Saturday, 30 June 2012

Turning to the Dark Side

So, I have finally joined the Dark Side and bought myself an Apple computer. One of the new MacBook Air laptops in fact. And it's lovely! (Hello!) I know that not everyone will agree with my casting of Apple as the Dark Side. For years, Microsoft seemed to be the corporation that everybody loved to hate.

Microsoft never achieved the monopoly of Apple, though. With a PC, you could change components yourself, therefore benefiting from a free market. The same even applies to operating systems - if you really hate Microsoft, put Linux on your PC. (I did recently on my little Dell netbook after the upgrade to Windows 7 at work made it utterly useless.) Different hardware. Different software. Different strokes for different folks. PCs were the computers for the real geeks.

Apple, on the other hand, made pretty gadgets but always seemed greedy. Oh, you want to connect one of our devices to the rest of the world, not to another one of our devices? That'll be another £15 for a special adaptor, please. Want to upgrade your memory? Well, you'll have to get that from us too. Etc.

On the other hand, there is something to be said for a monopoly. Apple control their products. There's none of the PC irritation of buying a game only to find that the two hundred different graphics cards supported does not include the one you have or that, for unknown reasons, your particular motherboard/memory/hard drive combination just doesn't seem to work together as well as the individual numbers would suggest. Then there are all the things claiming to speed up your system, or clean your registry, or check for viruses and spyware and yadayadayada. When I was young, I enjoyed finding out about this stuff but it doesn't seem like such fun anymore. An Apple, in contrast, just works. And if it doesn't, there is one person to blame: Apple.
Luke: Is the dark side stronger?

Yoda: No. Quicker. Easier. More seductive.
I still think I am a geek but maybe I am getting old, or computers are just a lot more complicated than they used to be, but these I want something where everything just works! And boy, does the new MacBook Air work! Everything about it is a joy. Lovely to look at, lovely to use. I'm still getting used to the different short-cuts and the like, and no delete key (only a backspace - Fn+BACKSPACE is the PC "delete", by the way) but, on the whole, I am really liking what I see. Best of all, there's no stupid Windows compatibility or performance issues. So far, at least. (I am still in the Honeymoon period and even Windows 7 takes a while before it seems to grind the whole system to a halt at random.)

Someone accused me recently of becoming an Apple advert (I'm already in the iPhone and iPad fan clubs) and I think I may be just about there! My only real criticism (other than dark rumours about the usual shenanigans of a multinational giant that is bigger than many countries) is the usual cable nonsense. Happily, I don't really intend to plug my MacBook into anything other than USB devices - this is for play, not work, so no projector connection or PowerPoint issues for me!

Will I ever go back to a PC, now I have tasted the Apple? It's early days. I am yet to try any programming on it, or see if MS Office works (including Excel Macros) but early indications are probably not. They say that "once you go Mac you can't go back".
Once you start down the Dark path, forever will it dominate your destiny.

Congratulations, Globe-Town!

Back in April, I posted about Globe-Town, a website made by some of the students in Southampton's Web Science Doctoral Training Centre as part of the World Bank's "Apps for Climate Change" challenge. Well, they achieved third place. Well done, Jack and all the Globe-Town team!

Thursday, 28 June 2012

Putting photos on Picasa with an iPad

5-in-1 connector kit for iPadRecently, I posted about the short-comings of the iPad for certain input-intensive activities. The focus of the post was writing. Until recently, I would also have included digital photos in this category.

Much as I am increasingly becoming an Apple convert, I still despair of their odd (or, perhaps, cynical) business decision to equip with their products with a bunch of IO ports that are incompatible with the rest of the world and then fleece their customers for more money, buying cables that overcome this apparent design flaw. I guess it's good business: unlike PCs, they have a clear monopoly on their products and can get away with such behaviour because their customers - myself included - are willing to fork out the extra cash when needed. It doesn't win any friends but I guess they can just buy friends with all their billions. (Apparently Apple is worth more than all the tea in China and has an annual turnover greater than the GDP of 160 nations, including Syria and New Zealand.) As a result, it came as no surprise that, using only what comes in the box, it is impossible to connect a digital camera to an iPad and upload pictures.Uploading photos to iPad

The technology does exist, though, and I recently invested in a 5-in-1 iPad Connection Kit, which I tried out following the recent kite festival. Beyond the irritation of the need to invest in such a piece of kit for what should surely be a basic and obvious function for any tablet or notebook, I am happy to report that this item works really well and conveniently solves my iPad digital photography woes. It's plug-and-play, and you simply attach your camera as normal, select which photos you want to upload (and, in usual iPad fashion, the interface for this is great) and away you go. As with any normal import tool, you are then given the option to delete the uploaded photos from the device.
Import photos
Once on your iPad, the photos are helpfully collated in an Album called "Last Import" with all imported photos in another album imaginatively called "All Imported". These are then available for all your usual iPad activities, such as blogging. You also then have the option of saving the photos individually to your camera roll, which will make them appear on your Photostream and thus available for other devices (if you have iCloud enabled). Happily, they do not all automatically appear in your Photostream - I was worried about filling up my iPhone the first time I tried this.
Albums
Of course, once you have your photos on your iPad, you need to do something with them. In the past, I have had to go via a PC with the good ones (essentially relegating the iPad to a viewing device (oPad!)) but now I use the Best Album App to put them up on Picasa. For some reason - competition, maybe? - Google websites like Picasa do not seem to work very well on iPhones and iPads, in my hands. I've tried a few apps claiming to work well with Picasa in the past and found them disappointing. This might be because I have stuck to the free ones. For a couple of quid, Best Album is well worth it. It just works really well. (So far, at least.)
Best Album Upload Picture
Once logged on to your Picasa account, you can view, edit and create galleries easily and then uploading photos is a simple as picking the photos you want from the Photo Library and then uploading. My only real gripe was that I did not find it easy at first to work out the size at which my photos would be uploaded to the website. I cannot remember now whether the default was too big (I don't have unlimited space on Picasa) or too small but it was easy enough to remedy in the Settings once I realised.
Best Album picture info
Once up, album details can be altered and the cover art set. Individual photos are also really easy to add captions to, and the like. My kite photos are here and the whole process of uploading them, flicking through to find the ones I liked, creating a Picasa album and uploading them, only took a few minutes and gained a bit of the iPad feeling of fun into the bargain. If you own an iPad and like digital photography then I can heartily recommend this combination of kit and app.

(I haven't gone into editing photos at all here because I don't do a lot of it. The main thing that I do is to re-crop photos, and the crop tool in the standard iPad Picture Gallery is perfectly adequate for that.)

Wednesday, 27 June 2012

MapTime: visualising Deep Time using Google Maps

A couple of days ago, I blogged that MapTime was coming soon... So, what is MapTime?

MapTime is a website that we are developing to make time lines as described in:
Parker, J. D. (2011) Using Google Earth to Teach the Magnitude of Deep Time. Journal of College Science Teaching 40(5): 23-27
The paper was featured in a Science 2011 Editor's Choice, "A destination in time." (Science 332: 1360.)

Evolution took a long time to happen and humans are not really built to intuitively grasp how long that time really was. By using Google Earth, (or Google Maps in the case of the website,) one is able to plot a route between two locations that resonate with students by showing key dates along the way using a comprehensible scale. This allows them to "feel" the magnitude of deep time.

An example route between Big Ben in London and to the entrance of Southampton Bargate reveals how the analogy works:

On route from Big Ben, as this graphic shows:
  • Life begins on the M25 at Heathrow
  • Multicellular animals do not arise until just south of Winchester.
  • The age of the Dinosaurs runs from around the M3/M27 junction down the Inner avenue to Middlestreet
  • Humans first appear about 18 and a half feet in front of the Bargate
  • British life expectancy (80 years) is the thickness of a eurocent coin from the front of the Bargate.
Now imagine driving 70 mph through the single celled phase of life from the M25 along the M3 to Winchester with a human lifespan the thickness of a eurocent coin.

Visit the MapTime Blog and subscribe to keep abreast of new developments - including the imminent launch of the website! The last few bugs are being ironed out and then we will be looking for interested testers. (And, of course, you can watch this space too!)

Monday, 25 June 2012

Natural Selection: a mechanism, a theory AND a fact

There are a bunch of science/research social/professional networking sites these days, vying to become the Facebook or LinkedIn of Academia. One of these is ResearchGate, which looks like it might be one of the better ones. (One day, I might do a proper comparison.)

One of the features of ResearchGate is the ability to pose questions to the community. Occasionally, when it's an interesting topic or I think I can help, I chip in. Unfortunately, ResearchGate is not devoid of Creationist trolls it seems, and in a discussion about random mutation as the source of biological innovation I responded to comments that
"Natural selection does not explain anything. It is not a scientific theory."
and
"Darwinism is an ad hoc narrative that lacks both quantization and predictive power."
Responding was possible ill-advised (don't poke the crazy!) but, as evolutionary biologist, it saddens and offends me to see such nonsense in what is supposedly a scientific forum. I responded thus:
Natural Selection is a well documented fact of nature. It is an inevitability given a certain set of circumstances (heritability, variation, competition and non-random differential survival) and those circumstances are all individually and collectively documented both in the lab and in nature. (Read "Why Evolution is True" for some examples of both.) It is not the only, or even necessarily the main, driving force of evolution as most change at the genetic level is neutral. However, it remains as the primary mechanism of ADAPTIVE evolutionary change. It explains in general terms how exquisite adaptations can be ultimately caused by random events (mutations) through non-random survival. To call it an "ad hoc narrative" is just plain wrong unless you are trying to applying it to specific PAST events, in which case there is usually a great deal of speculation (and lack of certainty) involved. When used in laboratory (and field) experiments using fruit flies or bacteria, it is most certainly NOT an ad hoc narrative and has great predictive power. I am not sure that it can be "quantized" but it can certainly be quantified, as population geneticists have been doing for years.
This then elicited a very strange response and a complaint about the term "Natural Selection" that I have seen before but did not expect to find in a supposedly serious discussion:
OK, Richard, Natural Selection is a well documented fact of nature. It may be so.

Then also i agree that " It remains as the primary mechanism of ADAPTIVE evolutionary change.". It may be too.

The problem then is that Natural Selection does not explain anything. A fact does not explain,. Neither does a mechanism.

You need to decide whether Natural Selection is a fact, a mechanism or a theory. Theories are not facts, nor mechanisms. Using the same word for a fact, a mechanism and a theory is just creating confussion.
For me, the only thing confusing here is how anyone can seriously claim that "Natural Selection does not explain anything". "Natural Selection does not explain everything" would be fair enough but "anything"? Really‽ Even Creationists seem to be happy that Natural Selection can account for "microevolution" (ewww!) and antibiotic resistance! In case anyone else out there is also confused, I thought I would re-post my reply here:
Natural Selection is a mechanism by which random heritable variation is shaped through time through non-random survival to produce non-random evolutionary change. That the mechanism of Natural Selection is responsible for adaptive evolutionary change is a fact. (The big unanswered question is how much observed evolutionary change is actually adaptive.) It is also a scientific theory as it has been subject to scientific scrutiny and repeatedly confirmed through experiments and observation. I do not understand how this can be confusing. It explains how you can get non-random evolutionary change (adaptation) from random heritable variation. This is a BIG explanation and rightly rates among one of the top scientific theories/discoveries of all time. If you think it explains nothing, then try SCIENTIFICALLY explaining adaptation without it.
Natural selection is one of the most beautiful and elegant explanations/mechanisms/theories/facts in all of science. There is a reason that Darwin is so famous!

Monday...

...can't it just leave me alone?


Saturday, 23 June 2012

Virus Paper

With the recent Science special issue and controversial publication of the mutations necessary to convert H5N1 "bird flu" into a virus that can be spread between mammals, it seemed like a good time to give a quick plug for Virus Paper, a collection of short stories on the Kindle by a friend under the nom de plume, "Maxwell Jonathan".

Here's the blurb:
Virus Paper: An artist, infected with a deadly virus, races against time to complete his masterpiece.

The Dislocation of Sebastian Peters: A failed writer gets a second chance at life in the body of his dead son.

Ratskin Bedsocks: A mother stops at nothing in order to keep her child alive in the aftermath of a nuclear apocalypse.

The Apostate: A boy raised in a satanic cult starts to question its dark faith.

In all four of these short stories from Maxwell Jonathan, ordinary people find themselves in extraordinary circumstances. Through love, hate, fear and hope they are pushed to the very extremities of human endurance.
This is not my usual genre (I normally go for something a little more detached from reality) but I am happy to recommend it nonetheless. Tied together by a general theme of life, death and personal identity, each story stands alone. Bleak and harrowing in places, these are not stories to be read when feeling a bit glum but they are very well written and will give you plenty to think about. For me, the latter three did not quite live up to Virus Paper, which was my favourite, but I think that if you like the opening pages, you will like the rest of the collection. (And I am sure that others will have different favourites.) It's on the kindle so why not download a free sample and see what you think? (And, whilst you're there, why not download a sample of The Cabbages of Doom too‽ ☺)

Friday, 22 June 2012

Cakes! (And nematode cookies!)

CupcakesCRUK LogoToday, we had a charity cake sale at work. Mmmmm! Chocolate cupcakes with a peanut butter frosting are highly recommended! Being a bunch of science geeks, there were even some baked DNA gels and C. elegans worms!

It was all in aid of Cancer Research UK and if you want to support the idea of cookie nematodes from afar, you can sponsor the "Girls of B85" for the upcoming 5k Race for Life Southampton.
I am happy to report that the C. elegans were very tasty!

Wednesday, 20 June 2012

Well done, Flying Fish and L-Katz!

serpentsLast weekend was the Southampton Kite Festival and the Flying Fish Kite team were performing their first public routine. I'm always a bit nervous when I go to see friends perform because, well, I'm not very good at lying and so I worry about how I will respond if they turn out to not be very good and I'm asked for my opinion. On top of that, I know that the weather of late has been pretty atrocious and so they probably have not had the chance to practice as much as they would have liked. On top of that the conditions on Sunday were a bit windy (although better than Saturday) and one of the pairs performing earlier in the day (the pairs team ranked 10th in the world, no less) had to restart their routine after one of their lines snapped in the wind!

Happily, all such worries were totally unnecessary and the Flying Fish were really good. For a pair that have only been formation flying for about a year, they were amazingly well synchronised and, given that this was their first public performance (including having friends watching), they showed no nerves at all. The routine was well structured and fun to watch.
Flying Fish
There was a slight hiccup at one point when the kites got a little too close and experienced a tangle but, to be honest, I was really glad it happened because it meant that they started their routine again and we got to watch the first half of it for a second time. And they nailed it.

The Flying Fish also returned to field a bit later in the day as part of their other team, the L-Katz. This time, it was a four kite display. The first time I saw a four kite display, I think my jaw may have literally dropped. It's not just what the kites are doing, although that is impressive enough: it's a bit like watching the red arrows and as the kites swoop after and around each, performing fly-bys etc., you sometimes almost forget that there are people on the ground controlling them. The red arrows, though, are not attached to ground with strings. As well as the aerial ballet, making sure that the kites themselves do what they are supposed to in the air, there is a second ballet going on down below, with the flyers moving forwards, back and around each other to make sure that the kites do not get entangled in the wrong way. (The lines are so silky that they can actually control the kites well even when the lines have crossed each other a few times but it can still limit the range of motion and enforce some maneuvers that "unwrap" the kites.)

Anyway, just as with the Flying Fish pairs effort, the L-Katz turned out a great routine, especially when you consider it was their first public performance as a team too. Well done, guys (and gal)! You can read their take on the event here - if nothing else, it's worth a visit for a video of some crazy 11 kite action near the end of the day. (We missed that, unfortunately.) I also have a few more pictures at my Picasa Album of the event.

frogegg and sperm kiteThe rest of the Kite Festival was also a success, I think. It was raising money for the Air Ambulance and we got a little visit from their helicopter during the Flying Fish routine. There was the usual array of funky (and sometimes disturbing) kites and some great demonstration flying. The stunt kite demo was particularly impressive this year. We also got to see the British national champion team at work, which was extremely impressive: the precision and synchronisation of these guys is unbelievable.

Last, but not least, I have to mention Biggles Do'nut van. She may not look like much, but she's got it where it counts, kid: it's hard to beat freshly cooked donuts, still warm and coated in cinnamon sugar. Mmmm.

Biggles Donuts

Tuesday, 19 June 2012

When it comes to writing, it's more of an oPad than an iPad

This is my 200th blog post and I've had my iPad for around a year now, so it seemed like a good time to reflect on using the iPad for writing in general, and blogging in particular.

I'll start by saying that I really love my iPad and it's great for the main things that I had in mind when I bought it. It's handy for conferences, makes email feel like fun rather than a chore, and is a joy for web surfing - as long as you don't need flash of course! Reading PDFs is good with iBooks and better still if you need to annotate them and invest in the iAnnotate App. With ArtStudio and a stylus, it's great for drawing too. I love the way it's so easy to share and access files between my iPad and other devices using Dropbox, and the way that pictures taken with my iPhone are almost instantly available on my iPad through Photostream.

But... there are situations in which the iPad is not great, which are basically any situations in which a lot of typing is needed. For text-rich output, the iPad is fantastic but text-rich input just isn't its thing.

The problem is not a software issue. The OfficeHD App that I invested in early on is rather rubbish and buggy, to be honest, but the later Apple offering, Pages, works really well (even if it is one of the more expensive Apps out there). The problem is just that, even with the big touchscreen keyboard, you just can't type so quickly and instinctively as with a "real" keyboard.

I did invest in a wireless keyboard when I bought my iPad and, as a piece of kit, it works really well. It pairs cleanly and easily via bluetooth and has the usual delightful Apple keyboard feel that makes it a pleasure to type with. The problem is that it is just not that practical to use it with a iPad. You cannot easily, for example, balance both the iPad and the keyboard on your lap, as you can with a laptop. (It's called a laptop for a reason!) Although you can set up the iPad on a desk and sit the keyboard in front of it, this solution only really works if you only want to type. Without a mouse as well, it is a real pain whenever you want to use any of the functions that require touching the screen.

This is a particular problem when blogging, possibly due to my choice of blogger as host. In my hands, the WYSIWYG "Compose" mode does not really work on an iP* device and, even on Windows, it tends to add lots of unwanted HTML. (Too many divs!) For this reason, and being a bit of an HTML purest (hence my (X)HTML ASCII code cribsheet), I do my blog writing through the "HTML" mode. Writing HTML is especially bad on an iPad because of the need to toggle between letters, numbers and symbols. For blogging, my current solution is therefore to email blogger the subject and photos for a blog post from my iPad (or iPhone), and often the core text (if it's short) without any links or formatting, and then use a laptop (or my little netbook, on which I put Linux after Windows 7 killed it), to tidy up, format and/or add to the text/images.

It works but it's a bit clunky. And progess on "Mystic Mog and the Exploding Tortoise" has slowed to, well, tortoise pace. Happily, the answer might be in hand. Having stalked Mac Rumors for several months awaiting the new MacBook Air - and saving up my pennies - the new version was released last week and mine should be winging its way to me before the end of the month. My website might get some much-needed attention too! ☺

Monday, 18 June 2012

The Cabbages of Doom has its first review!

The Cabbages of Doom has its first review! As it's a nice one ☺, I thought I would reproduce it here (with permission):
★★★★★
By Joel Parker

This exciting and entertaining first novel exceeded all of my expectations. The story itself is a very imaginative chase across the English country side involving inter-dimensional travellers culminating in an entirely unpredictable hilarious and action packed final confrontation. The story had me laughing out loud and genuinely invested in routing for the good guys (okay, cabbage and small animals). Unlike most self-published first novels in this price range this one was very well spell-checked and surprisingly grammatically correct. If you are in the mood for a smile, a fun story and groan or two for some amazing puns and references to classic films, then this is the best 99p you can spend.

Sunday, 17 June 2012

Life's too short to drink bad wines

Life's Too Short to Drink Bad WineLast Friday was the last University of Southampton wine club tasting and the theme was wines selected from Simon Hoggart's Life's Too Short to Drink Bad Wine: 100 wines for the discerning drinker. Clearly, we did not do them all but we did manage to taste an impressive eight. (The wines themselves were sourced from The Wine Society and any prices quoted are from there. Names are from the evening's handout, so apologies if any are not quite right.)

In total, we got through three whites, five reds and one Prosecco. I did not remember to get pictures of them all but I have my favourite five from the night. First up was the Muscadet Sevre-et-Maine sur Lie, Chateau de Chasseloire, Cuvee Centenaires, 2007. This was a crisp, white wine that was very drinkable and a bargain at only £9. A very good start and my favourite white of the evening. It was accompanied by an amusing passage from the book but, sadly, I cannot remember any of that.

Muscadet Sevre et Maine sur Lie Madiran Chateau Montus 2005
Muscadet Sevre-et-Maine sur Lie, Chateau de Chasseloire, Cuvee Centenaires, 2007 Madiran Chateau Montus, 2005
The star wine of the evening for me, though, was the Madiran Chateau Montus, 2005. At £19 a bottle, it's over twice the price of the Muscadet but also over twice as nice and I might invest in a bottle or two for special occasions. (Although, sadly, I cannot find it on the Wine Society website.)

In between the Muscadet and Montus were two more whites and three reds, most of which were very drinkable. The book sold itself on being for the wine enthusiast and not the wine snob and, definitely not being a wine snob, I found this to be a refreshingly honest and down-to-earth approach. I'm not sure that I have the knowledge (or sophisticated palate) to class myself as a wine enthusiast (although this does complete a round dozen posts about wine) but I was pleasantly surprised to find myself appreciating the majority of Simon Hoggart's suggestions that we tried that night. (The exception was the Cassis Chateau Barbanau Kalahari, 2007, which I found to be very hard work and definitely not one to revisit at £18 a pop. Still, one failure out of eight is not bad at all.)

My favourite three of those five are shown below. (The second white of the night, a Fefinanes Alabarino, 2010, was not omitted deliberately but neither is it worth £11.50 a bottle by my taste/budget.) Of these three, I think the best bang-for-buck goes to the 2005 Hochar at £10.50. This was a fair bit nicer than the slightly more expensive 2009 Morellino di Scansano. The 2004 Chateau Musar was nicer than them both but at £18 I think I would rather spend a pound more and get the 2005 Madiran Chateau Montus. I wouldn't say no to a glass (or two) if offered, though!

Morellino di Scansano Chateau Musar Hochar 2005 Chateau Musar Gaston Hochar 2004
Morellino di Scansano, 2009 Chateau Musar, Hochar, 2005 Chateau Musar, Gaston Hochar, 2004
The evening was rounded off with a glass of Prosseco di Conegliano-Valdobbiadene NV, which was perfectly quaffable, even if not noteworthy enough to warrant a photo. It seems a little wrong to review a book based on 8% of its contents but if they are a representative 8% then this book is well worth buying!

Pigeon Chess: not just debunking Creationist lies but destroying them!

Via WEIT, I came across a great new blog today, called "Playing Chess with Pigeons" by Troy Britain. (New for me, that is!)

In a recent post, “Gill slits” by any other name…, he goes after common Creationist misconceptions (and deceptions) regarding the evolution and vertebrate development of "pharyngeal apparatus". Not only does it make a really interesting read but it does a beautiful job of highlighting - and then destroying - the common Creationist fallacies regarding this particular bit of anatomy.

Why "Playing Chess with Pigeons"? Apparently, it comes from a quote from an Amazon book review:
"Debating creationists on the topic of evolution is rather like trying to play chess with a pigeon; it knocks the pieces over, craps on the board, and flies back to its flock to claim victory."
- Scott D. Weitzenhoffer

Friday, 15 June 2012

Manga cats

Manga cat: MiaAs part of my quest to develop artistic skills, I invested in a copy of The Complete Book of Drawing Manga by Peter Gray. (This explains the slightly Manga-esque nature of my recent self-portrait, in case you were curious. I must confess that I have not really read much Manga but it is quite an appealing style to emulate, with bold colours and a distinctive appearance.

The Complete Book of Drawing MangaThe book is really good and talks through the basics for drawing Manga with step-by-step instructions for drawing faces, figures and animals etc. What's really helpful is that it shows you how to build up the guide lines before adding the outlines and finally some colour. The layers in ArtStudio are particularly good for this. At first, I thought it would be limiting only having six layers but it's really easy to duplicate and merge layers, allowing you to build work up in stages and then flatten it and move on if you need more layers. I've found that four layers works really well for my style: a background layer, one for sketching guides, one for block colouring and one on top for outlines. It's then possible to insert an extra layer between block colours and the outline layer to safely experiment with highlights and shadows.
Manga cat: Arthur
Although I have had an attempt at drawing people, and I have a few ideas in this area, I thought one fun thing to do (as much for the sake of having a focus as much as anything else) would be do make some manga-style characters from The Cabbages of Doom. To this end, I decided to do the cat tutorial from the book. As with the ArtStudio cat tutorial, I modified it a bit to be like our cat, Mia (above) and then repeated it as a bit more solidly-built tabby to be more like Arthur (left). There's definitely room for improvement but I'm fairly happy with the results as a first effort.

They look quite happy too.

Wednesday, 13 June 2012

Artstudio: like being a kid again (It's great!)

Artstudio cat tutorialI'm a bit obsessed by the Artstudio App for the iPad at the moment. I find that there's something incredibly relaxing about colouring in. Perhaps it's regression to childhood or something! One of the nice features about ArtStudio for the novice is that it comes with a bunch of tutorials with step-by-step instructions to follow for drawing some basic stuff like faces and cats.

Here's a screenshot of my version of their cat tutorial, with a little customisation to make it look a bit more like one of our cats, Mia.

I really can't say enough good things about this App. It's incredibly easy and intuitive to use. The colour palettes, brush controls (e.g. thickness etc.) and layers are really quick and convenient to switch as you work. It all makes for a very pleasing and user-friendly experience. For art newbies like me, having good undo controls is great too!

Magicwand StylusJust before getting the App, with a view to using my iPad to explore my artistic a little, I invested in a Magicwand stylus. When it arrived in the post, I was a little disappointed. It got great reviews on Amazon but I could not get over how thick the stylus itself is: you can get finer control than a finger, for sure, but it is not exactly great for precision stuff. (There must be something about the way the touchscreens work that limits how small a stylus can get.) With Artstudio, it's not a problem, though: you can zoom in and out with such ease that fine control is possible, and the undo button is quick and convenient if you mess up. (I played around with Paper by 53 before investing in Artstudio (it's free) but it was really frustrating.)

At the end of the day, what I really want from an Art App is something that works well enough for my skill to be the limiting factor, not the technology. As you can tell by my first attempt at a "Mangafied" self portrait (below), Artstudio is just that. Five stars, 10/10, a definitely my favourite App of 2012 so far.

Mangafied self-portrait

Sunday, 10 June 2012

The Cabbages of Doom: now only 99p!

Perhaps somewhat predictably, copies of The Cabbages of Doom are not exactly flying off the virtual shelves. This could, of course, be that's it's rubbish and no one likes the sample chapter enough to cough up the price of McFlurry to read the rest. My web sleuthing (and ego), however, suggest that it's a lack of reviews that is the issue: why would someone invest their precious time on something with only the author's recommendation?

This is therefore an unabashed plea for some kind folks out there to write some nice words on Amazon, Lulu or iBooks - assuming you have read and liked the book, of course! It's not that long, should you want to find out! What better way to spend a lazy Sunday than in the company of homicidal vegetables and vegicidal animals on a whirlwind adventure of carnage, romance and silliness. (Mostly silliness.)

As an extra motivator, the PDF Edition of The Cabbages of Doom is now only 99p, in line with the iBookstore price - and you can try before you buy! If you read the sample chapter and are sitting on the fence, I'll even send you a copy - as long as you agree to write a review if you have anything nice to say! If you do buy it, I might even share my McFlurry with you.

(Don't mind Frankie, there. He is just trying to use his mind-control powers to convince you.)

Saturday, 9 June 2012

Let's go fly a kite...

...or two. In formation!

I've already posted on flying squid and flying squirrel( suit)s, now it's the turn of Flying Fish! This picture is my ArtStudio homage to The Flying Fish Kiting Team, who joined the Blogosphere this week. Unlike their biological namesakes, however, these guys really do fly. The kites do, at least. (Unless things go a bit wrong in high wind, the humans stay firmly on the ground.)

I've dabbled a little in flying kites - and no doubt will again when the sun decides to grace our fair isle with its presence again - but I'm at the level where I consider it a success if I don't crash. Getting one kite to do roughly what you want is not too hard if the conditions are right. Getting it to do exactly what you want is something more of a challenge. Doing it to music, synchronised and in formation with a partner... that's not easy. It looks really good, though: there's something very relaxing about watching a pair of kites swooping around after - and sometimes at - each other.

The Flying Fish are currently practicing for their first public routine at the 16th Southampton Kite Festival next week, so if you're in the area, come along and give them some support. The festival is always fun (if the weather behaves) and features some crazy kites - as well as rather fine donut van. This year, it's raising funds for the Air Ambulance Service, do that's another good reason to go if you can.

Even wasps can be cute

Over on MYRMECOS, Alex Wild asks if this is The Cutest Wasp Ever? I reckon it's a contender. I recommend clicking on the picture (or link) to go and see the original high res version. (I've deliberately only put on a low res copy here because Alex Wild deserves the traffic - his photos are amazing!)

Friday, 8 June 2012

Who does Microsoft Academic Research think you are?

A while ago, I posted some thoughts about Microsoft Academic Research. Today, I was sent a link by a colleague about one of the features on the site - the Co-Author "Academic Degrees of Separation" path. She sent me the path between us - we're five steps apart. The only problem was, it wasn't me! The picture was me and the name was me but all the other details were wrong!

Here's the entry:

The worrying thing for me, is that I did not create this entry and yet they have somehow affiliated both my picture and one of my genuine URLs - my Southampton Computational Modelling Group homepage - with a tiny handful of wrong publications and an institution where I have never worked or visited. Perhaps more worrying, I cannot work out how or why. I can only guess that they have some kind of data-mining algorithm that has gone badly wrong. Very badly wrong!

Here's the real me:

As you can see, I have a totally different set of metrics, keywords and interests to the spurious me. My colleague is not really to blame, though. Search my name, and up pops the wrong entry complete with my actual photo before the real me:

The sooner they roll out ORCID, the better! For now, I guess I need to work out how to get the wrong Richard Edwards removed and/or merged with the right one.

For those interested in the Co-Author path, here it is for the real me to the fictitious me:

Of course, any one of these links could be through a totally incorrect entry. This whole scenario just reinforces my views of Microsoft Academic Research: they have some nice tools but until they can sort out the underlying data, it remains essentially useless and possibly worse than useless.

If you have a remotely common name, even if you have no interest in a profile on Microsoft Academic Research, go and look yourself up now! You never know what someone else might be finding out about "you".

UPDATE. I was able to log on and remove my picture and URL from that entry, although it looks like it will take a week to take effect. Hopefully, it will work...

Postdoc position available: one week to go before deadline closes

This is just a quick unashamed plug for the postdoc position currently available in my lab. (Who wouldn't want to work with me?) Follow the link for details. Closing date is June 15th.

Thursday, 7 June 2012

Intelligently designed ignorance gets a boost in Korea

Having just said that the Why Evolution is True website is a bit too anti-religion at times, Nature News has just reported some worrying developments in South Korea that make it clear why the likes of Jerry Coyne and Richard Dawkins continue to take the fight right to the door of those trying to spread misinformation in the name of religion.

The piece, "South Korea surrenders to creationist demands" (Nature 486, 14), reports that high-school textbook publishers have agreed to remove examples of evolution from their books following pressure from Creationists in the country. (A group using that old oxymoron of "Creation science", which demonstrates that the people involved understand "science" in the same way as they understand "evolution": through a twisted misrepresentation of the underlying principles and mechanisms of action.)

I feel sorry for some Creationists - I used to be one - as there are those that have been fed lies by people they trust and, therefore, believed them. (Often, the lies are passed on in ignorance and without malice for several "thought generations".) I have no such sympathy for the spawners of such nonsense, though. You need to be pretty damn sure of yourself to start imposing your thoughts on others by trying to influence textbook content, so these people are either wilfully deceitful or woefully ignorant. (Ignorance itself is not a crime, until you start try to teach others your ignorance. If you don't understand evolution, leave it to those that do. I don't try to teach quantum mechanics.) This is doubly true if what you are trying to teach flies in the face of the well-established scientific consensus.

The focus seems to be on the removal of Archaeopteryx as a possible avian ancestor and the fossil series evidence for the evolution of the horse. I am all in favour of specific examples of evolution being updated in the light of new data, or replaced with clearer ones. (Archaeopteryx may not be the ancestor of modern birds and may instead represent an extinct off-shoot of feathered dinosaurs. Plenty of other fossils and species exist, though, and it does not change the overwhelming evidence that modern birds evolved from therapod dinosaurs.) The crucial thing here, though, was that the Korean biologists say they were not consulted, and the move was made in response to a petition from the Society for Textbook Revise (STR), an independent offshoot of the Korea Association for Creation Research (KACR) that:
aims to delete the "error" of evolution from textbooks to "correct" students' views of the world, according to the society's website.
In other words, you should teach what we want because we don't like the scientific consensus.

One of the most worrying aspects, as pointed out by the authors, is that (next to, say, America), Korea is not a particularly religious country - according to the article:
About half of South Korea's citizens practice a religion, mostly split between Christianity and Buddhism.
The article cites a 2009 survey in South Korea, which found that less than one third of respondents did not accept evolution. (Compared to over 40% in the US, for example.) Less than half of those denying evolution, however, claimed to do so for religious reasons and instead cited a lack of evidence and/or understanding. This is both depressing and encouraging, I think. It is depressing to think that Creationist liars are spin doctoring so well that the central tenet of biological science for the past 100 years can still be poorly understood in the 21st Century - especially with all the good online resources now available. (It only takes a Google search and an open mind to debunk most of the Creationist fallacies.) It is encouraging, on the other hand, because the solution seems obvious: better education.
Until now, says Dayk Jang, the scientific community has done little to combat the anti-evolution sentiment. "The biggest problem is that there are only 5–10 evolutionary scientists in the country who teach the theory of evolution in undergraduate and graduate schools," he says. Having seen the fierce debates over evolution in the United States, he adds, some scientists also worry that engaging with creationists might give creationist views more credibility among the public.
I wonder how much it would cost to put a copy of Why Evolution Is True in every school library in South Korea?

How to root a phylogenetic tree

Teaching phylogenetics, it is clear that one of the things that causes a surprising amount of confusion is rooting the tree - defining the position on the tree of the (hypothetical) ancestor. Here, then, is my basic introduction to rooting a phylogenetic tree and why it is important.

Unless you are modelling recombination or Horizontal Transfer, a phylogenetics is explicitly based on a model of a single common ancestral lineage that splits over time into multiple lineages. For species, these splits are speciation events. For molecules (e.g. genes or protein sequences), these splits can also be duplication events. But how do you know where that common ancestral lineage is?

With respect to rooting a phylogenetic tree, there are three main strategies that are routinely employed. In approximate order of confidence in the ancestry, these are: (1) No rooting (leave the tree unrooted), (2) Midpoint rooting, and (3) Outgroup (not outlier!) rooting.

Unrooted. I'll start with the unrooted tree because most methods produce an unrooted tree. Note that, although phylogenetics as a general approach assumes there's a common ancestor somewhere, many of the actual methods for constructing trees from data make no direction/ancestry assumptions. (The obvious exception is UPGMA, which is not used that much for serious phylogenetics.)

Leaving the tree unrooted is also the easiest because it essentially involves doing nothing! In the figures below, the left-hand image shows the unrooted tree. The key thing here is that there is no assumption about ancestry and therefore no statement about the direction of evolution. If you trust the approximate branch lengths, it is still possible to say things about the topology, such as A and B are closer to each other than they are to C and D (with an important caveat covered below), but you cannot make any direct inferences about the common ancestor. Whilst easier, therefore, you are limited in terms of analysis and interpretation.

This kind of representation is best used in situations where you have three or more well-defined clades (such as different members of a gene family) that radiated a long time ago over a relatively short period, such that the placement of the root and the order of branching is not known. You might still be able to say something with confidence about some of the individual radiations but you avoid making unsupported claims about the precise history and relationships of those clades. (Another option here is to "collapse" the root into a multifurcation (one-to-many split) but I will not deal with that here.)

The alternative when the actual root placement is unknown, is to use midpoint rooting:



Midpoint Rooting. As its name suggests, Midpoint rooting attempts to root the tree in its middle point. It does this by calculating all of the tip-to-tip distances and selecting the longest - A to E in the tree above. The root is then placed exactly half-way between these two tips. If the tree is behaving and the rates of evolution are pretty constant throughout, this point should represent the ancestral point. It is therefore useful in situations where the actual root is not known but the assumption of a reasonably constant "clock-like" rate of evolution is quite sound. The other situation it generally works well for is when a tree is fairly balanced with some closely-related clades separated by a long branch in the middle - if midpoint rooting places the root far away from any nodes, it is less likely to be wrong (i.e. moving it a little due to rate discrepancies would not make any difference).

The main problem with midpoint rooting is that it is very susceptible to large deviations from a constant evolutionary rate, especially if these are not "balanced", i.e. they only occur on one side of the actual root. The other time midpoint rooting tends to go wrong is when it places the root in amongst a rather dense set of short branches, where quite small deviations will place the root on another branch. For these reasons, whenever possible, outgroup rooting is generally the method of choice.



Outgroup Rooting. Unlike midpoint rooting, in which features of the tree itself specify the root, in outgroup rooting existing knowledge is utilised to place the root in the right place. This is done by using an "Outgroup" - a species or molecule that is known to be more distantly related than everything else in the tree. In the example above, kangaroo is used to outgroup root the tree, as it is known that marsupial mammals diverged from the ancestral lineage of all placental mammals.

This tree emphasises the point made above about evolutionary rates - the midpoint root was wrong because the rodent lineages (mouse, rat and their ancestor) are evolving faster than the rest of the tree, probably due to relatively short generation times. (This pattern is often seen with real trees.) This can sometimes be obvious if deleting one of the nodes used to midpoint root the tree changes the position of the root: for a perfect clock-like tree, it should make no difference (as long as you do not delete the outgroup). This will not always work, though - in the example above, it would not make a difference, for example.

Why does the root matter? There are a couple of reasons why correct rooting is important. The first just comes down to interpretation and understanding - it would be wrong to get too obsessive about the superficial differences between the three trees in the above figure - they are all essentially the same tree (same topology) and the differences are all down to rooting. The second is more important and comes down to the direction of evolution and conclusions about relatedness. If you want to infer anything about ancestry, you obviously need to have the right root. From the midpoint rooted mammalian tree above, it might not be obvious that placental mammals form a Monophyletic clade. Coming back to my earlier caveat when interpreting an unrooted tree, you might determine that the kangaroo, lemur and human were all more closely related to each other than to the mouse and rat. In terms of pure sequence divergence (on which the tree was built) this might be right but, in evolutionary terms, it is wrong: all placental mammals are equally distant from kangaroos due to the shared common ancestor.

Related post: How to read a phylogenetic tree.