Natural England and the 2022 cull licences

Over the last three years, the science base for badger culling has shrivelled away from ‘not very much’, to nothing. It has regressed from speculation that it might enable a modest annual reduction of bTB in cattle, to the reality that after 7 years of study, there is no measurable benefit when comparing herd breakdown rates in culled and unculled parts of the High Risk Area. It doesn’t work. This is one reason the government refuses to talk about it. Not only did the 2018 spike in bTB breakdowns in Gloucestershire show how unlikely it is that the killing of badgers is linked to the epidemiology of cattle breakdowns. It showed how cautiously the model-based claims of the Animal Plant and Health Agency (APHA) after 2 and then 4 years of culling should be considered. Subsequent detailed examination of all the government data this year in a peer reviewed paper (Langton et al) showed the badger culls to have failed.

Following a ridiculous three months of trying and failing to block and then rubbish the new scientific paper, Defra stopped communicating with the authors and enquiring journalists, leaving Natural England (NE) with the difficult decision of whether to continue issuing licences. The government response was to re-deploy Andrew Robertson from the government’s TB HUB information service in Exeter to Natural England in May of this year “because of a lack of expertise” inside the NE organisation. The outcome was that Natural England supported Defra’s position and issued yet more badger culling licences. Initially more Supplementary culling licences were approved by NE in May, this despite the fact that there was no benefit after 4 years to maintain for a further 5 years. Then in August, NE were somehow prepared to extend their belief in the killing of badgers and to continue culling badgers based on their own unpublished ‘secret’ science.

Instead of stopping culling as they should have done, NE have taken a nebulous stance on the science. It has refused to provide any written justification for its position, perpetuating its belief in the use of secrecy to prevent public scrutiny of their competence and decision making. The public have a right to see the rationale for their decisions, but this has been withheld. It is clear that NE have worked very very hard this year to facilitate continued issue of licences. They do this for a combination of reasons. They are likely fearful of contradicting Defra and APHA. Perhaps it would be too difficult to admit to failure on such a sensitive area.

Over the summer, NE Chairman Tony Juniper chose not to reply to communications, preferring to talk vaguely on public panels about NE not wanting culling and preferring vaccination. This summer he had a big chance to stop badger culling. He didn’t. He has now been in charge during the culling of most of the approximately 200,000 badgers. He and George Eustice have carried out what some call the near eradication of badgers over large parts of England.

NE eventually responded this week following a legal pre-action letter, sent in early October. They claimed that the death of the Queen and changes in government had prevented the licensing paperwork from being shared with those asking for it. These are embarrassing excuses for the lack of provision of legally required documents, on such a controversial subject of high public interest, and they reflect poorly on those responsible.

Information released late on Friday 28th October, showed 11 new cull areas, and the potential for tens of thousands more badgers to be killed. Over 30,000 or so could have already been shot over the last 8 weeks in a further sickening Natural England licenced ‘bloodfest’ of largely healthy badgers. One thing is certain, this is Natural England’s work. Natural England carry the torch for badger culling even if they say they are only following orders. As they have since 2012, when someone thought it would be a good idea for NE to carry it out and control it. They certainly have. It is the legacy of those involved with NE past and present, as much as anyone.

Tony Juniper, a new King, and the ecological impact of killing badgers

Dominic Dyer, chairing the State of the Earth evening session at Birdfair on 15th July this year, asked two of his assembled panel guests about badger culling. The first, Sir Iain Boyd, the former Chief Scientific Advisor (CSA) to Defra commented, beyond his usual emphasis that the problem is more with people than badgers, that he “suspected that the evidence is suggesting it doesn’t work”. And  “if badger culling isn’t working it shouldn’t be done, that’s absolutely clear.” Presumably, a reference to the most recent peer reviewed science (here).

The second guest, Tony Juniper, currently chairman of Natural England, freshly reappointed for another 3 years, was asked about the ecological impact of changing ecosystems by removing most of a dominant species.  His response was slightly less coherent. Knowing his staff had just issued more supplementary killing licences and were in the final stages of lining up licences for a further 40,000 mostly healthy badgers to be killed this and the following three autumns. He picked words carefully: “we did say that it wouldn’t be a good idea” and “Natural England’s advice was that it probably wouldn’t work and we should try other methods” and (not answering the question) “will it have an effect on protected sites and protected species?..  we are looking at that too.”

Not mentioned by him,  Juniper’s hands were tied due to a legal case that would play out a fortnight later in the High Court, that turned into a spectacular environmental travesty (here), remining us just how far government and the judiciary are now leaning towards unsound, politically expedient policies. Briefly, Defra remade its improper decision not to look at impacts from badger culling, supported by Natural England, without telling the court or the claimant. It rubber stamped its do-nothing approach in a way that meant Defra and Natural England could carry on doing little or nothing, escaping justice via the back door. It was ‘too late and too expensive’ now to study and deal with the problem anyway, was their best position, and that was their final decision. Looking at it was all they were doing.

Natural England had promised the courts in 2018 that they were on the case, with a research programme that was kept secret. Secret, it turns out because the BTO analysis used to justify continued culling had mistakes in it, and so had to be held back for two years while culling continued and Natural England staff worked with BTO to get the work through peer review. More recent events in the sorry saga have been exposed thanks to wildlife stalwart Mark Avery (here) and his guest blogs by the main expert witness for the three Judicial Reviews, Dominic Woodfield (here). Dominic has, in his blogs and comments, unzipped the whole matter from start to finish and dealt with the response from BTO during the sordid passage of the work over its last five years.  It is worth taking the time to read the new blog and those that went before, to get a firm understanding of how Natural England have obfuscated their statutory duty and worked hard at minimising effort to examine the problem, while at the same time helping badger cull companies with advice and support to find their cull targets.

Juniper is aware of this of course, and efforts to get funding from Defra to look at the issue may have been turned down. But he has another problem. He has a relationship with and has written a book with Prince Charles. Who is a known lobbiest for badger culling, with his ‘black spider’ letters urging Tony Blair to start culling, a notable royal intervention (here). There followed a concerted effort to neutralise badger culling opposition in mainstream wildlife ngos between 2008 and 2013. Now Prince is King, what will happen? The King faces the reality that the tenuous evidence of badger involvement in bTB in cattle fifteen years ago, then presented as strong evidence, remain tenuous. Critically, recently published research using all of the relevant government data suggests that badger culling since 2013 simply shows no sign at all of working. This is despite Defra’s attempt to use small selective amounts of data with over-elaborate variables to try to show that it does. Defra used their most senior staff CSA Gideon Henderson and Chief Vet Christine Middlemiss to try to rebut the new published research, but this has only made them look foolish. They published, then retracted flawed data (here) that showed huge benefits from badger culling in its first two years, while insisting in their rebuttal of the new analysis that there is little or no benefit to be had in the first 2 years. Leaving professional vets, scientists and commentators completely baffled. Juniper and Charles III now have a big opportunity to help put things right that have gone terribly wrong on their watch.

Most of all, with the BTO paper just published (behind a pay wall), there is a final piece of chicanery. There is no sign of the all-important last line of the conclusions in the papers introductory abstract. The latest BTO magazine simply says that a similar (to the new publication) minimal approach might be repeated. Yet in the BTO paper, the authors call for a landscape-scale quasi-experimental approach: “to provide stronger inference about the complex potential ecological effects of culling predators such as the badger” 

More and more journals are making sure that study limitations are placed in scientific papers and their abstracts, partly a response to the science reproducibility crisis. What this all means is that Natural England corner-cut to address important questions about the effects of the ecological impact of culling. It now admits that the minimal approach it employed is inadequate, and points to the kind of study it now agrees should have been done. This, in truth, is confession of guilt when there is little chance of a retrial before thousands more badgers are gunned down.

You can read Dominic Woodfields new blog ‘New paper same old same old’ here.

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

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 30th August and names Eleanor Brown as the senior official who wrote to VR Editor Susanne Jarvis on 2nd 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 (31st 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’s efforts to pervert the course of science

Today the Daily Mail lifts the lid on Defra’s attempts to interfere with scientific progress (here).

Defra were caught out by freedom of information (FOI) disclosures, leaning heavily on Veterinary Record journal staff, and using emotive language, over an  accepted academic manuscript. This  new scientific paper analysed the governments own bovine TB and badger culling data. It was published by independent researchers on 18th March (see here).

Defra lashed out in an extraordinary way at the authors, peer-reviewers and journal staff via a media blog and made half-baked attempts at manufacturing  graphs using selective bits of (incorrectly calculated) data pushing what they wanted to see. They reached a new low level in efforts to keep badger culling going to prop up the failed policy. Their science and statistics is all over the place and they then refused to communicate over their embarrassment.  Defra staff are now in bunker mentality with their advisers unable to help.

It should be all-over for badger culling – will the Defra, APHA and Natural England blinkers remain on,  or will we see the change that the new science demands?

Read the FOI’s here.

 

Human TB – Bovine TB. Lessons to be learnt and three simple questions for DEFRA

While Defra hold on to a now disproven view that badger culling is needed for control of bTB in cattle, there remain important omissions, contradictions & unanswered questions in their approach to the current management policy.

For a start, the management of Bovine TB (bTB) is still plagued by the inaccuracies of currently used tests and testing systems. Importantly, none of the primary tests currently used can identify the presence of live Mycobacteria which is core to the central dogma of bacterial diagnosis developed by Robert Koch, one of the main founders of modern bacteriology.  He discovered the causative organisms of anthrax (1877), septicæmia, tuberculosis (1882) and cholera (1884). Koch’s dogma or principle, specifies that definitive diagnosis is dependent on the identification of the presence of the infectious organism.

There are major concerns about elements of the front-line bTB tuberculin skin-test. Firstly, it misses a substantial proportion of infected animals, thus allowing undetected infection to circulate in and between herds. Secondly, repeated injection with the tuberculin injection used for the skin test may potentially render an animal skin-test positive, despite there never having been any infection. Thirdly, the implementation of the skin-test is laborious and time-consuming, and requires multiple visits to the farm by a vet, hence while it creates work for vets, it is expensive.

In Human TB (hTB) the basic biology is similar. Recently, however,  the human TB clinical fraternity have become increasingly concerned about the TB skin-test. In fact the concern has been such that the Centres for Disease Control (CDC), based in the US, now recommends the use of the TB blood tests (IGRAs), such as QFT-Plus (similar to Bovigam) over the TB skin test (TST) for most risk groups.

To illustrate the importance of this change of approach, clinical studies on the phage-based test ‘Actiphage’ have shown for the first time that live bacteria can be detected in the blood of people with incipient TB infection, including contacts of infected patients. This success was mirrored by the data produced by vet Dick Sibley at Gatcombe who used Actiphage and Bovigam (gamma interferon) to effectively eradicate bTB from the farm on two occasions. Those studies showed clearly that the best way to identify infected animals was the combined use of Bovigam and Actiphage, and not skin-testing. They indicated very strongly that the biggest problem in the eradication of bTB is the inability of skin-testing to identify infected carriers which actually maintain the infectious burden within the herd. They also imply that there is no significant involvement of external non-bovine hosts in the propagation of the disease.

So, the questions we would like to put to  George Eustice and DEFRA are:

1) Why have you not implemented a controlled trial on the efficacy of different testing strategies for Bovine TB?

2) Why will you not take note of the human TB data? This  clearly shows that identification of the live bacteria is the critical key to controlling this disease.

3) When will you recognise that all the data from both bovine and human TB indicates that there is no justifiable scientific rationale for the involvement of an external host to maintain persistent infection in the herd?

 

DEFRA called out over flawed bovine TB claims at international vet conference

The UK’s Animal and Plant Agency statistician Colin Birch was roundly criticized for his presentation yesterday (12/08/22) at the 16th International Symposium of Veterinary Epidemiology and Economics (ISVEE 16) held at Halifax Convention Centre, Halifax Nova Scotia, Canada.

Birch presented data from badger killing zones in England in recent years, with no proper explanation as to why he had not also used data from unculled areas to compare. He claimed  that a reported 50% reduction in bovine TB herd incidence in culled areas was due to badger culling.

The audience seemed less than convinced. At the end one question pointed out that it is not possible to attribute the reduction in bTB incidence to badger culling as the reduction in the unculled area had a similar trajectory. Cattle measures (Testing and movement controls) that were introduced prior to and over the same period (in both culled and unculled areas) would reduce incidence in the manner observed.

A further point was made from the audience that it looked like Birch and APHA were trying to make and promote ‘policy driven evidence’ to satisfy the ministry (Defra). Birch had no coherent response to this but said that he did not agree.

The unpublished manuscript by Birch and others is yet to be fully disclosed, but comes at a highly sensitive time for Defra and Minister George Eustice and Natural England Chairman, Tony Juniper and his scientific staff. They want to sign off the killing of another 40,000 largely healthy badgers from September of this year, despite the science suggesting that complete failure is the most likely outcome.

In March of this year, Defra issued flawed data (see here) in response to a detailed peer reviewed paper (see here) published in Veterinary Record which showed that badger culling in England since 2013 has failed. In a response to the paper, Defra produced a media outburst designed to undermine it, that claimed badger culling had little or no effect in the first two years, and therefore the analysis used was flawed. Observers have been left baffled and talking about government competence, since all the Defra data presented shows large drops in herd incidence over the first two years, suggesting that it is cattle measures that are responsible for these declines, and not culling.

Despite high public interest in this most controversial of policies, Defra have become tight-lipped on their home-made dilemma since March 2022, and defiantly issued more cull licences in June. But despite well and truly losing the science argument they still  appear desperate to try to show some reason to prop up their policy and to enable them to keep killing badgers. This fell flat at today’s conference as the science community strongly questioned Defra’s handling of data.

A letter to the Prime Minister

A letter signed by 30 veterinary and environmental professionals has today been sent to the outgoing Prime Minster Boris Johnson and other members of the government calling for an immediate moratorium on badger culling in England. Those signing the letter include the three authors of a recently published peer-reviewed paper (read here) on the efficacy of the badger cull using government data.  

A moratorium would allow time for independent scrutiny to establish the veracity of the independent scientific evidence as well as Defra’s claims, and to consider whether culling should be permanently ended as a result. It would also allow for a re-evaluation of the bovine TB eradication policy based on the latest scientific evidence rather than received wisdom that is decades out of date.

Green Party MP Caroline Lucas said:

“It couldn’t be clearer – badger culling simply doesn’t stop the spread of TB in cattle. Yet even when presented with this evidence, DEFRA has its fingers in its ears, and continues to kill at will. We need to see a moratorium to allow time for independent scrutiny of the evidence – which I have no doubt will reinforce the message that this cruel and counterproductive badger cull must come to an end.”

Tom Langton, the lead author of the independent study said:

“Defra have painted themselves into a ridiculous scientific corner and now simply refuse to discuss it. This is the sign of a government that has lost its grip and cannot accept that its own data now shows badger culling to be a cruel and ineffective failure. It’s Defra’s version of ‘Don’t look up!’.”

Veterinarian Dr Mark Jones, Head of Policy at Born Free and one of the co-authors of the scientific analysis, said:

“Huge numbers of badgers have been killed across vast swathes of the west of England over the past decade, ostensibly to control the spread of TB in cattle. However, in spite of Government claims, evidence that the culls are working is lacking. No further badgers should suffer and die for the sake of this failed policy. It’s time that badger culling was ended.”

The letter can be viewed here. The letter is featured in an article in The Guardian here. More from Mark Jones, Head of Policy at Born Free, and an author of the scientific analysis which led to the letter can be found here.

Defra in Denial?

A new peer reviewed scientific analysis (Langton et al.) of the effects of the current badger cull was published in Veterinary Record on March 18th 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:

Donate


Thank you.

Christine Middlemiss, Gideon Henderson and the Defra bovine TB data fiasco

In March 2022 the Chief Veterinary Officer (CVO) Christine Middlemiss & Chief Scientific Advisor (CSA) Gideon Henderson joined Defra Media Centre in attacking a peer-reviewed, freshly published scientific paper on bovine TB control (Langton et al.), stating that they thought it was flawed, and had ‘inappropriate’ analysis, see here.

The graph the CVO & CSA produced (top right) looked odd, and the authors of the original paper immediately suspected an error in the data, and wrote to Defra with an enquiry to this effect.  In addition, much of their written rebuttal seemed invalid. Further, the CVO wrote a personal blog highlighting her criticisms of the new paper. The blog then received a number of posted comments from external observers and academics which reiterated the papers’ authors’ concerns about potential errors in Defra’s analysis and incorrect conclusions. A response to the CVO & CSA from the authors of the paper was printed in Vet Record on 02 April, see here.

It took more than six weeks before Defra admitted that it had got it wrong and published a new graph of data (above, bottom right). But they maintained that this did not change their overall conclusions about the new paper; basically that it was ‘wrong’. They did not respond to the rebuttal arguments that the authors put forward in the 02 April issue of the journal Veterinary Record. On this there is still strange silence.

The authors of the paper had a further letter published in Vet Record on May 21st responding to Defra’s admission of data errors and their replacement graph. You can read this here

This week, CVO Christine Middlemiss made a small adjustment to her blog, but did not change her faulty graph. She added some wording to the following paragraph (in bold).

“Our analysis indicates a clear reduction in OTFw cattle breakdowns, relative to unculled areas, in culled areas from cull year 2 onwards (Fig 1). For example, TB incidence in the areas where culling started in 2016 has dropped from 17.2 OTFw breakdowns per 100 herd years at risk in 2016/17, to 8.7 in 2019/20.

Similarly in the areas where culling started in 2017 it has dropped from 15.3 in 2017/18 to 8.4 in 2019/20.

In contrast, in the parts of the high-risk area (HRA) where no culling took place, incidence has only fluctuated slightly from year to year, from 10.9 in 2015/16 rising to 12.8 in 2016/17 before returning to 10.9 in 2019/20.”


It is a shame that the CVO does not seem to have grasped that the first bar in the graph represents the first year data after culling and not pre-cull incidence. Incidence levels before culling began are missed off, and these better shows the pattern of change in the first two years that they focus on.

The CVO & CSA’s main criticism of the new paper is that (they imply) bTB does not come down enough in the first two years for those years to be grouped with later years of culling. Looking at their graph, this is clearly not the case and the CVO and CSA’s position is a paradox and nonsense. There is a drop in culled and unculled areas if you examine all the culled and unculled data, and not just a sample of unculled (never-culled) area. The steady decline in incidence, as shown in the Langton, Jones and McGill paper, is attributable to cattle testing and movement control measures. Defra’s attempt to show otherwise falls at the first hurdle. It is something Middlemiss and Henderson seem reluctant to address. It is understood that Defra intend to ignore their own faulty response, and endorse an APHA study at a disease conference in July in Canada as justification to carry on culling in September.

Christine Middlesmiss doubled down on her position in an interview on Farming Today on 26th May (the focus of which was Defra’s badger vaccination licensing scheme), using very strong language and stating that in the Langton, Jones and McGill paper, “the whole methodology was wrong and so the conclusion was wrong.” Again, she claimed that the authors had not used a robust methodology to examine and assess it and therefore the conclusions are wrong, they’re not scientifically valid.”

This is a bold claim about a rigorously peer reviewed paper in a leading scientific journal, and one that it could be said she should be able to clearly and concisely articulate in a debate, or at least to the authors. It is not good enough for the CVO to just claim, as she did in her interview, that “it is complex“.

Further she said we believe that culling is effective, apparently relying on faith rather than understanding of published science. She must be able to explain her reasoning for dismissal of peer reviewed science. She also said that “It’s not absolutely my decision to release it [the data], implying political interference? The authors are still waiting for a response to their April invitation to discuss the CVO’s criticism with her.

You can listen to the CVO’s interview on Farming Today, available here.

The CVO & the CSA must look again and accept the findings of the new robust peer-reviewed research. Prevailing science shows the current badger culling policy to have failed, with no detectable impact from it on the incidence of bovine TB in cattle herds in the High Risk Area. The 29 Supplementary Badger Culling licences authorised this Wednesday were issued on the back of a government veterinary service in denial.

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Badger culling and BTB data:

Middlemiss and Henderson say sorry for getting it wrong

As previously blogged on 18th March here, the respected journal Veterinary Record published a new scientific appraisal of the effect of badger culling on bovine tuberculosis (bTB) in the High Risk Area of England using government data collected from farmers and vets for over a decade. This extensively peer reviewed paper is available open access online, in full here. The paper concluded that badger culling has not been associated with reductions in bovine TB (bTB) incidence or prevalence among cattle herds.

Alongside a one-page summary of the paper in the Vet Record print edition, the Chief Veterinary Officer (CVO) Christine Middlemiss and Chief Scientific Adviser (CSA) Gideon Henderson published an un peer-reviewed letter rebutting the paper’s main findings. They produced their ‘alternative analysis’ in the form of a graph, and claimed it showed that badger culling was ‘working’ in reducing bTB in cattle. The graph indicated very rapid declines in bTB in culled areas following the commencement of culling, with little change in unculled areas. The CVO Christine Middlemiss also posted a blog on the Defra website using the same graph.

The graph could not be reconciled with publicly available data. There followed repeated requests for Defra to supply the data and methodology, but these were not met. Then last week, six weeks after publication, Middlemiss and Henderson  sent an email to the authors of the original paper stating:

“Following your recent correspondence about how incidence in unculled area was calculated we have re-examined our analyses and discovered an error we wish to bring to your attention.  The incidence in the area unculled throughout the period was calculated incorrectly. The incidence in cull areas is unchanged. We attach a corrected graph, with the corresponding data and workings as previously requested. We apologise for this error..”

A new graph was provided (see below). After further requests and delay, we have data from Defra to allow us to reproduce their corrected graph but not to check its origination. Defra’s original published graph shows bTB herd incidence higher in unculled areas in four of the five years, while in the new one it sits at the same levels as in culled areas.

As previously, Defra are still disregarding huge areas of unculled land in their blue-bar ‘never culled’ areas, which is problematic. Notably, however, the error bars between ‘culled’ and ‘never culled’ overlap more extensively, so the difference between the two is unclear.  It seems that Defra’s corrected calculations corroborate the findings in the Langton et al., and that there has indeed been no significant impact from badger culling on bTB incidence among cattle herds.

Defra’s graphs from their 19th March letter and 5th May email:

19th March (withdrawn): Unculled incidence is higher than culled in 4 of the 5 years.
5th May: Now incidence levels in unculled areas are shown well within same levels as culled areas.

Defra’s “never culled” areas are likely to include significant land areas where bTB is less of an issue, with landowners having a lower incentive to coordinate a cull, whilst the “waiting to be culled” portion of the unculled area will have significant areas where bTB is a major problem. Defra is engineering a highly selective use of the available data. It adds up to a misleading picture that is bringing Defra into disrepute. Without access to their full data source, it is not possible to fully understand their rationale.

Further, when you don’t limit the data as Middlemiss and Henderson did, and add “all culled areas” bars (green), and include 2013/14 and 2014/15 (see below), it shows the true extent of decline of bTB incidence in unculled areas that mirrors culled areas.

Revised Defra data with Langton et al’s unculled green bars

The 5th May ‘apology’ email from Middlesmiss and Henderson maintains that “this does not change the overall argument in the letter”, yet over six weeks on, they have failed to address a response by the authors to this criticism (published in Vet Record on 2nd April). This response shows that their main argument on ‘incorrect grouping’ of data does not undermine the peer-reviewed statistical analysis.

Specifically, Middlemiss and Henderson claimed that using data from the first two years of culling ‘masks’ any overall effect from badger culling, making it ‘impossible to see’. But Defra’s counter argument rests upon a steep decline in herd incidence over those first two years! Defra’s argument falls and the answer is that taking all the data, herd breakdowns reduce in culled and unculled areas at similar rates, due to cattle measures both before and after badger culling is rolled out.

So, the senior Defra scientists have no answer, and continue to use delaying tactics, while still providing only limited access to the available data that might enable independent researchers to assess their new graph. This is shocking and does not serve the public interest. Cattle-based measures implemented from 2010, and particularly the introduction of the annual tuberculin skin (SICCT) test have been responsible for the slowing, levelling, peaking and decrease in bovine TB in cattle in the High Risk Area (HRA) of England during the study period, before badger culling was rolled out in 2016.

Last week, the authors of the badger culling paper, Tom Langton, Mark Jones and Iain McGill wrote to George Eustice (read here) about the continuing fiasco and asking for badger culling to be suspended and for additional clarification and dialogue.

This is what all stakeholders and the public deserve. Clear, open government responding to the facts in an honest and professional way.  No more delay, secrecy, and avoidance of the real issues. It is time things changed.

On Friday 20th May, the paper’s authors response to Defra’s apology and clarification was published in Vet Record. You can read this here:

Farming Today featured the debate around Defra’s data miscalculation on 20th May; you can listen here from 7:18 minutes in.

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Why were you Wicked to Badgers?

Book Review:  A History of Uncertainty – Bovine Tuberculosis in Britain 1850 to the Present,  Peter J Atkins, 2016, Winchester University Press
(Link to the online chapters of this book (free subscription required) here.

By Tom Langton

 

Back in 2016, having just begun a detailed examination of the Randomised Badger Culling Trial (RBCT) (1), this book escaped my attention. Now with a tatty ex-library copy from ebay, its value and place is clearer. As with the 2019 review by Angela Cassidy (2), it is I believe a substantial contribution to the understanding of the English bovine TB (bTB) epidemic and control policy in the period since ‘badger blame’ emerged in the 1970s.

Peter Atkins, has been a prolific food and drink geographer and historian at Durham University, including inevitably, the disease-related issues. Much of the book is a detailed account of the technical and political context surrounding livestock management and milk production, including pasteurization since 1850, as a threat to human health. This is a compelling blend of what happened and why, regarding the once extremely debilitating and widely lethal bovine TB threat to human health in the UK.

Atkins book was published before the announcement of the 2016 badger cull roll out, which Atkins misjudged as unlikely to happen. Despite this, insight generally seems well evidenced and often convincing, and the book is especially worth reading in terms of what has unfolded since 2016.

Don’t be put off by the cover of the book, that shows nose to nose proximity between a tame badger and a cow, in an unlikely day-time event. This is, according to research done before and since publication, a rare event even at  night, which is when badgers are most active above ground. In fact, it is one of a group of photos that has unintentionally proliferated misunderstanding of the transmission of bovine TB from badger to cattle.

Although bovine TB and badgers occupies only the last quarter of the book (chapters 12-15), it manages to get through a good amount of epidemiological practicalities at pace, and provides bouts of eloquent summary. There is a useful collection of around 800 author-indexed references at the back of the book, several of them obscure, with handy library reference numbers too.

Spat between the ISG’s John Bourne and CSA David King

Chapter 12 on epidemiological understanding provides some useful detail on factors such as cattle herd density changes over time, government expenditure on disease control and potential infection pathways. Its thoroughness extends, at least to some extent, to referencing international examples and molecular consideration of spoligotype distribution. Chapter 13 is a rapid road trip from the period where bTB was found in badgers in 1971 in Gloucestershire, through the uncertainties of the badger-cattle disease relationship and infection of badgers by cattle. There is good descriptive summary, albeit with historical account of certain research findings as fact, rather than placed in any measured scientific context of the strength of findings. This is not a criticism as this was not a scientific appraisal.

There is a short history of badger culling from 1971, a rapid summary of the RBCT and the Independent Scientific Group 2007 report and of David King: the government chief scientific advisor’s critique of it. Plus, the spat between the Independent Scientific Groups’s John Bourne and King, that followed. Of some interest is the report that in 2007, it was the Labour government, under Gordon Brown and the MAFF-centric Lord Rooker, that laid the foundations for mass badger culling, even if there followed a delay by Hilary Benn until Labour lost the election to the coalition government in May 2010. There is some basic material on badger cull opposition and the period leading up to the culls starting, but nothing comprehensive. The threats from uncertainty and risk, the focus of the book, are well measured at appropriate points in the narrative. While several of the uncertainties are better understood due to research in recent years, the text for the most part stands the test of time well and is a good general foundation for the student.

Civil Service prone to massive policy mistakes and blundering?

Chapter 14 is likewise an admirable summary for the time of bTB testing protocols, and test accuracy. Examining what is termed the ‘recrudescence’ of the disease in England and Wales since its near eradication in the 1960s, it touches on important disease eradication cost-benefit issues and a more condensed history of disease administration, with even a brief sortie into cattle and badger vaccination.

But perhaps what is most interesting of all, is saved to the final chapter 15: ‘Is uncertainty the future?’. As the writer puts it, ‘what are the lessons the historical geography of bTB has for us?’ There then follows, as a warmup, a look at complexities of some of the spatial questions in bTB epidemiology, raised earlier in Atkins and Robinson (2013) (3) and more recently reinforced by findings from Whole Genome Sequencing. There is an amount of conjecture over ‘scenarios’ that to the historian may seem like useful wondering, but to the scientist perhaps are rather speculative.  Maybe a bit of original conjecture is okay, but it stands out a bit  in contrast to the bulk of careful documentary.

Then, for me the book turns even more compelling. It addresses the question of why the bTB response has been so sluggish and ineffective, and what is framed as the ‘grotesque cost’ of dealing with diseases of the intensive cattle industry: BSE, Foot and Mouth and bovine TB over the last decades. It looks at the punitive demise of MAFF after Foot and Mouth, and how the British Civil Service seems somehow prone to massive policy mistakes and blunders. Should, asks Atkins, bTB handling by Westminster be added to the ‘hall of infamy’ of policy disasters?  But then ‘no’ comes the answer, with a slightly unconvincing defence. His forgiveness is founded on his perception of complexity and uncertainty in the science.

Bang on cue, a sub-section is set up, that chimes with recent discussions over England’s covid-19 early response management entitled ‘A rule of experts?’. The building of policy-lead science (4) to address difficult questions is laid out, leading to the introduction of the concept of dealing with complex and politically tangled issues, framed as ‘wicked’. Based partly on the fact that the problem is dire, unforgiving, labelled as unsolvable and hence apparently justifying unconventional resolution. So ‘Yes Minster’ style consequentialism – where the ‘ends justify the means’: your often ‘tribal’ (5) bad behaviour is excused, and where whatever you decide, you become blameless.  Does this government approach sound familiar?

Wickedness unveiled

The last few pages of the book, ‘Bovine TB: a wicked problem?’ may both delight and annoy. They delve into the philosophy of addressing problems that are rated so unbalanced, complex, and frustrated, that the strategy is to manage them, based on continued uncertainty over long periods of time.  So bTB is allocated to ‘wicked’ philosophy (6), something that the very senior government officials and scientists may have latched on to at the start of culling as interest in its use began to grow (7). Meaning, that the uncertain outcome of badger culling wasn’t an important issue; it didn’t have to ‘work’ if it induced the livestock industry to accept tougher disease eradication measures that they were resisting. Such approaches are also nicely framed as a ‘clumsy solutions’. All government scientists and vets had to do, whether in the know or not, was roughly comply with a top-down ‘yes, it is the badgers’, undertake a bit of low inference analysis, then maintain ‘you will never actually know directly how much badger culling has contributed to disease control’ and ‘we are going to use every tool in the box’. This of course nullifies a range of professional and ethical pledges, and may be unlawful. But hey, this is a ‘wicked’ problem, these are different times and so anything goes? Those who have said badger culling is criminal may actually have a point?

One must ask who was ‘in’ on the badger cull wickedness, who fixed it, made it happen and who drove the car?  It is getting easier to see now. Anecdotally, government staff will apparently not deny it in private. This has been clear from multiple sources since Atkins book. But outwardly, in-post, their job comes first and they will follow the tribal line. This helps explain why Defra have reacted so ferociously (and clumsily) to the now emerging data on the badger culls (8) that shows them for what they are; ineffective. The problem must and needs long-term to remain ‘wicked’ for the emperor’s clothes to remain visible. But Environment Secretary Minister George Eustice has lost cull architects Ian Boyd and Nigel Gibbens, and those replacing them may not have been told and thus have greater exposure.

Atkins almost spoils it at the last, as Angela Cassidy did in her book in 2019. He had already come up with his own esoteric home-brew idea that badgers pose more of a risk at certain densities. He points at uncertainty in the epidemiology and the pathogenesis, but not to any deficit in ‘formal sector expertise’, which is a bit over-simplified. He denies ‘selfish individual motives or special interests’ which also looks a tad naïve, given the strength of influence of commerce in the mix. Atkins suggests no one is to blame, or that the blame is evenly spread, which is the diplomatic nice story, but  one cannot help feeling that in doing so, like Cassidy he drops into the ‘sticky trap’ of badgers and bTB (9).

Of course, scientific evaluation is not  Atkins forte,  and there is failure to balance scientific findings according to their limitations. BTB is a scientific problem and you can see as he cites and runs through much of the key relevant literature, that he is not pausing on the uncertainty and hindsight problems within them.

Despite this, Atkins logically foresees the time of effective use of cattle measures that were starting to bite in the High Risk Area as he finished this book, and that they need further tightening with better testing and/or cattle vaccination, to finish the job. Such disease control achievement however, is not the consequence of any ‘wicked’ approach. It is simply what would have happened with strong leadership and without badger culling. And, with all due credit, Atkins also rightly concludes that badgers are likely to be seen as a distraction to the bTB problem when all is said and done in years to come. Again, this book was published before the announcement of the 2016 badger cull roll-out and his last page makes salutary reading, as he was unaware of the mass butchering of largely completely healthy badgers that would immediately follow, and that should hopefully soon be abandoned.

This is a great ending if you are concerned by the repeating car wrecks of government veterinary epidemiology when addressing livestock disease control in England. And how the manipulation of logic and science for expedient high risk approaches, can be endorsed and nurtured in the tribal institutions in public service, given a few wicked people pulling the strings. 

A link to the online chapters of this book (free subscription required) is available here.

References

  1. Bourne J, Donnelly C, Cox D, Gettinby G, Mcinerney J, Morrisson I, et al. Bovine TB: the scientific evidence. A science base for a sustainable policy to control TB in cattle. Final report of the Independent Scientific Group on Cattle TB presented to the Secretary of State for Environment, Food and Rural Affairs the Rt Hon David Miliband MP; 2007.
  2. Vermin, Victims and Disease. Book review.
  3. Atkins, P.J. and Robinson, P.A. (2013) ‘Bovine tuberculosis and badgers in Britain : relevance of the past.’, Epidemiology and infection., 141 (Special issue 7). pp. 1437-1444.
  4. Kao, R. Simulating the impact of badger culling on bovine tuberculosis in cattle. Vet Record 176 February 18 2012. “An underlying problem in this debate is the contrast between the burdens of proof demanded by the scientific and policy constituencies. The burden of scientific proof requires near certainty in outcome; the classic limit for scientific confidence is that 19 times out of 20, a repeated experiment will produce a stated result (ie, the result is within the 95 per cent confidence interval).  Policy, however, must balance the efficacy of a potential measure with social, economic and political requirements, and in the event that a decision is to be made, it is made only when the balance of probabilities is in its favour. Thus, there is an inherent paradox in the need to take statistically rigorous, scientifically sophisticated recommendations and view them through the relatively fuzzy lens of sociopolitical realities.”
  5. Boyd, I. 2021. Scepticism, science and statistics. December 2021 Significance. The Royal Society of Statistics. P 42-45. 
  6. See Pellezzoni I. 2014 Technoscienza 5,2,73-91 and a raft of associated ideas discussed in the Atkins book and elsewhere. 
  7. Badger culling emerged from scientific endorsement but there was no real link between a large experiment with equivocal results and its real-time application. Culling badgers was simply ‘Bourne’s carrot’ using Kao’s (3) acceptance that an arguable balance of probability it might work (see (3) above) was sufficient. 
  8. Thomas E. S. Langton, Mark W. Jones, Iain McGill, 2022. Analysis of the impact of badger culling on bovine tuberculosis in cattle in the high-risk area of England, 2009–2020 Veterinary Record Vol 190 Issue 6. 18 March 2022 
  9. https://thebadgercrowd.org/vermin-victims-and-disease                

It must surely be time to kill the badger cull?

A new article for BBC Wildlife Magazine by James Fair takes a look at newly published peer reviewed research that concludes that the badger cull isn’t working. It’s worth a read because it puts the new analysis into the context of the historical background of bTB and the previous analyses of the results of badger culling.

It is of note that the conclusions of the Independent Scientific Group (ISG) in 2007 are mirrored by the conclusions of the latest study;

ISG: “After careful consideration of all the RBCT and other data, including an economic assessment, we conclude that badger culling cannot meaningfully contribute to the future control of cattle TB in Britain,”

And

Langton, Jones and McGill 2022: “This examination of government data obtained over a wide area and a long time period failed to identify a meaningful effect of badger culling on bTB in English cattle herds.

Despite this confirmation of the expected & predictable results of nine years of badger culling, Defra (Chief Vet & Chief Scientific Adviser) have kicked back strongly with accusations of partiality on the part of the authors. This is somewhat ironic as (nearly) all published English bovine TB science to-date has been published by Defra or their funded contractors. Commentary on the paper via the Science Media Centre was supplied by two recipients of Defra contracts who are or have been heavily engaged in bTB policy.

The paper’s authors are still waiting for a reply to their request for an explanation of how Defra manipulated data in their un-peer reviewed rebuttal analysis letter, published in Vet Record, which claims to show culling does reduce bTB in cattle.

You can read James Fair’s article here, and Langton, Jones and McGill (2022) here.