Monday, December 28, 2009

My 2009

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...

Wednesday, December 23, 2009

Even more distilled procrastination - animal links

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?

Tuesday, December 22, 2009

More distilled procrastination

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!


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.


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.

Tuesday, December 01, 2009

First Lines

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.

  1. 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
  2. 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
  3. 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
  4. 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]
  5. 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
  6. 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
  7. 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
  8. 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)
  9. The escalator strained slowly upward. In an old station like this what else would you expect? Night Watch, guessed by Rachel
  10. 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

Monday, November 16, 2009

Just some webcomic links

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.

Tuesday, September 01, 2009

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

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:

Tuesday, August 25, 2009

Changing the size and colour of placemarks in Google Earth

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">

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:


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.


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">

Friday, August 21, 2009

Multiple placemarks in Google Earth

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="">

The footer to:


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

<name>Hole name</name>

Where the coordinates are longitude, latitude and altitude respectively.


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



Lesson learned, and shared.

(Image and original code below.)

<?xml version="1.0" encoding="UTF-8"?>
<kml xmlns="">

Wednesday, August 05, 2009

For your procrastinating pleasure

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


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


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.


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.


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.


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.


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.

Tuesday, June 30, 2009

What I did at NAPC

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.

Monday, June 15, 2009

Bits and bobs

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




Sunday, June 07, 2009

Dinosaur supertree - now zoomable!

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.

Monday, May 25, 2009

My Top 9 Tips For Fantasy Football

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.

Thursday, May 07, 2009

A thought

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.

Friday, April 03, 2009


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.

Wednesday, February 18, 2009

Rube Goldberg machines

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.

Friday, January 30, 2009

Gibbon vs. tiger cubs


My top 20 most important fossil sites

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!

Thursday, January 29, 2009

If you go down to the grasslands today...

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

Saturday, January 24, 2009

The 20 most important fossil sites

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.

Wednesday, January 21, 2009

Thursday, January 08, 2009

Dating phylogenetic trees of fossils

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.

About Me

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Currently I am founding member, president elect and entire membership of SWEMP (the Society of Wonky-Eyed Macroevolutionary Palaeobiologists). In my spare time I get paid to do research on very dead organisms and think about the really big questions in life, such as: What is the ultimate nature of reality? Why is there no room for free will in science? and What are the implications of having a wardrobe that consists entirely of hotpants?