Valerian

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For a minute Rudolph McMurdo had been wor­ried. He was hardly old. At the age of eighty-two he was still a year short of another media mag­nate, and his own news empire sup­plied him with the best health care money could buy. Yet he had been warned by med­ics that he had car­diac prob­lems and the crush­ing pain in his chest had felt like the end. It wasn’t entirely com­fort­ing to real­ise it was. At least he had the sat­is­fac­tion of know­ing his demise proved he wasn’t has heart­less as the smug bas­tards in the lib­eral media claimed. Nevertheless, it was cruel that death had finally come on his hon­ey­moon night with his fourth and pre­sum­ably final wife.

It was a sense of injustice over this that gave him an anchor in this new place. It was hard to tell exactly where he was. It was black, but well lit — though from no vis­ible source. It cer­tainly wasn’t dark. He could see him­self well enough, a curs­ory exam­in­a­tion of the back of his hand revealed the usual mottled. That was another thing someone would have to sort out. If he was dead then there was no need for him to be old.

The noise from behind was quiet, but was the only sound in the oth­er­wise silent place. Rudolph spun round in sur­prise. Some dis­tance away an old man in what may have been a robe, or pos­sibly a toga, was sham­bling towards him. His gait was hindered by the need to avoid his over­grown beard that could have slipped beneath his feet as he walked. His head was stooped, like the most fas­cin­at­ing things in the world were his toe­nails. The image was everything Rudolph asso­ci­ated with reli­gious nut­ters. Christ! You can’t even escape the bleed­ers in the after­life. The man seemed to be mut­ter­ing to him­self. As the fig­ure got closer it wasn’t what Rudolph had expected.

…and then someone says ‘let’s have some religiously-inspired gen­o­cide.’ It would be nice if, just once, they thought of the poor sods who have to pro­cess every­one after­wards. I told him ‘Thou shalt not kill’ and ‘Turn the other cheek’ were too ambigu­ous, but would he listen? Ooof!”

The final syl­lable punc­tu­ated the man’s col­li­sion with a fas­cin­ated Rudolph. The man looked up and into Rudolph’s face with benign incom­pre­hen­sion. Rudolph waved his hand in front of the man. “Hello? D’yer work here?” Rudolph asked.
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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.