And May All Your Dreams Come True

For as long as I can remember, I have wanted to be a writer.

As a child, I filled endless notebooks with my stories. They were mostly stories about animals, or thinly veiled replicas of Lord of the Rings. I may even have tried my hand at the odd love story. At school, I kept a private tally of how often my essays were read aloud, or made a teacher cry. I love the written word.

When I was 29 years old, an editor approached me and asked me to write a book. That book, Animal Personalities, is currently available for pre-order.

Of course, when you achieve your childhood dreams, a weight lifts from your heart, a divine confidence settles in your soul, and you never again doubt yourself or your abilities. You become as happy as you always believed you would be . . .

I recently wrote a short case study about being a postdoc for Edinburgh’s “Thriving in Your Research Position” document from the Institute of Academic Development. In the case study, I talk about a spectral figure who has haunted me throughout my whole career: the Perfect Postdoc. She is always better than me. When I wrote my book, she somehow wrote a better one. She’s like a funhouse mirror version of me, and when I change, so does she. I’ll never be able to outdo her.

If you’re a long-term reader of this blog, you’ll know I’ve been thinking about failure lately. I explored my failures as an animal trainer, and meditated on how academia breeds an anti-failure culture. I’m also critical of the idea that all scientists have to be specialists – I’m not a specialist. I’m interdisciplinary and I love it. This leads me to another area of my academic life where the Perfect Postdoc is always one step ahead of me.

The Perfect Postdoc understands R much better than I do. I’ve spoken before on this blog about my frustrations while trying to learn R. While I have taught research methods and statistics for several years now, I’ve always hesitated to teach R. I’ve hesitated because, well . . . because I’m not brilliant at it. My code is ugly and often cobbled together, and I often find the community around R, places like stack exchange and stack overflow, are hideously unfriendly.

I’ve been lucky enough enrol on the Leadership Foundation for Higher Education’s woman-only Aurora programme this year. The first session was called Identity, Impact and Voice, where we explored how we can make a difference in our workplaces and communities. There were two-hundred plus women at the Aurora event in Edinburgh this month, and so many of us spoke about being afraid of ‘not being the best’.

The curious thing is, when I was listing my strengths, I never said I was “the best at [thing]”. My strengths are my communication skills, the fact I’m approachable, and my willingness to try new things. I firmly believe that in five years time anyone who doesn’t have R skills is going to find it very difficult to get a job in academia. Hiding my bad code means I’m not contributing to the R conversation happening right now. I have a voice. And I can have an impact too.

Hadley Wickham, who wrote some fabulous R packages, says:

So with that in mind, I’m going to start sharing my own R teaching materials more widely.  You can find my resources on Github (scroll down to find direct links to the exercises). The worst that can happen is that someone tells me my code is ugly. The Perfect Postdoc’s code is of course much prettier, but do you know what? Just like writing my book, writing that exercise was pretty fun.

Glory in your bad code. Glory in saying “I don’t know how to do that” in your local programming club meetings. Glory in your voice. There is nothing else like it.


Badger Fortnight – The Cull

This week on Badger Fortnight we turn our attention to the rogue of the tale, the humble badger.

Did you ever read the Redwall books as a child? If the story of Bovine TB was told Redwall style, I imagine the badger would be a travelling bard, handy with a bow, flirting with the bovine ladies at the bar, upsetting the status quo and just generally causing a fuss.

Badgers biggest problem in this story is that they are a host for Bovine TB. When they catch TB and it becomes an active infection the disease develops and they become weak and emaciated but rarely actually die from the disease. They can transmit this infection back to cattle out in the fields, again through aerosol droplets.

Badgers are group living animals which are highly territorial. They live underground in setts which are protected by law in the UK. For this reason, Defra’s randomised culling trials needed special permission. You cannot simply go and shoot badgers in the UK.

The culling trial was supposed to be the humane solution to the problem of the spread of bovine TB. As you may have seen in some other posts of mine, I have no welfare problems with humane culling (although I may not like it from an ethical standpoint).

In this post I’m going to briefly go over the final Defra reports on the culling trial and discuss why I would consider it to be an abject failure.


Humaneness of the Badger Cull

The Humaneness Monitoring protocol for the cull (Version 0.4) states that:

“Killing techniques that are instantaneous without imposing any stress on the animal are universally accepted as being the ideal and having a low welfare cost. Welfare costs are assessed in two dimensions: duration and intensity of suffering.”


I’m fairly content with this definition. If the process doesn’t stress the animal and the death is fast, I consider that to be a ‘good’ death. The protocol itself states how they recorded the whether or not the cull was humane. They investigated:

  • Time from being shot to death
  • How many badgers escaped after being shot at?
  • What do badgers do after being shot at?
  • Where on the badger are the wounds located?
  • How injured are the shot badgers?
  • Is there a relationship between time till death and type of injury?
  • Is there a difference in the wound type between shootings observed by researchers and unobserved shootings?

This protocol also features the cutest little wound plot you ever did see.


Taken from the Humaneness Report Protocol, 2014, Version 0.4
Taken from the Humaneness Report Protocol, 2014, Version 0.4


These are the objectives the independent panel used to decide whether or not the badger cull was considered humane. But of course the cull had another objective too.


Population Control

The cull’s purpose was of course to control the badger population in the region. The Animal Health and Veterinary Laboratories Agency 2014 Report into the efficacy of the cull (Version 1) describes how the AHVLA judged the success of the cull on a population control level.

Their aim, stated at the very start, was to reduce the badger population in the Gloucestershire area and Somerset area by at least 70%. Pretty early in this report you’ll notice the words ‘cage trapping’ being used. And if you’ll scroll up just a few paragraphs you’ll notice the humaneness protocol mentioned nothing about cage trapping.

Yes, the cull, in the end, did allow for cage trapping followed by shooting. Does being confined in a small area, unfamiliar to you, for up to a day, before a human approaches and shoots you sound like a stress free death? There’s a reason ‘like an animal in a trap’ is a saying.

Moving swiftly on . . . the AHVLA sampled the number of badgers in the area using hair traps – by placing little pieces of barbed wire near setts and badger runs they collected badger hair and DNA sampled that hair to build up a profile of how many badgers were in the area. They then compared the DNA of culled badgers to their profile.

They also investigated sett disturbance by monitoring the setts and placing, in a slightly Nancy Drew esque fashion, sticks outside the setts and noting which ones were disturbed. This method was not very reliable and they stopped using it because it was estimating that the cull had taken out over 100% of the badgers in the area, even though the observers were clearly seeing badger activity.

So they stuck with DNA sampling.

Now as you may have heard, it’s important for the cull to take out at least 70% of the badgers or the disturbance in the population will simply lead to badgers redistributing within the air and increased disease transmission. The cull had to take out a large proportion of the badgers to be successful.

Now read on . . .


Cull Success – Numbers

The AHVLA report estimates that in the Gloucestershire area, the highest estimate of the number of badgers culled was 65.3%. And it could have been as low as 28%. In Somerset they removed a maximum of 50.9% of the population and as few as 37% of the population.

All of those numbers are less than the target of 70%, even the maximum estimates.

In Gloucestershire, more setts were active after the culling than before (suggesting that the cull had resulted in increased badger movement, increasing the perceived disease transmission risk). Although this didn’t happen in Somerset.

The AHVLA report concludes with the following verdict:

“From the results presented above we conclude that industry-lead controlled shooting of badgers during the entire culling period (including the initial six week period and the extensions) did not remove at least 70% of the population inside either pilot area. In both areas significantly fewer than 70% were removed by controlled shooting. The combined approach of controlled shooting and cage trapping also did not remove at least 70% of the population inside either pilot area; substantially fewer than 70% were removed in both areas. Populations of badgers were highly likely to persist within both pilot areas following culling.”


Verdict: Fail.



Cull Success – Welfare

The Humaneness Report (2014) found that only 36.1% of the carcasses they post mortemed had the first entry wound in the target location. When the contract shooters were observed this jumped to 42.9% and when they were unobserved it was 31.5%


As you can see from this figure, a proportion of badgers were found some metres away from where they were shot, clearly suggesting functioning behaviours and implying suffering and pain after being shot.

Taken from the Defra report into humaneness.
Taken from the Defra report into humaneness.


The Independent Panel Report’s Conclusion

Professor Munro’s Independent Panel Report (2014) takes both these reports into account when it delivers this damning conclusion:

“We concluded, from the data provided, that controlled shooting alone (or in combination with cage trapping) did not deliver the level of culling set by government. Shooting accuracy varied amongst Contractors and resulted in a number of badgers taking longer than 5 min to die,others being hit but not retrieved, and some possibly being missed altogether. In the context of the pilot culls, we consider that the total number of these events should be less than five per cent of the badgers at which shots were taken. We are confident that this was not achieved.”


In summary, the cull failed to eradicate enough badgers to be worthwhile and it failed to do this in a method that we would consider humane.

The report also makes this  mention of the problems surrounding the humaneness of the cullings:

“Further concern about the accuracy of shooting stems from the following observations:

a. Seven badgers required at least two shots, with one Observed shooting recording six shots fired at a single badger.

b. A further seven badgers (in Category C) may have been missed completely. In one of these cases two shots were fired at two badgers, with both shots being considered misses on the basis of thermal imaging observations and subsequent analysis of thermal imaging recordings.”


So on the two criteria by which the culls were launched, they failed. They are not an option for controlling bovine tuberculosis.


So what happens now?


Tune in next week  . . .

Fluffy Friday – Keep a Pen Handy

At the end of 2007, I was sitting on a high plastic stool in the feed prep area, scribbling with a biro on the corner of the admittance card of C390. The radio in the corner played inoffensive, slightly out of date pop music through a soft veil of static and in the corridor beyond one of my colleagues was folding freshly tumbled towels into the linen cupboard. It was called a feed prep area because it was for animals, a food prep area would be for humans, though having worked in both I was equally squeamish about eating meals in either. We just called it the kitchen.


In the far corner beside the bin, which stank in summer, I had learned how to skin, de-limb and de-yolk day old chicks in three quick hand movements. It was remarkably easy to do. You could use scissors, of course, but that involved finding scissors. In the middle of summer in a wildlife hospital, scissors are not always in ready supply. In the middle of summer there’s not enough of anything, not enough time, not enough staff, not enough food, not enough dry towels, not enough clean cages. And far too many orphaned animals. But right now it was winter, and I was wrapped up in a blue mac over blue overalls, my fingerless gloves tucked into one pocket, my latex gloves crumpled on the table beside my elbow. My boots were muddy and so had been left by the door. I’d have to sweep and mop the lino at the end of the shift, no sense in making it harder for myself by tracking animal shit through the kitchen whenever I came in to do some paperwork. So my be-socked toes were curled around the support of the stool as I worked on the biro. The ink would not flow.


At the time, I was sick of it. I earned decent money in child care, my part time job, and the animal work was fun but not nearly as rewarding. Less responsibility too. My first week into the internship, my boss sat me down and gravely intoned that if I didn’t do my job properly, animals would die. Sitting in the hot, stuffy little office, I thought back to the job I was going to leave for wildlife. If I didn’t do that one properly, children would die. But I’d a get a Masters, so I nodded and agreed and now, with a little over four months of placement left, I had been given a new project to turn into a master’s thesis.


There was considerably less shit involved with children. People who think babies make a lot of mess should work with orphaned animals. Or ill animals. Or animals. My hair, just growing out from an ill-advised short crop, was a regular refuge of feather lice and other beasties. Though never yet a bat, despite the myths. My hair, which I was growing long on the self-promise that I’d wear it down more often, was pulled back in a tight ponytail to keep it out of the way. This look, blue overalls, navy mac, welly boots, hair up high, a faint dusting of shit on my face, had become de-rigour for me.


Irritated as the project had made me, there were aspects of the wildlife work that I enjoyed. Namely, the clinical stuff. Dressing wounds and administering drugs were like a balm to my ego. Look at me, look how casually I wield these implements of miracles. Injections were the best, intramuscular the most fun, especially for birds. Do it in the wrong place and you stab through the heart. Working outside there was little opportunity to give an injection, but when you did, the joy of walking purposefully outside with a syringe gripped in your teeth, or gingerly placed atop the feed in a bucket, was unmatched. More often, outside drugs were continuations of antibiotic courses. These most often took the form of tablets. In the winter, I would stuff each animal’s dose down a separate finger of my latex gloves and write the ID number of the animal that needed the course on each plastic coated digit. This was less glamorous. Swans were the most common offenders. There’s nothing purposeful about chasing a large, grimy white bird around a fully enclosed paddock, cursing when it makes it into the water, only to catch it in the mud, hold it down and squat above it, wrestling with your glove to get the tablet out, try not to drop it in a puddle, and then stuff it down the bird’s very long throat. BD (bis in die) was worst. First thing in the morning and then at the very end of your shift, so you’d have to go out after you’d swept and cleaned, to return and clean after yourself again. The ineffectiveness of it grated on my soul.


Inside there was much more opportunity to look important. Microwaving saline for example. Hedgehogs, the little bags of disease, were always needing saline. That involve sub-dermal injections, so easy you could do it in your sleep, but impressive looking enough to any observing students. Changing a dressing involved a mechanical challenge, a puzzle component that was always fun, as well as the need to assess the progress of the recovery. There was also tube feeding, which was a pain if only because it was so tricky. It also looked more like torture than TLC and I did not enjoy it. Although, tube feeding a snake once was fun, if only for the mechanical challenge.


Working in the isolation unit looked very important. White overalls and white wellies, lots of drugs too. All kinds of clinical procedures, as well as assessments, and also a good chance there’d be a vet around to let me try some more advanced techniques. I had decided against the veterinary life but the intravenous injections and blood sampling I did in isolation did make me wonder if I would have enjoyed the veterinary life after all. These procedures could only be done under veterinary supervision, and only because we were working on wild animals. I enjoyed the physical challenge, sensing the pressure of the blood flow beneath the needle, trying not to blow it, trying to deliver the whole dose before the animal got too stressed. The  physics of blood flow, the chemistry of hormones, and all of it slotting together to form an animal who feels something. I still love that puzzle.  After the solution makes itself known you feel invincible, right up until your cheap Biro fails as you try to write it on the admission card. It’s a hard fall back to earth.


When you need to gear yourself up to every encounter in your day you want the little things to go smoothly. When you’re wiping sawdust from your eyes and spitting out feathers from your mouth, scooping up an admittance card from the freshly mopped floor – that would have to be cleaned again because you’re currently dripping blood on it – the ability to simply write on the card your name and the time you administered the medication is like a small miracle you have tamed and made your own.


After my masters project, I returned to university to complete my course. The backwards way that my university functioned not withstanding, it was odd to go back to the life of lectures and exams after working day in, day out. Lectures mean pens, you need at least three pens to make sure you can continue to follow the discussion leaping around taxonomy. The main writing colour, the highlight colour, and a back up just in case. I became a fan of the gel pens that stained my hands terribly but smudged on the paper less than biros. For all my love of laptops, tablets and phones, I will always have an inkstain on my right ring finger’s knuckle.


I write in my lab books, I write in post it notes, I write on papers to review, I write on my own papers. Pens are part of my trade, cheap pens, branded pens, giveaway pens. My one advice for working in animal welfare . . . keep a pen handy.

How To Read Science News – It’s Okay To Be Smart

The science blogger Joe Hanson has uploaded a video on ‘how to read science news’. I definitely recommend watching it.

His first two points pertain to aspects of journalism that very few people get – print journalists do not choose their headlines or even their bylines. I’d also argue that we scientists ask for press releases because we want to communicate our science, rather than free advertising. And he’s clearly never submitted a paper to some of the conferences I’ve been at, where peer review is more rigorous than some journals I know, but apart from all that it’s still a very interesting watch. Take it as a guide.

And maybe in the future we can cut out the middle man – come to the scientists for your science news. If they’re like me, they might even be blogging about it!