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y get very close under the rwc scenario while sage s view remains that school closures constitutes one of the less effective single measure to reduce the epidemic peak it may nevertheless become necessary to introduce school closures in order to push demand for critical care below nhs capacity however school closures could increase the risks of transmission at smaller gatherings and for more vulnerable groups as well as impacting on key workers including nhs staff as such it was agreed that further analysis and modelling of potential school closures was required demand supply and effects on spread and on the 18th sage advises that the measures already announced should have a significant effect provided compliance rates are good and in line with the assumptions additional measures will be needed if compliance rates are low they even argued that the measures implemented on the 18th including the new school closures were probably adequate to fully suppress the pandemic sage reviewed available evidence and modelling on the potential impact of school closures the evidence indicates that school closures combined with other measures could help to bring the r0 number below 1 although there is uncertainty summary the claims that the govt was responsible for a week of delay at this time and that sage was arguing for much more immediate and stringent action is not supported by a reasonable reading of the evidence indeed sage had no reason to be doing this since they still believed contrary to vallance s testimony above that the pandemic was doubling at a rate no more rapidly than 5 days at worst and furthermore as they explicitly stated on the 18th was probably being significantly slowed beyond this figure by existing policies already introduced at that time all of the quotations i have given above are directly copied from official documentation available on the govt s own web site other than that taken from the youtube video of the pm statement and press conference of the 16th march which is my own transcription please contact me if you require any help in validating the provenance or accuracy any of this evidence regards james annan jdannan blueskiesresearch org uk posted by james annan at tuesday november 28 2023 2 comments email this blogthis share to x share to facebook share to pinterest labels covid 19 saturday november 25 2023 vallance vs vallance vs sage why does doubling time matter one thing that all the protagonists myself included agree on is that sage s estimate of doubling time in mid march was of critical importance vallance testified forcefully to this effect in 2020 when the sage sub group on modelling spi m saw that the doubling time had gone down to three days which was in the middle of march that was when the advice sage issued was that the remainder of the measures should be introduced as soon as possible and then confirmed in this exchange with a committee member sir patrick vallance knowledge of the three day doubling rate became evident during the week before q1080 ed this number has changed from the previous time i posted about this graham stringer did it immediately affect the recommendations on what to do sir patrick vallance it absolutely affected the recommendations on what to do which was that the remaining measures should be implemented as soon as possible i think that was the advice given and again sir patrick vallance the advice changed because the doubling rate of the epidemic was seen to be down to three days instead of six or seven days we did not explicitly say how many weeks we were behind italy as a reason to change it was the doubling time and the realisation that on the basis of the data we were further ahead in the epidemic than had been thought by the modelling groups up until that time but why does the doubling time matter so much and is the difference between 3 days and 5 day really important the point of this post is to answer these questions i ll start by repeating a couple of plots i first made way back in april 2020 when it was just dawning on me what a colossal cock up sage had made of it these graphs are generated by a simple seir model that i ve shown to reasonably replicate more sophisticated ones in the below the blue calibrated line uses data up to 14 march to estimate doubling time which comes out at 3 days the red uncalibrated line uses parameters from ferguson s march 16 paper which has a doubling time of 5 days so one obvious point is that the blue curve does a much better job of predicting what was going to happen ie the magenta x which were not used to calibrate either model but that s not the point of this particular post rather it s just that the predictions for 3d vs 5d doubling are radically different here is the longer term view now without the logarithmic scaling on the axis note the we are here point is mid march when the red and blue curves are visually indistinguishable there are several reasons why the doubling time matters firstly the estimate of current pandemic size is based on historic data edmunds specifically talks of a 12 day delay from infection to illness to testing to finally test data reporting so 100 cases reported today means 100 infections 12 days ago and that s 4 doublings at 3d doubling meaning 1 600 cases now if the doubling time was only 5d then the 12 day delay is just over 2 doublings and we wouldn t be at 1 600 cases for another 8 days 4 doublings is 20 days so that means 12 just past and another 8 in the future so one immediate consequence of a change in perceived doubling time is that we ve lost just over a week in terms of pandemic progression these calculations all ignore the proportion of infections that are undetected which can reasonably assume to be roughly constant and thus not affect the argument secondly the 3d doubling means the pandemic comes much sooner and thirdly reaches a much higher peak as shown in the 2nd graph above what was expected some time over the summer is now happening next month and it s going to be a lot worse than expected getting on for twice as many cases per day at peak finally the more rapid doubling implies a higher r0 number and this makes it harder to control with r0 2 4 ferguson s 16 march number a reduction of contacts to 40 of normal would control the virus because 2 4 x 0 4 0 96 which is less than 1 whereas a 3d doubling implies a rather higher r0 let s say 3 2 this then requires much stiffer action because 3 2 x 0 4 1 28 which is still greater than 1 a reduction to 30 of previous contact levels to get the r number below 1 3 2 x 0 3 0 96 as before is obviously much tougher to achieve especially given that family members essential work etc mean we can t really isolate perfectly quibbling over the exact value of r0 to use doesn t invalidate the general point that a higher r0 is harder to control so changing the estimate of doubling time from 5d to 3d would be a real oh shit moment for anyone involved in pandemic planning it means a we ve instantaneously lost 8 days of lead time b the pandemic peak is going to be coming a month sooner than expected c the peak is going to be almost twice as big as expected and d the control measures we were hoping to use are much less likely to be adequate any plan predicated on a 5d doubling time would immediately have to be revisited in the most extreme and urgent manner i hope i have convinced my reader that whatever plans were in place in early march under the assumption of a 5 day doubling the new understanding that the doubling time was instead 3d would cause an abrupt and substantial change of perspective this from a scientific perspective is inevitable and obvious posted by james annan at saturday november 25 2023 3 comments email this blogthis share to x share to facebook share to pinterest labels covid 19 thursday november 23 2023 vallance vs vallance vs sage introduction ok i m going to do a bit of analysis of vallance s evidence to the uk covid 19 inquiry focussing specifically on the events of the mid march 2020 period up to the imposition of the first lockdown on 23rd march on monday 20th nov 2023 he was interviewed by the inquiry and also provided some written testimony this is broadly speaking a more detailed version of the testimony he provided back in july 2020 to the house of commons science and technology committee which i blogged about at the time but appears significantly inconsistent with the documentary evidence provided by the minutes of sage meetings and other records of that period if you already agree with me that vallance misled the s tc with his testimony in 2020 then you might not find this very interesting but i think i might as well go over it again as there s a lot more testimony to consider including other participants in sage i ll break it up into sections in order to make it digestible and also to avoid me going round in ever decreasing circles to start with let s consider some background concepts posted by james annan at thursday november 23 2023 0 comments email this blogthis share to x share to facebook share to pinterest labels covid 19 tuesday november 21 2023 uk covid 19 inquiry module 2 the currently ongoing module 2 describes its aims thusly this module will look at and make recommendations upon the uk s core political and administrative decision making in relation to the covid 19 pandemic between early january 2020 until february 2022 when the remaining covid restrictions were lifted it will pay particular scrutiny to the decisions taken by the prime minister and the cabinet as advised by the civil service senior political scientific and medical advisers and relevant cabinet sub committees between early january and late march 2020 when the first national lockdown was imposed i m particularly interested in this period as it s the time that the expert scientific analysis and advice from sage was so woefully inadequate i ve blogged about this at length but just to recap the scientists were mistakenly thinking that the doubling time of the pandemic was about 5 6 days various numbers appear in the sage minutes and that we shouldn t take too stringent measures as there was a genuine risk that by doing so we d put the pandemic off to the following winter when it would add to the normal seasonal pressures on the nhs they were quite anxious that we should get through it over the summer of 2020 instead vallance misled the science and technology select committee a while ago about this claiming that sage had recommended lockdown on the 16th or 18th of march this is contradicted by the minutes of those meetings and even if you try to argue that the minutes may not be completely definitive on that it is also contradicted by his accompanying statement that their change of heart was due to correcting their estimate of the doubling time to 3 days which the sage minutes document very precisely to the 23rd march he s due to give evidence to the uk covid 19 inquiry on monday so i await with interest to see whether he will correct the record or also mislead them this error was not just an inconsequential comment in a committee that no one cares about but has been widely reflected in press comment for example the usually excellent lewis goodall on xitter doesn t seem to me that what uksciencechief said earlier has received as much attention as it should in the day s tsunami of news in saying that sage advised the govt to lockdown a week earlier than they did yet more space is opening up between them pic twitter com ckuwxlh7vh lewis goodall lewis_goodall july 16 2020 posted by james annan at tuesday november 21 2023 1 comments email this blogthis share to x share to facebook share to pinterest labels covid 19 monday november 20 2023 uk covid 19 inquiry i can see i m going to have to go over all this again it s not a task i really face with much enthusiasm but it doesn t seem like anyone else is prepared to do it to say i m disappointed at the revisionism sleight of hand and downright misleading testimony from several senior scientists to the uk covid 19 inquiry would be an understatement i had naively hoped there might be some element of humility introspection and self reflection concerning their errors at the start of the outbreak but i ve seen no hint of this if anyone wants to reassure me that lessons have been learnt internally then i m all ears but would want to see evidence of this unfortunately neither the inquisitors themselves nor the journalists following the process nor the array of commentators eagerly quoting the juicy messages seem to have the will or perhaps the scientific skills to unpick the story that s not to say it is hugely complicated but a basic understanding of the underlying mathematics is vital for piecing together how it all played out and why and it s very clear that most people start out with an agenda and go looking for support rather than really being interested in understanding the truth the scientists are delighted to have found a route to blaming the politicians and the politicians are too focussed on knifing each other to question what the scientists are now claiming the history to be that s not to say i m perfect far from it but on this particular topic i happen to be correct a more difficult question is whether anyone else cares anyway on with the show posted by james annan at monday november 20 2023 0 comments email this blogthis share to x share to facebook share to pinterest labels covid 19 sunday november 19 2023 retired as you may have noticed there hasn t been a lot of science getting done here recently the basic reason for this is that we ve decided to retire and close down blue skies research ltd we set it up about 10 years ago when we returned from japan and have had a lot of fun continuing our research in a private setting but over the last few years have been gradually winding down the research activity and increasing the other than research activity and want to focus on the latter from now on there s a paper in the works with paper charges still to pay so the company isn t completely shut down yet we aren t looking for new projects but if something exciting comes up we might change our minds to be honest we haven t been particularly inspired by new ideas for a while and simply don t have any burning climate science questions that we need to answer after all we have worked out what equilibrium climate sensitivity is actually we worked it out in 2006 but everyone else took 15 years to catch up there are lots of other scientists quite capable of taking the field wherever they choose to and we look forward to seeing where they go posted by james annan at sunday november 19 2023 1 comments email this blogthis share to x share to facebook share to pinterest labels blueskiesresearch careers friday november 18 2022 no comment necessary posted by james annan at friday november 18 2022 0 comments email this blogthis share to x share to facebook share to pinterest wednesday september 21 2022 chess ma...
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