this life's a fiction

Batman links

2011-03-09T22:04:00.029Z

(Click image for more.)

Turbine powered batmobile.

Bibliophile links

2011-03-01T11:05:00.031Z

How books work.

Judgemental Bookseller Ostrich.

How to get insulted by authors

Another personal library to be jealous of.

Why we should all read fiction.

Unusual new library stock.

My 2010 reading list

2011-01-09T19:12:00.005Z

For no particular reason here is a list of stuff I read in 2010.

Fiction

'Salem's Lot. My first Stephen King book. It was OK, but not enough to make me into an instant fan.
Fragile Things. A collection of Neil Gaiman short stories. Mostly pretty good.
American Gods. Another Gaiman, the longest one I've read of his. It's pretty good.
The Name Of The Rose. I was curious to read this for ages. It's good, although more interesting for the historical exposition than the whodunnit.
The Confusion and The System Of The World. These are the last two books of Neal Stephenson's Baroque Trilogy. I can't praise them highly enough, easily my favourite read of the year and one of the few books I've ever read that I can say I would instantly read again.
The Girl With The Dragon Tattoo, The Girl Who Played With Fire and The Girl Who Kicked The Hornet's Nest. Almost everyone has probably already read these. Personally i found them entertaining page turners, particularly the latter half of the second book, but these will not be classics for the ages.
Pirate Latitudes. A farewell to the author I have been most faithful too as a reader. It's typical Crichton fare, but without the opinionated ranting of his latter offerings.

Non-fiction

Bad Science. Most of you will already be familiar with Ben Goldacre's stuff, but this was a good read and I did learn a bit about medical science.
Life: An Unauthorised Biography. This was part of my bookmark liberation resolution. I started reading this back as an undergrad a decade ago. I don't know why I stopped, it's very well written and despite covering so much stuff I should already know, entertaining and informative.
Undaunted Courage. My first book of the year and a Christmas present. I wanted to read this as my 2009 US road trip followed a similar route to this biography of the Lewis and Clark expedition. It's interesting stuff.
Fearless Symmetry. This is a maths book about the proof for Fermat's Theorem. It's pretty well written, although I can't claim to grasp it all I did come away with a better understanding of why it eluded a solution for so long. Of course it still doesn't answer the question of whether Fermat really did have a proof, but it seems unlikely it was the same one.
Theology And The Scientific Imagination. Another bookmark liberation tome. This is tough stuff, a lot of untranslated Latin and Greek quotes. No doubt a more informed reader would get more out of it, but nevertheless it contains some interesting ideas.
The Palaeobiological Revolution. This was a review copy so I should just refer you to what I wrote in the PalAss newsletter.
Love All The People. I read this after watching American: The Bill Hicks Story. It's basically just transcripts of his shows plus some other bits and bobs. Apart from a lot of repetition it was good to relive some of his material.
The Prehistory Of The Mind. Probably my first venture into human origins popular science reading. He has some interesting ideas, but I'm still skeptical about how testable such anthropological/archaeological ideas are, but then perhaps I'm just a scientific snob.

Comics/Graphic Novels

2010 was marked by my getting into comics/graphic novels in a big way. Previously I'd basically only read Calvin and Hobbes and The Far Side, plus a little Manga. However, I decided I wanted to reread Tintin and Asterix from my youth as well as explore Batman, a character I've always loved.

The Complete Maus. Recommended by a friend who hadn't even read it. This is an important book and grown up enough to be the obvious go-to when ignorant people tell you comics are for kids. (I should point out that its subject matter is the holocaust.)
Adventures Of Tintin (Vol. 1). The first three Tintin stories. This is the only book I've read that comes with a special red sticker warning you of its racist content (referring to the Congo story). Although the Russia story is more historically interesting as clear anti-communist propaganda.
Asterix The Gaul and Asterix And The Golden Sickle. The first two Asterix books. It's interesting to revisit these as I haven't read them since I was a kid. Sadly despite my many years of education since I still don't get all the Latin jokes.
Batman: The Killing Joke. The first Batman I read. It's a pretty good story and I liked the art.
Batman: Year One. Although top of most people's Batman lists I wasn't that impressed by this. Mind you having learnt a lot more about the character since it's probably worth revisiting.
Batman: The Dark Knight Returns. I liked this story, although I'm not a fan of the art. It's always fun to see Batman take down Superman.
Batman: The Dark Knight Strikes Again. Again I liked this follow up story, but not the art.
Batman: Dark Knight Dynasty. This is the only 'Elseworlds' tale I've read and I hated it. The whole what-if-Batman-existed-at-other-times-and-places thing is not for me.
Batman: Strange Apparitions. My only taste of 70's Batman. It's not for me, things have definitely improved, although having read the first few stories they likely took a turn for the worse before they got better. So far the best stories are from the early 2000's.
Batman: The Wrath. Not so good, basically this is a what-if parallel tale of a guy with a similar history and resources to Batman that became a bad guy.
Batman: Death And The City. I liked the art, particularly Scarface and his new 'handler', but the story wasn't great.
Batman: The Bat And The Cat. I really liked this, easily the funniest Batman I've read (although he barely appears in it). The jokes are in both the writing and the visuals. Recommended. (Just don't read it on the bus/train.)
Batman: New Gotham 1: Evolution. This was mostly confusing for me as it follows up the much longer No Man's Land story arc. The art is from a very restricted colour palette and didn't really work for me.
Batman: Contagion. The first issue of this is the worst Batman art I've seen, I honestly think I could do better. However, it improves and it's a good story that precedes Cataclysm and No Man's Land.
Batman: No Man's Land 1 and Batman: No Man's Land 2. These are the first two of five volumes. I really like them, the story is great and so is some of the art. Probably the best story arc I've read so far.
Batman: Arkham Asylum. The best selling Batman story, but undeservedly so in my opinion. Morrison's writing is unbelievably pretentious and although the art is technically amazing, it's not for me. I especially hate the pointy-shouldered Batman.
Batman: Deathblow. Again, the art here is technically impressive, but I think this more photo-realistic approach actually works against the believability of it all. This story is also a bit too gritty for my (Batman) tastes and besides there wasn't enough Batman anyway.
Batman: War Games Act 1, Batman: War Games Act 2 and Batman: War Games Act 3. This is a pretty good story arc with some good art and includes a character death. (Unfortunately I still haven't encountered this character much so it's a bit lost on me who they are.)
Batman: The Long Halloween. A very different feel to much of the Batman I've read, but this whodunnit is a really good story and includes a Two-face origin to boot.
Batman: Dark Victory. Follow up to the latter and best read that way. This is just as good if not better, I certainly prefer Sale's art on this one - I particularly think his Selina Kyle/Catwoman has improved between the two. This also contains the only decent Robin (Dick) origin story I've read.
Batman: Bruce Wayne: Murderer?. The first volume in a what may turn out to be my favourite story arc so far. What if Bruce Wayne got arrested for murder? How can he be Batman from in prison? Did he do it or was he framed? If he was framed, was it Bruce Wayne's enem(ies) or Batman's?
Batgirl: Silent Running and Batgirl: A Knight Alone. The first two collections of the Cassandra Cain Batgirl. She's an interesting character and has turned up in several other story arcs I've read. I find her costume the scariest of the batman 'sidekicks'.
Robin/Batgirl: Fresh Blood. Art a bit too cartoony for my tastes and the story felt too much like a segue rather than a stand alone.
Robin: Year One. The story here is OK, but it was the art I really liked as it has a cool retro feel.
Huntress: Year One. A cool albeit peripheral character from the Batman universe that I wanted to read more of. I mostly liked the story and the art.
JLA/Titans: The Technis Imperative, JLA: Pain Of The Gods and Titans: Titans East. This is my attempt to try out some JLA and Titans stuff. It's not for me. I can't be doing with superheroes with superpowers. I'm just waiting for Batman to show up.
Iron Man vs. Whiplash. My only flirtation with Marvel. This was probably a bad choice as it's basically a rubbish spin off from the second film. However, I like the character so might try again in the New Year.

Some additional link blogging for Batman is here:

Audio Books

Finally here are some audiobooks I listened too for free from librivox.org/

Alice In Wonderland
From The Earth To The Moon and Round The Moon
My Man Jeeves
War Of The Worlds

Update

Oops, forgot some:

Batman: Hush. How could I forget this? Definitely the prettiest comic I've read, Jim Lee's art is amazing. The story is pretty good too, although there is a bit too much exposition re: Batman's back story. However, this does kinda make this ideal for a first Batman comic if you're thinking of getting into these things.
Batman: Under The Cowl. Not a story arc, but a collection of different issues where, for many and eclectic reasons, the guy under the cowl isn't Bruce Wayne. To be expected I liked some and not others, but there is an amusing gem in here.
Watchmen. Moore's opus magnum. This is really good, although it no doubt improves the deeper into comics you get. Another one I can't believe I forgot!

Bibliophile links

2010-10-03T17:34:00.004Z

Just some link-blogging this time.

Here is yet more library porn, and I have now discovered bookshelf porn (more here).

No discerning bibliophile can be without these awesome bed sheets.

I'm not sure if i agree with this list of authors and the people who read them.

Here is a useful web app to help you read at speed.

Here is a bibliophilic origin for a theological construct!

An interesting video diary of a disappointed book.

I feel rather embarrassed that I never knew about the story of Hay-on-Wye.

Here is the coolest ever library information desk.

The book as technology.

Finally here are not one, but two important pieces of advice. (I can honestly say I've adhered to the latter, I'm probably safe from the former.)

Well that's it for now, but I am looking forward to a bibliophilic pilgrimage I have planned for next month with The Oregon Trail to the world-famous Powell's. I have wanted to go there for at least a couple of years and will finally be proximal enough with a post-GSA trip.

Tropical Zoo

2010-10-03T08:21:00.026Z

We couldn't find Cynthia...

...but here's Elvis

Yesterday I went with a friend to Brentford. It's pretty dull round there, but if you know where to look there is a cooler place hidden away inside: The Tropical Zoo.

Toitles

This isn't a normal zoo though. Firstly because it is populated to a large degree by animals seized by UK customs and donations, often of exotic pets that got too much for their owners. However, what really makes it cool is the interaction they offer.

They have a lot of African Greys

We saw two of their shows, the first being reptile-dominated with various lizards, a couple of snakes and finally a caiman crocodile being brought ought by the keepers. The second was a flying demonstration with an Asian Eagle Owl. However, unlike a normal show the audience is invited to touch and even hold some of the animals. It was pretty cool to feel the heft of a massive constrictor and stroke a crocodile although I wasn't brave enough to hold the tarantula.

A jealous cockatoo

All in all this was a pretty cool experience for a (cheap for london) £6.50 entry so I am duly recommending it to all you Nodnol residents. It is worth a trip before health and safety regs step in and such things become impossible. Also, due to development they are about to lose their present home and need the money to fund the cost of their new site.

We weren't brave enough to check what the label meant

Drunky Monkey

2010-08-05T21:40:00.001Z

If palaeontology was an xbox game...

2010-07-28T13:54:00.011Z

Oh dear...

2010-07-15T11:32:00.003Z

Just put my last post through this site and, oh dear...

I write like
Dan Brown

I Write Like by Mémoires, Mac journal software. Analyze your writing!

Open source: doing my bit

2010-07-10T17:07:00.021Z

Although I can hardly claim to be a prolific blogger I do visit this page regularly to look for updates of other people's blogs (see list at left). One of these (The Open Source Paleontologist) is concerned with the public availability of both data and primary literature. Needless to say I agree with much of what is written there. As many of my readers wll know I also maintain my own site: http://www.graemetlloyd.com, where I try and do my bit. As is often the way with these things my ambition for what should be there goes well beyond my actual motivation to produce it. However, there is some stuff that people apparently do find useful and prompted by some recent comments I thought I'd take an opportunity to advertise what is there for those that haven't visited.

1. Dinosaur supertree bonus material

First off there is extra data from my dinosaur supertree paper, produced with my colleagues over at Raptor's Nest and Museological Meanderings. This includes the MRP matrices (as NEXUS files), the original tree and XML files, as well as R source code for the subsampling analyses. Apparently somebody has used this code so it was worthwhile!

2. Dinosaur matrix list

In conjunction with the above I have been collating a list of published cladistic analyses of dinosaurs. Many of these come from the supertree project, but I have kept an eye out for more recent things and just yesterday updated my list, so presently it is current. I also include NEXUS files of the matrices plus MPTs where I've had time to produce them. Again, this list has been used by at least a few people, but I have no doubt there are publications I've missed so for those keen enough to point them out I would be glad of the info. My eventual aim is to produce a proper relational database that allows automated creation of MRP files and hence an "instant" up-to-date formal supertree of the group.

3. Tree dating code

I wrote a post a while back about the problem of dating phylogenetic trees of fossil taxa. I subsequently wrote code to do it in R and know a lot of people already use it. There are plans to include this with some other functions in a full-fledged library - watch this space.

4. Palaeo-polygon area

I have also written some code to measure the area of the polygon described by the convex hull of a bunch of palaeolatitude and longitudes (now available as a downloadable field in the PaleoDB). Again, this was prompted by an old post. However, it should be noted that there are issues with this function. I now have it working better, but have yet to update the page (email me if you're desperately interested and I'll give you the latest one).

5. Red Queen PDF

On a trip to Chicago where I interviewed for their PhD program I was able to get my hands on Leigh Van Valen's ridiculously well cited, but poorly read Red Queen paper. As I got asked for this a lot I ended up scanning it in and making an OCR'd PDF and have made this available (with permission).

6. Endnote libraries for edited volumes

Being of a macroevolutionary bent I have a large personal library and spent a good chunk of my PhD entering everything into Endnote. Services like WoK were great for entering my journal runs of Palaeontology and JVP (I could just download everything from between a starting year to present), but no such electronic resource exists for my several edited books. These I had to enter manually, at no little effort. It seemed prudent then, to make these freely available once I was done and so you can browse and download copies from this page. I ended up using BibTeX for my thesis in the end and so hope to one day add this format too. I have also added links to these volumes on Amazon (if you buy via this link I get money!) and a bookfinder search (which will usually be cheaper, probably why I haven't made any yet).

Well, that's it for now. Hopefully some of you find at least one of these things useful. It is gratifying to me to know people are using it so please let me know if you like it or if there is anything else you'd like to have. After all, blogs are supposed to be interactive, right?

Iron Sky Trailer

2010-05-12T13:34:00.000Z

Looks set to be the best Nazi sci-fi comedy of all time....:

A meme of one's own

2010-01-18T13:23:00.007Z

Memes have to start somewhere, so I though I'd have a go at one. The image above is a tag cloud of the song titles in my iTunes library. Of course a meme only works if other people follow suit, so here's how I did it:

1. Fire up your iTunes (or equivalent) and select all your songs and hit Ctrl+C.
2. Open up Excel (or equivalent) and hit Ctrl+V. On most OS's this should just paste your library in text form, with separate columns for song title, artist etc.
3. Select just the song title column and hit Ctrl+C.
4. Point your browser at Tag Crowd and paste into the "Paste text to be visualized" box.
5. Click "Visualize!"
6. Screenshot the results and post them to your blog.

Stuff I'm totally going to do in 2010

2010-01-02T11:41:00.019Z

I'm not much into New Years resolutions, but there are a few things I hope to do this year, apart from the usual publishing papers and writing grants. In essence these are about digitisation and downsizing.

1) Digitising my DVD collection
Towards the end of last year I purchased a nifty 1-terabyte external hard disk and I've since been ripping my DVD collection onto it using the excellent Handbrake. Most other rippers are actually two programs, but this is really easy to use and does the whole thing for you (with plenty of options for customising the output). I've even set up a separate iTunes library just for this purpose so I can have all the nice DVD covers and everything, but my music remains on my laptop. (There is a trick on the Mac when you load iTunes by holding down alt first that allows you to pick which library you load.) Currently I'm about half way through the ripping, but there are still lots of covers to scan.

2) The great paper reduction
My second, much bigger project, is to try and digitise my entire academic library so that I can take more stuff with me on my (fingers crossed) next post-doc. Being a macroevolutionary type my library is quite large and runs to several feet of books and tens of boxfiles. Again, I have already started this, purchasing a nice Epson multi-purpose device that includes a paper feed scanner allowing automated scanning of multiple pages, so less work in creating the initial digital files for the ones I can't just download a PDF for. I then tend to clean these up in Photoshop, usually by ramping up the contrast so OCR is easier, as well as rotating them so the text is nice and straight and cropping any black edges. Initially each file (usually one or two pages) is saved as it's actual page number(s) in the paper (so I can quickly see if any are missing) and each paper is a separate folder. I then combine them into a nice PDF using Acrobat Pro, OCR it for text recognition and then optimise it for a smaller file size. I have PDFs for several boxfiles already, but what I really want to do is link these up to my Endnote library before discarding the original, in a recycling bin of course. Not sure I'll complete this in a year, but hopefully I will be able to clear some space from under my desk where I keep the boxfiles that I have no shelf space for.

3) Selling stuff
During my years at Bristol I managed to acquire far too much stuff - I took one carload to Bristol and two van loads out. I have had to downsize to some degree already in my move to London, but there is still a lot of superfluous stuff in my room that I really need to get rid of, either by selling or giving it away. I haven't been ruthless enough in my life so far in getting rid of things I don't use anymore, but hopefully I can finish 2010 with just the things I really need or love.

4) Getting back into running
Just before my PhD I ran the Bristol half marathon and enjoyed it. Since then I haven't really done any running at all, but I now really need the exercise and for a while now I have been thinking of doing the New York marathon, although this will likely have to wait until 2011 due to a clash with this year's GSA. The only way I'm going to get back into it though is if I sign up for another half marathon as I need the incentive to get training again and it looks like I might be going in for the Budapest half marathon in September.

5) Bookmark liberation
In my end of year review I mentioned that I am now getting into reading in a big way, but there are still several books on my shelves that I started reading, but for whatever reason stopped. It is my hope that I can finish these off over the space of the next 12 months, and indeed more generally reach a point where I have actually read all the books I own (with the exception of things like reference books and the like).

My 2009

2009-12-28T11:25:00.021Z

Because I'm so awesome I'm sure you'll all be fascinated to read a recap of stuff I did in 2009.

1) Leaving Bristol
I moved to Bristol in September 2002 and lived there until March 2009, a huge chunk of my adult life. During that time I completed my Masters and my PhD, but most of all it was where I made pretty much all of the closest friends I've ever had and it was certainly a bit of a wrench to leave.

2) Moving to Nodnol
The reason for my leaving was to take up my first post-doctoral position as a research assistant at the Natural History Museum. I was initially hesitant about returning to London, the city where I spent my (much less happy) undergraduate years, but I found somewhere quiet and pleasant to live and the project I'm working on is really great and ought to lead to lots of quality publications.

3) US Road Trip
Although one of the joys of palaeontology has to be the traveling I hadn't been on what I would consider a "proper" holiday since before my PhD so I spent most of the year looking forward to a US road trip with John and Phil. Our starting point was NAPC 2009 in Cincinnati, Ohio, our goal: Seattle, Washington. A good 2,500 miles away. I certainly enjoyed myself and as we never came to blows hopefully my traveling companions did too. We managed to take in Ashfalls, The Badlands, Deadwood, Rushmore, Dinosaur Park, Custer State Park, The Bighorn Mountains, Yellowstone and even Cicely, Alaska clocking up some 3,000 miles along the way. We got to Seattle in under 8 days, just in time for the Independence day fireworks and a whistle stop tour of the city. It was slightly depressing to then fly back across the same expanse in just a few hours.

4) Reading
This was the year I discovered the trick to getting through books more quickly: spend more time reading. This was prompted by a couple of things. Firstly I am now a commuter again after four and a half years of walking to work I now get the tube and hence can read on the way to and from work. Secondly I finally read Harry Potter after seeing the sixth film convinced me it would be worth it. I ordered the paperback box set and plowed my way through them in enough time to go and see the film again before it came off release. I certainly enjoyed them and the process got me back into reading novels and I now read more than ever. A quick scan of my book shelf shows that I managed to finish a minimum of 24 books this year, pretty good for me!

5) Lego advent calendar
December has been all about my Lego advent calendar and I've decided I just don't care anymore if they are supposed to be for kids. Lego is awesome, end of.

6) Footy
Although Liverpool turned out not to claim the Premiership I did manage to make it back-to-back wins in the fantasy football. However this season isn't going well on either front. I did manage to see another live game, but this turned out to contain the now infamous beachball incident. I didn't even get to see this goal as the queue to get in meant I couldn't see the pitch until about 10 minutes in. I'm going off football...

Even more distilled procrastination - animal links

2009-12-23T15:07:00.004Z

Some more links for your delectation.

It seems that dog torture is doubly popular, as is that traditional pastime of cat-waking. (Although I prefer cat buckaroo.) If you want a guaranteed smile then I recommend this. I have no idea what could have inspired this, but it is just a little bit brilliant.

I recently finished this book about the sadly extinct Thylacine and was directed towards this collection of the only surviving footage of the animal in life. I really liked this gorilla photo and found this bird's appearance amusing.

This appealed to my sense of humour, reminds me a bit of the "Matt Damon" bit in Team America. Finally, didn't someone once say you can judge a nation by the way they treat their animals?

More distilled procrastination

2009-12-22T17:41:00.010Z

Whilst I wait for some code to run I thought I'd post a little update with some book- and dinosaur-based links partly cannibalised from my stupidly long post. Enjoy, and Happy Christmas!

Dinosaurs

In my limited experience of being interviewed as a "dinosaur expert" I am always asked what my favourite dinosaur is and in all honesty it is still T. rex if for no other reason than our arms are the same length. Not one, but two cartoons make use of this fact to humorous effect. Presumably this is the creationist version of dinosaur extinction. Although this is more season-appropriate. Alternatively this cartoon has an eye on the bigger picture, whereas this is just silly.

Bibliophilia

I do enjoy these lists of books none of us has read most of and found these, what I can only describe as, children's books for adults kind of intriguing. I also shamelessly indulged in this hefty collection of library porn, have now discovered bookstore porn and even ceiling porn. (OK, the latter isn't book-related, but it fits here better than most places.) I found this incredibly useful blog on awful library books as well as this interesting list of things found in second hand books.

I keep finding really cool t-shirt sites, but unfortunately they are pretty much all US-based, like this collection. Other bibliophiles may also appreciate this, this, this and this.

First Lines

2009-12-01T22:52:00.011Z

OK, I've added a clue to the last one

I haven't done a meme since my first post so thought I'd try this one stolen from A little bit of babbling about nothing. Basically the idea is I pick ten of my favourite books or series and then copy out the first lines. Then you (dear reader) can make guesses as to what they are. I suspect my readership will have encountered many of these before so no googling and away you go.

Nel mezzo del cammin di nostra vita mi ritrovai per una selva oscura, che la diritta via era smarrita. Dante's Inferno, guessed by Mike
The late twentieth century has witnessed a scientific gold rush of astonishing proportions: the headlong and furious haste to commercialize genetic engineering. Jurassic Park (I couldn't resist), guessed by Mike
Far out in the uncharted backwaters of the unfashionable end of the western spiral arm of the Galaxy lies a small unregarded yellow sun. Hitchhikers Guide To The Galaxy, guessed by Sarah
Idle reader: Without my swearing to it, you can believe that I would like this book, the child of my understanding, to be the most beautiful, the most brilliant, and the most discreet that anyone could imagine. [Clue: windmills]
On 24 May 1863, which was a Sunday, my uncle, Professor Lidenbrock, came rushing back towards his little house, No. 19 Konigstrasse, one of the oldest streets in the old quarter of Hamburg. Journey To The Centre Of The Earth, guessed by Carlos
They put the behemoths in the hold along with the rhinos, the hippos and the elephants. A History Of The World In 10 1/2 Chapters, guessed by Sarda
It was 7 minutes after midnight. The dog was lying in the grass in the middle of the lawn in front of Mrs Shears' house. The Curious Incident Of The Dog In The Night, guessed by Sarah
It seems increasingly likely that I really will undertake the expedition that has been preoccupying my imagination now for some days. Remains Of The Day, guessed by Sarah (covertly) and Jenny (via Facebook)
The escalator strained slowly upward. In an old station like this what else would you expect? Night Watch, guessed by Rachel
You don't know about me, without you have read a book by the name of The Adventures of Tom Sawyer, but that ain't no matter. Huck Finn (OK, major clue in this one, but not as easy as the opening line from Lolita I almost included), guessed by Sarah

Just some webcomic links

2009-11-16T20:09:00.007Z

Ages ago I started preparing another post of stuff I found on Stumbleupon, but it got ludicrously large and unwieldy so I've broken it up instead. These are some of the webcomics that I find amusing/interesting/thought provoking etc. Enjoy!:

This little piggy went into, um, well see for yourself (not exactly a comic).
I mostly don't get The Warehouse but this really appeals to my - no doubt autistic - sense of humour.
Apparently only men can be sexist. Ok, it's silly, but it amused me.
The undisputed champion of the webcomic (at least for geeks like me) has to be xkcd and this is just one of the many that I have enjoyed. (Brings back fond memories of childhood when I built my own sewer out of cardboard and toilet roll tubes for my figures to play in.)
I have always felt that marking off the days since the moment of birth is a somewhat arbitrary measure of a lifespan and this somewhat encapsulates this.
Two great novels on dystopian futures battle it out in this really thought provoking comparison between Orwell and Huxley. I am yet to read 1984, but it looks like I've read the more terrifying one.
Not exactly a comic, but a pretty accurate description of meetings.
Ever wondered what the truth about opticians is?
Another one from xkcd, I admit it took a bit of thinking for me to get this. Definitely one for the statisticians amongst you.
I enjoyed this lampooning of a certain magazine. Some of the covers are just priceless.
Here is a perfect retort to the kid who wants to grow up too soon.
I always like scientific jokes such as this entomological one.
I had to finish with one from my favourite comic of all time: Calvin and Hobbes. No doubt my readers will already be familiar with it, but it will always be worth revisiting and this strip perfectly encapsulates the thoughtful, funny and beautiful nature of Bill Watterson's work. Warning: it may bring a tear to your eye.

You can tell I was going to be a palaeontologist...

2009-09-01T16:23:00.014Z

Something from my misspent youth this time. As kids my siblings and myself hit upon the great idea of producing a calendar as a Christmas present for our grandparents, quite probably because it was cheap. Basically we decided on a theme and then got drawing (in pencil first, then inking in later so that our dad could photocopy it at work). I suspect I had a pretty big hand in picking the 1994 theme (see below), the fact that Jurassic Park came out in 1993 was surely a coincidence. Anyway, as this resurfaced recently I thought I'd scan it in and post it here for posterity.

The front cover Pretty sure I've just copied these from JP merchandise:

January Pfft! This is clearly a Deinonychus...:

February We even ripped off the JP typeface for the months:

March An interesting mutant:

April Proof that randomly including Dimetrodon in dinosaur books does confuse kids:

May Apparently Toyota landcruisers were always associated with dinosaurs...:

June Obviously I didn't have great editorial control:

July Well it is the party month:

August Here we erect a new species:

September A reconstruction worthy of Waterhouse:

October Are those feathers?:

November Nice to see our notes section got used:

December It's all been building up to this:

Changing the size and colour of placemarks in Google Earth

2009-08-25T12:49:00.005Z

In follow up to my previous post I have now found out how to change the size and colour of my placemarks. The trick here is to create a "style" of placemark right at the top of the file. Again, this is pretty simple when you get down to it. This time you need to post a little bit of code at the top of the file, just after the <Document> tag:

<Style id="normalPlacemark">
  <IconStyle>
    <color>ffffff00</color>
    <scale>5</scale>
  </IconStyle>
</Style>

The id part of the opening <style> tag is important as it gives each style a name that we can then refer to later for each individual placemark. This allows the user to create different styles of placemark that can be used together in the same file (rather like CSS does for HTML). Colour (<color>) and size (<scale>) are then defined as elements of the <IconStyle> tag. Colours are in a hexadecimal format:

The range of values for any one color is 0 to 255 (00 to ff). For alpha, 00 is fully transparent and ff is fully opaque. The order of expression is aabbggrr, where aa=alpha (00 to ff); bb=blue (00 to ff); gg=green (00 to ff); rr=red (00 to ff). For example, if you want to apply a blue color with 50 percent opacity to an overlay, you would specify the following: 7fff0000, where alpha=0x7f, blue=0xff, green=0x00, and red=0x00.

Whereas scale is just a number.

Now we just need to make an addition to our <placemark> tag to state that we want to use this style:

<Placemark>
  <name>110_671B</name>
  <styleUrl>#normalPlacemark</styleUrl>
  <Point>
    <coordinates>-58.73,15.52,-1622</coordinates>
  </Point>
</Placemark>

So now I am able to plot my holes as giant green pushpins:

Unfortunately it is not easy to modify the colours of the pushpin icon as it has a yellow overlay to it and I have yet to work out if there is an easier way to colour placemarks exactly as I want. This will have to wait until next time.

Update:

OK, this last bit has been solved by someone who asked to be referred to as "my clever volcanologist friend." Basically a white pushpin needs to be called in the <style> tag like this:

<Style id="normalPlacemark">
  <IconStyle>
    <color>ffffff00</color>
    <scale>5</scale>
    <Icon>
      <href>http://maps.google.com/mapfiles/kml/pushpin/wht-pushpin.png</href>
    </Icon>
  </IconStyle>
</Style>

Multiple placemarks in Google Earth

2009-08-21T16:47:00.010Z

In my current job I am producing a database of fossil occurrences from the North Atlantic deep sea record and one of the fields in the data base is latitude-longitude for each of the IODP holes included. For a while now I've been wanting to export this data to a KML file (Google Earth's HTML-like file format). At first I figured this would be easy. I created an SQL query in Access to get my data out as a comma-delimited file which I then import into R. All I need to do is create a table of unique lat-long occurrences (holes) and their names then format them in the KML-style. However, I came up against a bit of a snag.

The first part is easy. Just set the header of the file to:

<?xml version="1.0" encoding="UTF-8"?>
<kml xmlns="http://www.opengis.net/kml/2.2">

The footer to:

</kml>

Then each hole is entered as a Placemark using the following syntax:

  <Placemark>
    <name>Hole name</name>
    <Point>
      <coordinates>-122.0822035425683,37.42228990140251,0</coordinates>
    </Point>
  </Placemark>

Where the coordinates are longitude, latitude and altitude respectively.

Simple.

But once you import the whole file into Google Earth it only shows the first point (hole) and skips all the others. Google's own code site wasn't much use on this, and the few forum's I looked at seemed to be missing a proper answer to this problem. In the end I figured out that all that needs to be done is wrap the placemarks in a simple

<Document></Document>

tag.

Lesson learned, and shared.

(Image and original code below.)

<?xml version="1.0" encoding="UTF-8"?>
<kml xmlns="http://www.opengis.net/kml/2.2">
<Document>
  <Placemark><name>110_671B</name><Point><coordinates>-58.73,15.52,-1622</coordinates></Point></Placemark>
  <Placemark><name>110_672A</name><Point><coordinates>-58.6,15.5,-1581</coordinates></Point></Placemark>
  <Placemark><name>110_673B</name><Point><coordinates>-58.64,15.53,-1875</coordinates></Point></Placemark>
  <Placemark><name>110_674A</name><Point><coordinates>-58.9,15.5,-2003</coordinates></Point></Placemark>
  <Placemark><name>110_676A</name><Point><coordinates>-58.7,15.53,-1494</coordinates></Point></Placemark>
  <Placemark><name>149_897A</name><Point><coordinates>-12.47,40.83,-5320</coordinates></Point></Placemark>
  <Placemark><name>149_899B</name><Point><coordinates>-12.26,40.77,-5291</coordinates></Point></Placemark>
  <Placemark><name>149_900A</name><Point><coordinates>-11.6,40.68,-5037</coordinates></Point></Placemark>
  <Placemark><name>149_901A</name><Point><coordinates>-11.05,40.67,-4719</coordinates></Point></Placemark>
  <Placemark><name>152_914A</name><Point><coordinates>-39.72,63.46,-533</coordinates></Point></Placemark>
  <Placemark><name>152_919A</name><Point><coordinates>-37.46,62.67,-2088</coordinates></Point></Placemark>
  <Placemark><name>157_950A</name><Point><coordinates>-25.6,31.15,-5438</coordinates></Point></Placemark>
  <Placemark><name>157_951A</name><Point><coordinates>-24.87,32.03,-5437</coordinates></Point></Placemark>
  <Placemark><name>157_952A</name><Point><coordinates>-24.5,30.79,-5432</coordinates></Point></Placemark>
  <Placemark><name>159_959A</name><Point><coordinates>-2.73,3.62,-2091</coordinates></Point></Placemark>
  <Placemark><name>159_960A</name><Point><coordinates>-2.73,3.58,-2048</coordinates></Point></Placemark>
  <Placemark><name>159_961A</name><Point><coordinates>-3.05,3.44,-3292</coordinates></Point></Placemark>
  <Placemark><name>159_962B</name><Point><coordinates>-3.18,3.25,-4637</coordinates></Point></Placemark>
  <Placemark><name>160_966F</name><Point><coordinates>32.7,33.79,-923</coordinates></Point></Placemark>
  <Placemark><name>101_627B</name><Point><coordinates>-78.29,27.63,-1026</coordinates></Point></Placemark>
  <Placemark><name>160_967E</name><Point><coordinates>32.72,34.06,-2553</coordinates></Point></Placemark>
  <Placemark><name>160_969B</name><Point><coordinates>24.88,33.84,-2202</coordinates></Point></Placemark>
  <Placemark><name>164_994C</name><Point><coordinates>-75.54,31.78,-2799</coordinates></Point></Placemark>
  <Placemark><name>165_998A</name><Point><coordinates>-82.93,19.48,-3180</coordinates></Point></Placemark>
  <Placemark><name>101_628A</name><Point><coordinates>-78.3,27.5,-964</coordinates></Point></Placemark>
  <Placemark><name>105_646B</name><Point><coordinates>-48.36,58.2,-3106</coordinates></Point></Placemark>
  <Placemark><name>101_635B</name><Point><coordinates>-77.3,25.4,-3081</coordinates></Point></Placemark>
  <Placemark><name>103_637A</name><Point><coordinates>-12.9,42.1,-1243</coordinates></Point></Placemark>
  <Placemark><name>101_626C</name><Point><coordinates>-79.54,25.6,-844</coordinates></Point></Placemark>
  <Placemark><name>149_898A</name><Point><coordinates>-12.12,40.68,-5279</coordinates></Point></Placemark>
  <Placemark><name>103_638B</name><Point><coordinates>-12.19,42.15,-1890</coordinates></Point></Placemark>
  <Placemark><name>103_639A</name><Point><coordinates>-12.24,42.14,-1829</coordinates></Point></Placemark>
  <Placemark><name>103_640A</name><Point><coordinates>-12.5,42,-1363</coordinates></Point></Placemark>
  <Placemark><name>103_641A</name><Point><coordinates>-12.18,42.15,-1918</coordinates></Point></Placemark>
  <Placemark><name>104_642B</name><Point><coordinates>2.92,67.22,-1283</coordinates></Point></Placemark>
  <Placemark><name>104_643A</name><Point><coordinates>1,67.7,-2769</coordinates></Point></Placemark>
  <Placemark><name>104_644A</name><Point><coordinates>4.57,66.67,-1215</coordinates></Point></Placemark>
  <Placemark><name>107_651A</name><Point><coordinates>12.8,40.2,-2974</coordinates></Point></Placemark>
  <Placemark><name>107_652A</name><Point><coordinates>12.1,40.4,-3094</coordinates></Point></Placemark>
  <Placemark><name>107_653A</name><Point><coordinates>11.44,40.26,-2821</coordinates></Point></Placemark>
  <Placemark><name>107_654A</name><Point><coordinates>10.7,40.6,-2209</coordinates></Point></Placemark>
  <Placemark><name>107_655A</name><Point><coordinates>12.46,40.17,-3234</coordinates></Point></Placemark>
  <Placemark><name>108_657A</name><Point><coordinates>-20.94,21.33,-2332</coordinates></Point></Placemark>
  <Placemark><name>108_658A</name><Point><coordinates>-18.58,20.74,-2264</coordinates></Point></Placemark>
  <Placemark><name>108_659B</name><Point><coordinates>-21.02,18.07,-3073</coordinates></Point></Placemark>
  <Placemark><name>108_660A</name><Point><coordinates>-19.24,10.01,-2221</coordinates></Point></Placemark>
  <Placemark><name>108_661A</name><Point><coordinates>-19.38,9.44,-2541</coordinates></Point></Placemark>
  <Placemark><name>108_662A</name><Point><coordinates>-11.73,-1.39,-2740</coordinates></Point></Placemark>
  <Placemark><name>108_663A</name><Point><coordinates>-11.87,-1.19,-2856</coordinates></Point></Placemark>
  <Placemark><name>108_664B</name><Point><coordinates>-23.22,0.1,-2747</coordinates></Point></Placemark>
  <Placemark><name>108_665A</name><Point><coordinates>-19.66,2.95,-1813</coordinates></Point></Placemark>
  <Placemark><name>108_666A</name><Point><coordinates>-20.2,3.5,-2037</coordinates></Point></Placemark>
  <Placemark><name>108_667A</name><Point><coordinates>-21.91,4.56,-3029</coordinates></Point></Placemark>
  <Placemark><name>108_668A</name><Point><coordinates>-20.92,4.76,-2690</coordinates></Point></Placemark>
  <Placemark><name>108_668B</name><Point><coordinates>-20.9,4.8,-2693</coordinates></Point></Placemark>
  <Placemark><name>174A_1071A</name><Point><coordinates>-72.72,39.38,-88</coordinates></Point></Placemark>
  <Placemark><name>174A_1072A</name><Point><coordinates>-72.69,39.36,-98</coordinates></Point></Placemark>
  <Placemark><name>174A_1073A</name><Point><coordinates>-72.27,39.22,-639</coordinates></Point></Placemark>
  <Placemark><name>1_1</name><Point><coordinates>-92.18,25.85,-2827</coordinates></Point></Placemark>
  <Placemark><name>1_2</name><Point><coordinates>-92.05,23.04,-3572</coordinates></Point></Placemark>
  <Placemark><name>1_3</name><Point><coordinates>-92.04,23.03,-3747</coordinates></Point></Placemark>
  <Placemark><name>1_4</name><Point><coordinates>-73.79,24.47,-5319</coordinates></Point></Placemark>
  <Placemark><name>1_5</name><Point><coordinates>-73.64,24.72,-5354</coordinates></Point></Placemark>
  <Placemark><name>1_6A</name><Point><coordinates>-67.64,30.83,-5124</coordinates></Point></Placemark>
  <Placemark><name>1_7</name><Point><coordinates>-68.29,30.13,-5182</coordinates></Point></Placemark>
  <Placemark><name>4_25</name><Point><coordinates>-39.24,-0.51,-1916</coordinates></Point></Placemark>
  <Placemark><name>4_26A</name><Point><coordinates>-44.04,10.89,-5169</coordinates></Point></Placemark>
  <Placemark><name>4_27</name><Point><coordinates>-56.87,15.85,-5251</coordinates></Point></Placemark>
  <Placemark><name>4_28</name><Point><coordinates>-65.62,20.58,-5251</coordinates></Point></Placemark>
  <Placemark><name>105_647A</name><Point><coordinates>-45.26,53.33,-2695</coordinates></Point></Placemark>
  <Placemark><name>11_100</name><Point><coordinates>-73.79,24.68,-5325</coordinates></Point></Placemark>
  <Placemark><name>11_101A</name><Point><coordinates>-74.43,25.19,-4868</coordinates></Point></Placemark>
  <Placemark><name>13_125</name><Point><coordinates>20.42,34.62,-2782</coordinates></Point></Placemark>
  <Placemark><name>14_137</name><Point><coordinates>-27.06,25.92,-5361</coordinates></Point></Placemark>
  <Placemark><name>14_141</name><Point><coordinates>-23.99,19.41,-4148</coordinates></Point></Placemark>
  <Placemark><name>150_905A</name><Point><coordinates>-72.28,38.61,-2698</coordinates></Point></Placemark>
  <Placemark><name>151_910A</name><Point><coordinates>6.59,80.26,-556</coordinates></Point></Placemark>
  <Placemark><name>151_911A</name><Point><coordinates>8.22,80.47,-902</coordinates></Point></Placemark>
  <Placemark><name>152_915A</name><Point><coordinates>-39.78,63.47,-533</coordinates></Point></Placemark>
  <Placemark><name>152_918A</name><Point><coordinates>-38.63,63.09,-1869</coordinates></Point></Placemark>
  <Placemark><name>38_338</name><Point><coordinates>5.38,67.78,-1297</coordinates></Point></Placemark>
  <Placemark><name>39_354</name><Point><coordinates>-44.19,5.89,-4045</coordinates></Point></Placemark>
  <Placemark><name>41_367</name><Point><coordinates>-20.04,12.48,-4748</coordinates></Point></Placemark>
  <Placemark><name>41_370</name><Point><coordinates>-10.77,32.83,-4214</coordinates></Point></Placemark>
  <Placemark><name>44_390A</name><Point><coordinates>-76.11,30.14,-2665</coordinates></Point></Placemark>
  <Placemark><name>47_398D</name><Point><coordinates>-10.71,40.96,-3910</coordinates></Point></Placemark>
  <Placemark><name>49_407</name><Point><coordinates>-30.57,63.93,-2472</coordinates></Point></Placemark>
  <Placemark><name>49_408</name><Point><coordinates>-28.91,63.37,-1624</coordinates></Point></Placemark>
  <Placemark><name>49_410</name><Point><coordinates>-29.47,45.5,-2975</coordinates></Point></Placemark>
  <Placemark><name>76_534A</name><Point><coordinates>-75.38,28.34,-4971</coordinates></Point></Placemark>
  <Placemark><name>77_537</name><Point><coordinates>-85.46,23.93,-3123</coordinates></Point></Placemark>
  <Placemark><name>77_538A</name><Point><coordinates>-85.16,23.84,-2742</coordinates></Point></Placemark>
  <Placemark><name>77_540</name><Point><coordinates>-84.37,23.82,-2926</coordinates></Point></Placemark>
  <Placemark><name>79_545</name><Point><coordinates>-9.36,33.66,-3142</coordinates></Point></Placemark>
  <Placemark><name>79_547A</name><Point><coordinates>-9.34,33.78,-3938</coordinates></Point></Placemark>
  <Placemark><name>80_548</name><Point><coordinates>-12.16,48.91,-1251</coordinates></Point></Placemark>
  <Placemark><name>80_549A</name><Point><coordinates>-13.09,49.08,-2513</coordinates></Point></Placemark>
  <Placemark><name>82_558</name><Point><coordinates>-37.34,37.77,-3754</coordinates></Point></Placemark>
  <Placemark><name>82_563</name><Point><coordinates>-43.76,33.64,-3786</coordinates></Point></Placemark>
  <Placemark><name>93_603</name><Point><coordinates>-70.02,35.49,-4633</coordinates></Point></Placemark>
  <Placemark><name>93_603C</name><Point><coordinates>-70.03,35.49,-4633</coordinates></Point></Placemark>
  <Placemark><name>93_605</name><Point><coordinates>-72.6,38.74,-2194</coordinates></Point></Placemark>
  <Placemark><name>94_606</name><Point><coordinates>-35.49,37.33,-3007</coordinates></Point></Placemark>
  <Placemark><name>94_607</name><Point><coordinates>-32.95,41,-3427</coordinates></Point></Placemark>
  <Placemark><name>94_608</name><Point><coordinates>-23.08,42.83,-3526</coordinates></Point></Placemark>
  <Placemark><name>94_609</name><Point><coordinates>-24.23,49.87,-3884</coordinates></Point></Placemark>
  <Placemark><name>94_610</name><Point><coordinates>-18.88,53.22,-2417</coordinates></Point></Placemark>
  <Placemark><name>95_612</name><Point><coordinates>-72.77,38.82,-1386</coordinates></Point></Placemark>
  <Placemark><name>210_1276A</name><Point><coordinates>-44.78,45.4,-4549</coordinates></Point></Placemark>
  <Placemark><name>173_1067A</name><Point><coordinates>-11.59,40.68,-5021</coordinates></Point></Placemark>
  <Placemark><name>2_8A</name><Point><coordinates>-67.55,35.38,-5184</coordinates></Point></Placemark>
  <Placemark><name>2_9</name><Point><coordinates>-59.19,32.77,-4973</coordinates></Point></Placemark>
  <Placemark><name>2_10</name><Point><coordinates>-52.21,32.86,-4712</coordinates></Point></Placemark>
  <Placemark><name>2_11</name><Point><coordinates>-44.74,29.94,-3571</coordinates></Point></Placemark>
  <Placemark><name>2_12C</name><Point><coordinates>-26,19.69,-4557</coordinates></Point></Placemark>
  <Placemark><name>173_1068A</name><Point><coordinates>-11.61,40.68,-5044</coordinates></Point></Placemark>
  <Placemark><name>3_13</name><Point><coordinates>-18.22,6.04,-4585</coordinates></Point></Placemark>
  <Placemark><name>4_23</name><Point><coordinates>-31.04,-6.14,-5079</coordinates></Point></Placemark>
  <Placemark><name>4_24</name><Point><coordinates>-30.89,-6.27,-5148</coordinates></Point></Placemark>
  <Placemark><name>4_29</name><Point><coordinates>-69.32,14.78,-4247</coordinates></Point></Placemark>
  <Placemark><name>4_30</name><Point><coordinates>-63.38,12.88,-1218</coordinates></Point></Placemark>
  <Placemark><name>4_31</name><Point><coordinates>-72.02,14.94,-3369</coordinates></Point></Placemark>
  <Placemark><name>173_1069A</name><Point><coordinates>-11.77,40.72,-5075</coordinates></Point></Placemark>
  <Placemark><name>101_631A</name><Point><coordinates>-75.7,23.6,-1092</coordinates></Point></Placemark>
  <Placemark><name>101_632A</name><Point><coordinates>-75.4,23.8,-1997</coordinates></Point></Placemark>
  <Placemark><name>101_633A</name><Point><coordinates>-75.6,23.7,-1679</coordinates></Point></Placemark>
  <Placemark><name>151_908A</name><Point><coordinates>1.36,78.38,-1274</coordinates></Point></Placemark>
  <Placemark><name>151_909A</name><Point><coordinates>3.07,78.58,-2519</coordinates></Point></Placemark>
  <Placemark><name>151_912A</name><Point><coordinates>5.45,79.95,-1037</coordinates></Point></Placemark>
  <Placemark><name>151_913A</name><Point><coordinates>6.94,75.48,-3319</coordinates></Point></Placemark>
  <Placemark><name>152_916A</name><Point><coordinates>-39.8,63.48,-514</coordinates></Point></Placemark>
  <Placemark><name>154_925A</name><Point><coordinates>-43.48,4.2,-3042</coordinates></Point></Placemark>
  <Placemark><name>154_929E</name><Point><coordinates>-43.74,5.97,-4356</coordinates></Point></Placemark>
  <Placemark><name>157_953A</name><Point><coordinates>-15.14,28.65,-3578</coordinates></Point></Placemark>
  <Placemark><name>157_954B</name><Point><coordinates>-15.53,28.43,-3485</coordinates></Point></Placemark>
</Document>
</kml>

For your procrastinating pleasure

2009-08-05T16:05:00.002Z

Here's what I've been wasting my internet time on this past few weeks.

Photography

I've always wanted to know how to photograph fireworks, especially when you can get results like this awesome picture.

Animals

I tend to come across lots of dinosaur stuff, including useful pointers on why you really should keep your T. rex off crack, a case of some dinosaur revisionism and this, frankly confusing, t-shirt. I also find this simple joke quite amusing.

Entertainment

If you haven't already come across it, I really like the idea of this wedding entrance. Some more creativity comes into play in a performance of 80's classic Africa and finally there was this darkly comic animated feature, Billy's balloon. I also recommend checking out the art of this guy.

Science

First up is this cool toilet paper experiment. That nice chap Bill Gates has also purchased and made freely available these Richard Feynman lectures. Then you can make friends with your glands.

Humour

Despite being a throwback to the early part of the internet age animated gifs still seem to be going strong, my favourite being this one. One wonders what the elephant makes of it. I enjoyed several of these workplace training videos. Ten is probably the funniest, number four is just wrong (who says such things?) and two is perhaps painfully true. However, I found this collection of 1950's propaganda to be more disturbing than funny. For those with a non-PC sense of humour this garage door opener should appeal, although I much preferred the Wayne's World echoing twist to this fast food folk song. Finally this "remix" of an NWA classic is just awesome.

Geekdom

One of the joys of this internet age is that the powerbase of the world is shifting ever more towards the geeks of this world. I found this short talk by the guy who brought you captcha (you'll know what it is when you see it) to be really interesting. Although this vision of the future of dating may be less encouraging. Finally, this really appealed to my sense of humour.

What I did at NAPC

2009-06-30T03:59:00.009Z

1) Wrote my talk at the last minute.
Always a great idea. It's not like I ran over and had to be booted off stage. Worst of all I realised later that I must have been completely oblivious to my two-minute warning. Still, apparently it came across OK.

2) Saw some of my heroes speak.
Including Ken Miller and Sean Carroll, both of whose popular science books I have read as well as Michael Donoghue (whose contributions to evolution have been truly diverse), Steven Stanley (father of macroevolution) and Phil Gingerich (of fractal rates of evolution fame) - all legends.

3) Became addicted to shuffleboard.
A bit like a dry version of curling, but without the brushes. I exclusively play the doubles version and it turns out I have a penchant for the violent 'kamikaze'-type shots.

4) Got my ass whupped at basketball.
It seemed like such a good idea. I mean, how good can a bunch of palaeontologists be at sport? Weren't we all the geeks at school who hated physical education? Anyway, I entered myself and a couple of friends in the 3-on-3 tournament under the name "The Bristol Deciders" (retrospectively the Chickencows would have been better). It seemed victory would be ours when at one stage we were the only team to enter, but as it turned out there was one other - not enough for a tournament. Instead we played a pick up game with such luminaries as Arnie Miller, Mike Foote, Tom Baumiller and Shanan Peters involved. It's safe to say against the average American I am atrocious at basketball.

5) Visited the Creation Museum.
This was a truly bizarre experience. Some 80 palaeontologists, including Arnie Miller, Mike Foote, Christine Janis and myself boarded a couple of school buses for the short drive into Kentucky. I got photographed by the Cincinnati Enquirer, Akron something-or-other and the New York Times. In the end the story made both the New York Times and Bucyrus Telegraph Forum, but the highlight has to be the back of my head appearing in this article, justifying my claim to be the back of the head of palaeontology. It's a shame I'd already gotten my business cards done.

6) Enjoyed a mini PBDB summer course reunion.
It was the first time I had seen three folks from the PBDB summer course in two years and we even squeezed in a reunion photo. All of our instructors were also at the conference and it was good to see them again (and have them remember my name).

7) Learned how to play bocce ball.
Not as fun as shuffleboard, and Bristol taking on Berkeley ended disastrously. Still bocce ball was good fun.

Bits and bobs

2009-06-15T15:45:00.003Z

Here are a few more things I've found whilst stumbling.

From http://www.vivapixel.com/:

From http://farleftside.com/:

From http://www.birdandmoon.com/:

Dinosaur supertree - now zoomable!

2009-06-07T10:35:00.002Z

I just got an email from Mike Klymkowsky with a link to an online, zoomable version of the dinosaur supertree. A preview is shown below. To see the site yourself click here (the link to the dinosaur tree is on the left hand bar). It's cool to see other people making use of it, especially as we couldn't fit this figure into the actual paper.

My Top 9 Tips For Fantasy Football

2009-05-25T10:06:00.009Z

For a few years now I have been playing the official Fantasy Premier League game. Not only has this been a distraction from the heartache of watching Man United reach 18 league titles, but it is completely free and allows you to be entered in both a global competition as well as smaller leagues with friends. Having just won the latter for the second year in a row I thought I'd post some tips on what I think is the best strategy for success.
1) Make the best player your captain. Even if they appear to cost the Earth picking the highest scoring player and making them your captain is key for the simple reason that the captain's points count twice. To save money here is a false economy as the doubling cancels out any expense. Of course the trick is actually picking the highest scoring player, but usually this is the best midfielder at a top four club, i.e. Fabregas, Gerrard, Lampard or Ronaldo. Choose wisely, however, as their great expense will make transferring them later tricky, e.g. if you want to 'upgrade' to a more expensive player you will often need to make two transfers, costing you gameweek points.
2) Fill the bench with the cheapest players. Don't waste money on players that you will never use. Sure, it's great if you get injuries to have cover, but it is a false economy to have someone decent on your bench when the money could be better spent on filling your starting eleven with high scorers.
3) Play your wildcard early. You get one chance per season to make as many transfers as you want in a gameweek without it costing you points. It is pointless to save this for later as by the end of the season players will cost what they are truly worth and bargains are hard to find. Everyone makes mistakes with their initial selection as in my experience preseason form is pretty awful indicator of how players will do when the PL kicks of for real. In addition there is almost always someone who makes the headlines early on for unexpectedly strong performances, e.g. Hull's Geovanni at the start of the 2008-09 season, and you want to get these cheap, but high scoring, players in your team as early as possible. Use your wildcard early to draft in the form players and get rid of the dross. If you need any further convincing then you sould note that the 2008 winner played his in gameweek 2 and the 2009 winner in week 6.
4) Check the fixture list. To get the most out of a player you need them playing when they are on form, but it also helps if their upcoming games are either mostly at home, against lesser opposition or, as is often the case later in the season, are twice in a gameweek. Similarly, it can hurt you if you bring in some wonderkid just before they go on the road against the big four.
5) Don't panic! Just because you get an injury, a suspension or a team doesn't play in a gameweek don't drop good players. Apart from it costing you points if you go over your one transfer per week you may find with shifting prices you can't afford to buy them back. Generally speaking you should only transfer out players that aren't performing for you anymore.
6) Never make more than one transfer a week. As this costs you 4 points it is almost always a false economy, see point 6. The only exception to this is the wildcard, see point 3. I make one (free) transfer a week and so did the 2009 winner.
7) Watch football. A simple one really, but checking a player's fantasy stats won't tell you how well they are actually playing. Just watching Match of the Day can really help identify your next acquisition, or who to get rid of. Apart from anything else I have found that injuries and suspensions can be slow to be added to the Premier League's website. It won't help your cause to make captain someone who got stretchered off in their last game.
8) It's not all about goals. Some of the highest point scorers in the game are defenders and these are often the most value for money. Strikers are actually the least efficient players (in terms of points per million cost). Don't rule out playing 5-3-2.
9) Pick a balanced side. Finally, distributing your team across multiple different clubs is alway a good idea. This is basically "don't put all your eggs in one basket", but it can severely affect your gameweek total if you rely heavily on just a few teams who end up with bad results. In addition, you may actually like to rotate some of your cheaper players. For example, I had both Schwarzer (Fulham keeper) and Jaaskelainen (Bolton keeper) for most of 2008-09, and would regularly switch who started depending on who Bolton and Fulham were playing.

A thought

2009-05-07T13:41:00.005Z

A brief post to keep this ticking over, but recently I've had a geeky thought probably from watching too much Battlestar Galactica*. In the show the ships are able to make "jumps" across space exceeding the speed of light. This made me think if we could "jump" away from Earth, but still within an unobstructed view of it then we would essentially be looking at a past Earth, potentially much older than present. Better still if we could magnify our image to a high enough resolution, and through gaps in the clouds, we ought to be able to see what was going on at the surface and hence ultimately get the best picture of past life we're ever likely to see. OK, OK, we can't make supra-light speed jumps and currently we can't even get high enough (i.e. literally "life-size") resolution of nearby objects like the Moon. However, there is a theoretical possibility of achieving the former through something like an Einstein-Rosen bridge - the plot vehicle used in Deja Vu - and our imaging could still get a lot better, e.g. even correcting for the bending of light by gravitational bodies between the viewer and the (past) Earth.

What's more if we could continually traverse away from the planet at supra-light speed instead of stills we could actually get a (greatly speeded up) movie of life in reverse. Of course, being a palaeontologist I'm thinking of things like dinosaurs - we could know once and for all what killed them, but there would be immense scope for viewing human history too. The possibilities are almost endless (if restricted to plan view). Am I the first person to think this? Anyone out there from Hollywood want to buy the rights off me?

* no spoilers please - I'm only up to season 4.

Stumbling

2009-04-03T16:27:00.003Z

Greetings (y')all. It's been a while since I've put something up here, partly because of moving to a new city and new job, but also because my internet time has been dominated by a new obsession, namely "stumbling". If you haven't tried it yet I recommend it. Here's what I've learnt so far:

1) According to Leviticus, I should really be allowed to own a Canadian.

2) The Japanese have some have odd ideas about Obama.

3) Despite what you may have heard, paper can actually be folded 12 times.

4) My knowledge of the states could be worse.

5) There is such a thing as library porn. (I must confess, I am a fan.)

6) A best man can really ruin a wedding.

7) Kids really shouldn't be allowed to use the internet for their homework.

8) True random numbers can be gotten if you really want them.

9) The Tauntaun sleeping bag may become a reality.

and, 10) I have some new tips for indulging in my my favourite pastime.

Rube Goldberg machines

2009-02-18T22:09:00.005Z

We've all seen these - most famously in a Honda advert - but I've just found my new favourite. Learn more about the man here.

Gibbon vs. tiger cubs

2009-01-30T17:33:00.001Z

Bizzare...

My top 20 most important fossil sites

2009-01-30T16:18:00.015Z

I have made my decision. I've basically gone for (what I believe is) a good mix of age, geography and recency of discovery/time of greatest interest. In chronological order, oldest first.

1. Ediacara Hills, Australia

Geologic period and biota named after them
Amongst earliest unequivocal evidence of multicellular life
True affinity of the frond-like taxa still disputed (possible early animals or something altogether unique)

2. Doushantuo, China

Precambrian sediments that include embryos of earliest animals
Astonishing preservation (embryos have perhaps the lowest preservation potential of any living thing!) at very important and poorly understood point in animal evolution

3. Burgess Shale, Canada

Most famous of several Cambrian lagerstatte (sites of exceptional fossil preservation)
Soft-bodied preservation of diverse taxa
Important window on the early diversification of animal life

4. Soom Shale, South Africa

Ordovician age, perhaps the period when biodiversity increased most rapidly
Important site for early vertebrate evolution with soft tissue preservation of the conodont animal as well as various arthropods

5. Herefordshire lagerstatte, UK

Unique form of preservation: fossils have to be destroyed to reveal their affinity (successive slices are ground away and a picture taken leading to a exquisite 3D reconstructions)
Some of the rarest fossils known from here (e.g. one of only 4 sea spiders known from last 500 million years)
Only real lagerstatte from whole of Silurian
Exact location a secret

6. Rhynie Chert, Scotland

Volcanic preservation of Devonian lake biota
Predates vertebrate colonisation of land and is one of the earliest terrestrial ecosystems preserved
Plants, fungi and terrestrial invertebrate fossils

7. Gogo Formation, Australia

Fantastic 3D preservation of reef fossils
Particularly important site for fish, with muscles and nerves preserved in microscopic detail

8. Mazon Creek, USA

Carboniferous age
Preserves both land and sea floras and faunas as casts
Extremely diverse (hundreds of species known)

9. Joggins, Canada

Preserves forests of ‘coal age’ (Carboniferous) in situ
UNESCO world heritage site

10. Karoo, South Africa

One of the longest periods of continuous sedimentation (Permian through Triassic)
Spans largest ever mass extinction (“When Life Nearly Died”)
Famous for showing step-like evolution of mammals

11. Jurassic Coast, UK

Historically important to founding of palaeontology and geology
Abundant marine fossils of Jurassic age (e.g. ammonites, belemnites)
Marine reptiles also found here most famously by Victorian collector Mary Anning

12. Solnhofen, Germany

Late Jurassic age
Lagoonal deposit with very rare fossils
Forever associated with most iconic fossil of all: Archaeopteryx

13. Morrison Formation, USA

Late Jurassic age
Abundant dinosaurs (Allosaurus – most completely known carnivorous dinosaur, Stegosaurus and various iconic sauropods)
Historically of interest in ‘bone wars’ between Cope and Marsh
Still important field site at present day

14. Jehol, China

Fantastically diverse terrestrial biota of Early Cretaceous age
Includes almost all known feathered dinosaurs, which have proved instrumental in closing the morphological gap between dinosaurs and birds
Many other rare finds include: gliding lizards, two-headed reptile, early birds

15. Santana, Brazil

Early Cretaceous inland sea deposits
Includes fish, many pterosaurs (a very rare fossil elsewhere), insects, turtles, plants and various invertebrates

16. Green River, USA

Eocene age
Extremely rich preservation of fossil fish: literally millions of specimens
Consequently rare acts are preserved, e.g.:

One fish preserved midway through eating (swallowing) another
A stingray giving (live) birth

17. Messel Pit, Germany

Eocene age
Diverse terrestrial biota
UNESCO world heritage site

18. Dominican Amber, Dominican Republic

Oligocene to Miocene age
Dominican amber, unlike Baltic amber, is clear and so fossil inclusions are more easily seen
Insects and spiders common, but a lizard has also been found
‘As is’ preservation as tree sap has unique bacteria-killing property that means even the bacteria present inside the individual prior to death are unable to effect decay

19. Fossil Hominid Sites of N.W. South Africa (Sterkfontein, Swartkrans, Kromdraai, and environs)

Various fossil hominid sites spanning over 2 million years of human evolution
Includes fossils (Australopithecus africanus) as well as evidence of cave dwelling, fire domestication etc.
UNESCO world heritage site

20. La Brea Tar Pits, USA

40,000 to 25,000 years old
Fossils preserved in tar pits many of which are still bubbling up out of the ground
Many, many fossils of dire wolfs, sabre-tooth cats etc.
Specimens from here in many museums around world (if you’ve seen a sabre-tooth cat it is almost certainly from here)
Located close to downtown LA!

If you go down to the grasslands today...

2009-01-29T13:04:00.001Z

A friend pointed me at this recently. I guess it's pretty old, but still pretty amazing!

The 20 most important fossil sites

2009-01-24T12:30:00.008Z

As part of my consulting job with Dorling Kindersley I have been asked to compile a list of the top 20 most important fossil sites and was hoping that my small, but extremely intelligent, readership might want to contribute. (Not that I'm trying to get you to do my job for me mind.)

Here is a few starters for you:

Jehol
Solnhofen
Burgess Shale
Chengjiang
Hell Creek
Patagonia
Isle of Wight
Soom Shale
Karoo
Doushantuo
Rhynie Chert
Gogo Formation
Mazon Creek
Joggins
Santana
Green River
Dominican Amber
La Brea

I make that 18. Of course I could always just steal Wikipedia's lagerstätte list, but there are far more than 20, and does something have to be a lagerstätte to be important?

All comments greatly appreciated.

I propose a new era...

2009-01-21T14:21:00.003Z

Dating phylogenetic trees of fossils

2009-01-08T15:25:00.015Z

A problem I have encountered repeatedly in my PhD is that the way palaeontologists date their phylogenetic trees means lots of branches represent zero million years. In fact, at every single bifurcation one branch is always zero million years in length. This fact is somewhat hidden graphically as published trees drawn against stratigraphy (like this one) usually include some additional default length so that individual branching events can easily be seen. In reality, with branch lengths appropriately scaled, they look more like this:

Phylogeny with branch lengths scaled to time and taxon names removed

So why does this matter? Well the primary reason (as far as I am concerned) is that this screws up the standard calculation of evolutionary rates. (A rate being some change over time; with a denominator of zero the result is infinity.) A secondary problem, then, is that zero-length branches simply aren't realistic.

How to get around this? Well early authors (notably Karl Derstler and Peter Forey) independently went for the simplest option - simply add something to the divisor in each case, 1 million years, 2 million years etc. This may be fine in some cases, but for large phylogenies this divisor can end up pushing branching events really far back in time. (In one example I worked on, lungfish appeared back in the Precambrian.) Not so good.

The best method I am aware of was developed in a paper by my colleague Marcello Ruta and co-authors. They argued the best approach was for zero-length branches to 'share' some time with a preceding branch of positive length. Furthermore, they argued that the proportion of sharing should be linked to the number of character changes on each branch. This essentially assumes an underlying model of equal-rates of character change and hence is biased to what would normally be the null hypothesis.

The Ruta et al. approach was adopted by us in our Science paper, but with a slight modification. As we were using a manual implementation we (by which I mean Steve) used a simpler approach whereby the shared time was split up equally.

Recently I have returned to this problem and have now constructed R code to automate the process. Here is what the above tree looks like using the equal sharing method:

And here is what it looks like using the Ruta et al. method:

For the rate calculations (and the group) you will have to wait for the paper.

My 2008 Highlights

2008-12-31T11:57:00.018Z

Time for a brief vanity post as this year has been reasonably good for me. Here are my ten highlights in roughly chronological order:

1) The Boss and E Street at Old Trafford
This was my first stadium gig and my first trip to the 'Theatre of Dreams'.

2) Fantasy Football
After a couple of years of dismal perfomances I finally won my fantasy football league thanks in large part to signing Ronaldo at just the right time and making him captian.

3) Radiohead at Malahide Castle
My first ever Radiohead gig and an enjoyable weekend spent in the area just North of Dublin.

4) Three peaks
I finally climbed Ben Nevis as well as return trips up Snowdon and Scafell all in one weekend.

5) Media-whoring
(My degoratory term for the courting of radio, newspaper and TV by scientists). I must confess that my earlier scoffing at such things was tempered somewhat by my own experience. I enjoyed being interviewed although some of the resulting articles had the typical ring of inaccuracy and the "quotes" assigned to me were hilarious - apparently I have predicted that we will eventually find the Triassic was when dinosaurs were most diverse.

6) My first Science/Nature paper
Almost by accident a study conducted by Steve Brusatte that I had helped out on with some of the numerical analyses was ready to go at a time when Science were publishing a number of Triassic archosaur papers. I suggested we at least give them a try and lo and behold the best reviews and quickest acceptance that I am ever likely to experience occurred. Quite rightly most of the credit goes to Steve, but this was (and is) a fantastic addition to my CV - thanks Steve!

7) My first lead-authored paper
The media-whoring mentioned earlier accompanied the online publication of my first lead-authored paper, although technically it didn't appear in proper print until November.

8) My first post-doctoral position
Just as I was finishing up my PhD a job was advertised at the NHM that well suited my rather odd set of skills (being a paleontologist who doesn't look at fossils) and I was lucky enough to get an interview and an offer. This means 2009 will see me move to London's fantastic Natural History Museum.

9) PhD
Exactly six days after being offered the job came my dreaded PhD viva. I can't say it was an enjoyable experience, but it was one I survived with only minor corrections.

10) Newcastle United 1 Liverpool 5
As she did last season, my Mum managed to get tickets at St James Park for the visit of my beloved Liverpool. Sitting with the home fans meant I had to keep quiet as we romped to our most convicing victory of the season as we close out the year top of the Premier league. Now let's have no mention of this...

How big is your species-area polygon?

2008-12-13T17:42:00.038Z

Following on from my dino world post I have recently been trying to work out how to calculate the area of a species' (or other taxon's) range given a set of occurrences as latitudes and longitudes. In theory this is very simple: you draw a convex hull around your occurrences, split the resulting polygon into triangles, measure the area of each and sum the results. Simple, right?

Trouble is, when your coordinates are actually latitudes and longitudes things aren't as easy. Imagine this simple scenario:

Which polygon is largest, the blue or the red? On this projection they appear equal and this is because the distance, measured in degrees of latitude and longitude, between each set of points is exactly the same. However, although latitude is truly a measure of distance (one degree is 111km) longitude is not. At the equator one degree of longitude is equal in distance to one degree of latitude, but closer to the poles this distance declines to zero. This is because our polygon is really a spherical polygon.

How do we measure the area of a spherical polygon? Well, in the same way. we split it into spherical triangles and measure the area of these. However, to measure the area of a spherical triangle we need to know, not the lengths, but the angles (A, B and C, given in radians) as well as the radius (R) of our sphere:

So all we really need to do is work out those angles, but our data is latitudes and longitudes. More technically, we are providing the location of our polygon's vertices.

The easiest way to do this (Bevis and Cambareri 1987) is to artificially move each point to the pole, then the angle can be calculated as the difference between longitudes. However, this isn't quite as simple as it sounds as each angle can be measured twice, once for the 'interior' and once for the 'exterior'. So, for example, there may be 40 degrees of separation in one direction and 360 - 40 = 320 degrees in the other. The reason this confusion arises is that the sides of a spherical polygon are actually the sides of two spherical polygons, both an 'inside' and an 'outside'. (Both are finite, and hence, both are measurable).

Bevis and Cambareri (1987) suggest a way around this is to use an algorithm that measures the area based on the sequence the points are fed to it:

If the points are fed in clockwise order then the internal angles, and hence internal polygon (1) is calculated (shaded area, left-hand plot). If in anticlockwise order then the external polygon (2) is measured (shaded area, right-hand plot).

So how big is your species-area polygon? Well, if you really want to know you can calculate it using the Bevis and Cambareri method (I have put an R implementation on my website here).

Reference:

Bevis, M. and G. Cambareri, 1987. Computing the area of a spherical polygon of arbitrary shape. Mathematical Geology, 19, 335-346.

Interesting new website

2008-12-09T09:55:00.004Z

I recently stumbled across this new website:

http://www.academia.edu/

It is basically a network of academics, but you have to sign up to be part of it. Notable members are Richard Dawkins and that Stephen Hawking chap. Definite lack of palaeontologists at the moment though. Sign up! Be my contact!

My page here:

http://bristol.academia.edu/GraemeLloyd

Dino World

2008-12-07T20:25:00.011Z

I am about to give a lecture on dinosaur palaeobiogeography here in Bristol and was tinkering with some data from the Paleobiology database (PBDB) and thought I'd upload the above image for your delectation.

The PBDB recently added two new data fields: palaeolatitude and palaeolongitude. I'm not entirely sure how these are done, but basically any fossil occurrence that has latitude and longitude data added also gets a palaeolatitude and palaeolongitude. Whilst preparing my talk I thought I'd stick up a world map with all of the dinosaur occurrences included on it, but decided to plot out the original positions too.

The above graph shows the modern location of each fossil locality (a light blue circle), it's original position (dark blue circle) and, so you can see how these link up, a red line connecting the two. The resulting image thus shows the 'tracks' along which the modern continents moved. (FYI: the graph was produced in R using the 'maps' library).

There are problems with this plot, however. There are three lines which are quite long and cross over other lines quite obtusely. The upper one of these (leading from the northeast of Russia to somewhere North of the Bering Strait is likely an artefact of drawing the plot on this particular projection. (In reality it should cross the Date Line and not wrap around the Earth in a whole different direction). The two others (the very southern line and the Japan-to-Atlantic line) are a bit harder to explain, but likely they are the result of some kind of error.

Still, I'm quite happy with it.

Who is my best friend, statistically speaking?

2008-11-09T00:48:00.013Z

Those of you who use the social networking site facebook may be familiar with the Friend Wheel application which takes your friends and plots them out as nodes along the edge of a circle. It then joins with a line each of your friends who are friends with each other.

My friend wheel is shown above, but who is my best friend?

I reckon I can outgeek John with this one. Surely (!) my best friend ought to be the person who has the most friends in common with me, i.e. the one with the most lines emanating from their node above. Because it would take me too long to work this out for everyone I will limit myself to those who blog: John, Manabu, Sarda and Dave.

It turns out my best friend is easily Manabu (53 friends in common), then Dave (34), Sarda (31) and John (29). However, a raw count might not be the best measure. For example if John only had 31 friends and Manabu had a thousand then surely John would be my best friend because almost all his friends would be my friends. Visually this could be represented as a Venn diagram like this:

Each circle is a person and the area of the circle is the total number of friends they have. In this example I am circle A (I'm very popular, of course) and I have two friends (circles B and C) who share friends with me (represented by the area of overlap). The raw number of friends is about the same, but friend C's circle overlaps with mine much more and so between the two I would consider C to be my best friend. (Of course B and C may also share friends, but representing this would be where Venn diagrams get complicated).

So mathematically speaking my best friend would be the one whose number of friends in common with me is the greatest proportion of their total friends. Let's call this the BFI (Best Friend Index), which logically ranges from 0 (no friends in common) to 1 (all friends in common). It turns out that Manabu has the highest BFI (0.47), but what if I wanted to draw the Venn diagram reflecting this relationship accurately? This is where it gets really geeky.

First we need to draw two circles (one for me, one for Manabu) with the area being the total number of friends we each have. This is easy, right? The area is πr², so to draw the circle we simply divide our area (number of friends) by π and then root the result. This gives us the radii needed to draw the circles.

Now it gets a bit more complicated. We know the size of the area that the overlap should be (53 friends), but this area has an odd shape that represents two segments of a circle. One for me and one for Manabu. But we cannot simply halve the total area between the two circles as the chord lengths will not match if the circles are different sizes (which they are).

This hurt my head for a bit until I found the answer here. So the area of overlap (A) is given as:

Where (R) and (r) are the radii of our respective circles and (d) is the distance between the two centers - the thing we need to know. So by rearrangement we get:

Um, actually this was a bit hard for me so I posted a question on a maths forum and it seems that this equation is not rearrangeable. The only way to get d then is by an approximation method. I tried to do this using the Newton method, but this requires establishing the derivative of the above equation. Again, beyond my abilities. But after enlisting the help of a friend it turns out this too is impossible as it involves the root of a negative. So the only solution was to write my own extremely inefficient approximation method in R. Here, then, is the Venn (or is it Euler?) plot for Manabu and myself:

This may all seem a bit silly, but it could easily be adapted to cover other things (e.g. favourite music and films in common etc.). If I were a more adept programmer I might have even turned this into a facebook application.

Deepest fish ever

2008-10-07T18:58:00.004Z

Arent they cute?

Famous again

2008-09-11T21:22:00.004Z

I'm famous again. Well, sort of. I played a fairly minor role in some interesting new research on the rise of the dinosaurs that suggests it was their competitors, the crurotarsans (crocodiles and their antecedents), that had the greater range of body plans and indistinguishable rates of evolution back in the Triassic when both groups first appeared. The dinosaurs came to dominate, perhaps not because they were superior, but simply that they got lucky with two rounds of mass extinction hurting the crurotarsans much more, leaving only the true crocs to soldier on through the Mesozoic.

Goat-based humour

2008-09-10T20:45:00.007Z

Goats seem to provide a decent history of humorous stories, at least on the BBC website. First was the Sudanese man forced to marry a goat, that sadly later died. And most recently a number of goats were freed from prison after being unfairly "charged with being sold illegally by the roadside." This put me in mind of perhaps the funniest youtube clip I have ever seen:

Reading level

2008-08-31T07:09:00.004Z

I saw this on John's blog and thought I'd see if I could match him. (Apparently so). But how does it work?

Back once again

2008-08-30T16:37:00.005Z

Hi all. It's been a long time, but I have decided to attempt resuscitation of this blog (which still gets more traffic than my 'proper' web site). Check back soon for a post on my fifteen minutes of fame following the publication of my first lead-authored paper on a new dinosaur supertree.

Mystery organism revealed

2007-04-02T16:18:00.002Z

The culprit is the model organism, Onthophagus nigriventris. Although most of us will know it as a dung beetle. So Sarda was right, if vague. John Orcutt's brave descent of the Linnean hierarchy went unrewarded, but John Hopkin came closest - even going so far as to provide the correct genus. I, however, was spot on.

Well done me.

You might like to know that the striking horns in the original photo are just one of a variety of phenotypic expressions in this species (see photo below).

Mystery organism

2007-04-01T15:04:00.002Z

As Sarda has instituted the 'mystery fossil' I thought I might steal her idea (which she stole from someone else anyway) and have a mystery organism instead.

I came across the above in a paper I was recently reading. Can you guess what it is?

The imaginings of children

2007-03-23T20:23:00.002Z

Comedy may be about timing, but humour is about juxtaposition. I came across this on the New Yorker's website:

The Wisdom of Children, by Simon Rich

A Conversation at the Grownup Table, as Imagined at the Kids’ Table

MOM: Pass the wine, please. I want to become crazy.
DAD: O.K.
GRANDMOTHER: Did you see the politics? It made me angry.
DAD: Me, too. When it was over, I had sex.
UNCLE: I’m having sex right now.
DAD: We all are…

Not another gliding reptile...

2007-03-20T20:15:00.001Z

I haven't got hold of the paper yet, but PNAS is supposed to be carrying a contribution by Xu Xing and colleagues that describes a new lizard from the Early Cretaceous of Liaoning China. (Cue groans of 'oh no, not another spectacular fossil from China'). It's not just the preservation that is spectacular this time, but the splayed ribs supporting a skin membrane that look remarkably like wings. In fact that is their most likely function - not true flapping wings, but something that could be held open enabling the animal to glide.

For once though, China hasn't got there first. This is now the fourth group of reptiles to have independently evolved the same peculiar trait.

We have to go all the way back to the Late Permian, some 260 million years ago, for our first example. Back then it was Coelurosauravus and Weigeltisaurus from Germany and Madagascar respectively. United together in the family Coelurosauravidae it is assumed that these two taxa had a common ancestor in which the splayed-ribs-as-support-for-gliding-membrane adaptation first evolved, but these strange creatures disappeared almost as soon as they had arrived.

Only 40 millions years or so later (in the Late Triassic) it happened again. Icarosaurus and Kuehneosaurus from the US and Europe did pretty much the same thing - evolved this bizarre trait, spread out across the globe, then disappeared.
Another 60 million years later and we have Xianglong zhaoi, our brand new rib-splayed glider. Unlike it's predecessors Xianglong is a true lizard and yet it is not closely related enough to the living Draco (our fourth rib-glider; see movie) to share a gliding ancestor. We could be forgiven for thinking that there must be something about reptilian skin that stops them from making the (presumably) much simpler shortcut to a gliding membrane - just stretching some skin between the forelimbs and hindlimbs, as flying squirrels do. Only that's not true.

At the same time as Icarosaurus and Kuhneosaurus were taking in the Late Triassic air in what would become modern day Russia a creature called Sharovipteryx had made an appearence. Undoubtedly reptilian, although beyond that it's relationships are unclear, Sharovipteryx had developed not just a membrane between the two pairs of limbs, but another between the legs and tail and even one between the neck and arms. Overall this made a triangular-shaped membrane that is unique in nature. Although some authors have suggested Sharovipteryx may be the ancestral pterosaur it is more likely another oddball that disappeared as soon as it had arrived.

There are a number of mysteries here. Why did so many lineages go down the gliding route the 'hard way'? Why did none of the groups possessing this odd trait persist for for more than a few million years? Why do we have so many fossils of a group of animals that have such a low preservation potential?

Any ideas?

Where is evolution fastest?

2007-03-16T11:47:00.001Z

An incontrovertable fact of life is that species diversity is highest in the tropics and hence it has long been thought that rates of evolution are also highest there. Just last year this was put to the test by Shane Wright and colleagues from the University of Auckland in a paper published in PNAS last May. They examined rates of molecular evolution and showed that tropical plants did indeed seem to be evolving at a faster rate than species from the same genus found in temperate latitudes. Their preferred explanation was elevated rates of mutagenesis.

However, today in Science the whole notion of evolution being higher in the tropics was cast into doubt. Jason Weir and Dolph Schluter at the University of British Columbia took a different approach to examining speciation rates. They took sister-pairs (two species who are more closely related to each other than anything else) of birds and mammals and plotted out the time of divergence against the probable latitude of their common ancestor. Although most of the taxa had shared ancestors at low (tropical latitudes) those with a recent ancestor were concentrated at higher latitudes. When they fitted their data to a birth-death model using maximum likelihood they show a linear relationship between latitude and speciation rate (lineages per million years).

So, who's right? As a student of both evolutionary tempo and biogeography I find such links between the two interesting. Leaving the issue of taxa choice (plants versus birds/mammals) aside, I think it is crucial to point out that the two sets of authors are looking at two fundamentally different questions. Wright et al. were interested in the rate of molecular (DNA) change whereas Wier and Schluter were only examining the frequency of speciation (when one lineage splits into two). These two phenomena aren't necessarily interlinked. In fact Wright and colleagues even stated that, "greater rates of speciation in the tropics do not cause higher rates of molecular evolution."

Perhaps the most interesting conclusion from today's announcement is that tropical diversity was built up over an extended period, suggesting that it is the environmental stability of this region that has led to the huge build-up in species.

The world gets a new cat

2007-03-15T14:05:00.001Z

It is very rare to find new species of living mammals and rarer still a top predator like a big cat, but in the news this morning it was reported that clouded leopards from Borneo and Sumatra are genetically distinct enough from their mainland cousins to be considered a separate species. Although this is yet to be published in a scientific journal (where a formal name will be attached to it) there is a video!

This is yet another example of how technology has changed the way we recognise species. It was DNA that told us the clouded leopard should be split in two, but now that has happened we are noticing subtle differences between the 'halves.' For example the new species has smaller 'clouds' and different patterns on the pelage that gives these cats their name. The Borneo/Sumatra species also has the largest canines of any big cat.

Andrew Kitchener of the National Museums of Scotland is quoted as saying "it's incredible that no-one has ever noticed these differences." Indeed, I looked up the clouded leopard in Kitchener's 1991 book The Natural History of the WIld Cats, where he states:

"The clouded leopard is an animal of tropical forests , being found at altitudes of up to 2,500 metres. In Borneo, however, it was found to be mostly terrestrial."

Back then it was only considered as a subspecies under the name diardi, and perhaps the recent divergence date (of one million years) is enough to forgive us for not noticing sooner. In any case this is a welcome new addition to our "entangled bank" and another neat example of evolution in action.

Ten wierd things about me

2007-03-14T22:29:00.002Z

1) I write my eights as two circles.
2) I have a burning desire to know Lemar's thoughts on mixed herbs.
3) I get emotional everytime I watch the climax to Brassed Off.
4) I think 'Endless Love' by Luther Vandross and Mariah Carey is one of the greatest songs ever recorded.
5) I collect my favourite quotes in a little book.
6) I have a pet lungfish.
7) When I was little I thought Harrison Ford was two people (Harris and Ford).
8) I also thought that all the superheroes and cartoon characters were once real, but like dinosaurs became extinct.
9) Before I wanted to be a palaeontologist I wanted to be a fighter pilot.
10) ...erm.