Langton et al. – The Badger Crowd – standing up for badgers

The Daily Mail, Defra and the bTB story that just keeps growing

Posted on 04/09/2022 by The Badger Crowd

Has Defra had enough of experts? Its own experts that is?

Last week The Daily Mail published a story (here) around the release of a Freedom of Information request (here). This FOI showed that the Deputy Director of the bovine TB Programme at Defra wrote to the journal Veterinary Record (VR) trying to influence the peer-review process of a new scientific analysis of badger cull data, Langton, Jones and McGill, (here), and largely failed.

The Mail story was published on Tuesday 30^th August and names Eleanor Brown as the senior official who wrote to VR Editor Susanne Jarvis on 2^nd March 2022, just a few weeks before the paper appeared in print. It laid down extensive criticisms aimed at the manuscript that they had been sent ahead of publication, where they stated that it was the VR Editorial Board’s (Headed by Lord Trees) decision as to whether to publish it or not. Defra thought it should not be published and made that very clear to a journal that extensively publishes government science.

The original Mail article implied that VR had been ‘forced’ to seek changes to the manuscript. The VR Editorial Board had in fact called a special meeting to discuss challenges to the paper, that Defra’s email in early March claimed was full of errors and flaws. However, the VR Editorial Board found that there was nothing wrong with the statistical work, which was found to be robust. These senior national and international veterinarians, with the VR staff, resting on the detailed reviews of no less than four peer reviewers decided that Defra’s accusations held little substance, and published the paper largely unaltered. The paper showed badger culling lacked any signs of working. Badger culling has not affected bTB herd breakdown in the High Risk Area of England since 2013.

The Daily Mail then republished the article the next day (31^st August), removing the claim that Defra had ‘forced’ the Veterinary Record to make changes to the paper. The truth was that in order to proceed with publication, VR had required the authors to write-in Defra’s apparent intention to publish something in the future, using data it had kept secret, and describe it as a limitation to the study. Something that was dubious, but was made a condition of the paper not being blocked. So the Mail got it right in that there was an element of ‘watering down’ due to the Editorial Board meeting, but nothing that impacted the full force of the paper’s findings that showed that Defra’s badger culling policy had been a total failure.

Defra’s view that the analysis was flawed was therefore roundly rejected by over a dozen leading experts in the field. However, Defra had been invited to comment on the new paper for a short news piece to accompany the publication of Langton et al in the same edition of the journal. But this ‘comment’ somehow morphed into a full-page critique, fronted by the Chief Scientific Adviser Gideon Henderson and Chief Veterinary Officer Christine Middlemiss. This contained and expanded on the sentiments of Eleanor Brown’s email. It persisted with the claims that the paper was ‘flawed’. This was published under the guise of a ‘letter’ in the very same issue.

These highly unusual events then became farcical when commentators immediately recognised errors in Defra’s alternative view. But Defra then held out for six weeks before admitting that their letter was flawed. They then revised it. Saying it didn’t matter anyway because they were right and in effect, that the study, Vet Record editorial staff and the peer reviewers were all wrong (here). In response to last weeks Mail story, Defra even put out a defiant blog on 30 August repeating their original nonsense and unchecked views using small amounts of data for the unculled area comparison (here).

The 30 Aug Defra blog stated:

“As we had been invited to, we presented our findings to Vet Record to help inform its editorial decisions around publication of the paper, with the journal deciding to publish the study alongside a letter of response from the Chief Vet and Defra Chief Scientific Adviser. There was absolutely no attempt to make changes to the scientific research, as the Mail claims was the case.”

For some reason any comments made to this blog criticising Defra’s restatement of their flawed position were removed. Interesting.

So Defra now say that it never attempted to try to get changes made to the science. Yet it wanted to go over the head of the VR staff and peer-reviewers to the Editorial Board? And turned an invite for a news piece comment into a mini-paper that was wrong, dressed up as a letter.

Readers can be the judge of whether science was handled ethically in this instance. Defra say they made no attempt to make changes, yet they wrote to VR in very clear and emotive terms a few weeks before publication, and having been ignored, completed a hurried un-peer-reviewed missive that itself was full of error, ambiguity and secrecy. They were successful in getting the VR Editorial Board to require a smattering of changes stating that Defra had other ideas. Un peer-reviewed science of the future influencing peer-reviewed science of the present?

This actually all looks more than a bit dubious from the perspective of publishing ethics. It has to be asked, who is going to look into it? Having re-stated their views on their new blog, Defra have begun signing off new four-year intensive badger cull licences in 10 new cull areas this autumn, with 40,000 or so more badgers condemned. But Defra are wrong. They (wrongly) claim large benefits from badger culling in the first two years of culling, as they did in 2017, yet say this data cannot be used in the Langton et al analysis. And then they won’t talk about it and neither will Natural England’s statistical expert Peter Brotherton. Natural England as a whole have clammed up, presumably because Defra won’t explain their thinking to them either.

The Minister George Eustice owns the badger cull policy and is closely managing it. He must now be aware of what his staff have done. He may even be a part of it. They have painted themselves into a corner and gone to ground. Has he had enough of his experts yet? If he survives the reshuffle that is. If not, perhaps the dodgy legacy will be his, and a new Minister will get to grips with the ridiculous, unscientific yet defiant behaviour of Defra and its agencies on bovine TB and badger culling. As hundreds of badgers a day are shot for no good reason, the evidence clearly points to bad government and desperate measures. This policy of killing largely healthy, protected animals in a manner found cruel by the British Veterinary Association is out of control.

Defra in Denial?

Posted on 10/06/2022 by The Badger Crowd

A new peer reviewed scientific analysis (Langton et al.) of the effects of the current badger cull was published in Veterinary Record on March 18^th this year. Alongside the summary of the paper, Defra published a rebuttal of the science. There followed a conversation in Vet Record over the Langton et al. data versus the Defra data, and six weeks later Defra admitted that they’d got their data wrong. This is very worrying as it suggests that they have not been accurately monitoring the effects of culling as they should be, and as they assured a High Court Judge that they would back in 2018. Importantly, however, Defra maintained that although they had got their calculations wrong, this didn’t change their overall conclusion that the Langton et al. paper was ‘wrong’.

So what have Defra said is ‘wrong’ about the Langton et al. analysis? Let’s take a look……

Their main argument seems to be that data has been ‘inappropriately grouped’ because the impact of culling on cattle takes some time to appear. They claim this because Langton et al. add culled areas into the analysis in the years following commencement of culling. However, since Defra originally forecast an average annual 16% benefit from badger culling starting from year one, this is an appropriate approach. Indeed their own graph shows substantive declines in bTB herd breakdown incidence in year 1 and year 2. It is not clear how Defra’s argument can be valid on its own presentation. And even if there was some ‘dilution’ or ‘masking’ effect created by having early-year cull data in the analysis, if badger culling was, as claimed by Defra, ‘working’, it would still be possible to pick up a signal of any so-called ‘benefit’ from culling. But there is no detectable effect. None. Twenty-six statistical models failed to find any effect. Four independent peer reviewers, including epidemiological statistician specialists agreed and found the analyses robust.

OK, so actually there is nothing ‘flawed’ or ‘inappropriate’ or ‘wrong’ about the methodology as used in the paper, but Defra seem to carry on in denial, not wanting a conversation about it. How about the data analysis that Defra’s Christine Middlemiss and Gideon Henderson present in Vet Record, and which is also presented by Chief Vet Middlemiss in her 18th March blog?

Well, their graph starts in September 2015, not 2013 when the current badger culling policy began. Why might they do this? bTB had been rising in the High Risk Area for years, with the same trend being observed in nearly all areas. By starting their graph in 2015, Defra is obscuring the fact that bTB had already peaked before badger culling was rolled out to any extent, and has subsequently been declining in all areas. The Defra approach is called ‘selective use of data’, and it conceals the bigger picture of what is more likely happening, as shown in the published paper.

Again, Defra selected a subset of ‘never culled’ badger cull areas to compare with ‘culled’ areas. Why have they done this? Because if you compare ‘all’ the unculled areas with ‘all’ the culled areas, those 26 different statistical models used in Langton et al. fail to find any difference in levels of bTB between them. What is the difference between Defra’s ‘never culled’ data area & Langton et al.’s unculled data area? Well for a start Defra’s never culled area is very much smaller than Langton et al’s unculled area (see figure), about 30% of it in fact. Defra are are comparing only the blue (unculled) and red (culled) area data, but none of the green unculled area data; all area data were used in the Langton et al. analysis. The weakness of Defra’s analysis is their use of a smaller dataset. This could potentially exaggerate any difference between the compared areas. Again, Defra is selectively using data and adding uncertainty to claim a benefit, when impartial analysis using all suitable and available data shows there to be none. Defra’s approach is arguably less appropriate than that of Langton et al.. And of course their analysis is not peer reviewed, i.e. properly checked by independent experts. It is disappointing to see it being published.

What Defra are doing is picking pieces of data from areas of their choosing, using data from years of their choosing, holding them up, and saying, ‘look, we can see a difference’. It’s simply not acceptable to try to criticize a piece of peer-reviewed science like this, using hastily cobbled together snippets, to get your calculations wrong, and still claim that you are right.

What Middlemiss, Henderson and a few paid Defra contractors seem unable to accept, is that the analysis in Langton et al. points very convincingly to cattle testing initiating a reduction in bTB in Englands High Risk Area. Of all the statistical models used in Langton et al., it is the the one in which the cull is excluded that gave the greatest support i.e. a model that did not include culling as a covariate. So without the cull as an effect in the decline in bTB rates, it is cattle measures that are likely to be the driver and this is the best scientific evidence of that to-date.

There is a Crowd Fund for the upcoming Judicial Review Appeal of the ‘ecological impacts of badger culling’ case. You can donate to help cover essential costs here:

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Defra ‘tribalism’ tries to undermine bTB study?

Posted on 01/04/2022 by The Badger Crowd

A recent scientific paper in Veterinary Record (1) by independent researchers Tom Langton, Mark Jones and Iain McGill, showing the effects of badger culls on bovine TB herd breakdowns over the last decade, has been met by criticism from officials at the top of Defra. There are accusations that it is ‘flawed’, and in the Daily Telegraph, even of data ‘rigging’ . You can view a 3 minute video of the main findings here.

Further details on the origin and contents of the paper are discussed in a 40-minute Off the Leash interview by Charlie Moores with two of the authors Tom Langton and Mark Jones, here.

Many badger campaigners will know Mary Barton, aka Betty Badger, who stands up for badgers outside Defra offices each Thursday, and has done for many years. On Thursday 17th March, she was granted a meeting in person with Environment Secretary George Eustice. He told Mary that he thought the study was ‘flawed’. Then on 18^th March, Defra put out a dramatic press statement, criticizing the content & motivation of those involved in writing, reviewing, and publishing the paper (2) :

“This paper has been produced to fit a clear campaign agenda and manipulates data in a way that makes it impossible to see the actual effects of badger culling on reducing TB rates. It is disappointing to see it published in a scientific journal.”

and

“Experienced scientists from the Government’s Animal and Plant Health Agency have reviewed the report and found its analysis is scientifically flawed. It has manipulated the data in a way that makes it hard to understand the actual effects of badger culling and therefore its conclusions are wrong. Today, the Chief Veterinary Officer, Christine Middlemiss, and Chief Scientific Adviser, Gideon Henderson, have also published a letter in Vet Record, which rebuts the report’s claims. The CVO has also written a blog about this.”

Which stated (3):

“We do not believe the scientific methodology used is credible as the analysis has been carried out in an unusual manner ”

These are confident words from the chief vet, informed no doubt by James McCormack (Head of Science Advice to Defra TB policy) and Eleanor Brown (Defra’s Veterinary Head for TB Policy Advice) to try to prevent acceptance of what are the plain and simple findings from Defra’s own data. The new analysis has been extensively checked using appropriate models, peer-reviewed by 4 reviewers, and accepted as a solid piece of research. In truth the 2021 badger culls should have been put on hold in June of that year because the basic findings were clear then and Defra knew about them.

However, the Defra Chief Scientific Advisor and CVO claimed in a letter to Vet Record on the day of publication (4) that “This analysis has been carried out in a manner that masks the effect of culling by incorrectly grouping data.”

Defra’s alternative analysis, shown above, has done something strange to diminish ‘unculled’ area data, that is not explained, yet which appears to undo their own argument. The letter states that the ‘impact of culling on cattle outbreaks takes some time to appear’ while showing steep decline in bTB in the first two years of culling. Oops!

All scientific studies have limitations and none are 100% correct. What Defra are doing in their letter is adopting a pro-cull narrative to promote their policy publicly, with an un-peer reviewed analysis. They are avoiding the sharp reality of what their data is really telling them, and George Eustice and the government should be very concerned about this.

Defra have defended their pro-cull policy in Parliament and in the High Court using a government study from 2019 that uses very small amounts of data (Downs et al. 2019 (5)), wrongly, as ‘proof’ that badger culling ‘works’. That paper in fact admits that there are enormous limitations to its conclusions. The position that ‘culling works’, however, has been widely adopted by the Minister, MPs, the NFU and farming stakeholders.

It’s in the herd: cattle measures are the answer

Defra have dismissed in a short soundbite, one of the most interesting findings of the published paper: the disease slowing, peaking and declining between 2011 and 2016 across the HRA counties, and before badger culling began in all but one area. Defra want to adjust the data for confounding variables. Such adjustment is something that only Defra can do, as they alone have access to this ‘secret’ data. But adjustments are hardly likely to substantially change the conclusions, when such a huge dataset has been used in the analysis (over 20,000 herd a year). Mention has been made of changes in badger cull buffer areas and badger population numbers, but the strength and validity of that data is questionable and presently obscure.

The Defra letter is particularly disappointing, given that Defra/APHA should have been using data to closely monitor and inform the public on the effects of bTB interventions and to ‘adapt and learn’ from their analysis. As they intimated would be the case in a Judicial Review of culling in the High Court in 2018, and as the judgement anticipated. And to encourage and inform those involved in the grueling cattle testing effort. Shouldn’t the public, who are after all paying for all of this, demand that too? Ask a simple question: why didn’t Defra do an analysis with the large data set they had available in 2019 and show the results? Was it because it showed that bTB was peaking and falling in both culled and unculled areas, well before badger culling was rolled out?

But that would mean admitting that cattle measures are the key ‘tool in the box’ to bTB control and need to be extended. BTB decline since 2015 has averaged around 5% per year in the HRA, very similar to the picture in Wales where badgers are not culled and also in Republic of Ireland (RoI). Badger culling is now being phased out in RoI, with long term use of annual SICCT and gamma testing, and with bTB OTFW incidence no lower than around 4%, due to the limitations of the SICCT test. International evidence points to cattle measures alone being the solution, as predicted by experts for over 20 years.

The answers are all here. BTB should keep coming down in the English HRA if it follows the RoI trend over the next 3-5 years. If modern PCR testing is applied, it could be dealt with well before 2030. If the will is there. The Edge area crisis is another matter, but could be turned around too with correct thinking and the right interventions.

Other specialist comment:

Prof Paul Torgerson from the Section of Veterinary Epidemiology at the Vetsuisse Faculty of the University of Zurich wrote an opinion editorial for Vet Record on 19^th March (6) offering insights on why badger culling doesn’t work, as predicted by the government researchers conducting the Randomised Badger Culling Trial back in 2007.

The Defra and the Middlemiss/Henderson arguments have been more than dented.The authors of the new analysis have responded in the Veterinary Record (2^nd April) letters pages (7), saying that Defra’s criticism of the paper is baseless, and their attempt to show alternative science lacks explanation in the way they have handled the data. Defra have discounted around half of the data and the figures they use do not match figures from the reference material. There is also a dead end Link. This could be interpreted as ‘data manipulation’ to try to defend existing policy-based science. Defra’s refusal to accept the Langton et al. analysis using all of the cull data over the whole period of culling, is effectively limiting consideration of one of the most important debates of farming and veterinary concern of the last 50 years.

Over £100 million of public money per year is paid to farmers each year to support bovine TB control, and over £90 Million has been spent killing around 180,000 badgers since 2013; £500 per badger.

Defra’s position is that it wants yet more ‘thinking time’ to privately consider data and internal reports. Meanwhile, concerned observers can only watch while the decision on the course of the badger cull, where Defra aim to kill a further c.110,000 badgers from this June through to January 2026, hangs in the balance. The matter of efficacy needs settling. But Defra want to begin culling again this June and September with the issue of further licences.

‘Scepticism, science & statistics’, by Ian Boyd

There is an irony here in as much as the attitude of Defra employees towards the new study appears to have formed a classic exemplar of what the retired Defra Chief scientific advisor (2012-2018) Prof. Iain Boyd has described recently as departmental ‘tribalism’ in his article in the Royal Society of Statistic journal Significance entitled ‘Scepticism, science and statistics’. Staff behaviour includes hostile over-reaction to anyone questioning government policy.

We can only hope that those involved will now resist that ‘unjustified tribal confidence’ and the ‘traditions embedded within their professional tribe’ and find the ‘social licence to break out’. For the sake of badgers, cows, farmers, the countryside and the public, they need to do it now.

Northern Ireland

DAERA (NI Department of Agriculture Environment and Rural Affairs) have been pressing for a badger cull in NI for some time and have rushed a consultation through recently to try to copy ‘English-style’ badger culling.

For many years Mike Rendle and the Northern Ireland Badger Group (NIBG) have been working with legal and scientific support from the Badger Trust and Eurobadger. Working and meeting with government at Stormont to discuss the issue.

Developments since 2020 have been very disappointing and many who have been watching closely feel the DAERA process of considering interventions has been bungled and that it should have followed the Welsh model. For example, on the government’s own data there is a distinct lack of association (see below) between high badger density areas and high bovine TB incidence areas. The matter of DAERA’s concealed ‘business case’ for badger culling and why the badger intervention with highest environmental impact has been chosen remains unexplained. DAERA even dropped their ecological impact assessments (SEA/HRA) in favour of an earlier ‘dumbed down’ version. This followed an extensive critique, submitted by NIBG describing multiple failures in the proposals and with useful input from eco-regulations expert Dominic Woodfield.

Illustration from the Bovine Tuberculosis Eradication Strategy for Northern Ireland.

Now Wild Justice (8) (Chris Packham, Ruth Tingay and Mark Avery) have come to the fore and with NIBG are Judicially Reviewing the decision to shoot badgers on the basis of improper consultation regarding the business plan and cost-benefit analysis. This includes reference to the new paper on badger culling efficacy in Vet Record. Cattle movements in NI are less controlled than in England, and cattle measures alone should control bTB if a higher level of herd management discipline and more accurate testing could be introduced to cattle controls. But if Defra have been coaching DAERA, the road to ruin may have been laid.

References

(1) Langton TES, Jones MW, McGill I. Analysis of the impact of badger culling on bovine tuberculosis in cattle in the high-risk area of England, 2009–2020. Vet Rec. 2022;e1384.

(2) Defra media statement 18 March 2022.

(3) Christine Middlemiss blog 21 March 2022.

(4) Christine Middlemiss and Gideon Henderson letter to Vet record 19^th March 2022.

(5) Downs S H, Prosser A, Ashton A, Ashfield S, Brunton L A, Brouwer A, et al. Assessing effects from four years of industry-led badger culling in England on the incidence of bovine tuberculosis in cattle, 2013–2017.

(6) Paul R Torgerson, P. R. Editorial in Vet Record, 19th March 2022.What is the role of badger culling as a control measure for bovine TB?

(7) Badger culling to control bovine TB, letter to Vet record, Thomas ES Langton, Mark W Jones & Iain McGill. 2nd April 2022.

(8) Wild Justice Judicial Review

(9) Interview with Tom Langton & James Wood, Head of Department of Veterinary Medicine at the University of Cambridge, BBC Radio 4 Farming Today, 19th March 2022. Clickable button below.