On Friday 26th September, Defra changed the “Bovine TB strategy review update” but simply made things worse by adding another layer of confusion.
The correction of reported Information Criteria as now shown in the Godfray Review
An error was reported as “a revision to a line of code”. In the document itself, the change is referred to as a ‘cut and paste error.’ Red text in a box next to the correction (see above) suggests that ‘The rest of the analysis and interpretation is unaffected’.
The replacement red numbers, now show the outputs from their 4 models described, but this time the difference between models 3 and 4 is insignificant. To put it in technical terms, a delta (difference) AICc of 0–2 suggests both models have similar support from the data.
However, far from the analysis and interpretation being unaffected as they suggest, the revision does have serious implications for the inferences drawn. The ‘update’ is actually a correction due to the wrong results being inserted into their models in Annex 4. The results reported as AICc (Akaike Information Criterion) were in fact the results from Baysian analysis (BIC) (which they did not report on).
However, BIC is not the correct IC for model selection, due to the small number of data points and large number of coefficients to estimate. The small sample size equivalent (was this really not tried?) would be appropriate (BICc), especially for logistic regression. Applying BICc favours a model which suggests that the incidence of herd breakdowns is independent of culling (i.e. culling produces no effect).
If AICc is used for model selection, a model suggesting a weak effect of culling is only slightly favoured, model 3: 173.58 vs model 4: 173.87. This difference is too small to draw any inference from; it is effectively a toss-up between the two models. The incorrectly reported IC results showed a bigger difference: model 3:151.58 vs model 4:159.38). It is this greater significant difference, which is what the peer-reviewers seem to have picked up on. Hence the big question, what were the peer reviewers sent? And given that one or both reviewer assumed the code was right, were they commenting on the wrong results?
Apparently Defra have been asked this all-important question and an answer is pending. Maybe they don’t know and need to ask? The answer could alter the Chapter 6 discussion hugely. A very large number of people are interested to find out who knew what and when.
The Information Criteria as originally presented in the Godfray review
One might pose the question “did the Godfray group try the small sample size BICc?” Given that they obviously tried BIC (as that is the output they incorrectly reported), the correct form of BIC would be the small sample size correction as there are only 20 data points. Interestingly, when BICc is applied, model 4 (without badger culling at 196.00) is favoured over model 3 (with badger culling at 200.96). I.e. badger culling has no effect.
However, notwithstanding all this incredible muddle, it would have been more appropriate to select the most favourable model of a series of over-dispersed models, using the quasi version of AICc, which is QAICc, especially as the quasibinomial model was subsequently used for statistical inference.
When the QAICc is applied to their models, the results strongly favour a model which again suggests bTB incidence in cattle is independent of badger culling (i.e. culling produces no effect).
A pre-print outlining some of the problems with the new analysis is available here.
Reasonable people can disagree….
When dealing with the recent academic publications on the RBCT, (which have been reported on here), and which arrive at different conclusions, the Godfray review has stated at para 6.LXX:
“…reasonable people can disagree about the best way to analyse complex data such as these.”
That is an interesting response to the current differing views. A short article entitled “When Can Reasonable People Disagree?” is quite insightful on this. We borrow a couple of apposite quotes below:
“To say that “reasonable people can disagree” can encourage suspension of judgment in response to important matters of personal and social concern.”
“There is a related tendency to use the expression “reasonable people can disagree” to create an equivalence when it comes to conflicting beliefs that large groups of people hold. A common perception exists that if a large enough group of people believes something, it has met the litmus test for being a “reasonable’ belief and the people involved “reasonable people.” This is a familiar critical thinking error. The fact that a large group of people believes something does not provide us with a compelling reason for thinking it is true.”
“Respect for persons might require engaged listening. It might require careful consideration. It does not require treating weak evidence as if it is strong nor does it require treating unsound arguments as if they are sound. Far from being kind, we are actually doing one another an injustice when we engage one another as if all arguments are equally compelling.”
The point is, and it is a point made by Prof mark Brewer earlier this year in his review of Torgerson et al 2025, it is more a question of can reasonable people agree? And the answer to that appears to be not yet. But there needs to be conversation. So far Defra has refused to have that conversation. Will that continue or does it have to wait until there is an inquiry into the crisis?
In any event, this muddle is so bad that the Godfray review will need to be rewritten. That is unavoidable now. The mistakes are too obvious, too profound and too important to remain as a part of the narrative.
While there is a ‘it doesn’t matter anyway’ type sentence to cover up any exposure, it is quite clear that it really does matter. The mistakes alter everything, including the economic forecast on badger culling benefit.
Its time for Defra to change the way they do business.
In December 2024, rather than have an independent review, Defra re-appointed some of its familiar advisors to update their 2018 Bovine TB Strategy Review. To consider “new evidence or analysis” published since 2018 that affects the recommendations made seven years ago. The reported aim was to assist work on a new bovine TB (bTB) strategy for England for the spring of 2026. The DEFRA panel was mandated to:
review evidence and analysis published since 2018
look for improvements on BTB interventions set out in their 2018 Review
advise on gaps in the available evidence and disease control tools.
The authors were charged with producing these outputs as three chapters. But the result looks more like an effort to refresh old beliefs and hopes, aiming to keep the little acted-upon 2018 document afloat. The new report says it should be read alongside the 2018 review, but that is hard, with what is now overlapping groups of ideas across two documents. No one seems to have asked if the 2018 review was actually worth building upon or if perhaps ordering it in a more effective way was in order, so as to better the 2018 review.
In the report, the authors have looked selectively at the science, but not discussed its merits in any depth. Instead they have used their preferred thoughts and policy suggestions, and much ‘hunch’ opinion comes through. And rather than accept peer-reviewed published science on the RBCT that they don’t like, they have done some of their own analyses – as posted earlier (here). These analyses are selective and lack scientific rigour. They then finesse the muddle by saying any demise of the RBCT does not really matter anyway. So why did they go to all the effort of the unsuccessful rescue effort then?
The overall impression is of a report trying to help Defra to ‘carry on regardless’, with failing measures and with a few changes here and there, rather than looking forward with clear fresh direction and determination, as the exercise required. After all, the 2018 recommendations were largely, either rejected, not adopted, adopted in part or merely paid lip service to. The result has been a failure to reach the 2025 mid-point policy targets.
The fact that Daniel Zeichner (now fired and replaced as Minister of State by Angela Eagle, after only a little over a year), reappointed largely the same conflicted group of individuals from 2018, may relate to him coming into the job with the wrong briefing on bovine TB.
Zeichner failed to recognize, and act on considerable issues within his struggling bTB department. A department too embedded in the wrong moves, he was too slow to realise. Zeichner and DEFRA simply chose to dismiss early concerns over lack of impartiality in the Godfray re-appointments. A 50,000 strong petition calling for scrutiny of Oxford’s statistics, a six thousand strong petition and public demonstrations in Oxford about the lack of independence of panel members, some of whom held multiple conflicts of interest, made no difference to the Defra back-room advising the Minister. Academics most conflated in the scientific controversies at Oxford and Cambridge Universities would be ‘marking their own homework’ for Defra again, at taxpayer expense.
Labour’s incoming policy emphasis last July was all about moving away from badger culling. But it did not let go of the Defra obsession to focus so highly on badgers, as their unproven significant vector. This suggests that the usual suspects within DEFRA and APHA, by now captured and tribalised by industry interests saw that their best strategy was to play for time. It seems that their aim was to slow down policy change to phase out culling. They were perhaps keen not to risk the truth being made public, which might enable the NFU to reclaim huge costs spent on killing badgers to no effect. Perhaps to play a waiting game in order to bring culling back in a few years time to satisfy strong industry beliefs, spawned by bad (Godfray) science. It is, after all, the measure that Defra has long ‘hung it hat’ on, as the key tool in its mythical tool box. The measure that Boris Johnson as Prime Minister took away from George Eustice back in 2020. The measure that originates largely from Oxford University getting the science wrong, time and time again. And now getting it wrong once more.
This outcome has been on the cards since Defra announced they had made the Godfray panel appointments earlier this year (see here). The panel included Professors Charles Godfray and Bernard Silverman from the University of Oxford, and Professor James Wood University of Cambridge. Godfray and Wood had major roles in supporting badger culling for Defra, and were unlikely to change their rewarded positions on the issue. Also on the panel was Professor Glyn Hewinson, who has spent a professional lifetime (now at Aberystwyth University) working to try to seek new testing methods, and Professor Michael Winter of the University of Exeter. Professor Christl Donnelly was recused from the panel, with prior concerns raised over RBCT badger cull policy statistics.
The update report looks like it has been collated by Defra staff with major input from James Wood, with excessive detail on worries about cattle vaccination. With Bernard Silverman looking at Badger cull statistics. Use of a mix of numbers and roman numerals for paragraphs looks a bit clunky.
The report suggests that there is a ‘small chance’ of being TB-Free by 2038. Saying that it is ‘challenging but achievable’ is not so much a stretch as an impossibility, and Defra have confirmed they have no position on when TB Freedom will occur.
Here the departure from reality looks a bit desperate, it shows a detachment from any understanding of where the epidemic control crisis is truly positioned. Farmer representatives cannot possibly look at this document with anything other than grave concern and scepticism.
This ‘small chance’ of TB-Freedom in 2038, must be maddening to those at the ‘coal face’ who know that the disease control policy is failing and poor scientific advice is the major driver. And it is not due to a lack of investment, but how finances have been managed that is at fault. The self-praise that TB Hub is ‘very good’ is revealing. It has long been a mouthpiece for dubious ideas and advice.
Chapter 3: Surveillance and diagnostics in cattle.
After the introduction and background, the first topic chapter recognizes some of the more obvious and burgeoning issues with the current approaches that were underplayed in the 2018 review and are already published for anyone caring to look:
Mother to calf infections are important
That TB-Free status awarded on release from breakdown is often false, undisclosed residual infection is rife, and is driving the epidemic in cattle (and wildlife)
The low sensitivity of the SICCT test means it should be replaced with the SICT test, the test used successfully in other countries
Better testing will significantly contract the cattle industry due to the volume of infected animals that have been generated by the failed system since 2001
Ways to safely quarantine infected cattle for slaughter to prevent spread both to other cattle and wildlife and avoid industry contraction have not been determined
Data sharing is incoherent, despite £183 Million being spent to-date
Yet there is a nod to the work by Robert Reed and Dick Sibley and others at Gatcombe Farm in Devon, and elsewhere, as expounded in the ‘Brian May’ BBC Panorama documentary of 2024. The need to be able to use alternative tests is recognized, as is the use of tests without compulsory slaughter of reactors. This opens the way for a more nuanced system. These avenues are mentioned but lost in a list of many other things without weighting or priority. The system to implement such measures is another story and could have been mapped out. Defra is stuck in ‘can’t afford it’ mode, but a report like this won’t help them.
The media headline announcement of the review update on 4th September was a warning that Covid-style control funding is needed – so perhaps a few hundred £Mn or £Bn per year? How likely is this in the current economic climate? How much is really needed and for what? Where is the cost-benefit analysis or doesn’t it look too good? Will the government simply look to pass on the problem to the next administration, as previous ones have done, or look to sort out the long running disaster? Other neglected animal health crises suggest ‘wait and see’ is the present strategy, so the reports vagaries might not have bothered Defra too much.
Chapter 4: The Disease in Cattle
Reading through all the uncertainties and caveats in this section, the reader is led to the conclusion that bTB cattle vaccination is unlikely work any better than it is working now any time soon, and that it might be undeliverable at scale. Some of the claims are un-evidenced and a DIVA test that works is the unconvincing ‘maybe’ of old. This could almost be interpreted as a recommendation to drop the whole thing and let those involved slip away, rather than invest yet more shiploads of funding. It is hard to see any excellence in this direction.
Chapter 5: Cattle movements and Risk-based trading
Obviously linked to diagnostics, the general lack of cattle movement control monitoring and poor biosecurity offers bleak prospects. The problems are well known, but little is being done to improve them. Suggesting that only 25% of Low Risk Area infections are due to cattle movements implies continued denial and/or incompetence. The update fails to identify a credible and rapid way forward to stop what the EU call ‘the British national sport of moving cows around’. The links between biosecurity, risk-based trading, slaughter compensation and a potential insurance approach are further covered in Chapter 8. But until the basic elements of disease control are sorted out (moving diseased cattle infects the herds they are moved to), and the truth separated from the fiction, it is hard to see who is going to believe in, support and enforce any such extensive controls.
Chapter 6: The Disease in Wildlife
Here the authors are writing to defend a failing battle to promote badger interventions. Charles Godfray and James Wood are two of the academics who have pushed them as effective. Godfray via the original Randomised Badger Culling Trial RBCT experiment where he was a DEFRA audit contractor, and Wood being the post 2013 media cheerleader for culling “working” generally, and attacking those questioning biased government propaganda. Predictably they recommend that badger interventions are still necessary to control bTB in cattle.
With Bernard Silverman replacing Christl Donnelly (both at Oxford University Statistics), the face-off between the Paul Torgerson and Donnelly camps over the RBCT analyses that has played out recently in the Royal Society Open Science journal comes to the fore (see here). The review finds in favour of Torgerson on statistical use of rate/count in the ‘battle of the models’, but Silverman has gone beyond his remit to review, and has actually done his own analysis, with code published as Annex 4. He attempts to ‘rescue’ the RBCT, albeit with low statistical significance. However, having diminished the holy-grail RBCT study significance from strong to weak, he has used the wrong output data for his result. When his published model is followed properly, badger culling is shown to have no effect, (see pre-print here). Thus the Godfray report fully invalidates the RBCT – this may take a few weeks to sink in across academia. And of course with the Donnelly 2006 analysis relegated, the plethora of papers that reply on it and/or use the same analytical method fall with it. And there are a lot of them.
Silvermans substantial oversight unravels the arguments made in the rest of the chapter to try to justify the badger interventions since 2013. It is embarrassing for the authors to try to bury their past positions on this issue, and this is the reason so many people said they were unsuitable to undertake the review update. This surely cannot be lost on Defra who put them there. It undermines the whole report.
What else did they get wrong? Well for a start, the pre-printing of the ‘Robertson’ analysis (currently un-reviewed). This work was, one suspects, commissioned by Defra officials to try to discredit (see here and here) the 2022 study showing badger culling to be ineffective. Robertson was seconded to Natural England from APHA for some months to undertake the work. Badger Crowd understands that Godfray suggested that it be pre-printed to back up his unwavering view that badger culling has “worked”. This analysis using unqualified guesswork and simulated data has not moved on since it was shared by Natural England back in 2023. Requests for the code used in the work have been ignored. Badger Crowd understands that it has not been submitted to a journal, and it is not difficult to see why. More on this red herring will be revealed shortly.
Perhaps the largest deception of all is that the Godfray review update attempts to characterise the badger issue as one where key decisions are political not scientific, with progress hampered by unmovable positions by those with extreme views. This is a gross simplification. Hard-core protagonists or deniers have little or no hands-on involvement or power. It is the scientists who have got it wrong, and blaming politicians has come from overconfidence, and an apparent need now to blame others for a mess of their own creation, over nearly three decades.
This smokescreen report is an unsuccessful effort to excuse poor progress and to hide the academic mistakes on this issue over the last 25 years. Godfray and his Oxford colleagues are themselves implicated. The flaws and deceptions have the potential to damage Oxford University and Defra very badly, as Zeichner was warned in the spring. They will damage Labour as well, on whose watch the errors were constructed. If they don’t recognize the scale of the problems immediately and involve a broader team of visibly independent scientists, nothing can change. What is needed is an independent inquiry along the lines recommended by Professor Mark Brewer, head of Biomathematics and Statistics Scotland, in June of this year. Unless that happens, the British cattle and dairy industries are doomed to years, if not decades, of more failure with taxpayers footing the growing bill. £Billions more wasted, decades of cruelty and misery for animals and farmers.
Trying to use genomics arguments to sustain badger interventions as a last ditch effort is fanciful, but that is the route that Defra have taken. They may be preparing to use trap-side testing in the predictable back-route preparation for Test Vaccinate Remove (TVR). It is an effort to replay the very old record to ‘blame the badgers’ to ‘keep the farmers happy’. Who was it who first named the policy ‘lies, deceit and negligence?’ Surely this time the farmers are wiser?
In short, the Godfray reviews in 2018 and 2025 have simply failed to deliver when it comes to setting the scene for resolving the bovine TB crisis in England. Defra is set on a path that was presumably decided with the NFU once Labour took targeted culling away last August. There is practically no chance that central government will fund a Covid-style response to bTB when the science as presented is so incoherent. Maybe confusion and no change is the plan? There is important work to be done to get bovineTB under control, but there is no sound evidenced route to a TB free England in this review. Bring on an independent Inquiry.
Why was the use of Gamma interfreon testing, alongside use of the tuberculin test (SICCT), under-declared in APHA’s central bovine TB control evaluation paper (Birch et al 2024) last year, and also in the newly published ‘Godfray’ report?
Gamma reactors by cull year 2009 – 2023
A letter published today 19th September, in Veterinary Record, details the amount of supplementary Gamma testing that was introduced in the High Risk and Edge Areas before and during the post 2013 mass badger culls. It shows how Gamma testing was under-emphasised in the Birch et al. analysis on the effect of the poorly labelled ‘Badger Control Policy’, (see here). Considerable disease benefit is being claimed for badger cull in its first two years and beyond, but is far more likely to simply be linked to the increase in cattle testing with Gamma, as recorded publicly by number of gamma test reactors found.
What this shows is that Defra knew well that Gamma could find undisclosed infection, no surprise as it has been used in other countries for decades. They used it to help lower the spread of disease, then purposefully eased off, as badger culling was phasing down in more recent years. Who, you have to ask, was controlling this behaviour? And why?
As Badger Crowd has pointed out before (see here), all disease measures implemented, including extensive testing, were analysed together, with no control areas. There was no comparison of culled and unculled areas as the recent Godfray Review very strangely mis-reported.
Data presented with the Vet Record letter shows how easing off of the use of Gamma testing to supplement SICCT testing in 2022 is likely to have hindered disease control. This reduction in Gamma was said to be due to lack of EU funding, but this was surely predictable. So why were farmers and the public not told that the strategy was being derailed? A freedom of information disclosure in April 2025 concerning the likelihood of bTB freedom being achievable under present conditions of testing and cattle controls, produced the following response: ‘APHA has not yet produced models suitable for predicting whether TB eradication will be achieved in England by 2038, or when TB eradication will be achieved.’ The 25-year bTB eradication strategy published in 2014, with a 2038 projected target of bTB freedom (elimination or near elimination) now, on current trajectory, has an end point beyond 2060.
As has been pointed out many times before, there is an urgent need for the use of other immune-assay tests and phage testing to be authorised alongside SICCT and Gamma IFN-γ tests, and for farm vets to be provided with extensive new advice and guidance. With freedom to test bTB out from herds – this is mentioned in the Godfray report but it should have been front and centre.
The money raid on central government funds requested in the Godfray review would have been credible with a report triaging essential priorities. But instead, like the 2018 report, the 2025 report is muddled and incoherent. Progress, especially in England, Northern Ireland and the Republic of Ireland simply will not materialise if Defra continue along his line.
The interest and outrage generated by the English badger culls over the last thirteen years is huge and continues to grow. But as time has gone on, the problems have also attracted a growing international following. Bovine TB is, after all, an international problem. Since 2019, there have been multiple readers from 96 countries and dependencies:
Austria, Algeria, American Samoa, Argentina, Australia, Azerbaijan, Bahrain, Bangladesh, Belgium, Benin, Bermuda, Brazil, Bosnia & Herzegovina, Bulgaria, Cambodia, Canada, Chile, China, Colombia, Costa Rica, Croatia, Cyprus, Czechia, Denmark, Egypt, Estonia, Ethiopia, Finland, France, Gambia, Germany, Gibraltar, Greece, Guernsey, Hong Kong SAR, Hungary, Iceland, India, Indonesia, Ireland, Isle of Man, Israel, Italy, Jamaica, Japan, Jersey, Kenya, Kuwait, Kyrgyzstan, Latvia, Lithuania, Luxembourg, Malaysia, Malta, Mauritius, Mexico, Monaco, Montenegro, Morocco, Netherlands, New Zealand, Nepal, Nigeria, Norway, Pakistan, Peru, Philippines, Poland, Portugal, Romania, Russia, Rwanda, Senegal, Slovenia, Switzerland, Spain, Singapore, Sri Lanka, Serbia, Slovakia, South Africa, South Korea, Sweden, Syria, Taiwan, Tanzania, Thailand, Türkiye, Ukraine, United Kingdom, United States, United Arab Emirates, Uruguay, Vietnam, Venezuela and Zambia.
How do other countries view the disastrous situation the UK has got itself into? Do they also have government departments committed to upholding out of date analyses and opinions at the expense of adopting newer and better disease control protocols? They must surely be baffled by the obvious reluctance of the decision makers in London to engage with scientists who offer real hope for progress in the disease control process, with potential benefits that are readily apparent. The refusal of government to involve published scientists who have called out errors and oversights must be perplexing, as must the refusal to place any value on the lives and welfare of badgers as part of the wildlife wealth of the UK. The latter remains an unexplained moral and ethical black hole. This is a major international embarrassment for the UK in front of an academic and veterinary world audience.
We hope that despite England’s ongoing intransigence on this distressing issue over decades, our reporting of the science of bovine TB in recent years is helping to inform other countries who need to know the limitations of the tuberculin and gamma tests, as they are used in UK and Ireland. They need to know, where whole herd depopulation is not an option, how a new protocol to remove the disease from a herd is what is needed; a wider range of cattle tests used more frequently and according to need is vital.
In the UK, it is now clear that badgers have not been shown to play a significant role in the persistence of bTB in cattle herds. While more research is needed into this disease in all manner of wildlife, its respiratory nature suggests that the source of new infection in cattle is overwhelmingly other cattle; the necessary close contact between cattle and deer/badgers/fox etc just doesn’t happen in normal circumstances. Cattle that are carrying bTB, however, are able to remain undetected for many years by DEFRA’s tests of choice, the SICCT and Gamma tests. And infected cows get traded and moved, and take their infection to a new area and new animals. Only when this is better understood and accepted will vets and farmers be able to sustainably manage livestock in rural areas without disrupting ecosystems nearby that are vulnerable to careless exploitation.
The parliamentary summer recess has begun. There can be no more Parliamentary Questions until the recall in September. Which is more than a shame, because there are questions that still need to be answered about the badger cull and bovine TB policy, by a government that does not engage properly with many stakeholders and the public. Supplementary badger cull (SBC) and Low Risk Area licenses were issued in May, and badger shooting is underway, with more authorisations expected for intensive culling shortly. These last intensive cull licenses will almost certainly be issued later this month to allow even more culling in the autumn. But the science to support this policy has been successfully challenged in the literature, with independent verification and a call for proper investigation – yet we still have silence from a government that just wants to finish its ugly killing spree.
Zeichner visit to Gatcombe Farm
The Minister of State for Food Security and Rural Affairs Daniel Zeichner visited Gatcombe Farm in Devon a few weeks ago. This is the farm at the centre of the ground breaking Save Me TrustBBC documentary last year that was attacked by some of the nastier elements of the bTB world, including Defra-funded bodies. Gatcombe is where an innovative protocol for cattle testing has been investigated over the last ten years or so, using carefully managed, newer and more sensitive tests. Each test can be used to target bTB to better increase chance of detection. Used in combination, in a manner prohibited for general use by current rules, the new protocol has been successful in identifying infection that would previously be left hidden in the herd. Let’s hope Zeichner sees the potential to finally start on changes to policy that were needed many years ago, using the cattle measures that DEFRA staff have fought so hard to resist.
Godfray Review report postponed
The current review of bovine TB science, the first one published back in 2018, was commissioned by the new Labour government last year and was due to report by the end of June. But in June, this was officially changed to ‘from the end of June’. Badger Crowd understands that it will now appear towards the end of the year, but an exact time has not been announced. This could, perhaps, be partly due to the publication on June 11th of a paper in Royal Society Open Science that confirmed that previous core Government reference science, the RBCT, was in fact based on ‘a basic statistical oversight’, and that more plausible analyses of the results showed no effect of badger culling from the £50 Million experiment.
APHA produces a pre-print to oppose the 2022 appraisal finding no cull benefits
A pre-print has appeared on BioRxiv: ‘Evaluating the effect of badger culling on TB incidence in cattle: a critique of Langton et al. 2022’ authored by DEFRA’s Andy Robertson. Robertson has worked for TBHub, APHA, Natural England and is based at DEFRA. His publications have twice wrongly claimed badgers are a known maintenance host for cattle TB.
The new pre-print, three years in the preparation, claims that if badger culling had ‘worked’, (created disease decline benefit), the Langton et al analysismight not have detected it. As ever with DEFRA bTB publications, computer code for the model and simulations used is not provided, so it is impossible to check that what has been done is correct or plausible. Code was requested from DEFRA on July 21, but there has been no response at all.
Much of the text leans heavily on published studies that have now been shown to be uncertain at best. The Animal and Plant Health Agency (APHA) paper (Birch et al., published March 2024) in particular is misrepresented as evidence of a positive effect of badger culling. Accurate interpretation of that paper shows that there was no attempt in it to see if badger culling contributed to the general decline in bTB in herds under progressively tighter cattle testing methods. The critique glosses-over an important finding in Langton et al. 2022 (that Defra acknowledged at the time), that at the county level, bovine TB incidence stabilised, and started to decline, well before badger culling was rolled out.
Badger Vaccination
The governments new agreement to fund the NFU £1.4 Mn badger vaccination trials in Cornwall has been widely reported since January. It has been in the news again recently, yet there are still scant details available on the scientific and analytical protocol of the work. Aspects follows a similar project in Wales many years ago, that led to it being dropped as a strategic option.
Requests for further information from DEFRA have met the usual wall of silence. DEFRA’s Minister Sue Hayman half-answered a PQ on the project last week saying “Unlike previous badger culling studies, the Cornwall Badger Project is focused on testing different methods of delivering badger vaccination, rather than evaluating the impact on bovine TB in cattle.” So the use of badger vaccination as a tool in cattle TB control is not being measured? This despite NFU saying that is the essential question that needs answering. It all looks so half-baked and ‘un-joined up’ at DEFRA.
Jeremy Clarkson’s herd is OTF-S
As reported here, it was bad news for Jeremy Clarkson recently. Positive and inconclusive tuberculin tests on his cattle mean that Diddly Squat Farm now has the status Officially TB Free-Suspended. With viewing figures of 4-5 million, Clarkson is in a good position to put the disastrous government bovine TB policy into the public consciousness. Costing over £100Mn a year, the result of the policy has been an immense waste of time and resources. With a hidden epidemic that is still not being effectively detected, and 250,000 mostly healthy badgers culled, many cruelly, due to ‘statistical oversights’ and a government mired in its inability to get a proper grip. If Ministers want to do farming a huge favour, they will get the right experts to look at the evidence, and having procrastinated for over a year, instigate immediate radical change. Forget badgers, it is correct cattle testing and movement control procedures that will rapidly bring herds into manageable condition, as it did in the 1960’s.
Will anything new be offered before the intensive badger culling starts again in September? Probably not. The lack of urgency on this issue is incredibly disappointing. Whatever Labour’s manifesto intentions were, it seems that the civil servants have the whip hand here, holding on to their dogma and their wrong advice and roles, resisting rather than following the new science. It is the public purse, the farmers, cows and badgers who are paying the price of ineffective government.
The Diddly Squat Farm, owned by TV presenter Jeremy Clarkson and a part of the ‘Clarkson’s Farm TV show’, was the subject last week of multiple media reports on positive bovine TB tests in their small cattle herd. Perhaps the most dreaded event for any cattle owner and the prelude to an often long, expensive and heart-breaking series of events.
Reports suggest that a pregnant cow, with a calf that has been separated, is a positive reactor and to be slaughtered, while a bull and a few other cattle have produced tuberculin test results labelled ‘inconclusive’. Inconclusive results usually indicate an active infection, but not one where TB lung lesions are necessarily detectable.
England uses a SICCT test system that is failing and outdated; see the explainer here. In Wales, the SICCT test, with its extremely high specificity, is now read at ‘severe interpretation’, meaning that the ‘positive’ cut-off point (difference in bump size) is lowered so that some animals classified as ‘inconclusive reactors’ at the standard interpretation are now classified as full ‘reactors’ for management purposes. Wales has made similar progress to England without badger culling. Not finding TB on culture (in the lab) at post-mortem for some cows at slaughter, often happens simply because the infection is at too early a stage for the lesions to be visible to the eye, but that doesn’t mean they are not infectious.
The Daily Telegraph immediately, and relying on traditional anti-badger rhetoric, jumped to the conclusion that the infection was from badgers:
“Clarkson has spoken before about how badgers are rife on his farm and how he has tried to keep them away from his cows. But even with an Amazon budget and celebrity profile, the presenter was unable to stop transmission of the bacteria from badger to cow.”
But Clarkson confirmed that badgers have been heavily culled in his area in multiple yeas of culling ending last October. There are even reports that some of the badger setts in the area have been stopped up by others. So in an interview on Times Radio he is rightly uncertain as to how the disease arrived.
As with the majority of new bovine TB infections, the source is most likely to be undisclosed TB in purchased stock. Government’s external veterinarian of choice, Cambridge University’s James Wood claimed recently (on Farming Today) that:
“The challenge is with this [testing] system, the controls are imperfect, so that when we clear a farm with TB we know that a proportion that maybe as high as 25 or 50%, a proportion will have one or two animals that are still likely to be infected.“
Infection embedded in herds and traded onwards to new herds is the real problem. A simple check on the bTB status of herds that Clarkson has bought from in recent years will soon show if individuals are from herds that have had infection over the half dozen years or more. This is towards the upper bounds of the length of time that bTB is known to ‘hide’, due to some individual cows not responding to testing and the poor sensitivity (lots of false negatives) of tests used.
Clarkson recognises that the bTB system is a failure and questions why if TB meat can be eaten, the strict measures are absolutely needed. The fact that since pasteurisation was brought in bTB is not a significant human health risk is important, but Defra have rejected a rethink to relax massive public spending, and for it to be dealt with in a similar way to Johnes disease. Which is caused by a similar and widespread bacteria, spread by faecal contamination. Hence farmers face a draconian system imposed without access to alternative and better tests that Government have long-suppressed.
If Jeremy Clarkson can shine a light into the murky depths of bovine TB control policy and he does so with the appropriate seriousness, he will be doing farming a huge favour. But he will have to careful where he gets his advice and information from; that will dictate how successful he is. There are plenty of people giving bad advice, for all sorts of reasons.
“To ask His Majesty’s Government what assessment they have made of the paper by Torgerson and others published in the Royal Society Open Journal on 11 June claiming that other studies of badger culls contain methodological weaknesses; and what plans they have, if any, to ensure that the Cornwall Badger Vaccination Pilot has a peer-reviewed protocol before any work can continue.”
The reply from Sue Hayman was as follows:
“Work has started on a comprehensive new bovine TB strategy for England, to continue to drive down disease rates to save cattle and farmers’ livelihoods and end the badger cull by the end of this Parliament. The evidence surrounding bovine TB control, including recent studies such as the paper by Torgerson, is being independently reviewed by a panel of experts led by Professor Sir Charles Godfray, which the Government has reconvened. Unlike previous badger culling studies, the Cornwall Badger Project is focused on testing different methods of delivering badger vaccination, rather than evaluating the impact on bovine TB in cattle. The project is being delivered by the NFU in partnership with the Zoological Society of London, who have a track record of publishing peer-reviewed research on the subject of badger vaccination. The project will continue to be regularly reviewed by Defra as it progresses.”
“By working together to compare different approaches, we can develop a shared understanding of the evidence and use it to identify TB control solutions which are effective and sustainable.”
And it quotes a farmer as saying:
“What we hope to ultimately get out of [the project] is whether [badger vaccination] affects the cattle levels of TB – that remains to be seen, but I think it’s well worth doing.”
So Sue Hayman is telling us that “the Cornwall Badger Project is focused on testing different methods of delivering badger vaccination, rather than evaluating the impact on bovine TB in cattle”. Meanwhile, the researcher and farmer participant infer that the results will give an insight into the control of bovine TB in cattlebecause it seems they think or have been told that disease benefit in cattle is ‘likely’? This approach is highly questionable. The Government statement implies that three or four years down the road, we will still have no evidence of whether badger vaccination effects TB in cattle one jot.
Importantly, the PQ asked if any analytical protocol for the research and subsequent analysis would be published before the work starts to avoid a repeat of the problems of the Randomised Badger Culling Trial (RBCT) (see here). But this was not answered.
The Guardian article states:
“The project will assess three vaccination approaches to determine which works best: annual vaccination over four years, vaccination every other year or reactive vaccination based on TB infection on farms.”
But this is a three year project? Is ‘working best’ just a reference to a rough idea of TB prevalence change in badgers using a difficult test ?
The NFU said previously in their January project announcement and in defiance of Government policy:
“The NFU is clear that badger vaccination cannot be used as a direct alternative to culling and evidence is needed to give the NFU and wider farming industry the confidence that badger vaccination has any effect in reducing bTB in cattle, before proving its ability for delivery at the necessary scale, cost-effectively.”
So in summary, NFU are being given around £1.3 MN to see if farmers in some apparently badger-friendly areas of Cornwall can vaccinate badgers with a bit of training, and Sue Hayman says, quite rightly, that it will shed no light on whether vaccination is of any value in controlling bTB in cattle. In contradiction, the researcher quoted suggests the work will identify TB control solutions which are effective and sustainable. So why, in the midst of an expensive damaging disease crisis are the NFU being set up to spend public money on something that cannot deliver their stated needs? Do ordinary farmers in Cornwall know this? – apparently not according to what those involved are saying.
In any case the public, or at least independent specialists, should have access to the project design and the analytical protocol before work starts, whatever it is actually doing. For example if there are three treatment areas, will there be treatment ‘control’ areas and what proportion of badgers will be vaccinated, and what are the expected sample sizes?
Of course since the publication of Torgerson et al. papers (2024 & 2025), there is no sound scientific basis to continue with any badger culling or vaccination for bTB control. The RBCT did not show any benefit from badger culling, so any benefit from badger vaccination is unlikely. Cattle measures alone on the other hand, are proven to be effective. Are public funds being frittered again at a time when decisive action to protect badgers, cows and farmers remains long overdue and overlooked?
Have you noticed how quiet the NFU have become over badger culling since Labour came to power? Why could this be?
Badger Politics
In 2024 there was an agreement between the NFU and Labour not to make an issue of badger culling during a general election year. This was on the basis that Labour would ‘honour’ existing licences if they came into power – thinking that might be after the 2024 cull was over. But the election was called early by PM Rishi Sunak, and the surge in the Reform party popularity split the Tory vote and resulted in a Labour landslide. Labour’s undertakings meant they would go on to kill around 17,000 badgers in 2024.
Intensive culling programmes get go-ahead to continue to give ‘clarity’ to farmers
The first news from the new Secretary of State for Environment, Food and Rural Affairs Steve Reed in 2024 was confirmation of the agreement with NFU that the current badger culling programmes set to end in January 2026 would continue until then to give the farmers ‘clarity’. This decision went against advice from Natural England, who preferred the introduction of badger vaccination to seek a disease control benefit. But this advice was itself flawed, with growing evidence that there is unlikely to be any disease benefit from culling, and benefit from vaccination is entirely speculative. Natural England simply failed to properly consider evidence that badger culling has no likely benefit, and simply cherry-picked the evidence they wanted to get past the task. ‘Freedom of Information’ now shows us that they also relied on unchecked manuscripts, claiming naively that badger culling had robust effects.
The death of targeted culling?
Around six weeks after getting into office, Labour moved to scrap the NFU/Defra pre-election ambition to get mass (targeted) culling going (along the lines of LRA hotspot culling) in the HRA and Edge Areas. This targeted culling, developed under Rishi Sunak’s tenure as PM, was in defiance of the 2020 ‘Next Steps’ Boris/Carrie Johnson/Zac Goldsmith policy which was to phase out badger culling. Phase it out “other than in exceptional circumstances”, that is. This caveat was the toe-hold for future culling that pro-cull interests in the civil service managed to keep on the job-sheet, to fight back with, now that Environment Secretary George Eustice had been overruled.
But a new Low-Risk Area cull was then given the go-ahead
Under strong NFU pressure, Labour still gave in to a new Low Risk Area cull in Cumbria. Was this an attempt to appease their industry masters by keeping new culling going, aware of the long planned unpopular Farm Inheritance Tax news that was about to be released? Did Labour use badger culling to indulge the farmers, in an attempt to distract from the freight train coming?
New Minister – new policy? Or just more of the same DEFRA dogma?
Excerpt from the Labour Manifesto, 2024
The problem for DEFRA was how to balance Labour’s manifesto position that culling is ‘ineffective’, with the claims made by the Conservative Government politicians and their usual external contractors, of badger culling ‘working’; see the Downs et al 2019 and Birch et al 2024 papers. These publications have a pick-and-mix of confirmation bias, repeat of previous flawed analytical methods, stretched arguments, unevidenced speculation, confused presentation, key omissions and complex caveats. Of course many of the Government scientists who produced science that has facilitated badger culling for so many years are still in post. So how do they do a volte-face, and suddenly disagree with their own back catalogue of dubious science? Nobody likes to be wrong, and nobody is owning up to it so far. (see here for latest science update).
The Godfray Review
Another review of bovine TB control science (published since 2018) was commissioned secretly in 2024, and announced publicly in early 2025. The ‘Godfray’ review panel is soon to deliver its report, but it is hopelessly stacked with vested interest. Some panel members have a long history in badger cull science, with Oxford University’s Charles Godfray, together with James Wood from Cambridge University, publishing a re-statement in 2013 (of now impugned conclusions), which was needed to greenlight badger culling. Surely the most positive spin that the review can come up with is that Government post-2013 cull outcome research is inconclusive? Pro-cull cheer-leader James Wood said as much recently on Farming Today. But he couldn’t resist repeating his long held personal view that badger culling helps TB control.
The Westminster Hall Debate – waiting for a date
A large number of pro-badger killing MP’s were purged by the general election. It was almost as if their support of badger culling was proportional to the rejection of them by the voting electorate – dozens of them. So no longer will Richard Drax, Bill Wiggins, Robert Goodwill, Steve Double and many others be able to drivel on at Westminster Hall with anecdotal nonsense. Might the next one, resulting from the Protect the Wild petition, be fact-based perhaps? A date is yet to be allocated.
Back to the NFU
NFU get vaccination contract
So back to the question – why have the NFU been so quiet? Well perhaps they still hope to be granted their wish to keep killing badgers. DEFRA has now funded a badger vaccination project in Cornwall. The NFU have been awarded the contract to undertake the work, working with the Institute of Zoology.
The new £1.4 Million project hopes to train farmers to swap bullets for syringes (think banned RSPCA poster) in a so-far rather loosely described project to vaccinate badgers in the county for three years (2026-28) and compare it with somewhere else – either unvaccinated areas in the county or elsewhere. Details at present are scant, but have been requested. Pre-experiment plans are vital for the delivery of useful results in a verifiable way and should be open to scrutiny, especially those concerning statistical approach.
Vaccinate or Exterminate. Will DEFRA’s new approach ignite further controversy?
But why would the NFU take the money to do something they are supposed to be inherently against, according to farm research (see here)? The reason could be, either with or without DEFRA Minister Zeichner’s permission, that NFU have been preparing ‘under the radar’ with Defra/APHA to head towards ‘Test Vaccinate Remove’ (TVR ) – where farmers learn to trap badgers, test with a dubious trap-side DPP test (see here) that in Wales was a disaster (see here), and cull the badgers that test-positive.
Is this the dirty secret about badgers that is keeping the NFU quiet?
Perhaps Godfray and his panel of not-very-impartial reviewers, (see here) who have been asked to lean towards Labour’s preference for non-lethal badger intervention options, would be expected to leave the door ever so slightly ajar, hence open to TVR, simply by saying that badgers remain a TB risk to cattle.
This would satisfy the Defra/Civil Service ambition of bringing one single approach to disease control to three UK countries; Wales (possible new Reform/Welsh Nationalist government pro-cull wish in 2026), NI (UFU currently frothing at the mouth to cull) and England. This may be the fantasy result for Defra, but it would be the grotesque, disastrous result of using selective and plain-wrong science. It would be an extension of the UKs failure to tackle livestock disease effectively over the last 25 years (see National Audit Commision report here).
Will the NGO’s want to help the NFU vaccinate badgers?
It is interesting to note that the NGO’s are becoming less keen on badger vaccination, including the Wildlife Trust and Badger Trust. Partly because most vaccination teams have been frozen out of funding for this work that they have undertaken to protect badgers from bTB. Government has been aiming to capture and control the whereabouts of badger setts and badger vaccination for some time (see here) and it is handy for them if the NGOs stand aside or assist. NGO’s do hold important badger sett information that Defra would be keen to get hold of for potential future culling – when the NFU have demonstrated that badger vaccination either doesn’t work or somehow isn’t enough – cover for another 5 years of ineffective cattle testing and compensation?
So there are a few possible reasons that the NFU are so quiet. It could of course be that they recognise that the failed cattle testing system with inadequate use of tuberculin and gamma testing, imposed by Defra, has destroyed farm interests for a generation while the food wholesalers continue to have uninterrupted supply. But they won’t stay quiet about that for ever will they? Why would they do that?
The new scientific Comment paper by Paul Torgerson and colleagues was published on 11 June in Royal Society Open Science (RSOS) (here), and is a comment on two 2024 re-evaluations of the Randomised Badger Culling Trial 1998-2005 (RBCT) statistics (here and here). These re-evaluations were, themselves, a rebuttal of the comprehensive re-evaluation by Professor Torgerson’s group earlier in 2024 (here) which was prompted by the heavily peer-reviewed published evidence in 2022 (see here) that industry-led post-2013 badger culling was having no effect on bTB cattle herd breakdowns. The latest RSOS Comment paper (and its notable peer-reviewer findings) is well timed to accompany the Government’s new general intention to end badger culling by the end of this parliament (2029).
The current bovine tuberculosis (bTB) epidemic flared up in 2001 due to mismanagement of cattle distribution. Officially TB Free-Withdrawn cases (OTF-W) peaked in beef and dairy herds in 2015, starting to fall after annual testing from 2010 and the gradual tightening of TB controls in cattle. But Officially TB Free-Suspended cases (OTF-S), that are also indicators of new infection, have slowly risen. BTB remains embedded in herds in many counties, and is a costly and destructive force across much of England and Wales, and throughout Ireland.
This area of epidemiology has been a hugely controversial subject, largely due to RBCT findings in 2006 that suggested the European Badger Meles meles (a legally protected mammal) plays a highly significant role in bTB spread in cattle. Subsequent Governments have culled approaching 250,000 largely healthy badgers in England since 2013. The policy has been justified using the RBCT’s ‘perturbation effect’ hypothesis, where one specific analytical approach was used to claim that this hypothesis could explain beneficial and negative effects of mass badger culling. It was hugely uncertain and speculative, but treated as ‘established science’ and ‘irrefutable fact’ by those seeking to see badgers culled for all kinds of reasons.
The 2024 Torgerson re-evaluation, looked at the way in which the differences in the number of cattle herds in ten paired comparison areas of countryside in the RBCT trial were adjusted for, together with the varied duration of experimental study periods. Further, model selection used in the original analysis was examined. The task of assessing the suitability of models from among the most likely candidates was undertaken, bearing in mind that the pre-experiment plan for data analysis was loose and open to interpretation – see Supplementary Material 1 of the Torgerson paper. In this part of the analysis it is the selection of the most appropriate model that is the most critical for verifiable results. More plausible models than that used in the original 2006 analysis (here) were readily apparent. The new study was able to demonstrate how these more plausible models show no effect of badger culling upon herd BTB breakdown rate.
Further, the team looked at how newer pathogenic evidence and interpretation, including better understanding of categories of TB-test reactor cattle, now more accurately informs decisions on what represents a new herd infection and herd risk status. The paper described the reality that using ‘all BTB breakdown’ data is by far the safest conclusion for policy application. And when ‘all data’ is used, there is no effect of culling over all models. APHA and Natural England still claim that they believe this is wrong, which enables them to carry on licensing badger culling.
So whilst the original conclusion of the RBCT study reported that culling of badgers can make ‘no meaningful contribution’ to the control of bovine TB in cattle herds remains correct, the true reasons for this being the case are surprisingly different to those given in 2006. It is not, as originally suggested, because of positive effects (in cull zones) and negative effects (in neighbouring zones), but because there are no measurable effects to be found. The ‘perturbation effect hypothesis’ is a major casualty of the new analysis – if it exists, the RBCT found no evidence of it.
Whilst direct or indirect transmission between wildlife and cattle cannot be ruled out on rare occasions, it is not present at the significant scale reported by the RBCT model choice and data selection. Wildlife infection should no longer be blamed for the inadequacies that are all but entirely due to poor disease management by Defra and APHA who dictate every move of the livestock industry.
All this is positive news for livestock, badgers and disease control. The 2020 policy direction to abandon lethal badger interventions is justified, with a renewed focus on cattle measures that are known to be effective. The ‘hidden reservoir’ of BTB is now sufficiently well understood for ‘new generation’ TB tests to deliver far better detection rates. If there was greater scope for their use (currently restricted), these would give a real opportunity to vets and farmers to work towards the bTB elimination rates last seen in the 1960s. The logical conclusion from these newly published findings is that since badger culling has no measurable disease control value, badger vaccination is very unlikely to either. Any badger vaccination field trials would be an expensive distraction, when it is proven cattle testing and movement measures that need to be implemented at scale to tackle the epidemic effectively.
A new article in Vet Times reports on the Torgerson et al (2025) paper published in Royal Society Open Science last month, that has prompted calls to stop all badger culling immediately. The badger culling policy has, it says, relied on a ‘basic statistical oversight’.
The article picks up on comments by the new paper’s reviewer, Biomathematics and Statistics Scotland director Mark Brewer, who argued that “in such a contentious area as this, it is naive to imagine that a single analysis by a particular group of scientists should be seen as sufficient”.
In a noticeable first and potential change of direction, the article quotes Chief Veterinary Officer Christine Middlemiss as saying that Defra is “really looking to protect our key species through vaccination and progress that with badgers, as a key wildlife species, but cattle as well.”
The peer-reviewer of the new scientific paper, Torgerson et al 2025, published on June 11th is the Director of Biomathematics and Statistics Scotland (BIOSS). The paper is concerned with analysis of the Ranomised Badger Culling Trial (RBCT). Below, you can see the text of the review together with the authors responses, as addressed to the editor. Also highlighted (bold italics) are a few points that seem particularly important & difficult to disagree with, even if you don’t understand statistics. It should be noted that the two reviewers of the Mills et al. (2024) papers that Torgerson et al. is rebutting, declined to submit a review of the new Torgerson paper. In other words, they praised the two Mills et al papers, recommended them for acceptance, but declined the opportunity to defend their decision by explaining their thinking on Torgerson et al (2024 & 2025). They remain anonymous, which is interesting from an integrity perspective.
Torgerson: The reviewer has made a number of comments. We have addressed these where necessary and made some amendments to the text. We would also like to thank the reviewer for these helpful comments which we hope have improved our manuscript.
Reviewer: Comment. Overall it seems there is strong disagreement over competing data analyses on what is already a highly contentious issue, which has significant implications in terms of ecology and agriculture. I have been asked to comment on one small part of the ongoing discussion, which I will do – however, my overall, strongest recommendation is that, given the importance of the underlying issue (both scientifically and politically) that a proper investigation be conducted to establish an agreed position involving all parties. A continuing to-and-fro among different sets of authors – each, I am sure, well-meaning in their own ways – serves little purpose, and there are better, more efficient and effective ways of resolving disagreements than in the pages of an academic journal.
Torgerson: The underlying issue (mass culling of largely healthy badgers across much of England and in Ireland) is the result of the original analysis by Donnelly et al, first published in Nature in 2006 and papers derived from that, and subsequent analyses. Although the merit of the analysis has been questioned, only by having alternative data analyses published in peer reviewed journals is it possible for the UK Governments to consider amending the policy. Nevertheless, we have contacted Donnelly et al previously in an attempt to meet and to find common ground, but our attempts were rebuffed. In order to give the reader a clear idea of the applied implications of both our re-evaluation and the peer review comments, we have added some text to the conclusions: “Accordingly a very substantial number of publications that rest extensively or completely on RBCT statistical analyses may require major qualification or retraction. The justification for lethal control of badgers to-date appears to have been based upon basic statistical oversight.” Also there is a reproducibility crisis in science. Therefore it is important for these issues to be published as we believe they provide an exemplar of a major driver to the reproducibility crisis and misdirection of disease epidemic management.
Badger Crowd Comment: A scientific seminar and evening presentation on the work of Paul Torgerson and his team (then a pre-print) was organised in Oxford in November 2024 in order to allow debate with the RBCT scientists. All declined the invitation. DEFRA and APHA sent no representatives. Natural England sent one staff member but gave no feedback. Badger Crowd very much welcomes the reviewers suggestion to hold a “proper investigation…to establish an agreed position involving all parties.”
Reviewer: Comment 1) Section 2.1. I agree with the authors of the current contribution here that use of an offset here is likely a requirement, and that the comments from the Mills et al. (4) are naïve at best – it isn’t helpful to think of an offset as equivalent to setting a regression coefficient to 1.0, as of course the issue is that this is a log-linear scale and the point is that (under the Poisson) we assume proportional rates. I agree that it does not seem to make sense that the herd breakdowns vary only very slightly (the parameter value of 0.04) with the number of herds, although I would caution here only that it is possible some other variable/term in the model might be related to the number of herds, hence suppressing the parameter value (when including number of herds as a regression term rather than as an offset) owing to collinearity.
Torgerson: This is quite possible, and the collinearity is likely to be between the co variates of “triplet” and “baseline herds at risk”. Hence the motivation to explore the results of models where triplet was removed (which always resulted in a considerable reduction in AICc). Although it is not clear if the reviewer required a response to this statement, we have inserted the following text into the manuscript “The removal of “triplet” may remove any hidden effects possibly due to collinearity with number of herds, as well as substantially reducing the number of covariates and hence largely eliminate the issue of over fitting.”
Reviewer: Comment 2) I have personally written (Brewer et al, 2016 – https://doi.org/10.1111/2041-210X.12541 ) about the dangers of relying on the theoretical distinctions between AIC/AICc and BIC, so it should be no surprise that I share the current authors’ suspicions on the preference expressed in Mills et al. (4) for BIC. Also, why are the AICc values for Models 1 and 3 so much higher than the null model in Table 1? Is this just a feature of the small-sample correction? Otherwise I would not expect this at all (if I’m understand what the null model is, correctly); in the absence of other explanations here, given the high number of parameters in models 1 and 3 I would suspect poor model fitting with inflated variances due to collinearity. So, I agree with the current authors here, on the basis of the evidence in front of me (Sections 2.2+2.3, Table 1, supplementary material).
Torgerson: This issue is well taken. This was part of our arguments. Although perhaps not completely clear. We have edited the relevant text which now reads “Brewer et al (16) have written about the dangers or relying on theoretical distinctions between AIC/AICc and BIC. Nevertheless, Mills et al. (4,5) state “…a wide array of statistical techniques and study periods allows us to make robust conclusions regarding the effects of proactive badger culling which are informed by consistent scientific evidence from trial data, irrespective of which approach to statistical inference is taken.” This is demonstrably untrue. The analysis of “confirmed breakdowns” (OTFW) show that results are highly dependent on the approach to statistical inference and information criteria used. However, absence of any cull effect on the incidence of bTB, when total breakdowns are considered, is robust, irrespective of statistical method.”
Reviewer: Comment 3) The discussion on Bayesian models claims that the authors of Mills et al. (4) made coding errors. I do feel that then Mills et al. should be able to examine and (if relevant) correct these errors, and formally issue a correction in the pages of the journal. Otherwise, I don’t feel I have sufficient information to comment further here.
Torgerson: Here the reader needs to refer to both the coding on GitHub, which is where Mills et al have made their statistical code available and the code we have given in the supplementary material. We give an example here. In Mills et al, they claimed an offset was used with the following R code: rs1aB←stan_glm.nb(Incidence~Treatment+log(hdyrsrisk),+log(Hist3yr), offset = log(hdyrsrisk), prior_intercept=normal(0,10), prior=normal(0,10), data = rbctconf, refresh=0) Here you will note (in red) that log(hdyrsrisk) appears twice in the code, both as an explanatory variable and an offset. The effect of this is to shift the parameters of log(hrdyrsrisk) by a value of 1, whilst other parameter values remain unchanged, thus effectively having no offset. The correct code if a parameter value is to be fixed as an offset is: rs1aB<-stan_glm.nb(Incidence~Treatment+log(Hist3yr), offset = log(hdyrsrisk), prior_intercept=normal(0,10), prior=normal(0,10), data = rbctconf, refresh=0) or alternatively: rs1aB<-stan_glm.nb(Incidence~Treatment+offset(log(hdyrsrisk))+log(Hist3yr), prior_intercept=normal(0,10), prior=normal(0,10), data = rbctconf, refresh=0) We refer the reader to our supplementary material where it is fully explained together with the other errors in the code of Mills et al.
Reviewer: I agree with the current authors’ concerns on the statistical audit. I would go so far as to say that, given the important of the topic of this discussion, any audit should be carried out openly and transparently.
Torgerson: We have added short text at the end of section 4 “ It is important that trials include an audit that is open and transparent.”
Reviewer: Comment 5) Section 5 on the neighboring area study – again, from what I can see here, I would broadly agree with the concerns of the current authors.
Torgerson: No response required
Reviewer: Comment. 6) To clarify; I have no issue with the modelling of counts, as the use of a Poisson-form log-linear model is, in effect, modelling rates. To be more precise, I would suggest that the problem is not that Mills et al. (4) modelled counts, but that they did not properly scale those counts by use of an appropriate offset – and again, I am saying this on the basis of the evidence of the current work (only).
Torgerson: Here the reviewer appears to be agreeing with our approach by using the offset. But for clarity so readers can see the derivation of the offset (in the Poisson log-linear model) in our previous manuscript where there derivation is explained. Thus we have inserted the text “The mathematical derivation of the offset is explained in our previous manuscript on this issue (3).”
Reviewer: Comment. 7) Finally, I would like to address the quotation from Donnelly (16): “the suggestion of requiring independent replication of specific statistical analyses as a general check before publication seems not merely unnecessary but a misuse of relatively scarce expertise”. The point to me here is not that work should be “replicated” as such, but that work should be verifiable. The authors of Mills et al. (4) have apparently made their work – at least that related to the 2024 journal papers – available openly, and this is the key; openness and transparency are vital. I would even go as far to say that, in such a contentious area as this, it is naïve to imagine that a single analysis by a particular group of scientists should be seen as sufficient.
Torgerson: Yes we agree, which is one of the issues with the original RBCT proactive cull statistical findings published in 2006, which was led by Donnelly: it was a single analysis by a particular group of scientists, and the Mills et al papers are also led by Donnelly et al. We think this is obvious and it should be verifiable. Nevertheless we have modified the text surrounding the quotation of Donnelly (16). It now reads: The position of Donnelly (17) that “the suggestion of requiring independent replication of specific statistical analyses as a general check before publication seems not merely unnecessary but a misuse of relatively scarce expertise”, needs revisiting. This case underlines the need not only for rigorous checks of statistical analysis but also validation of the statistical models and assumptions used within submitted manuscripts to verify them.
Badger Crowd Comment: For the last 6 months, Sir Charles Godfray and his ‘expert’ panel have been reviewing badger cull and bovine TB science published since 2018. Godfray was involved in the RBCT audit, the 2013 restatement of badger cull science and the 2018 science review. In other words, the single analysis (Donnelly 2006) that has supported the badger cull policy is being reviewed by (largely) the same ‘particular’ group of scientists who have been associated with the work for nearly 20 years. Donnelly herself has been ‘recused’, but has been replaced by another Oxford statistician from the same department. There is no outside scrutiny, and there is a case that there has been no “proper investigation ….to establish an agreed position involving all parties” as recommended by the peer reviewer. A proper investigation would be free from conflict of interest. Defra have refused to address this issue over the last six months.
In case you missed the point of all this, the new Torgerson paper shows how for multiple reasons that there is no evidence that culling badger delivers a disease benefit of bovine TB control in cattle herds. The current ‘closed shop’ of science at DEFRA has fallen flat in the past and should not be allowed to continue. They are selecting the scientists and science that they want to suit a civil service agenda and they don’t want to admit that they have been wrong for very many years. It is a flagrant example of policy driven science. And everybody is losing out because of it: the public (because of the enormous costs of policy), the farmers (because it is a policy that can never achieve its aims) and the badgers – because they are being inhumanely killed in huge numbers.
This intolerable situation cannot be allowed to continue. Badger culling must stop now, and an independent investigation or inquiry must be set up.
A prominent ecologist says an independent assessment of the latest study on badger culling is a “bombshell” takedown of the government’s evidence used to justify the policy. Tom Langton, a badger expert, said the conclusions by a top statistics professor should prompt the government to end the programme of shooting badgers to try to eradicate bovine tuberculosis (bTB).
Professor Mark Brewer, director of Biomathematics and Statistics Scotland, who reviewed the paper, praised the openness of earlier papers but wrote: “I would even go as far to say that, in such a contentious area as this, it is naïve to imagine that a single analysis by a particular group of scientists should be seen as sufficient.”
A study by Mr Langton and colleagues published by the Royal Society criticised scientists who believed badger culling was successful in reducing bTB, claiming they had made coding errors.
In the new study, Prof Paul Torgerson wrote: “The justification for lethal control of badgers to-date appears to have been based upon basic statistical oversight.”
Last week, The Independent revealed that government body Natural England had this year re-authorised supplementary licences to continue badger culls across England – against advice from their own scientific chief. The new culls will lead to an estimated 5,000 badgers being shot dead. The government has already begun establishing teams to increase badger vaccination and launched a badger population survey. It announced on Wednesday that badger TB vaccinations rose by 24 per cent across England last year, to what it said was a record high, with 4,110 badgers being vaccinated.
But controversially, ministers have also reconvened a panel of experts led by Prof Sir Charles Godfray, who has long backed culling and assessed the randomised badger culling trial (RBCT), concluding that culling reduced the spread in bovine TB.
Prof Torgerson wrote: “A very substantial number of publications that rest extensively or completely on RBCT statistical analyses may require major qualification or retraction.” And Mr Langton called for the earlier papers, on which successive governments have relied for evidence to continue culls, to be retracted.
He said: “The independent reviewer’s views should help take a wrecking ball to a large volume of accepted badger-culling science. “This shows how misjudgement can create bad government policy, if statistics are not checked properly and brings to life the many claims that the public have been cheated over badger culling for over a decade.”
Badger lobbyists argue that more scrupulous hygiene on farms reduces TB. The Wild Justice organisation, jointly led by naturalist Chris Packham, together with the Badger Trust, have won permission for a full judicial review of badger culling. The RBCT, which ran from 1998 to 2005, suggested a reduction in TB infections in cull zones, but its findings were disputed because of the “perturbation” effect, where badgers from targeted families moved further away from their natural areas, potentially carrying disease risk with them. It’s estimated 250 papers have been published using the results of the RBCT.
Epidemiologist Prof Christl Donnelly, professor of Applied Statistics at Oxford University, told The Independent that in the light of recent correspondence they would make some minor tweaks to some of their models.
“Crucially, the position does not change: repeated widespread badger culling can reduce risks of bovine TB to cattle inside culled areas, while increasing risks to cattle on nearby unculled land,” she said.
A spokesperson for the Department for Environment, Food and Rural Affairs said: “TB has devastated British farmers and wildlife for far too long.“We are rolling out a comprehensive TB eradication package that will allow us to end the badger cull and stop the spread of this horrific disease.
“This includes launching the first ever national wildlife surveillance programme to better understand the disease and work to increase badger vaccination at pace.”
Yet there is a nod to the work by Robert Reed and Dick Sibley and others at Gatcombe Farm in Devon, and elsewhere, as expounded in the ‘
The parliamentary summer recess has begun. There can be no more Parliamentary Questions until the recall in September. Which is more than a shame, because there are questions that still need to be answered about the badger cull and bovine TB policy, by a government that does not engage properly with many stakeholders and the public. Supplementary badger cull (SBC) and Low Risk Area licenses were issued in May, and badger shooting is underway, with more authorisations expected for intensive culling shortly. These last intensive cull licenses will almost certainly be issued later this month to allow even more culling in the autumn. But the science to support this policy has been successfully challenged in the literature, with independent verification and a call for proper investigation – yet we still have silence from a government that just wants to finish its ugly killing spree.
A prominent ecologist says an independent assessment of the latest study on badger culling is a “bombshell” takedown of the government’s evidence used to justify the policy. Tom Langton, a badger expert, said the conclusions by a top statistics professor should prompt the government to end the programme of shooting badgers to try to eradicate bovine tuberculosis (bTB).