep my own eyes out for good looking eye images. I am now wondering whether this particular specimen was the inspiration for London 2012
Olympic mascots, Wenlock and Mandeville.

For those interested in such things, Leptodora kindtii looks something like this and actually eats (among other things) the juveniles of the more familiar water flea, Daphnia:



(Picture from http://zoology.fns.uniba.sk/poznavacka/crustacea.htm)

The Relativity of Wrong

Isaac Asimov was a polymath and prolific writer. As well as writing and editing over 500 books, he contributed numerous letters and articles to magazines. Although I must admit that I cannot recommend his joke books(!), I can recommend the piece he wrote for The Skeptical Inquirer called The Relativity of Wrong.

Here's a taster:
The young specialist in English Lit, having quoted me, went on to lecture me severely on the fact that in every century people have thought they understood the universe at last, and in every century they were proved to be wrong. It follows that the one thing we can say about our modern "knowledge" is that it is wrong. The young man then quoted with approval what Socrates had said on learning that the Delphic oracle had proclaimed him the wisest man in Greece. "If I am the wisest man," said Socrates, "it is because I alone know that I know nothing." the implication was that I was very foolish because I was under the impression I knew a great deal.

My answer to him was, "John, when people thought the earth was flat, they were wrong. When people thought the earth was spherical, they were wrong. But if you think that thinking the earth is spherical is just as wrong as thinking the earth is flat, then your view is wronger than both of them put together."
Although written in 1989, this is still a great piece and worthy of a read now and again, especially if challenged about trusting current scientific explanations because they are "all wrong". Take evolution, for example. Whilst the details of evolutionary theory - a body of work, not a single theory - are subject to change, we can be as certain as we are of anything that the essence will not. Although conceptually evolution can be disproven by new evidence, the likelihood of such evidence is vanishingly small and diminishes further all the time. We may not have all the details but we can be confident that evolution is not "wrong".

Saturday, 19 November 2011

Resident Evil Afterlife versus The Walking Dead: Special Effects can't buy style...

...and bad acting alone does not make a villain.

Last night, I sat down to a bit of a zombie marathon, to catch up on a bit of missed TV that isn't quite to the taste of my wife, who is away for the weekend. To be fair, I can't say I blame her, especially where some of the films are concerned.

First up, though, was a couple of episodes of The Walking Dead, series 2. I've never been a fan of the supercharged high speed zombie but the "walkers" are good old school lurchers and shufflers. The more complete specimens can run a bit but nothing superhuman. Well, nothing more superhuman than being walking dead, of course. Furthermore, the non-superhumanity extends to the walking living too. OK, so the police guys and crossbow dude are a little more accurate with their weapons than I suspect is realistic (and their survival begs the question as to why more army marksmen didn't make it) but these are well within the "suspend disbelief" range.

Because the characters are believable, you care about them. Their struggles may be quite small (each episode) but that makes them more real. When a horde (or herd?) of zombies appears, they don't whip out pairs of firearms and fire of multiple head-shots whilst flying through the air or running up walls; they hide, or run away. Because you care about the characters, there is real suspense and after a couple of episodes I felt the need for some light relief, hence my next choice...

This was the latest offering from the Resident Evil series to make it onto the small screen, Resident Evil: Afterlife. Let's compare and contrast this with the Walking Dead, for a moment. The two are loosely based on the same general premise: nasty virus turns the world's population into zombies while a group of survivors try to continue being survivors. The Resident Evil zombies are also mostly lurchers. Mostly. This is where the similarity ends, though.

Whereas Walking Dead is all about placing characters in a series of plausible scenarios (given the implausible backdrop), Resident Evil is all about placing them in increasing ridiculous and hopeless scenarios and watching them leap, somersault and spray their way out with automatic firearms. And with the death of suspension of disbelief comes a death of any tension or caring about the lead characters who, even when supposedly stripped of their superhuman powers, all exhibit superhuman powers and are bound to escape essentially unscathed. Actually, I'm being a bit unfair in what I just wrote. Sometimes they use semi-automatic or even pump-action firearms. (Plus, of course, explosives and shiny, pointy things.)

This is particularly sad, in a way, because the computer games upon which the films were based were themselves all about tension, suspense and the feeling of panicked desperation when a zombie horde was approaching. (That and incredibly frustrating controls - a double irony is the one thing you often couldn't do in the games was move and shoot at the same time!)

Perhaps I am getting old but I am sure that action movies used to at least pretend to have a story worth taking an interest in, or heroes worth caring about. If you had to make someone superhuman, you at least created an excuse, such as making him a cyborg from the future, or a "chosen one" that was able to bend the fabric of the Matrix to his will. (Maybe a bad choice as even The Matrix went The Way of The Special Effect with parts II and III.) Now it's all about ever more ridiculous and extravagant uses of "bullet time", all the time trying to ignore the stupidity of a hero that is able to nail a foot soldier right between the eyes whilst in free fall down a lift shaft but somehow manages to lose all accuracy as soon as the main bad guy becomes the target. 

Then there's the bad guys themselves. In certain circumstances, the deadpan emotionless bad guy works really well. Again, think of The Terminator or Agent Smith. Most of the time, however, and certainly the case for RE Afterlife, an emotionless villain just makes a one-dimensional and dull villain. It comes across more as bad acting than bad attitude - more Arnie in Conan than Arnie in The Terminator. 

Perhaps the strangest thing of all is that all these effects don't really impress any more. The Matrix, Inception and others have used all these tricks to great effect in the name of the plot. Employing them for the sake of it is not impressive, it's just lazy. Possibly worse, it actually reduces the impressiveness of the stunts. I could forgive the dodgy dialogue and bad acting in a Jackie Chan movie just to see what Jackie Chan was going to do in the next fight and think "wow"! Can anyone honestly say that, when witnessing a random hero/villain dodging a bullet in slow motion while the camera pans round, they think "wow" rather than "Matrix rip-off"? It is certainly not enough to make up for a lack of coherent story or adequate plot/character development - except (sadly) on opening night at the Box Office, perhaps. It most certainly not enough to get me rushing out to watch Resident Evil Retribution when it comes out. 

On the other hand, I am looking forward to catching up with a few more episodes of the Walking Dead over the weekend.

Friday, 18 November 2011

Expelled: No Intelligence Allowed - No Integrity either.

Some time ago, I saw (and blogged) the terrible, terrible film "Expelled: No Intelligence Allowed". At the time, I thought its main failing was simply that it was vacuous crap, with all the intellectual content of the Jeremy Kyle show. The coverage of Intelligent Design - supposedly the focus of the "film" - was woeful and uninformative, for example. Instead, the filmmaker, Ben Stein, decided to spend a lot of time attacking evolutionary theory, and atheistic Darwinism in particular, as naturally leading to such atrocities as Nazi Germany and the holocaust. (A classic Godwin's Law violation, if only he had restricted such crap to an Internet forum.)

Whilst in many ways it really makes no difference whether Hitler was an atheist or not, or subscribed to "social Darwinism" - any idea can be corrupted and abused, after all - the fact is that there is no good evidence to support Stein's position. Worse, if one actually researched the source material - as presumably a reputable and honest journalist surely would? - one would actually find a great deal to support the opposite view.

In a great piece, "Nazi racial ideology was religious, creationist and opposed to Darwinism", Coel Hillier at coelsblog dispels this particular myth in no uncertain terms by doing exactly that and going to the source. With quotes from original sources throughout, the author neatly knocks down the lies that Hitler was an atheist or a Darwinist and, instead, reveals him as a(n albeit twisted) Creationist and Christian.

Does this in itself mean that Christianity or Creationism are bad? Of course not - no more than arguments about Hitler being an atheist or Darwinist would make atheism or Darwinism inherently bad if they were true. Let's face it, it was obviously plausible enough for people to believe it. Nevertheless, this is one myth I would love to see the back of. It would certainly be good to remove this particular attack strategy from the playbook of certain atheist-haters and anti-evolution lie-mongers; even if you don't understand the science well enough to appreciate the lies they tell on that front, this is a clear-cut integrity failure for all to see. (I think Godwin's Law is still safe, though!)

Friday, 11 November 2011

My best status updates of 2011 (so far!)

I'm a bit scared of Facebook Apps in general because I don't really trust them to behave but this one seemed worth the risk: My Top Status In 2010(!) I think it did a pretty good job of highlighting my 2011 (so far!) too. (Good to see a few silly ones made it to the Top 10 too.)


Tuesday, 8 November 2011

Mount Difficulty, Roaring Meg 2009 Pinot Noir

A couple of years ago at the University Wine Club barbecue, we had a delicious red wine from Mount Difficulty, called Roaring Meg.

They say:
This wine exhibits a lovely mix of dark red cherry and black berry fruits along with a hint of licorice. Further complexity is gained from oak spice. The wine has a sweet berry entry which displays these same characters in abundance. Lovely ripe textural tannins rise gracefully out of the mid-palate to finish the wine. These are balanced by the wine’s acidity and fruit, to produce a long fruit-driven finish.
A while ago, we invested in a couple of bottles for special occasions. Fortunately, investing in a couple of nice bottles of wine constituted a special occasion! We cracked one of the bottles open and I am happy to report that it was every bit as delicious as we remembered! Now, I'm just looking for an excuse to declare another special occasion.

Are science and religion compatible?

There's been a bunch of stuff flying around the net recently following the "debate" between John Haught (Catholic theologian) and Jerry Coyne (Evolutionary biologist & atheist). I am yet to watch the video, although I intend to, but I thought I would add my twopenneth to the discussion. (It will be interesting to see if I feel the same way after watching the video.)

My initial thought was that I felt a little uncomfortable with this topic as a debate - although upon further reading it seems that it wasn't really meant to be a "debate" in the usual sense. Nevertheless, there was a "for" (Haught) and "against" (Coyne) position. This implies that the answer is "yes" (they are compatible) or "no" (they are not). This, I feel, is a mistake. The answer depends on another question: which religion?

From what I have read, Haught seems to pull out some fairly standard arguments about "different types of explanation" (how versus why). This only holds if there really are different levels of explanation for the phenomena  being discussed, although this weakness in the argument can be ignored when one is only interested in compatibility. Even assuming that there are different levels of explanation for the Universe (there may be no "why"), however, this only allows compatibility if the religious position stays in its different realm and does not encroach into that of science - the what and how. (Actually, I think science can sometimes also answer the "why?" questions but probably not all of the "why?" questions that religions and philosophy attempt to address.) In other words, this holds true all the time that religion is not interventionist - if god leaves no trace.

Science and religion are compatible in the sense that one can conceptualise a scenario in which a deity exists and science does not know/care. I believe it's called Deism. (One can conceptualise them, yes, but conceptualisation does not make them true.) One can also conceptualise a different scenario in which god is regularly intervening, performing miracles, healing the sick etc. This type of god would leave traces that are in the realm of science to detect - traces that we simply do not see. (As an extreme case, think Young Earth Creationism.) These religions are not compatible with science, without a lot of intellectual gymnastics that raise serious questions (for me) about the nature of such a god.

The important thing is that not ALL religion is compatible with science and, for me at the least, the religions that ARE compatible are largely pointless and/or irrelevant. I'm yet to watch the video (although I will) but it sounds like Haught knows this and is playing the game of talking about a deist-like non-interventionist god, while at the same time trying to imply that is is also true for other religious positions, such as Catholicism. (I don't mean to pick on Catholicism, it's just the one that Haught is associated with.) From what I have read, he gets caught on this in the Q&A and has to reject Catholicism (in essence, if not explcitily) to maintain his position. 

It is right to attack his defence of universal compatibility and force him to explicitly recognise that not all religions - including most of the major ones - are compatible with science. On the other hand, I think the atheists need to be careful too. In "The God Delusion", Dawkins defines "God" (and hence religion) in a very particular way - Deist gods are excluded. (Who cares, or can say anything, about a god that does nothing?) This is useful for such a book and enables reference simply to "god" or "religion" but when targeting the wider population with the notion that "religion and science are incompatible", one has to remember that this is only true for some (albeit probably most) religion. Otherwise, one paints oneself into an uncomfortable corner where on has to start attacking legitimate (if, arguably, pointless) positions to maintain an over-zealous statement. (As I say, I have not seen the video yet, so I am not suggesting Coyne does this. I have seen it happen on discussion boards etc. though.)

So, are science and religion compatible? I think they can be but, personally, I would seriously question the value of the religion that was. If other people choose to believe such things then that, of course, is their decision. And here lies another area where I think atheists need to be careful. A lot of religious folks just don't care whether their religion is compatible with science. They don't care if their religion is apparently logically inconsistent. It's all part of the great "mystery" and not meant to be understood. This is not a position that I myself could maintain but they are not me. Furthermore, as long as they are not trying to structure society, impose moral values, or educate children based on these beliefs, I don't care what they want to believe. 

Monday, 7 November 2011

Delete cookies?!

Sometimes an act of simple genius comes along that just needs to be shared! Well done, Fernandez, whoever you are!

Sunday, 6 November 2011

Heron's Nest Cabernet Sauvignon Pinotage

I may not know how to write about wine but I know what I like and I like Heron's Nest Cab Sav Pinotage (2009). If you are in Ireland and like your red wine, I thoroughly recommend popping down to your local Dunnes and getting one or two of these boys.

Saturday, 5 November 2011

iAnnotate: what the iPad was made for

iAnnotate is probably the best App on the iPad, and certainly the best that I have paid for. If you ever need to read PDFs for anything other than pure interest (and even then, to be honest,) iAnnotate is the App for you.

It's great for organising your PDF library but it's the annotation tools that really make it. Notes are easy to add and the highlighter tool is great for flagging bits of interest - or pulling out quotes. You can even draw free-form, if you like. Once you're done, you can email the annotated PDF for printing etc. or just send the notes and, conveniently, the highlighted text. As an academic, this is the perfect tool for reviewing papers.

On top of all this, iAnnotate is probably the least buggy App that I have used. I'm not sure if it has ever crashed on me and it certainly hasn't lost anything I've done if it has. I initially baulked at the price but this App is worth every penny and I look forward to many happy years of iAnnotating my PDFs to come. Top stuff!



Thursday, 3 November 2011

My atheism in a nutshell: no evidence, need or desire for a deity

In a response to a comment on another post, I stated that I was a atheist because I had neither evidence nor need nor desire for a deity, in that order. Here, I thought I would expand briefly on this statement.

Evidence first, for this is what came first for me. It is also the simplest to express. Quite simply, everything I have ever experienced makes more sense to me in the absence (versus presence) of a deity. Furthermore, everything I know of the world - including religion itself - makes more sense to me in the absence of a deity. Personally, I don't rate "personal revelation" as a particularly reliable or trustworthy source of evidence. (As a scientist, quite the contrary in fact. We wouldn't need statistics otherwise.) When it comes to "evidence" for the divine/supernatural, I have simply never encountered any other kind - and even experiential "evidence" has been limited to that of other people. (And not from lack of trying, I might add.)

The lack of evidence is probably reason enough for me to be an atheist but I think it is important to acknowledge that there are other factors too. I think people often assume that atheism is a very negative and reactionary thing. Whilst I admit that my rejection of Christianity was negative, I see atheism itself as very positive. It is, I believe, embracing the true nature of the universe. There is more than enough beauty and wonder in this reality for many lifetimes of exploration and curiosity. There is power in shaping our own destiny, purpose and meaning. I just have no need to look to ancient texts for these things, although is interesting to see what ancient cultures thought. I feel like I have been there, tried that and life's too short. I prefer to spend my time pondering mysteries that might be solved in my lifetime. If I'm lucky, I might even solve some myself! This is really what I mean when I say that I don't need a deity/religion (although I also mean that I don't feel the need for one to "explain" anything nor to define morality).

It goes beyond just not needing a deity, though. I have no desire for one. And this lack of desire itself goes beyond my personal philosophical position that, if a god exists, it is either mean or insiginifacnt, and I am interested in neither. For me, a deity or supernatural element belittles and diminishes the true wonders of the natural world: the human brain; the way that unseeing, unthinking and uncaring molecules can interact to produce something as amazing as an ant, or a cat, or a person (or a bacterium etc. etc.); the way that unseeing, unthinking and uncaring cells and molecules can ultimately evolve into something as amazing as an ant, or a cat, or a person (or a bacterium etc. etc.); the truly awesome size of the Universe; the enormity of time; the insignificance of Man in the grand scheme of things but the ultimate significance of a man to a select few; true altruism. You get the idea. I know that my religious friends feel sorry for me and think that I am missing out on something but that's OK: I feel the same way about them.

In the same way, it goes beyond just not needing some externally imposed sense of purpose or meaning or, yes, morality. It is actively desirable that these things come from us, from people, explicitly and with all the limitations that comes with. No (sane) person ever claims to be omniscient. We will not get man-made ethics and morality "right" - there is no absolute "right" - but we can do our best and change our best in the light of new findings or situations. In the (hopefully immortal) words of Tim Minchin: "I don't go in for ancient wisdom. I don't believe just because ideas are tenacious it means that they're worthy." I'm proud to apply 21st Century knowledge and reasoning to 21st Century problems and come up with morality and ethics that may be flawed but can be explained and reasoned and changed if necessary.

Location:Southampton,United Kingdom

Wednesday, 2 November 2011

Goodbye, little dog. (Levi 1996-2011)

Today, my dog-in-law was put down due to failing health. (My wife's dog, Levi, who lived with her parents in Dublin.) I'm not entirely sure why I am blogging about it but I just feel like the little guy deserved a mention.

This picture is possibly a little mean, as he is wearing a bow and not looking his most masculine as a result. It reveals something of his character, though, I think: (generally) well behaved and good fun. He certainly always made me feel welcome whenever I invaded his home.

It also catches him when he was a bit younger and more spritely, taken as it was at Christmas 2007. He was already 11 at this point! We're going back to Dublin this Christmas and it will be strange not to have Levi snuffing at the dining room door while we tuck into the delicious feast that my mother-in-law has laid on.

He made it to 15, or 105 in dog years, which is pretty good going but it is still sad to have to say goodbye to a friend, be they human or animal. He will be missed.

Location:Dublin, Ireland

Tuesday, 1 November 2011

First authorship determined by coin toss!

This week's Science features the most complete and robust mammalian phylogeny to date, in the snappily titled: "Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification" by Jan Janečka et al.*

Apart from the beautiful figures (see the main phylogeny below), the thing that really caught my eye was the unusual superscripting of "First/Last authorship determined by coin toss." Never seen that one before! I've been on a couple of joint first author papers before but we've never had to resort to a coin toss to determine the "first first" and "second first" author order. Then again, they've not been Science papers, so I guess the stakes weren't so high.

*The listed first author is actually Robert Meredith but I thought I would play "parallel universe" for poor Jan Janečka, who missed out on the first author coin toss. (The last author coin toss is not so bad as papers do not get abbreviated to the last author in the same way as the first authorship; this paper will always be "Meredith et al.")

Zombie pumpkins (but not pumpkin zombies)!

Halloween is a time for reanimating the dead, so here are a couple of dead pumpkins from a previous year. First up, the first pumpkin I was involved with. We called him Henry:
The next two don't have names. Mine is the simpler one on the right. (Not sure you can have a zombie ghost!) The fancy one was carved by my wife, the pumpkin expert of our family!

Monday, 31 October 2011

Happy iHalloween

This photo is of the pumpkin that my wife carved for Halloween this year:
It was taken on my iPhone, uploaded to Dropbox, downloaded onto my iPad, cropped using PhotoPad and then blogged with BlogPress*. Isn't technology wonderful?

[*I'm actually a bit annoyed with BlogPress at the moment as it is refusing to pull anything down from online. Hopefully, iOS5 will sort that out, once I can persuade my work PC to let me upgrade. (My recent Windows 7 upgrade has done something strange to iTunes.)]

UK science gives great bang for buck!

One of the great things about going to International conferences is seeing some of the work that goes on "across The Pond". This can be both inspiring and depressing - the scale of some of the work is fantastic but, at the same time, it's the sort of stuff that can only happen on a generous budget.

In the UK, we typically have a smaller pot to play with but that doesn't mean that we don't do good stuff. Indeed, a recent Science news piece highlights two recent studies that show (1) the UK “"attracts more citations per pound spent in overall research and development than any other country", and (2) the UK now tops the charts when "ranked by average number of citations" (see figure). Above and beyond this, some of my beleaguered colleagues should also take heart that "The Thomson Reuters report says that ... biological sciences are the strongest area of U.K. research".

It's easy to get depressed with all the budget cuts but hopefully this will inspire us to keep "punching above our weight". (Or, better still, encourage more funding for what should be a source of national pride.)

(By the way, this image was grabbed from the PDF using iAnnotate on my iPad - a great App whose praises I must later sing.)

Thursday, 27 October 2011

Small but perfectly formed

After my recent post about bobtail squid, I felt that I should give some airtime (if you're using WiFi) to the little ocean critters that I am actually involved with: the beautiful Emiliania huxleyi. It's not really a "critter" as such at all - it's a tiny marine phytoplankton, so it's more like a plant really.

Emiliania huxleyi (fondly known as "E hux") is a "Coccolithophore"; the funky appearance comes from the armoured "coccolith" plates that cover the outside of these tiny single-celled organisms. Nobody really knows what coccoliths are for but they are one of the primary reasons for the interest in species as the plates are made out of calcium carbonate. This makes E hux and its relatives a potentially potent carbon sink despite their minuscule size. (The scale bar in the image is 2μm, which is 1 million times shorter than Darth Vader.) This is because huge numbers of coccoliths sink to the sea floor and ultimately become the chalk of the future.

Although it would seem to make more sense to make these plates externally, they actually make them internally and then export them whole, as this video (of a different coccolithophore) shows. In the words of the experts:
"The coccoliths are rather large relative to the cell size; if scaled up to human size it would be like a person giving birth to a car wheel or a dustbin lid."
The project that I am involved with is primarily concerned with Ocean Acidification, which is one of the lesser-known aspects of climate change due to rising carbon dioxide (CO2). Approx a quarter of atmospheric CO2 is dissolved by the world's oceans. As CO2 levels continue to rise due human activity, the amount of dissolved CO2 therefore also increases. This, in turn, lowers the pH of the ocean, which makes calcium carbonate - the stuff of coccoliths, skeletons and shells - dissolve more easily. The prediction, therefore, is that this will be bad for calcifies, making calcification itself more difficult and reducing the effectiveness of the calcium carbonate structures that they make. (Although we don't yet know what E hux uses its coccoliths for, it's a fair bet that their important.)

The good news is that, as Dr Ian Malcolm would say, "Life finds a way" and so there is every expectation that E hux and friends could evolve and adapt to the elevated CO2 levels. The bad news, though, is that rate of man-made CO2 increase is so fast that they may not have the time and capacity to adapt before the oceans get too acidic for them. It is therefore important that we understand both how calcification is regulated and what the capacity of E hux for adaptation to high CO2 is. Until we get a handle on this, we also don't really know how E hux will respond. Will the increased solubility of the calcium carbonate release more carbon into the ocean, making things even worse? Or, will E hux respond by making thicker coccoliths, incorporating more carbon and help to offset some of the effects of human emissions? (At least, that's my understanding of the main questions.)

In a future post, I'll outline a bit of what we are doing. (I say "we" but my contribution is actually pretty small.) For now, though, just marvel at their coccospherical beauty:

Monday, 24 October 2011

CreatureCast: awesome videos of crazy critters

In an interesting article about the need for evolutionary biology to go viral, I just came across a fascinating website called "CreatureCast", which features videos of crazy and awesome creatures, made by the Dunn Lab at Brown University. I have only watched the jellyfish one so far but it's well worth a watch. Click here or, alternatively, check out this collection on iTunes:

Cover Art

CreatureCast

Dunn Lab

Biology