My first Geocache find

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I star­ted with Geocaching at the week­end. It’s some­thing like hide ‘n’ seek for people with a GPS or smartphone.

So how does it work in prac­tice? I looked for geocaches near me, and one that caught my eye was Welcome to the Withybeds. I’ve joined Radnorshire Wildlife Trust, but I hadn’t been to Withybeds yet. I made it the first cache on my list of things to find, and found it pretty much where I expected.

The river Lugg at the Withybeds.

The river Lugg at the Withybeds.

The Withybeds reserve is small but pleas­ant, on the north side of Presteigne. I’m not sure how much longer it would have taken me to find the time to visit, if it hadn’t been for the geocache.
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I’m giving up writing at Medium

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I’ve been ser­i­ously think­ing about mov­ing to Ghost or Medium for writ­ing. Ghost uses Markdown, which I like is handy for when I write in StackEdit​.io. Medium has a very simple inter­face. It’s not cus­tom­is­able, but the flip side of that is that you don’t waste time try­ing to cus­tom­ise it.

I gave Medium a go with two short stor­ies I’d writ­ten. I was going to post some ser­i­ous and researched sci­ence art­icles, but I chose to put up the short stor­ies as I’d not be bothered if got no views. Here are the res­ults.
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5 Years On — Chemotherapy Works

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I wrote someone out of my will today.

It was five years ago I had chemo­ther­apy for can­cer. It should have been six, but I held off get­ting a dia­gnosis because I was in the last year of my PhD and help­ing out with eld­erly rel­at­ives. I wasn’t strictly in denial about hav­ing can­cer, but the tim­ing was bad. Relatives died which caused more prob­lems. When another close rel­at­ive was hos­pit­al­ised it was obvi­ous there wasn’t going to be a con­veni­ent time.

I was dia­gnosed on a Monday after­noon and oper­ated on the fol­low­ing day. It wasn’t that bad a situ­ation, someone else had can­celled their oper­a­tion due to snow. I was offered either their spot, or else wait a few weeks for the oper­a­tion. Hanging around with the tumour inside me seemed like a really bad idea, so in I went. The follow-up was a brief course of chemotherapy.

There’s been a lot writ­ten about how bad chemo­ther­apy is, but I had no prob­lem. Here’s a selfie from five years ago while I’m hav­ing chemotherapy.

chemo selfie

I pottered around the house and had no trouble at all. I didn’t have any prob­lem, though one day I did fancy some Jaffa Cakes and there were none in the house. So I went out to the shops to get some. This is a map of how far away the shop was.

Map via Google Maps.

Map via Google Maps

I was tired well before the first corner. Continue read­ing

WordPress shortcodes for DOIs and other research links

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I’ve writ­ten a plu­gin for WordPress that adds short­codes to link to research. To use it you’ll need a self-installed WordPress blog. A blog at word​press​.com won’t be able to use it.

[doi id=“10.1093/aob/mct148”]link text[/doi] links the link text to http://​dx​.doi​.org/​1​0​.​1​0​9​3​/​a​o​b​/​m​c​t​148 It also does a few more things.

If there are research codes used, the blog checks to see if it has cita­tions stored for them. If it does then it out­puts a References sec­tion at the end of the post. It’s not in this post, because I’m not actu­ally using the short­code in this post.

If there isn’t a cita­tion stored, the blog will go through each DOI and make one. It’s designed to make cita­tions com­pat­ible with the ScienceSeeker web­site. If you’re a sci­ence blog­ger then you would do well to sign up to this.

It solves a prob­lem with alt­met­rics too.

At AoB Blog we post about vari­ous papers, usu­ally from Annals of Botany or AoB PLANTS. If people like what they see and tweet a link to the post, the post gets credit for the link, but the ori­ginal paper doesn’t. It wasn’t the ori­ginal paper tweeted, it was the post. I’ve talked with people at OUP and Altmetric​.com and the answer we settled on was to add a meta tag in the header.

<meta name=“DCTERMS.isBasedOn” scheme=“DCTERMS.URI” content=“http://dx.doi.org/10.1093/aob/mct148”/>

This gives a way to con­nect a post to the paper it’s com­ment­ing on. It only works from the second time a page is loaded, but the first is usu­ally a pre­view by the author, so that’s not critical.

Not everything people want to link to has a DOI. What do you do if you have a mix of DOI and http:// links and you want to use them in the same ref­er­ence sec­tion? There is a url shortcode.

[url id=“http://aobblog.com/2013/08/brachypodium-is-not-arabidopsis/” author=“Chaffey, N.” date=“2013” title=“Brachypodium is NOT Arabidopsis(!)” website=“AoB Blog”]

…will out­put a cita­tion in a sim­ilar style to the DOI cita­tion, with a ‘date accessed’ note added, set to whenever you first run the short­code. If you don’t spe­cify a pub­lic­a­tion date then it sets this year. If you don’t spe­cify an author then it is set to ‘Unknown’.

You can down­load the code from Dropbox and install it, or have a laugh the at code. The code is not sleek, because I wanted to see what was hap­pen­ing each step of the way. As a warn­ing, I don’t know if this is secure code or not. That’s not likely to be a big prob­lem if it’s just you on your site, but it’s an issue if you have a multi-author blog.

Also it doesn’t handle a few other things yet. There is a space for an [arxiv] short­code. I haven’t added this yet because arxiv out­puts metadata in a dif­fer­ent way to dx​.doi​.org. Despite hav­ing DOIs, Figshare doesn’t work with it either. I don’t know why Figshare out their DOIs in a dif­fer­ent way, because I haven’t spoken to them yet. There’s prob­ably a good reason, so that might mean mak­ing a [fig­share] short­code to handle those links.

At the moment the code is up for dis­cus­sion. Once I’ve under­stood this page and added arxiv and fig­share sup­port then I’ll see about adding it to the WordPress plu­gin repository.

Download the plu­gin as a zip file

Update: Thanks to Stack Overflow I now know how to get data for an ISBN, so an [isbn] short­code will be pos­sible too.

Mick Aston

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Mick Aston was prob­ably the best-known archae­olo­gist in the UK. I’d also go so far as to say that he was the most influ­en­tial archae­olo­gist of the last 25 years.

Mick Aston

Mick Aston (centre). Photo by Wessex Archaeology.

The reason is Time Team, an archae­olo­gical series on Channel 4. If Sky at Night is Astronomy then Time Team when Mick Aston was in it was archae­ology. Its suc­cess massively expan­ded the uptake of archae­ology by stu­dents. Mick Aston’s idea was respons­ible sup­port­ing an incal­cul­able num­ber of jobs in uni­ver­sity depart­ments. It’s easy to over­look was an aston­ish­ing idea Time Team was.

The tra­di­tional doc­u­ment­ary places the aca­demic speaker at the author­ity speak­ing Truth. A recent example is Rise of the Continents, where Mantle Plumes are presen­ted as unques­tioned fact as noted in the post at The Theatre of Reason. A com­mon grumble is that sci­ence is a pro­cess not a body of fact, so how do you show pro­cess? Mick Aston reckoned you could pro­duce a usable brief eval­u­ation of an archae­olo­gical site in three days and this became Time Team. A cam­era crew fol­lowed an archae­olo­gical team as they dug for three days.

Below I’ve embed­ded the epis­ode from Blaenavon, which I hope 4oDDocumentaries have made widely access­ible.* You could make a drink­ing game from the num­ber of times someone says they don’t know some­thing. To steal a line from Paul Bahn: it’s not about find­ing things, it’s about find­ing things out.

As a meas­ure of impact, I offer another series, Bonekickers. Bonekickers was an attempt by the Life on Mars team to pro­duce a drama around an archae­ology unit. It was laughed out of the sched­ules because Time Team had demon­strated to a large chunk of the UK pop­u­la­tion how archae­ology worked. To be fair Bonekickers was pretty awful in its own right, but it’s thanks to the impact of Time Team that it became truly ris­ible. Can you ima­gine that hap­pen­ing with any other aca­demic discipline?

Mick Aston’s influ­ence meant that he became a ste­reo­type of an archae­olo­gist in his own time. That could sound snide, but rather it’s a meas­ure of how loved by the pub­lic he was.

He also had the poten­tial to keep innov­at­ing. After leav­ing Time Team, he’d been work­ing with Timothy Taylor on Dig Village. In some ways he was in the twi­light of his career, but he still could have shone for many years like the even­ing star.

Photo Time Team in Salisbury by Wessex Archaeology. This image licensed under a Creative Commons by-nc-sa licence.

*I’m not optim­istic that it’s vis­ible bey­ond the UK. You can search for Time Team on YouTube, but embed­ding those videos isn’t sens­ible. Uploading a pro­gramme whole­sale, breach­ing the copy­right isn’t neg­ated by say­ing “No infringe­ment of copy­right is inten­ded”. These videos will be com­ing down sooner or later. My per­sonal favour­ite epis­ode is prob­ably Llygadwy / Celtic Spring, but that’s not so typ­ical of the series.