Friday, 25 December 2009

Christmas Parties

It's been a year with a crazy number of Christmas parties. Unlike Erica I managed to make it to a good number of museum parties - 'the' museum party, PCU, workshop, life sciences and palaeontology. In addition there was a lunch for people on our floor, a meal with my relatives from Germany, the pantomime (Pamela Anderson and Brian Blessed), and the traditional Christmas Eve at the pub. Thankfully there is a break between now and New Year.

On her blog Erica mentioned the now (in)famous (in small circles) Dipsomania Dial - a celebration of joviality from 'Decent Chap' to 'Dead' (the party had a D and/or C theme). Here is the only photograph I have of it in full working order (thanks to a few people it sustained injuries caused by beer, cream and over-zealous handling).

Sunday, 13 December 2009

Bioinformatics and Norwegian pop bands

In the supplementary file to the recent paper on the Scratchpads project published in BMC Bioinformatics the Drupal module ahah_action apparently has the functionality required to provide 'a Norwegian pop band'.

Minor Flickr Fame

A photograph I took at the Pestival event this year and put on Flickr has been used by Schmap for a walking tour of Westminster. This is quite appropriate as Natalie and I did walk there from the Natural History Museum (stopping only for ice cream and traffic lights).

Sunday, 6 December 2009

Tuesday, 10 November 2009


For a few years I have been struggling along with JabRef. It has been pretty painful, but it is free and pretty portable (runs off a USB stick). Until a couple of months ago when I started using Mendeley. Mendeley comes with an in-build PDF viewer, metadata editor and the ability to upload my PDFs to a central server, so they are accessible (to me at least) from anywhere that has the internet.

The last few months of reference-managing have been absolutely wonderful (read 'have been as as wonderful as reference-managing can be).

Recently I hit the 500MB PDF limit, a bit of a bugger. Mendeley are planning on providing bigger accounts as part of a subscription service in the future, but have kindly agreed to give me a total of 1GB for now.

The killer question is will I pay for the premium service? Ideally I'd want to keep the free tool and get it to synchronise my files to a server of my choosing (I have many GBs of storage space to play with). Failing that though, as long as it's priced about the same as Flickr (i.e. noticeably less than vimeo), then I probably will.

Tuesday, 13 October 2009

In despair...

Some person on Facebook decided I should get an invite to the Facebook group this is ENGLAND!!!! STAND UP N B COUNTED!!! As if the random capitalisation and use of 'N B' as 'and be' didn't suggest these people were a little on the dim side the quote below is the group's description.

"this is our country where we choose illegal immigrants over our soldiers we make sure they are well fed n equipted over our soldiers who are dyin fightin sum f**ker elses war we live in a country where half of the ppl dont even speak our language yet get more rights than us i say ditch political bullshit send them bk we only have had problems since they came if you werent born here then fuck off home our priorites should be with gettin our boys home safe CHARITY starts at fuckin HOME

i would love for one ov us 'common ppl' t go for prime minister we live in this shit hole that is now england its not england though its a load ov political correctness went wrong if u ask me! if u agree JOIN THIS GROUP
STAND UP AND BE COUNTED !!!!!!!!!!!!!!!!!!!!!!!"

There is a remote possibility they'd have a point, but only if Britain was a single cohesive culture that had been that way forever. But instead we Britons are a mongrel race with origins in Denmark, Norway, Germany, the Roman Empire, France and elsewhere (and we haven't even hit the days of empire yet).

That aside, who chose to go to war? Our government. How many people speak English in our country? Most. Who can't spell people? You. Who doesn't recognise 'ov' isn't even a contraction? You.

If you understand the history of Britain isn't as a cohesive race, that immigration (sometimes albeit through invasion) has for millennia been part of our culture, and that we ourselves have been known to emigrate (often using force) then feel free to be proud of being British, I am (despite not being at all proud of some of our behaviour over the years). If you use patriotism as a thin veil for racism then the rest of us would quite like it if you didn't do it in our name.

Monday, 12 October 2009

I am not Ed Baker...

...or at least the one you may think I am.

In the last week I have been confused with E. D. Baker a (female) author of books for children ( see here and here) and also Ed Baker - a hymenopterist from Cardiff.

I am currently basking in the glory of other people's fame!

Saturday, 10 October 2009

Uncluttered Tube Map

Telling us what we always knew but never wanted to admit. People don't come to the Natural History Museum to look at insects, instead they want to see some statistical blips incapable of surviving beyond the K-T boundary. One day, they will learn.

Sunday, 27 September 2009

Writing for the Web

Writing for the web is a subject I've had some interest in for a while. Indeed, I have been writing here, with varying regularity, for the best part of two and a half years. So I had mixed expectations about spending a full day being taught just how I should go about it. Of course blogging is slightly different from writing for a more "standard" website, but it does share most of the same principles.

Our course was run by Dan Fielder from StickyContent and was very interesting (yes, I was pleasantly surprised). I have just checked their website and have noticed their logo has some cool ants on it too. Mixing invertebrates and the internet is always of interest to me!

The course was a mix of exercises based on various ideas and concepts shown to be important by research or previous experience. There has been a large amount of research into how people read the web! We had some fun dismantling various sections of theNatural History Museum website (amongst others) and coming up with better alternative structures and phrases.

There was a whole host of tips, including the inverted pyramid approach (summarise at the beginning and ensure that wherever you stop reading a page you have the whole picture). Perhaps the most important lessons were brevity and clarity. It is possible to be comprehensive, clear and concise.

I intend to make a few changes to a number of sites over the coming months, so I will post anything vaguely interesting here!

Sunday, 20 September 2009

DISQUS Commenting Enabled

DISQUS is a very tidy commenting system that I have just enabled on this blog, Invertebrate Diaries and In Defence of Reason. DISQUS has some very neat features, the main one being the ability to track all of those comments you have made to blogs all over the interweb from one place (as long as those blogs use DISQUS).

You can sign into DISQUS using your Facebook, Twitter or OpenID credentials, or make a new account. It also has some pretty good spam filtering and comment management options. So I'd ask you to have a go and see what happens!

Saturday, 19 September 2009

The Great nofollow

Flickr and Wikipedia among others are sites that append the rel="nofollow" automatically to all external links. What does this mean and how does it relate to the free web?

First of all the rel="nofollow" attribute is added to hyperlinks to prevent search engines using the link between sites as part of their ranking process. In some search engine routines a link from page A to Page B is considered a "vote" for Page B by Page A. Google uses this method, although it has further routines for calculating the voting power of a link compared to others (a link or "vote" from a more important site has higher authority or "voting power" than one from a minor site).

In strict terms I guess the search engine should not follow the link to Page B, although some do and some don't. What is clear is that the big players in search technology (Google, Yahoo, Bing) do respect the notion that links with the rel="nofollow" attribute have no "voting power".

Why was such an idea considered necessary? In order to overcome the havoc to search engine results that could occur by people posting comments that include links to a large number of sites, e.g. blogs, photo-sharing websites, etc. In fact the attribute was the brainchild of a Google/Blogger sharing of minds before Blogger became part of the Google empire.

In an ideal world there would be no need for such a tag. Spamming would be removed by caring blog owners (or blog platform operators), or could be corrected for by the search engines (this comment is spam, I will ignore the link). Unfortunately neither of these is entirely possible, or entirely foolproof.

Blanket use of rel="nofollow" however seems a bit mean. For example I use Flickr regularly and I also blog regularly. Strangely enough sometimes I even post photos and blog about the same thing! When this happens I tend to link from my blog to my Flickr photographs, and from some of my Flickr photographs back to my blog.

When I link from my blog to Flickr my votes count. My blog actively increases the importance of my photographs (at least as far as search engines are involved). When I link from my photos to my blog however Flickr automatically adds a rel="nofollow" attribute to my links. The importance of my photograph cannot be shared with my blog. Flickr keep all of its voting power for internal site links (a great way to increase its importance at my expense). I should point out that this is for photograph, set and collection descriptions - not only comments.

In this way Flickr has become a PageRank super-sink - it pulls in importance from thousands and thousands of sites across the web, and gives nothing in return. It's the start of a uncontrollable PageRank monster. In fact I have started calling Flickr 'The Great Importance Attractor' - probably because I like physics and maths too much.

Is this fair? No, of course it isn't. I'm not too fussed if the links in comments on my photographs and blog posts get their votes removed. This is where the majority of spam comes from (besides forums I imagine). But my content? I think I should be able to link it together in a way that doesn't contribute to the making of PageRank monsters.

Friday, 18 September 2009

Install Acrobat Reader (acroread) on Ubuntu Jaunty

The medibuntu repositorires only have the amd64 version of Acrobat Reader, however an i386 version is available from Adobe here:

Open a Terminal window and navigate to the folder where the file was downloaded to. Then enter:
sudo su
Enter your password followed by the enter key.
chmod +x AdbeRdr9.1.2-1_i486linux_enu.bin
Follow the instructions to install Adobe Acrobat Reader. Pressing enter at the installation directory choice will use the default [/opt].

Finally type
to exit su.

Hope that helps!

Thursday, 10 September 2009

BodyWorlds and the Mirror of Time

Gunther von Hagens is, there is no doubt about it, a unique character. Suffering bullying due to his haemophilia during childhood he became interested in medicine and anatomy. Perhaps the most defining moment in his life was his imprisonment by the soviet authorities for trying to escape across the Czechoslovakian border ro Austria. Eventually West Germany purchased his freedom and he continued his studies at Lubeck. Since 1977 he has developed the technique of plastination - preserving animal (mainly human) tissue in polymers.

His exhibitions have not been without controversy - particularly in Germany, with some accusations of uing executed Chinese prisoners - however no legal challenge has prevented von Hagens from displaying his exhibitions.

The latest of these, BodyWorlds and the Mirror of Time, has recently closed in London, UK. The exhibition itself was truly excellent, showing the process of aging and how it affects your body from the inside and out. von Hagen's methods might not be to the taste of everybody but I have seen no better way of showing how bodies work to a lay audience. Yes, it would have been nice if it was less crowded, but we did go on the last weekend of the exhibition.

Unfortuantely no photos were permitted inside the exhibition - so I don't have any to show you here!

Sunday, 23 August 2009

Science Online London 2009

Unfortunately I only made it to the first few sessions of this conference as I had already made plans to visit Body Worlds (I shall blog about this later). The conference had a good share of skeptics and science bloggers and from what I saw (and heard after) it was a pretty awesome event.

In addition to the programme, the vent was mainly held in the Faraday Thatre of the Royal Instiution (home of the Christmas Lectures).

The parts that I saw were as follows:

Jack of Kent (lawyer and blogger) and Petra Boynton (sex educator, agony aunt, academic and blogger) talked about the ethical and legal issues of blogging. Some good stuff here - although as Jack says, the legal advice should not be taken as legal advice - just a few sensible pointers as to how to behave. The fact that something posted online is deemed to be published by the law in some ways shows how the law is ahead of the ICZN.

The next asession was 'Blogging for Impact' - or how to manage blogging and a career. Again, some good stuff and some good examples of when it pays off. Unfortuantely some institutions are way behind the times when it comes to thinking of blogging as a productive activity.

The break-out session om 'What is a Scientific Paper' raised many issues that have been being raised for a long time. Different disciplines have different requirements, but making data citeable was considered important, as was a new metric for recognising the impact of data.

Monday, 27 July 2009

Treasury, Petra

Treasury, Petra
Originally uploaded by edwbaker
It seems no work of Man's creative hand,
By labor wrought as wavering fancy planned;
But from the rock as if by magic grown,
Eternal, silent, beautiful, alone!
Not virgin-white like that old Doric shrine,
Where erst Athena held her rites divine;
Not saintly-grey, like many a minster fane,
That crowns the hill and consecrates the plain;
But rose-red as if the blush of dawn,
That first beheld them were not yet withdrawn;
The hues of youth upon a brow of woe,
Which Man deemed old two thousand years ago.
Match me such marvel save in Eastern clime,
A rose-red city half as old as time.

by John William Burgon (1845)

Wednesday, 10 June 2009

Why doesn't Bob Crow try solidarity with London?

On the ITV news just a few minutes ago one of my least favourite people in the world appeared wearing this polo shirt.

"So what?" you may ask, "Do you think that self-serving greedy train union representatives have to wear a different shirt for each public appearance?"

No. I just think instead of showing solidarity with Cuba he should show solidarity with Londoners. Everyone has to make sacrifices in an economic downturn - if he accepted the offer on the table then he wouldn't be second to Nick Griffin on the list of evil Britons, and people could go to work to help fix the economy. Sadly he has turned tube drivers, his union, and himself into objects of hate and disgust.

Tuesday, 9 June 2009

Grammar Fail. Tube fail. Link?

I can barely contain my anger at the RMT, and, more importantly, Bob Crow. Mention either of them around me for the next few days and be prepared for a long diatribe. Imagine how my rage nearly boiled over when reading the below:

"dan i bet you look great in your brown shirt, these people are only acting on there legal right when faced with huge job loses, which also effect family's as well, i have a crazy idea, how about keeping people in there jobs, so they can pay taxies to the country, its an idea maggie never had"

david, San Diego, U S A

Originally posted here.

Where do people learn that kind of grammar? I know I make mistakes (often kindly pointed out to me), but this is crazy. Rightly, or, more likely, wrongly, I find it almost impossible to respect this persons opinion, solely on the basis of this. Let's take a look.....

"Dan I bet you look great in your brown shirt, these people are only acting on their legal right when faced with huge job losses, which also effect families as well. I have a crazy idea, how about keeping people in their jobs, so they can pay taxes to the country? It's an idea Maggie never had."

David, San Diego, U S A

It's still not perfect - but it's better. Am I wrong? Can you take this man seriously? Maybe I'm just semi-consciously linking this guy's lack of grammatical ability with my disgust at the tube strike? Let me know...

Tuesday, 2 June 2009


Part of the eBiosphere conference involved several break-out sessions, one of them being on cybertaxonomy. Within minutes of the session starting we ran into the first problem: what is cybertaxonomy?

This is bound to be fairly contentious. Many of the people who were there are involved in projects that involve taxonomy and the internet, and would like to define cybertaxonomy in a way that their project lies slap-bang in the middle of the definition. In the end I think that Vince Smith's definition is perhaps the most useful, given the breadth of ideas and projects that should fall under the cybertaxonomy umbrella. (Incidentally Vince is the world's first (and only?) official Cybertaxonomist.)

"Cybertaxonomy is using computers and/or networks for doing taxonomy."

Then the thing took a bit of a nose-dive as people tried to list ideas and projects that they thought were related to a (somewhat vague) definition of cybertaxonomy. This was (for me at least) rather tedious - most of the projects I knew about already (as did most people I think) and I'd have rather spent the time learning something new, or at least making use of the fact that all of these people were together in the same room at the same time.

The discussion then covered a few of the community's favourite 'hot topics'. Intellectual Property Rights (IPR) being one that has been mentioned many times before. Personally I doubt that publishers will freely give up their exclusive rights to content for nothing - they will need incentives. Whether the incentive is a carrot or a stick is a matter for debate.

Randy Pausch Time Management Lecture

A few people I know could do well studying this!

Friday, 29 May 2009

I'm Back and have Flickr

I am now back from my trip to Illinois and Costa Rica. I will post some information about various things I saw on my Invertebrate Diaries blog.

I have also (finally) started uploading a photographic version of my life to Flickr. You can view my photographs here - although it will take me a (long) while to get everything up and organised as I'd like it!

Monday, 25 May 2009

Google Analytics

I've been a fan of Google Analytics for a while now. I use it on a number of websites that I'm responsible for (or otherwise involved with). I have recently been to Champaign, Illinois, to visit the Species File team.

I am pleased to say that Google Analytics is now available to Species File administrators, making a wealth of useful statistics available to developers and site builders. I hope that having statistics available will encourage people to further develop their Species Files.

Saturday, 25 April 2009

Roy Davies and The Darwin Conspiracy

During a brief down-time moment in Champaign, IL I have discovered something that I wrote a few months back and did nothing with. Roy Davies, author of The Darwin Conspiracy, came to talk to the staff of the Natural History Museum, London. I jotted down some thoughts after the event, so here it is, not particularly timely, but hey!

I imagine that Roy Davies was just a little nervous sat before the assorted staff of the NHM. Evolution is part and parcel of their trade. In fact, the process of evolution and one of its results, speciation, is what they study. To accuse one of its founding fathers, Charles Darwin, of fraud (essentially stealing his ideas from Alfred Russel Wallace) may be considered a heresey.

Although heresy was not the mood in the room when Davies had finished, and nor should it have been. Surprise was certainly present in some, but for the majority it was probably curiosity. Davies gives his sources, and until those who weren't totally familiar with all of them had checked them his claims cannot be discredited. I don't have a thorough enough background in Darwin's works and letters to even begin to formulate a reasoned response. Neither do many of the countless people who will criticise Davies for attacking a person who to them embodies reason and science (and to many also atheism).

I would like however to welcome Davies, a TV hack and journalist, to the world of skepticism and reason. We believe that any idea is open to criticism and review. Darwin's contribution to evolutionary theory is one of those ideas. Davies has read more of Darwin's works than many of Darwin's defenders. Science should not be threatened by Davies' ideas. If they are wrong they can be disproved. If they are right the history books must be re-written. So what? It shows that is the scientific method is applied to the history of science then reason prevails.

One thing that did come out of the event was a near-universal view that Alfred Russel Wallace made a significant contribution that is being increasingly overlooked.

Monday, 13 April 2009

Emptying the trash in Ubuntu

A friend asked me how to remove files from the Trash (= 'Deleted Items' or 'Recycling Bin') folder on Ubuntu that they did not have permission to delete.

This is trivial task if you know where the Trash is stored, for Ubuntu 8.04 or later just enter this at the terminal:

sudo rm -rf ~/.local/share/Trash/ *

Sunday, 1 March 2009

Saving Streaming Video

For sites such as YouTube and Facebook that stream video it's possible to save a copy of the streamed video. The general technique is to clear your temporary directory, load the video in your web browser and let it play to the end. Without closing the browser copy the cached file from the temp directory to somewhere else on your file system. You may need to give the cached file a .flv extension and download the codecs required to play Flash video if you have not done so already.

Creative Spaces: Museum Social Not working?

Few people would doubt the rising power and influence of social networks such as Myspace and Facebook. Millions of people use them to communicate and express themselves. That some of the UK's greatest museums should be represented is clear. It just seems they don't know how to go about it.

The answer is not to create their own social networking website. Trying to find what you want on the Natural History Museum website should convince you that it's best to leave social networking to the experts.

But more than that it comes down to what people want. I don't want to use a hundred different accounts across a hundred different sites (even with OpenID). I'd much rather our institutions, once they have seen the need for social networking, to fit it into what I do already.

Creating a museum page on Facebook would allow me to stay up to date with what's going on. You could even create groups for different departments, or for people who have been to see a certain exhibition.

Social networking has the added advantage of breaking down barriers. I have had people contacting me about phasmids on Facebook that wouldn't have been sent to me in other setting. Quite often this results in me having scientifically useful data.

So I guess the answer is two-fold. First, embrace what people are already doing. Secondly, don't prevent your staff from referencing their employer on social networking sites (as one nameless museum has) - especially when the possibilities of them doing amazing things is so great.

Wednesday, 25 February 2009

Misquoted phrases

Having recently been corrected over my corruption of "another think coming" I almost feel like I shouldn't post this. But I am anyway. It's Britain's top 10 misquoted phrases (correct version in brackets)!

) A damp squid (a damp squib)

2) On tender hooks (on tenter hooks)

3) Nip it in the butt (nip it in the bud)

4) Champing at the bit (chomping at the bit)

5) A mute point (a moot point)

6) One foul swoop (one fell swoop)

7) All that glitters is not gold (all that glisters is not gold)

8) Adverse to (averse to)

9) Batting down the hatches (batten down the hatches)

10) Find a penny pick it up (find a pin pick it up)

Friday, 20 February 2009

Blogger feeds and Drupal 6 Aggregator Issue

If you want to import Blogger feeds using the Drupal 6 Aggregator (core module) then you must use the RSS feed (just add "/feeds/posts/default?alt=rss" to the end of your blog's URL). If you don't then the aggregator will list posts correctly, but the links will all be to the same post.

Wednesday, 18 February 2009

Google Toolbar for Firefox on Ubuntu

If running Google Toolbar for Firefox on Ubuntu and you can't see the majority of the buttons then just go to Tools -> Add-ons and disable the Ubuntu Firefox Modifications. Restart et voila!

Thursday, 5 February 2009

Formula 1 at the Science Museum

I quite like Formula 1. It's a sport, but there's more to it than that. To win a race you need to a skilled sportsman, but you need a team of skilled managers, mechanics, engineers, scientists and so on. It's a sport that pushes the capabilities of us as a species in so many different directions.

I have argued with people about how important F1 is in the grand scheme of things (outside of the realms of sport and general rapidness). Thankfully I ill shortly have a new weapon up my sleeve - the Science Museum is putting on an exhibition about how the technological innovations of Formula 1 filter down to us mere mortals.

Formula 1 is also far superior to football in that it doesn't turn pubs into rowdy idiot halls that interfere with good beer and good conversation*.

*Both of these are sadly becoming harder to find if your choice of pub is the Black Horse, Dedworth Road, Windsor.

Monday, 26 January 2009

Google Docs

Over the last few days I have been guest editing the journal Cockroach Studies. This has required getting various people to proof-read and correct papers. Instead of the usual e-mailing to-and-fro and then amalgamating comments and corrections I have given the appropriate people to edit papers using Google Docs. This has saved time, and also has the advantage of automatically saving revisions. I can also watch people edit documents in real-time. Overall I'm very impressed!

Monday, 12 January 2009

gTwitter vs Twitux

In an effort to reduce the number of 'always open' tabs that I have in Firefox I have been looking for a desktop Twitter client. The two most popular Ubuntu (and other Linux system) solutions are gTwitter and Twitux.

At present gTwitter is still in beta, and has the advantage of being able to read others' updates and update your own from one window. However you can only see the full text for one message at a time. This isn't a major problem, but isn't the interface I prefer.

Twitux annoyingly requires you to update Twitter from a second window, but I still prefer it. I can see the full text of all updates at once, and the graphics seem to be that little bit cleaner.

Thursday, 8 January 2009

Largest Value Banknotes

Hyper-inflation does strange things for the denominations printed on banknotes. There has been some talk of the recent Zimbabwean crisis creating world record denominations on bank notes, and in all fairness 50billion and 100billion are unusually large. The record, however, as far as I am aware, is a 500billion denomination banknote from the dying days of Yugoslavia.

50billion denomination Zimbabwe

100billion denomination from Zimbabwe

500billion denomination from Yugoslavia

Friday, 2 January 2009

Rip YouTube videos on Ubuntu

Ripping videos from YouTube using Ubuntu is a pretty easy process. First of all download youtube-dl from the Universe repository.
sudo apt-get install youtube-dl
Next get the URL of the video you wish to download.
youtube-dl http://
This will download the video you require in Flash Video (*.flv) format. If you want to convert this to MPEG then you will first need to install ffmpeg.
sudo apt-get install ffmpeg
Then get ffmpeg to do the conversion.
ffmpeg -i input.flv output.mpg
Incidentally I quite like using Tilda to manage consoles - I'd reccomend you take a look too.
sudo apt-get install tilda.