Early career researchers in Agriculture

Today I’m at a networking event for early career researchers in Agriculture and talking about, among other things, our mooc.

Looks like a good event for networking with industry and comparable researchers. Will be fun!



1052 and time for coffee and cake … and posters!

1458 talk over with only some small technical hitches, now listening to a talk on blueberries that’s making me hungry! Meanwhile my favourite poster illustration has to be below;

Badger Fortnight – The Solution?

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 . . .


Badger Friday! Shelter Part Two

I have a host of goodies for you this Fluffy Friday Badger Friday.

We have another Behind the Scenes blog post in our MOOC – remember to sign up for free here!

The Animal Welfare Hub has a new app for assessing horse grimaces and assessing pain in horses – join the Animal Welfare Hub here.

And there’s another Shelter episode. See you next week!


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  . . .

Badger Fortnight: TB

For the next couple of weeks I am dedicating Fluffy Sciences to the noble badger. Why, you ask? Well because the other day I ended up reading Defra’s independent panel report on the UK badger cull and the whole thing made me grumpy.

As someone who works both in animal welfare and in the agricultural industry, with a soft spot in my heart for cattle, I have heard a lot about Bovine TB and badgers in the past few years. I’m going to spend the next few posts telling that story, and where better to start but with Bovine TB itself? After all, without this insidious disease, badgers would be fondly remembered from the Animals of Farthing Wood, or the noble lords in Redwall. Instead they’re synonymous with James May and the word ‘cull’. An interesting turn of events.

So. Bovine TB, the villain in our tale. What are you?

When you’re reading or watching some trashy historical drama and the heroine coughs into her handkerchief, staining it gently with blood, you know she’s not long for this world. Satine, I’m looking at you. That disease is Tuberculosis, or consumption, if you’re still feeling gothic.

It’s a famous disease in science because of Robert Koch, who formulated the well known Koch Postulates, a set of rules to identify the causative pathogen of disease. While still very much remembered, they have been supplanted with other rules better capable of identifying things like parasites and even non-active infections.

  1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms.
  2. The microorganism must be isolated from a diseased organism and grown in pure culture.
  3. The cultured microorganism should cause disease when introduced into a healthy organism.
  4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent.

Koch identified the agent of TB, Mycobacterium tuberculosis, and he received a Nobel Prize for his troubles. Interestingly enough, he received his prize even though for years he’d been convinced that Bovine TB and human TB were not similar, and it was his results that forced him to reevaluate this position.

Fast forward a couple of hundred years and this disease which, at one point, was causing 25% of the deaths in the world was now on the run. Almost all Brits have a peculiar little scar on their left upper arm, the BCG (Bacillus Calmette–Guérin) scar. I have had some Americans quiz me about it and it turns out Americans never had a mass BCG immunisation. You guys missed out on some quality arm punching in school.

If you’ll think back to your school days, you’ll remember a thirteen year old you suspiciously watching a nurse inject you just under the skin on your arm. A few days later they inspect the mark and then decree whether or not you will receive the BCG  vaccination.

It’s often said that if you react to the skin test it means you are already immune to TB, but this isn’t quite true. It means that your body reacted to the TB (in a healthy person this means they got a red blister bigger than 15mm in diameter) which may be because you have a previous vaccination or because your body already has an active TB infection.

Regardless, those who escaped the skin blister get called back for the vaccine. The injection goes between the skin (large ulcerated BCG marks are often an indication of an accidental subcutaneous BCG). As vaccinations go, its quite painful (I remember it being more uncomfortable than three successive rabies vaccinations) and not helped by the traditional teenage sport of punching people in the vaccination spot.

Large keloid scars can form, although latterdays these scars are not so prominent due to improved techniques. I did try to take a picture of mine for you but mine is tiny and barely shows up. The mass BCG vaccination program has recently been suspended in the UK as the disease is now considered very rare. Only at-risk groups are vaccinated now.



Despite the fact that antibiotic resistant TB is on the rise (and that this is frightening) in the UK we manage the disease in humans fairly well. Other countries, such as India, haven’t been as successful as we have in using the BCG vaccinations – and it seems to be that the disease is harder to manage in equatorial regions, for reasons I’ll not speculate about here.

However Bovine TB is caused by the very similar pathogen Mycobacterium bovis, which can cause TB in humans if they drink the unpasteurised milk of an infected animal, or if they inhale aerosol droplets (e.g. cough, spits and sneezes) of a cow.

Being someone who has been coughed, spat and sneezed on by various cows, I’m not particularly worried about this myself, even though Bovine TB can cross the species barrier, TB itself rarely becomes an active infection in the person who has it.

So why do we worry about it in cows? Well we have a strange double standard here. When we test cows, we use a skin test very similar to the one we use in humans. And, like in some humans, there is a reaction to this skin test.

And those cows which react to the skin test must be culled. You’ll remember that only a few paragraphs higher up I mentioned that a reaction doesn’t mean immunity, it just means the animal is reactive. It doesn’t mean there is an active infection, it just means the animal is reactive. Yet we cull those animals specifically to prevent the spread of the disease.

You can sell the meat of the culled animal if you want, because cooking meat kills the Mycobacterium, but you cannot tolerate a TB cow on your farm.

And this isn’t considering false negatives and false positives in the test, as no diagnostic test is perfect.

The fear is that Bovine TB will either infect or reactivate a latent TB infection in people. Because of this fear we cull any cows infected with TB. Defra have also produced what they optimistically call a leaflet (at 21 pages) of ‘What happens if TB is identified in your herd’ which remind me of those Simpsons leaflets ‘So You’ve Ruined Your Life’.


The moment a cow reacts to the skin test the herd is classed as suspect and moving cattle out of and into the herd is restricted. Any reacting animals must be isolated from non-reacting animals and culled. The milk is to be dumped.

The reactor cows are tested post mortem, but even if your reactors show no clinical signs of TB, your herd status is still Officially TB Free Suspended. You will need a clear test (or two clear tests if TB was found in your reacting cows) for your Official TB Free status to be reinstated.

If you have a TB farm you also have restrictions on where you can spread your slurry and on what you can do if your cows die on farm.

It is, in short, a huge hassle, resulting in cow deaths and loss of farm profits, as well as posing a health risk to humans.


It is with these facts that the government turned its attention to badgers, and that, dear readers, we will discuss next week.

Granny and the Blackfish

New title for a band: Granny and the Blackfish.


TheDodo.Com reports that Granny, a 103 year old orca has been spotted off of Canada. Just another example of wild, long-living orcas. And another spit in the face to SeaWorld.

Fluffy Friday – behind the scenes

The marking and MOOC preparations continue this week.

On my morning run I came up with (what I think) is a great idea for one of our MOOC’s interactive sessions. Check out the preview below as I started working out the technicalities in my head. Spoilers? I guess? If you can understand them? Remember to check out our Massive Open Online Course in Animal Behaviour and Welfare which will start in the first week of July. Sign up! It’s free!

Plans Ahoy




And if that hasn’t whetted your appetite enough – check out the Jeanne Marchig Centre blog where you will find a particularly embarrassing video of yours truly capturing some of the behind the scenes action.


And to give you a sneak preview of what’s coming up on Fluffy Sciences next week  .  .  .

Do You Want to See a Magic Trick?

Do you want to see a magic trick?

As part of our Animal Welfare Indicators project I’m creating an online learning object which describes an experiment testing whether or not goats know an object is there when they can’t see it.

Now don’t go doubting the intelligence of goats just yet, this question is pretty multifaceted. It begins with human babies and the game of Peekaboo. If you’ve ever entertained a small baby, you might have fallen back on hiding behind your hands and enjoying the delighted giggles of this apparent magic trick.

There is some debate in the scientific community over whether babies are really fooled by this trick, or whether they don’t have an understanding of object permanence until they’re about two years old.

At some point babies develop the ability to understand that objects still exist even when they’re out of sight. Take a baby’s favourite toy and hide it behind a screen, the baby will look behind the screen. The fact that an object must exist outside of our perception of it can lead to some fun set ups. Check out this video to watch a magician performing a simple magic trick in front of some dogs. The dogs, fully expecting the object to reappear where it logically should, clearly act confused and start searching other logical places (such as beneath the hands, behind them, etc.)

The magic act Penn and Teller explain the anatomy of a trick that uses sleight of hand in this, slightly grainy video. The steps they include are: Palm – Switch – Ditch – Steal – Load – Simulation – Misdirection.

But none of these steps work if you can’t understand that an object should exist where you don’t know.

A psychologist named Piaget came up with a little experiment to test whether object permanance has developed in children – you can try it yourself with the nearest available baby or pet (please ask permission of the bill payer).

For this set up you will need an object and for an animal it will need to be something they’ll be motivated to look for. I suggest a treat (but preferably one which doesn’t smell too strongly).

Show your subject the object and then place it inside a cup or other container (or behind a makeshift screen, like a half open DVD case). Now for the magic trick. Place this container or screen, with the treat still hidden within, behind another screen (such as an open book propped up on the floor).

Watch what happens next. The theory goes that if your baby or pet understands that objects exist even when they cannot be observed, it will look for the treat behind the open book. This leap of logic means the subject must understand the object still exists when its inside the first container, and that when the first container is hidden, the hidden object persists even then.

Or you could hire a magician and get them to confuse the hell out of your pets and babies. Because that’s hilarious.