Tag: literature

100 Papers

This is as close as I’ll come to an academic year in review

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In 2019 I took part in the #100papers challenge. The idea is that you aim to read (fully) 100 scientific papers in a year. 

As I understand it, the challenge was born from the #365papers challenge. Some fools well-intentioned folks aim for averaging a paper a day for a year, and others thought “I’ll be lucky if I manage a third of it”. With both #365papers and #100papers, the idea is that you’ll commit to reading more if you’re publicly tracking it, and maybe also read more widely. I knew that #365papers would not be achievable for me, but #100papers might have been within my grasp (spoilers, it wasn’t). 

I really like setting myself challenges. I’ve done a variety of photography and reading challenges over the years. Tracking the papers that I read on Twitter is innately appealing to me. I also wanted to put a potted summary or key outcome from each paper onto my tweets to force me to read the papers instead of cheating the essence of the challenge by skimming. 

I have a pretty good work-life balance. I set aside a day a week to devote to research and I manage to keep that day protected about 60% of the time I’d say. How many papers did I read in their entirety in 2019? 

40. I read 40 papers cover to cover. 

I have some thoughts about this exercise. Firstly, I don’t think this is The Way to read papers. Something I noticed about reading whole papers was how pointless it often is. I teach students to be selective about how they approach papers, and when I was trying to find out how someone set up a study or I wanted an overview of a particular field, I wasn’t sitting down to read a whole paper, I was flicking to the relevant parts of various papers. So my first big takeaway is that reading whole papers isn’t something that I would prioritise over strategic paper skimming. 

With that being said, there is something quite meditative and indulgent about reading a whole paper. There were some very fun papers like Jenny Scoles’ one on messy boundary objects where the narrative itself is enjoyable. 

(There was also this deeply enjoyable rant where you could feel the authors’ visceral hatred of the right-brain-thinking myth.)

And I also really liked having the Twitter thread of all the papers I’d read, and the ability to jump back into that thread to share with people was massively useful. Bauer et al 2017, alongside reading Invisible Women, has changed my research practice quite considerably this year: 

The performative aspect of talking about the papers I’m reading online was also interesting. I think you can track what projects I was working on with this twitter thread. You can see when I started reading up on our Widening Participation cluster for example, and I like some of the conversations the spawned from the thread. 


In 2020, I’m probably not going to do the challenge again, but I’ll certainly be posting a papers thread, maybe #paperswotiread or something along those lines. The target of 100 fully read papers is not feasible for me, and if its not feasible for me, I’m not comfortable advertising it to those academics who may be following me. I’ve been thinking a lot this year about how I model what I view as ‘good’ academic practice, and I’m trying to make positive choices. So I’ll be doing something like this in 2020, just without the targets.  

Fluffy Friday – Peer Review Rings and MOOCs

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You’ll have to forgive the lack of original content in this week’s Fluffy Friday (and lack of content entirely in last week’s). The MOOC launches on Monday at 11 AM and this week has been spent polishing the course and obsessing over comma placements and going a little bit hysterical after watching ourselves present over and over. One of our hysterical moments was remembering filming this introductory video – you’re never more aware of your face than when you’re being filmed in the background!

 

But in other science news there has been yet another peer review scandal, this one reported by the Washington Post. The Journal of Vibration and Control (I will not make a joke, I will not make a joke) was apparently victim to a peer review ring, where a scientist made up false aliases to give himself and colleagues favourable reviews. Publishers SAGE have released a statement where they say:

While investigating the JVC papers submitted and reviewed by Peter Chen, it was discovered that the author had created various aliases on SAGE Track, providing different email addresses to set up more than one account. Consequently, SAGE scrutinised further the co-authors of and reviewers selected for Peter Chen’s papers, these names appeared to form part of a peer review ring. The investigation also revealed that on at least one occasion, the author Peter Chen reviewed his own paper under one of the aliases he had created.

 

What I would give to have been a fly on the wall when they came up with that idea. I imagine it happened in the pub as it was closing, a group of scientists huddled around their pints, and as they get hustled from their barstools one of them comes up with the inevitable words “Why don’t we just review our own papers?”

I think Kevin Spacey should play that scientist in the movie.

Elephants Who Marry Mice

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Don’t you just hate when you’re forced to face up to the fact you’re not as virtuous as you think you are?

One of the courses I’m currently writing for the International Fund for Animal Welfare came back to me with some corrections. My reviewer had changed the following sentence, the change in capitals.

“Dogs WHO showed pessimistic behaviours were more depressed.”

And try as I might, my gaze kept tripping over that word. Dogs Who, Dogs Who, Dogs Who.

Let us momentarily leap backwards in time to our English classes. My education contained very little formal grammar training, which may be obvious to the casual reader, but even I know that personal pronouns (e.g. who, he, she, they) are reserved for people. Animal are referred to as objects (e.g. which, it, that).

“The dog which barked” is preferable to “The dog who barked”.

“It is lying in the cat basket” may be preferable to “she is lying in the cat basket”.

This can lead to the English language treating animals very strangely. For example, say you visit a new acquaintance. You know this acquaintance has two cats, Gin and Tonic (this friend might be a bit odd), but you see one cat on the windowsill. You want to know, is that cat Gin or is that cat Tonic? You may ask “What cat is that?” or “Which cat is that?” seeing as you know it is one of two. It would be wrong to say “Who is that?”

Is it problematic to refer to animals as objects? Well first we have to ask if grammar affects the way we think. (And before we go any further I want to tell you that journals on grammar and semantics are almost as impenetrable as journals on molecular genetics)

Boroditsky (2009) investigated the differences in how speakers of English and Mandarin thought about time. In English we speak of time as a horizontal construct (you look ahead to the good times and back on the bad times) whereas in Mandarin time is spoken of in a vertical manner (the paper gives the translated example “what is the year before the year of the tiger?”).

The experiment itself is a bit odd to get your head around, but first they primed English and Mandarin speakers with either vertical or horizontal concepts (i.e. the black worm is ahead of the white worm, the black ball is below the white ball) and then given ‘target’ statements about time ‘March is earlier than April’, ‘March is before April’.

English speakers answered these questions faster after hearing a horizontal prime (similar to how they think of time) and Mandarin speakers answered these questions faster after they had heard a vertical prime (similar to how they think of time). Boroditsky concludes that the way we speak frames the way we perceive the world.

But does this happen in animal welfare? Well I’m not the only one who wondered about this. Gilquin & Jacobs (2006) wrote a paper which is whimsically titled ‘Elephants Who Marry Mice’. They reviewed style standards in various publication manuals. For example, the Guardian’s, which you can find here, says:

animals

pronoun “it” unless gender established

 

The Guardian also says:

any more

Please do not say “anymore” any more

 

So I don’t dream of writing a Comment Is Free column anymore.

Unsurprisingly, Gilquin and Jacobs found that it was the familiar animals (horses, dogs, cats, etc.) which scored a ‘who’ more often than the non familiar animals. Furthermore, publications aimed at animal-related interest groups were more likely to use ‘who’, e.g. Dogs Today.

They noted that in general texts or interviews, the personal pronoun was used when the author wanted to garner sympathy for the animal in question. It is “the poor cat who was stuck in a tree” rather than “the cat which was stuck in the tree”.

More interestingly, given some of my other posts on anthropomorphism, 60% of the sentences they found which used the personal pronoun for the animals attributed human-like characteristics to the animals.

Gilquin and Jacobs conclude that ‘who’ is used in English to refer to animals, although inconsistently. They suggest a wider adoption of this grammatical structure might engender more empathy for animals from humans, something which I think reflects what Ganea et al found in their work.

Should animal welfare scientists be calling for the personal pronoun usage?

I really can’t decide. I’m not convinced that it will completely change the way we think about animals. But it’s a nudge you might want to be aware of if you’re talking animal welfare science.

 

And for what it’s worth, I changed the text on the course.

Badger Fortnight – The Solution?

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But Jill, a fortnight is two weeks not three.

Shut up, that’s what.

 

This week I want to discuss two main studies – the first by Torgerson and Torgerson (2010) and the second a 2008 in the Veterinary Record. We have talked about why the disease is a problem, why the cull hasn’t worked, so the question becomes: What now?

The Torgersons start off with the claim that Defra’s continual fight against bovine tuberculosis is a misplaced use of public resources and we should just chill on the whole thing.

What’s their reasoning?

They start by going into the details of the few cases Britain has had of humans developing bovine TB. Between 1993 and 2003 they note that there were only 315 human cases of Bovine TB and only 14 of those were in people born after 1960 and were British Nationals.

Molecular investigation found that only 10 of the 25 spoligotypes of the bovine TB present in infected humans were actually present in contemporary UK cattle. They describe two cases from Gloucestershire where on-farm transmission from cattle to humans was likely. A third case in Cornwall where a veterinary nurse was infected was considered to have more likely come from her dog. (Interestingly, cats and ferrets are also known vectors of bovine TB and I know I’ve had more cats sneeze into my mouth than badgers, and I’ve probably worked with more badgers than most . . . Ragg et al, 1995). The more infamous six cases which sprouted up in Birmingham featured a UK national with a ‘history’ of drinking unpasteurised milk at home and abroad. And four of these six patients were likely immunocompromised.

Historically, Bovine TB did not come from cattle-to-human airborne transmission, but through milk. And as we pasteurise all our milk nowadays, the Torgersons conclude this risk is now negligible. I want to take a  moment to say that I have anecdotally observed a strange counter culture of people who love unpasteurised milk (in fact it is a topic of conversation that seems to leap up whenever I tell people I work with dairy cows). Unpasteurised milk drinkers are a little like foodies who insist you’re using the wrong kind of spice and I’m often asked if I drink unpasteurised milk – once I was fairly certain my optician wouldn’t sell me glasses until I converted to unpasteurised, but I digress – seeing as milk makes me ill at the best of times, the thought of drinking milk unpasteurised ‘gies me the boak’ as we say in Glasgow. Unpasteurised cheese is another matter . . .

Where was I?

Oh yes. The end conclusion of the Torgersons (are they brothers, or did they just think they would be epic scientific partners?) paper is that they believe our hypervigilant position on bovine tuberculosis in the UK is a waste of public resources. They don’t see a reason for spending so much money on a disease which so rarely affects humans.

The Veterinary Record article doesn’t quite agree, but following the randomised badger culling trial in 2007, they too realised that badger culling was not the way forward (yes we were having this discussion seven years ago) . In the article they propose:

  • More frequent testing of cattle using combined tests to detect active disease.
  • Research on post-movement cattle testing.
  • Research into a vaccine for cattle and badgers and immediate usage as soon as its developed.
  • Research into the disease.
  • Get farmers to understand the need for greater on-farm biosecurity.

 

Really, this article back in 2008, was proposing the oldest solution: identify, research, prevent.

So why aren’t we there yet? Well seven years in research and pharmaceuticals is not a lot of time. Defra’s old website has a page on cattle vaccinations and it points out that the EU prohibits vaccinating cattle against TB (because being vaccinated makes some cattle test positive for TB, ergo herds cannot be declared TB free because the vaccine may be masking infection. The EU prohibits trade of TB infected cattle).

The BCG vaccination is not brilliantly effective in cattle, so we either need a better vaccine, or to use that vaccine to protect some of the herd and reduce the number of cattle we need to cull. But it’s expensive and hampers trade with the EU.

This post will be published a week after I voted in the European elections. I can tell you I didn’t vote for UKIP or anything like that, I’m a good left winger who lives in Scotland, you get three guesses on my vote and the first two don’t count, but the role of the EU legislation in our Bovine TB problem can’t be ignored. The Farmers Guardian reports that the European Commission doesn’t expect a vaccine to be around until 2023.

There is definitely something to be said for better biosecurity measures on farms. There are some brilliant farmers, and there are some poorer farmers, and coughs and sneezes spread diseases. We have known this since Koch came up with his postulates. The good farmers resent being told what they already know and the poor farmers resent being told to do better. We come back to my old hobby horse – how do you communicate that science to a varied audience?

And finally the TB test – if we can find a test that can discriminate between infected, active infections, vaccinated and TB free, and do so reliably, we can still trade with the EU. These things all take time, money, and a little bit of luck.

We won’t find the solution to the bovine TB problem on a welfare scientists hobby blog. The answer is not badger culling. It’s not, as the Torgersons suggest, just letting the disease roam free. If we want to trade with the EU we need to deal with it.

 

Just wait till Defra finds out cats transmit TB . . .

 

How the Elephant Got Her Trunk

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When I was very small I had a beautiful picturebook Rudyard Kipling book of just-so stories. One I particularly remember is the tale of how the Elephant Got Her Trunk. She was staring at her beautiful nose in a pool every day until one day a crocodile swam up underneath her reflection, grabbed her nose, and pulled and pulled and pulled. The little elephant struggled for so long her nose was stretched all the way down to the ground before the crocodile finally released her. And that, children, is how the elephant got her trunk.

It’s silliness of course, we all know that evolution acts upon the populations, in random genetic mutations, and whatever happens to the individual, so long as it doesn’t stop them reproducing, doesn’t matter. All you need is to procreate, after that the genetic material is mixed and the next line of mutations start.

For the most part, these are the rules of evolution. But all rules have exceptions, and sometimes evolution works through a different mechanism, that of epigenetics.

You don’t come to FluffySciences to find out about cell mechanisms and inheritance (if you are coming here for that we need to have a conversation about our relationship) but you do come here for the real-world explanations. Epigenetics results in a kind of Just So story where a stressful event can result in a change that can be passed down to the next generation. And the Just So story we use to illustrate this isn’t so pleasant.

In the Netherlands in 1944 there was a Hongerwinter, when the Nazis cut off food and fuel transports in the river areas. Tens of thousands of people starved to death. Can you imagine the endless hunger, the enemy soldiers in your streets, the cold? At one point the daily calorie allowance was less than 600 calories.

The immediate effects of this horrible famine were obvious. Pregnant women gave birth to very small babies, children lost the ability to digest wheat, and Aubrey Hepburn developed anaemia. But what happened next?

In Painter et al’s 2008 study (which is open access and you can read here) they investigated the results of the Mothers who starved (F0), their sons and daughters who were born during the famine (F1) and their grandchildren (F2). Using a combination of historical health records, interviews and health checks, they investigated whether the ill health of the granddaughters could be attributed to what the mothers experienced.

Between the 07/01/45 and 08/12/45, children in this cohort were being born to mothers who had, during one of the 13 week periods of gestation, an average daily calorie allowance of 1000 calories. To put this in context, the typical pregnant woman needs 2200 calories per day to maintain both her body and her baby’s growth. In the Dutch Cohort study, children which were born between 01/11/43 – 06/01/45 and 09/12/45-28/02/47 were either born before the famine truly began or conceived after the words was over. They act as controls. They are from the same population, similar mothers, similar time period, even similar psychological stressed. They just don’t have that crippling 1000 calorie a day limitation during the important parts of the baby’s gestation.

The researchers monitored the F1 generation (remember that’s sons and daughters) weight, BMI, Socio-Economic-Status and blood tests to look at how they cope with sugar, and their good and bad cholesterol levels.  They did all this when the sons and daughters were 58 years old.

Then they asked about the F2 (grandchildren). Were the grandchildren premature, on time or late? What did they weigh at birth? Were they twins? How many kids? What order? How many girls? How many boys? How healthy are the grandchildren?

At this point the researchers know what has caused the ill health that F1 have suffered – it was the famine. The question is, has this ill health, which was entirely due to a short term environmental challenge experienced in utero, been inherited by the grandchildren? The two categories of disease they were most interested in were cardiovascular/metabolic diseases and psychiatric diseases.

They used a variety of mixed models (which allow you to have multiple children of the same parent, which would otherwise be a case of pseudoreplication), and regression models, among some other statistical tests which can cope with non-parametric (i.e. real world) data to investigate these questions.

Their results showed that the F1 generation were smaller at birth and as adults they had higher blood sugar levels two hours after eating than the ones who hadn’t suffered through the famine. So far so expected. The children of F1 women were also born smaller (though weighed the same) if the F1 woman had been in utero during the famine. This is the really interesting thing. The environmental effect was inherited. Also, the F2 children of the F1 generation who had been exposed to famine earlier in their gestation (i.e. when they were forming) were more likely to have poor health due to ‘other’ causes. Finally, and the one I consider to be most interesting, the F2 generation of those who had suffered in the famine were more prone to being fat babies.

The last point interests me the most. I’m working on a project looking at prenatal effects in farm animals and the way we talk about this phenomenon is to say that the offspring ‘samples’ the mother’s environment in early gestation. For example, if the offspring is receiving little food and lots of stress then it should prepare itself to be born into a world where resources are unpredictable and scarce. Whatever cellular changes it switches on to do this make it predisposed to obesity and heart disease in a normal environment, and can be passed on to its own offspring.

If you remember last week I ranted about nature vs nurture, this is why. This significant change in baby fat in the famine group is not genetics – the population is not genetically different. It’s not the environment, because the famine was long over when these kids were in the womb. It’s historical environment and the changes that produced. Remember, never use Nature Vs Nurture kids.

There’s still plenty we don’t know about epigenetics – how many generations can these effects last for? How cumulative can the total effect be? And when it comes to prenatal effects, what is the mechanism by which the offspring samples the mother’s environment? As a relatively new field, it’s sexy and cool and a lot of people are into it. Expect a lot more information about it in the future.

Just So.

The Other

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One of my colleagues recently took a sabbatical year and worked with another university’s anthropology department. This week she gave us a fascinating seminar about how anthropologists view human-animal relations and how different it is from the ethologist’s view.

I can only simplify what my colleague had already simplified for me (if you’re all interested we can harass her to write a guest blog post for us), but anthropologists don’t seek to understand and quantify their subjects like we do. Instead its more about a holistic documentation that incorporates the feelings and inherent biases of the observer. This is because the observer is coming in with their own culture and can never fully escape all those biases.

To me it seems as though anthropology does a lot of case studies, and as an ethologist I’ve been trained to look down on case studies. I’m not entirely au fait with everything that anthropology does (I worry about the inevitable changing of anything you observe so intimately) but I really like that they take the time to look at cases, and that they acknowledge how our own culture biases us.

But I do take issue with one thing in particular. They talk about their subjects as the ‘Other’. I don’t fully understand this concept from the brief seminar I got this week, but to the best of my understanding they are very concerned about their subjects being objectified. Therefore when they study animals they are reluctant to do anything that would objectify them, e.g. keeping them as a pet. The equivalence given was that you wouldn’t keep a woman or a tribesperson as a pet, so you can’t study an animal, ethically speaking, in that context.

I think this is forgetting just how ‘other’ the nature of animals can be. For example my colleague at the seminar quoted a paper by Smuts (2001 – and incidentally, what a wonderful name).  In the paper, Smuts investigates human-animal relationships. She details a revelation that occurred when the baboons she studied started to treat her like a baboon.

As a result, instead of avoiding me when I got too close, they started giving me very deliberate dirty looks, which made me move away. This may sound like a small shift, but in fact it signalled a profound change from being treated as an object that elicited a unilateral response  (avoidance), to being recognized as a subject with whom they could communicate. Over time they treated me more and more as a social being like themselves, subject to the demands and rewards of relationship. This meant that I sometimes had to be willing to give more weight to their demands (e.g., a signal to ‘get lost!’) than to my desire to collect data. But it also meant that I was increasingly often welcomed into their midst, not as a barely-tolerated intruder but as a casual acquaintance or even, on occasion, a familiar friend. Being treated like a fellow baboon proved immensely useful to my research…

To me this final sentence is a fundamental misunderstanding. We do not know that the baboons treated her like a baboon. I think they recognised her as an ‘other’, an ‘agent’ in anthropological speak (which, in fairness to Smuts, she does say in her lead in). They communicated with her in the only way they could and she responded as a human, therefore they knew she could understand some form of their communication. That doesn’t mean they recognised her as baboon, with all the inherent baboon culture. (I guess this then raises the question anthropologically speaking as to whether baboons tell science fiction stories of other species that have hugely different cultures – without the concept of another culture, can you truly have a culture of your own? I wonder).

We see this every day with pets – I’ve spoken before about how a special language can evolve between two members of a completely different species. Dogs, my favourite example for this kind of stuff, have so clearly adapted to us that they’ve survived across different human cultures, and yet they have their own dog language that they use within their species. When they don’t know this language they have huge problems interacting with their fellow dogs. When they don’t know the human language they have huge problems interacting with us. But do dogs understand the difference between dogs and humans, or do they just accept that humans are entities that are capable of interacting with them. (Possibly they accept that humans are entities that they can love, be loved by, etc., if dogs have a concept of love – I leave that for you to judge for now).

With that critique aside it is a very interesting paper.

Why do I go into all of this? Well there’s another interesting example of strange animal behaviour on the internet today. An Indian elephant was on a rampage, destroying houses as elephants are wont to do. At one house its wreckage disturbed a baby’s cot and the baby began to cry. The elephant stopped and picked rubble off the cot until the baby was freed.

Does the elephant recognise that the crying infant is an ‘other’? Does the elephant recognise that it has done something which has caused pain? (I’ve often wondered if cats recognise they hurt people when they scratch – or if it’s simply our emotional reaction they’re responding to). That’s quite a cognitive leap. We drill into children that our actions can hurt others and yet we’re forever hurting peoples’ feelings inadvertently.

Or has the elephant been distracted by an unusual noise and investigated (thus freeing the baby) until its curiosity was satisfied? With its energies so directed the rampage stopped.

I don’t  know because I cannot understand elephants. To me, the best way of getting to know elephants is to observe their behaviour, to objectify them, and to gather data on them (how often to elephants respond to infant cries, do elephants respond to any cries, etc.)

But I do like talking about the other possibilities.

LolCats and Doge, YouTube and Animal Behaviour

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In 2013 Nelson & Fijn published an absolutely brilliant paper in Animal Behaviour. It’s called ‘The use of visual media as a tool for investigating animal behaviour‘ and it’s about watching animals on YouTube.

I watch a lot of animals on YouTube so I love this paper. It provides a methodology for using YouTube videos in animal studies, all very simple rules, like not using videos with editing and the like.

Why is this important? How can YouTube contribute to the study of animal behaviour? Well have you seen this video? It was doing the rounds on the internet recently.

The video’s description says that the dog has become protective of the unborn baby, going so far as to defend the baby bump from the soon-to-be-dad. It’s a cute story and makes for good internet memes. I have to be honest that as a behaviour scientist my immediate reaction was to roll my eyes.

How does a dog know what pregnancy is, or that it will result in a baby that will be part of the family? How does a dog even know that a baby is a thing to be protected?  But as I thought about this I remembered our old cat who became fascinated with my mum’s belly when she was pregnant. According to my mum all her cats have been fascinated by her pregnancies. I’m sure they hear the second heart beat and it must be a fascinating thing for them.

This dog, I thought, is probably just responding to some weird behavioural cue that its owner is giving it. Like the well known story of Clever Hans, the horse who could count by reading its owner’s behaviour. This is actually a well known behavioural phenomenon, and is blamed for things like your dog looking guilty when its done something wrong (Horowitz, 2009).

Oh if only in this age of connectivity, I could somehow ask the owner if she might be aware of any cues . . .

It turns out the protective dog in this video is called Tebow, a 2 year old dog owned by Mekesha and her partner Justin. 3 weeks from her due date, Mekesha found the time to answer some of my questions.

As it turns out, Tebow is fascinated with Mekesha’s belly at the moment, just as I remember my cat being fascinated by my mum’s. Tebow will sit beside Mekesha with his head on her belly, or will lick it if he gets the chance. He’s also devoted to Justin’s young nephew and their younger dog, also in the video.

Something I thought was really interesting is that Mekesha wanted people to know Tebow isn’t an aggressive or mean dog. In fact she’s pretty upset that people think he might be. In the video you can see she’s laughing and she says everyone found it funny. As for whether she might be anxious in some way that Tebow is picking up on . . .

We have found it hilarious ever since, not threatening. I have no anxiety about my belly being touched and I actually don’t mind people doing it, I do know that certain pregnant woman who hate it, I am not that way.

I think that seems pretty certain! Of course, you can always argue that perhaps there’s some subconscious anxiety, that perhaps the anxiety is coming from Justin and not Mekesha – there are a hundred ways to interpret this video. But it’s interesting that most people who view it go with the ‘anthropomorphic’ one. That Tebow is protecting his family, even the ones he might not quite understand.

It might be easy to say “well this is somebody and their pet, of course they’re going to think the best of them”, but for another video doing the rounds this week:

National Geographic photographer describes a leopard seal’s attempts to feed him, graduating from live prey, to hurt prey, to dead prey, to partially eaten prey, as the seal becomes more and more convinced the photographer was incapable of feeding himself.

We should never forget that animals don’t think like we do. They don’t process the world like we do. But that doesn’t mean we should dismiss the similarities we do have in common. Videos like this get to the very essence of animal behaviour science – why do animals behave in the way the do? YouTube, and the internet, will help us by showing us more and more examples of these strange behaviours. What was once an odd story about something your friend’s dog did, becomes something an animal behaviour scientist might be able to analyse.

Plus I just want to get some funding to sit around on YouTube all day. Ethologists of the world, who’s with me?!

The Empathetic Spreadsheet

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Serendipity smiles on FluffyScience. I said I wanted to talk about the peer review scandal and the very next day I’m asked to act as the peer reviewer for the first time! If I ever needed an excuse to talk about peer review, I certainly have it now.

The peer review scandal everyone has been talking about is this: 120 computer generated conference papers were withdrawn by Springer. Including a delightful sounding paper about an empathetic spreadsheet. It sounds shocking. But it’s probably not quite as shocking as you think it is.

Let me explain using my own first hand knowledge of peer review. I don’t pretend to be an expert by any stretch of the imagination, but by fortunate happenstance I have enough publications, and enough different kinds of publications, to walk you through the process.

Have you checked out my Google Scholar profile? The link’s over on the right hand sidebar. Or just click here. You’ll see that there are currently five items in my profile. You can use Web of Knowledge instead but that requires an academic log-in, doesn’t update as quickly and isn’t as comprehensive in its record keeping. Therefore we’ll stick with Google.

All five of those publications have a Digital Object Identifier which basically means they have a permanent presence online. And they’re all linked to my name. The top three publications on that list are scientific papers. There’s MacKay et al 2012, MacKay et al 2013 and MacKay et al 2014. Then there’s a conference proceedings and a book chapter about the video game Halo (that’s another story).

Therefore I have publications in three categories: Papers, Conference Proceedings and Book Chapters. Now. Which publication wasn’t peer reviewed?

If you guessed the video game chapter, you’re correct. Video games, much as I love them, are not known for their rigorous peer review. You might be surprised to find that the Conference Proceedings (this one for the British Society of Animal Science (BSAS) 2012 conference in Nottingham) were, in fact, peer reviewed.

I’ve presented at two International Society for Applied Ethology (ISAE) conferences, two BSAS conferences, and two regional ISAE conferences. For all six conferences I have had to submit an abstract, a short description of what I intend to talk about. For BSAS the abstract is a page long, with references, subheadings and must present data in table or graph form.

This is quite unusual for my field, ISAE by contrast is something like 2000 keystrokes and frowns on references. On the other side of the fence, many of my colleagues have just submitted papers to the World Congress on Genetics Applied to Livestock Production (doesn’t it sound thrilling?) and these have been three pages in length. They’re papers more than abstracts.  But WCGALP only runs every four years and it is a very large conference, hence the extra work.

All of these conference papers will get comments back on them. Even the regional ones (although my last regional one was a comment simply saying I needed to be more explicit about what behaviour I was recording). The point being that a human has read these papers and passed judgement on it.

Here we stop and acknowledge the scientific committees of these conferences who have an extremely hard job reviewing so many small pieces of science.

So these 120 conference papers that were removed from Springer – what went wrong?

Well first off, many of the authors on these conference proceedings did not know they were co-authors. Someone submitted papers with their name on it without them knowing

But wait – I hear you say. Jill, your conference paper is on your Google Scholar profile. Wouldn’t you be suspicious if an extra publication cropped up? Yes, reader, I would. But note that despite publishing in six conferences only one of them is on Scholar. Why is this paper the lucky one? If I had to guess I’d say someone referenced something in that Proceedings, forcing Scholar to index it. But I may be wrong – Google’s not particularly clear on this. And some of these authors may be in the lucky position of having so many publications they genuinely don’t notice a few extra ones.

So why submit a fake paper with somebody else’s name on it? I’d be surprised if these papers are being presented at the conferences (although I’d love to hear the talk on empathetic spreadsheets). But what I do know is that those fake-papers have to cite other papers and another very important research metric is the number of citations you have. (Mine is a glorious 1).

Yes – fake papers are a problem. But it’s not a problem of bad results getting out there, it’s a problem of the system being gamed, and people using these kinds of research metrics as the only gauge of a researcher’s quality.

Research Metrics

There are ways around this. In the UK we have a new system for assessing research quality in Higher Education Institutes. It’s called the Research Excellence Framework (REF). Funding bodies use this to help them decide how to allocate funds over the next few years.

You enter REF as an institute. REF grades the papers submitted to them based on this framework.

  • A four star paper is world leading research, original, with great impact and the highest quality science.
  • A three star paper is pretty damn good, internationally recognised, good impact and high quality science.
  • A two star paper is internationally recognised as being original research, good impact and high quality science.
  • A one star paper is nationally recognised as being original research, good impact locally and high quality science.

 

The difference between these stars is really all about the impact of the science, which is great. Of course, REF has its own drawbacks. In the next few years you’re going to see a lot of UK papers with sweeping, statement titles instead of informative titles. A paper which would have been titled “The effect of indoor housing on behaviours in the UK dairy herd” will now be titled “Management systems affect dairy cow behaviour [and industry if I could wrangle that in there]”. You’ll also see a lot of new roles being created just before a REF exercise because the papers stay with the primary author. If you have a 4 star publication under your belt you become a Premier League footballer during the transfer season.

But one thing REF is  not vulnerable to is false publications. A panel of experts reviews all the papers that the institute chooses to put forward. No empathetic spreadsheets allowed.

We’ve just finished the first round of REF and it will be interesting to see how it affects research going forward. As animal welfare scientists we’re excited about the emphasis on impact, something we’re good at demonstrating.

Lastly, while 120 papers sounds like a lot, I’d like to direct you towards Arif Jinha’s 2010 paper which estimated that there are 50 million published articles out there. We are talking about less than 0.000001% of articles even if these were papers, never mind conference publications.

 

By that logic, my own publication records contributes 0.00000008% of the world’s papers. I’d better get cracking.

Blackfish

Jilly4 Comments

If you live in the UK or US you’re running out of excuses not to watch the documentary Blackfish. It’s had a cinematic release and been shown on the BBC, as well as being available on iTunes.

For the uninitiated, Blackfish is the story of an orca who recently killed its trainer at SeaWorld. As a result, SeaWorld trainers were prohibited from entering the water with the animals.

When I’m not slaving away over a hot computer screen and working on my next paper, I am a bit of a film geek. In fact I wrote the first draft of this post before heading to my monthly film pub quiz (we lost). Blackfish is a truly brilliant documentary. It takes you an emotional journey, is beautifully structured, and paints the orca, Tilikum, as a flawed, sympathetic character. I love it as a film.

But we’re scientists! Let’s take a critical look at the concept of keeping orcas in captivity. As I have access to scientific papers, I decided to do a short review of the literature. When talking about science I think it’s important to cite your sources (and no doubt I’ll say this many times in future) so I will link to papers. Unfortunately some of them, if not most, will be behind a paywall.

I wrote this post over a number of days, but it’s certainly not an exhaustive literature search. This is the kind of literature search I’d do if someone asked me what I thought of orcas in captivity.

So what did I find out?

Continue reading “Blackfish” →