Sunday, October 03, 2010

Bibliophile links

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

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.


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

Thursday, August 05, 2010

Drunky Monkey

Wednesday, July 28, 2010

Thursday, July 15, 2010

Oh dear...

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!

Saturday, July 10, 2010

Open source: doing my bit

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:, 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?

Wednesday, May 12, 2010

Iron Sky Trailer

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

Monday, January 18, 2010

A meme of one's own

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.

Saturday, January 02, 2010

Stuff I'm totally going to do in 2010

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).

About Me

My photo
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?