Thursday, August 30, 2007

A Trojan horse

At a recent meeting of the EFRA committee, Professor Bourne gave the following insight into his cattle control measures, and possibly how they may be achieved. We take this from the uncorrected transcript of evidence, which is of far more use than a draft which has been re-written and tweaked half a dozen times. It does what it says on the tin.

In its final published version, the RBCT Badger Dispersal Trial report roundly rebuffed the “at least 40 per cent” contribution that badgers make to the disease progression and despite admitting “there is no dispute about the fact that badgers do contribute to the cattle disease disease” . The diminutive Prof. then went on to outline the only option that was feasible which, in his opinion, was more (and more draconian) cattle controls.

This was ‘bourne’ of simple mathematical modelling undertaken by Prof. Donelly, who having tortured some unidentified (by the reader) data, weighted heavily - 2: 1 - in favour of cattle and against badgers (that bit was published) extruded a figure of 50 per cent of herd breakdowns attributable to cattle. We think. And it is on this illusive figure that Professor Bourne has fastened. He was questioned, including the progression of the disease through the 1960’s to the present day, and he came up with the following gems:

On the use of the tuberculin skin test:
“It was developed as a herd test. The obvious way to use a herd test is, if you find an infected herd, to take it out.”

On the increase in cattle Tb after the late 1980’s into the 1990’s.
“I suspect cattle testing was relaxed"

(It wasn’t, but badger culling in response to Tb outbreaks most certainly was –ed)
On cattle movement:
“Statistics show that there is a great deal more cattle movement because of wider trading activities of cattle farming”

(More than what? Drover’s roads from Wales and the Midlands to London, with herds stopping every ten miles or so? Cattle trains from Cumbria to the south? Just because a scientist hasn’t realised that a thing happened, it does that mean that prior to his Damoscene moment, it did not happen – ed)

And on ‘opposition’ to badger culling in ireland as opposed to the UK.
"There is no Badger Group in Ireland"

(And? bTb is a grade 3 zoonosis.)

On larger cull areas.
"Mathematical modelling in extrapolation from the trial data suggests that if you cull over a large area, you would ultimately get positive gains with respect to the area culled, relative to the area you were not culling"
(So that’s a yes?)

Er – no.
"I also stated [] that there would be extreme logistical difficulties in achieving this with respect to culling over a large area repeated regularly over a large period of time, and it could only be considered as a policy option, if there had been an adequate cost benefit analysis.”

(He means farmer’s would pay for cage trapping – ed)

Define difficulties?
“...the logistical difficulties of getting a trapping force into the fields, to do culling across the whole piece at the same time and continuing it for this very long period. ... Government have stated very clearly that they would not do this themselves. They would not be responsible for this, but farmers would in fact have to do this off their own bat..”

And is it possible, with such farmer participation?
“As an extrapolation, as a modelling exercise that was correct, but we are bound to write caveats to that, which I thought would have been a clear message to message to Ministers of the difficulty of doing that and the liklihood that the whole thing would not be achievable

(That’s a No then –ed)

So could badger culling have any effect at all on cattle Tb in the UK? And here we get the Trojan Horse, and the cattle measures that this open minded scientist has preached all along, while accepting political strictures from day 1, on his badger culling dispersal trial..

“What we are saying is that badger culling in the way it can be conducted in the UK, we believe, cannot possibly contribute to cattle TB control, and in using the word ‘ meaningfully’ what we mean there, is that if it is the only inducement that would encourage farmers to co-operate fully, and introduce effective cattle controls, it could have an effect”.

(Whaaaaat? - ed)

This was echoed, somewhat more politely by the EFRAcom Chairman:
“Can I make quite certain that my ears did not deceive me a moment ago, when you said with your almost impish smile, “Left to its own devices, culling is not the silver bullet but if it induced some other activity as a quid pro quo, it might have a role to play?”. Is that what you are saying to me?”

Prof. Bourne:
“It would be most unfortunate if that happened but that is exactly what I was communicating to you, because farmers have made it clear they will not co operate unless thay can kill badgers. Farmer co operation is absolutely essential to get this disease under control. It will be appalling thing for us if farmers were given the opportunity of knocking off a few badgers, just to get their co operation.”

Well that’s pretty clear, is it not? If government offer a few sacrificial badgers, at the same time as extra cattle controls, then a ‘package’ may be agreed?
A quid pro quo, the man said. Yes? The last industry 'package' was unceremoniously shattered by Defra, who are very adept at taking the 'quid' while failing to deliver the 'pro quo'.

So, cattle measures: in order that there is absolutely no illusion about what the good Prof. is proposing, the ISG final report (p.24 – 29) illuminated his audience with exactly what he had in mind as those extra cattle controls. They included:

* Pre and post movement testing, both combined with gamma interferon.(IFN)

* Strict animal movement control (zoning) of animals from high risk areas into low risk, and even between farms of the same status within a zone.(10.64)

* Gamma interferon widespread in low risk area breakdowns.

* Severe animal movement controls and only licensed to farms of the same status(10.71)

* In breakdown herds in high risk areas, one or two reactors at disclosing skin test and no recent history of infection would merit IFN in parallel use to the skin test.

* Within multiple reactor herds, with a previous history of persistent disease, slaughter of the whole herd or cohorts within it. It is advisable to be rigourous in these situations, and whole herd slaughter should be more readily excercised option for heavily infected herds.

* Expect a hard core of 5 per cent or more multiple reactor breakdown herds in high risk areas which have been difficult to clear; these pose a substantial disease risk and should be considered for whole herd slaughter.

And the contribution of infected badgers? Not a thing, except a throw away line that a few may have to culled, as a Trojan horse for what Bourne wanted all along. The draconian cattle controls which have so spectacularly failed in the past. And that delivered with a smirk "impish smile" to the Chairman of the EFRAcom, who remarked that he could not "be certain that his ears had deceived him".
Believe it. There's an election coming.


Matthew said...

Jim has sent the following observation on the RBCT's use of mathematical modelling:

It is interesting to see Bourne admit that “if you cull over a large area, you would ultimately get positive gains with respect to the area culled, relative to the area you were not culling.”

I've done some "mathematical modelling" (based entirely on the data in the ISG Report), and this "suggests" (to use modellers' language) that, if you take a cull area of 800km2 (as opposed to the RBCT area of 100km2), then the net number of herd breakdowns saved (i.e. the number of breakdowns prevented in the cull area minus the number of breakdowns induced by the perturbation effect in the 2km ring outside the cull area) would be 121.9. This is to be compared with the RBCT figure of 1.4 net breakdowns saved per 100km2 (or 11.2 for eight separate areas of 100km2 each).

This result is simply a (mathematical) function of the fact that the area culled is proportionately larger when compared to the perturbed area just outside the cull area. I've also taken account of the fact that the ISG found that the beneficial effect of proactive culling was about 50% in an inner core area 4 - 5km from the trial boundary - see para. 5.15 and fig. 5.1B - though this doesn't seem to be a finding they are keen to highlight.

It's worth noting that 800km2 is less than the combined area of the ten RBCT pro-active areas, and is a circle with a diameter of approx. 20 miles, as compared to some 7 miles for an area of 100km2.

Bourne's reasoning for not recommending larger cull areas (despite saying that "as a modelling exercise that was correct") seems to be the supposed logistical difficulties. Here, in my view, he is straying into the politicians' territory (possibly having been given a very strong steer to do so from on high).

Surely, if the mathematical modellers are saying that something would have a beneficial effect (i.e. culling over a larger area), then it's up to the politicians to find the will and the means to achieve that (or not, as the case may be). Instead, no doubt they'll hide behind the good professor, who has assured them it isn't practicable - and in the meantime they've conveniently sacked all the people with the necessary expertise.

I'm not advocating much larger cull areas as the only or necessary way forward (though an area only 7 miles in diameter, on which the ISG base their recommendations, strikes me as unrealistically small given the prevalence of bTB), but this does show what one can do with a bit of mathematical modelling.

I would prefer the more targeted approach advocated on this site but, if you take the ISG's own figures at face value, the question for the politicians is why not devise a way to carry out a cull over larger areas, as the mathematics shows that this will have a significant beneficial effect?

"For the avoidance of doubt", as they say, (a) in setting my calculator to work on the ISG data I'm not accepting that their report is anything other than fatally flawed, (b) if anyone thinks my maths is wonky, feel free to say so (though it appears to be in line with paras. 5.39 to 5.42 and fig. 5.4 of the ISG report), and (c) I realise that questions of badger ecology might influence the effects of a cull over a larger area (I'm just trying to show how a bit of number-crunching can affect one's conclusion).


George said...

But are these large cull areas actually needed?
During the period when gassing was used (1975-82) the removal areas were small - 3x3Km squares with the breakdown farm in the centre - a maximum of 10 square Km. Despite this, the cattle breakdown rate in the areas fell significantly. There was no sign of the ISG's 'edge effect' - which should have been very obvious, given the length of the edges. Mind you, the removal efficiency was very high.
So, providing the removal is efficient, small areas do work, and would be far more acceptable.

Matthew said...

There is a lot of information in the ISG report, much of which is not highlighted.
Jim's observations on the mathematical modelling of cull areas, are actually saying the same thing as George tells us about the much smaller targeted clearances of the 'clean ring' strategy.

The whole point of any disease eradication, is to remove the source. Completely. And in that Bourne totally failed by doing hit-and-run visits of just 8 nights, often in winter, with cage traps. So, he concentrates his efforts on cattle, including whole herd slaughter, but his results show that if a clearance of endemically infected badgers - which happened much more successfully in the centre of his culling zone than nearer its edge - is actually achieved, then the disease is reduced in cattle by a vast amount.
And this without the paraphanalia of any more cattle controls than 60 day testing and herd restriction until tested clear.

Smaller clearances, but more intense and for longer, have the effect of 'sucking out' (Rosie Woodroffe's delightful phrase) dispersers from neighbouring groups, as happened in the coastal areas of the trial in Cornwall. The trick is to avoid peturbation, not cause it.

Bourne's mathematical models are a politician's shield; the Bern Convention would not allow anything other than a 'targetted' clearance anyway, with the Irish 30 per cent as a likely benchmark. Anything else will be challenged, and a Judicial Review instigated.

The result will a repeat of the cattle carnage of Tait and Downie, but with absolutely no action on endemically infected wildlife, the diease will continue its passage. (And spillover into other species)

Anonymous said...

Jim's work is interesting. To put it's reliability into context, maybe we could have some information about Jim's qualifications and experience in mathematical modelling. And it would also interesting to know his plans for publishing in a peer-reviewed journal. The obvious thing would be to publish as a response to an ISG publication - maybe the IJID paper which showed final results.

Matthew said...

Anon; 12.11

I'm sure Jim can answer for himself, but peer reviewing was one question posed to Professor Bourne during the EFRAcom evidence contained in this post.

The Chairman commented " it almost as if you have peer-reviewed your own research and come back to the same conclusions as before. Is that a fair summary?"

Prof. Bourne replied that the ISG "constantly evaluate our [own]research" and it is published "in peer reveiwed journals".

EFRAcom Chairman then persisted with a question re the ISG final report. He asked Bourne if he was aware, if Defra were planning to have an independent audit of this work, and its conclusions.

Prof. Bourne: "I am not aware of that" He reiterated that the ISG work had been subject to audits, and to publicity in scientific journals, and thus an independent peer review of the whole was 'unecessary'.... "but if Defra want to do it good luck to them".

As far as I can see, our posts, including the latest which picks up on Jim's point, highlight parts of the ISG final report which the ISG seemed particularly reluctant to highlight, and their final report has not been peer-reviewed.
Matt 5

Jim said...

Anon asks about my qualifications. So far as relevant to the present discussion they are possession of a calculator and a maths O level, as I mentioned in a comment a while ago. (Oh - plus an, unwillingly embarked upon at the time but subsequently found to be surprisingly useful, course on statistics. I don't think my teachers were being unkind. They just wanted to broaden our minds.) Anyway, I thought I read something put up by (a different/the same?) Anon earlier this summer to the effect that one doesn't need to be an out-and-out boffin to be allowed to make comments on the ISG report. As soon as I have time - i.e. when I haven't got straw out in the field waiting to get rained on - I'll put up my detailed calculations for Anon to look at.

Anonymous said...

I wouldn't say that putting your calculations on a blog for an anonymous person to read would automatically make them reliable. For all you know, I don't even have a maths O Level or a calculator. On the other hand a peer reviewer would (plus a whole lot more!).

Matthew said...

Anon 9.26
Have a play on this link then.

It explains 'pi r squared' (sorry -can't do greek fonts)
To calculate the area of a circle: = pi(3.1416) x radius squared (x2)
or: pi (3.1416) divided by 4 x diameter squared (x2)
or: Circumference squared (x2) divided by 4 x pi (3.1416)

Working in rough terms, the area in the centre of a circle may be calculated thus:
Either 0.8 x diameter squared (x2)
or 0.08 x circumference squared (x2)

As an example, a circle with a 10 mile circumference (edge) would have an interior area of 8 sq. miles.
But a circle with a circumfernce of 20 miles contains an area of 32 sq. miles.
And a circumference of 40 miles, contains an area of 128 sq. miles.

So in theory, the ISG are correct (and they said it, but as a throw away remark, we suspect) that using these simple formulae the 'edge ' effect that they observed in their trial (no-one else noticed it in any previous trials) would be substantially reduced by a move to areas with larger centres - and in consequence a smaller (relatively) circumference.

Jim isn't making this up - it's standard mathematical calculus.

Anonymous said...

I don't think I've said - or even implied - that Jim has made anything up. I simply asked a couple of questions. One about Jim's background in the area, which he replied to, and one about whether he will put it forward for peer review, possibly in response to something by the ISG, which he didn't really reply to. Jim did suggest putting his calculations on a blog for an anonymous person to read, but you must have a fairly high opinion of me if you think I'm in a position to give them a stamp of approval. I personally would prefer a more universally recognised form of review. If Jim's point is reasonable, then scrutiny is something to be desired, not afraid of.

Jim said...

As requested by Anon, I set out below how I arrived at the figure of 121.9 outbreaks saved if one took a cull area of 800km2 (rather than the 100km2 used as the basis of the ISG recommendations). I put my original comment up on this blog since, being a mere farmer, somewhere such as this is just about the only form of “publication” open to me. I’m not at all afraid of scrutiny. If Anon finds that what I have said is reasonable, perhaps he/she would care to assist with getting it more formally reviewed/published.

My calculations assume a perfectly circular area and, to prevent my calculator running out of decimal places, I’ve taken the value of pi as 3.14 and I’ve rounded various measurements – e.g. the diameter of the cull area is 31.92km but I’ve called it 32km.

If 800km2 seems a large area, my earlier comment noted that a circle of this size would have a diameter of some 20 miles as compared with some 7 miles for a circle with an area of 100km2. It’s also worth noting something which Bourne said to the EFRA Committee on 07.02.06: “You have to recognise that TB hotspots do affect a very large area of the country. Even though 300km2 is a large area, you would need a number of those to cover all the hotspot areas.”

I have divided the hypothetical 800km2 cull area into an inner core and an outer core. The inner core is the part which is 4.5km or more from the edge, and the outer core is the part which is within 4.5km of the edge. The reason for doing this is to make allowance for the effect noted in para. 5.15 of the ISG report, viz. that “the beneficial effect of proactive culling appeared to increase at greater distances inside the trial boundary.” (This effect will obviously be more pronounced with a bigger cull area.) Looking at fig. 5.1B of the report it appears that 4 – 5km inside the boundary the beneficial effect of proactive culling was 50%. Again, in order to prevent this exercise becoming more complicated than it needs to, I’ve used a distance of 4.5km and I haven’t attempted to sub-divide the cull area further. My aim is simply to try and give an order of magnitude.

Based on the above, one has an inner core with an area of 415km2 and an outer core with an area of 385km2. It is also necessary to calculate the area of a ring 2km wide round the outside of the cull area, this being where the ISG’s perturbation effect would be seen. The area of this 2km outside ring is 217km2. I have then calculated the number of cases of TB saved or induced in the same way as paras. 5.11 and 5.31 of the ISG report (i.e. 1.25 herds per km2, 8 breakdowns per 100 herds per year, and 5 years of culling) but taking the 50% beneficial rate for the inner core and the “normal” beneficial rate of 23.2% for the outer core. This gives 103.8 cases saved in the inner core and 44.7 cases saved in the outer core (total: 148.5 cases saved). From this must be subtracted the number of cases induced as a result of perturbation in the 2km outside ring, which is 26.6. This leaves one with 121.9 as the net number of cases of TB saved.

By contrast, if one took 8 separate areas of 100km2 each (as per the ISG report), then the net number of cases saved across all 8 areas combined would be 11.2. This simply shows the powerful mathematical effect of taking a larger area. This is alluded to in the ISG report – see paras. 5.39 to 5.42 and fig. 5.4A, as well as the last sentence of para. 5.11, where they say: “The results of this and similar calculations clearly depend strongly on the size of area culled….” But, while they appear to accept it is a valid approach, they don’t actually present any figures. I am trying to fill the gap.

Presumably, if the instructions from on high given to the ISG had been to produce findings in support of a badger cull, they could have done calculations for themselves of the sort that I have done.

I have had the above “peer-reviewed” by (a) an Oxford graduate who did A level maths and (b) someone with a Masters in finance from Imperial College. The latter, who has plenty of experience of mathematical modelling, commented that modelling is “an art not a science” and “depends on certain key drivers, which you can tweak to make the results say almost anything you want.”

Incidentally, I assume from Anon’s tone that he/she must be at least a Ph.D., but perhaps Anon could let us all know what experience he/she has of farming, and specifically in relation to keeping cattle and managing a herd in the face of a TB breakdown. If the scientists expect us to bow down before their mathematical wizardry, it’s only reasonable for us to ask that they get their hands dirty before they condemn our animals to an unnecessary and preventable death.

Anonymous said...

Glad to hear you had some people look at it. I do not have a PhD (but interesting concept that people with PhDs have a certain 'tone') and nor do I have any experience in farming - which is why I wouldn't comment on any aspect of farming. If you reread my comments, I have said nothing against you. As an outsider, it just seems frustrating that people like yourselves have a lot to say on a blog but it's not pushed more into a place where it will get (a) read by people who have some influence over what happens in terms of TB policy (b) put up to the scrutiny that will mean that it gets taken more seriously.

Matthew said...

No offence intended. We have had quite a lot of veiled (and not so veiled) abuse over the 3 years this blog has been running. Prickles come with the territory.

My point was that peer reviewing a known mathematical formula is pointless. Pythagoras is what it is. Jim extended it and simply entered data from the trial, thus backing up what the ISG had already said - that in theory, larger cull areas would give a more substantial reduction in cattle Tb.
That said, we agree with Bourne (and that has to be a first) that logistically, morally and from an ecological point of view they are a no go. As George said, small more targetted clearances, worked well in the past and there is absolutely no reason to think they would not work again.