[tomtom]

The new normal won’t be the old normal and herein lies our freedom. Mourn the pleasures and recreate them screened off if you like. Or understand that pleasures mutate too and it’s time to find some new ones.

I rather liked this statement at the end of a Suzanne Moore column in the Guardian (I’m not usually her biggest fan).

[nik at work]

I’ll see if I can dig out the information I saw. But don’t hold me to the 8 weeks statement, as I said it was from memory so I could be way out on the timescale. The antibody drop off was definitely a thing though. As I recall this isn’t necessarily a sign that immunity is lost in a short time frame, and I don’t want to be seen as suggesting that it is.

Again dredging up from the depths of memory I’m fairly sure there is at least one other example of an immunisable disease which yields a cyclical level of antibody, meaning if you’re tested for immunity at the wrong time in the cycle you would “fail” the test due to having antibody levels that are sub-detectable, whilst still actually being immune. I’m afraid I can’t recall the specific example and a guess would be just that.

[Oldmanmatt]

I’ll see if I can dig out the information I saw. But don’t hold me to the 8 weeks statement, as I said it was from memory so I could be way out on the timescale. The antibody drop off was definitely a thing though. As I recall this isn’t necessarily a sign that immunity is lost in a short time frame, and I don’t want to be seen as suggesting that it is.

Again dredging up from the depths of memory I’m fairly sure there is at least one other example of an immunisable disease which yields a cyclical level of antibody, meaning if you’re tested for immunity at the wrong time in the cycle you would “fail” the test due to having antibody levels that are sub-detectable, whilst still actually being immune. I’m afraid I can’t recall the specific example and a guess would be just that.

It seems you don’t require a specific example, as it might be fairly common:
https://www.sciencedirect.com/science/article/pii/S0065277608602199?via%3Dihub

[teestub]

https://www.bbc.co.uk/news/technology-53095336

Change of tack on the tracing app.

[tomtom]

https://www.bbc.co.uk/news/technology-53095336

Change of tack on the tracing app.

The worst type of student to deal with are those who are not the brightest but arrogant. They belligerently carry on down the path they so strongly believe is right despite being told and having it pointed out to them (repeatedly) that it won’t / would not work. Only when they try - and fail as they always were going to - they realise and change tack. Time after time this government seems to follow this pattern.

As a lecturer when this happens you sigh - and try and take the perspective that at least they got there in the end. But this is our government ffs. Anyone been tallying up the U turns?

[Fultonius]

Saw this earlier today. Sounds kind of promising?

https://www.forbes.com/sites/michaeldelcastillo/2020/06/16/apple-and-google-admit-ethereum-app-to-let-employees-prove-theyve-been-vaccinated/

[Offwidth]

From Guardian live

https://www.theguardian.com/world/live/2020/jun/19/coronavirus-covid-19-live-news-update-us-questions-beijing-cluster-figures-who-vaccine-doses-latest-updates

"Researchers discovered genetic traces of Sars-CoV-2 - as the virus is officially known - in samples of waste water collected in Milan and Turin at the end of last year, and Bologna in January, the ISS institute said in a statement seen by AFP on Friday.

Italy’s first known native case was discovered mid-February.

The results “help to understand the start of the circulation of the virus in Italy,” the ISS said.

They also “confirm the by-now consolidated international evidence” as to the strategic function of sewer samples as an early detection tool, it added."

[teestub]

The results “help to understand the start of the circulation of the virus in Italy,” the ISS said.

Seems a bit mad sending the samples into orbit, but I guess it reduces the chance of cross contamination!

[Oldmanmatt]

From Guardian live

https://www.theguardian.com/world/live/2020/jun/19/coronavirus-covid-19-live-news-update-us-questions-beijing-cluster-figures-who-vaccine-doses-latest-updates

"Researchers discovered genetic traces of Sars-CoV-2 - as the virus is officially known - in samples of waste water collected in Milan and Turin at the end of last year, and Bologna in January, the ISS institute said in a statement seen by AFP on Friday.

Italy’s first known native case was discovered mid-February.

The results “help to understand the start of the circulation of the virus in Italy,” the ISS said.

They also “confirm the by-now consolidated international evidence” as to the strategic function of sewer samples as an early detection tool, it added."

I seem to remember taking some stick from you, on this subject, a couple of weeks ago...

[Oldmanmatt]

https://www.bbc.co.uk/news/technology-53095336

Change of tack on the tracing app.

Well, Apple say they’re lying and the UK Government haven’t contacted them at all:
https://www.bbc.co.uk/news/technology-53105642

[Offwidth]

From Guardian live

https://www.theguardian.com/world/live/2020/jun/19/coronavirus-covid-19-live-news-update-us-questions-beijing-cluster-figures-who-vaccine-doses-latest-updates

"Researchers discovered genetic traces of Sars-CoV-2 - as the virus is officially known - in samples of waste water collected in Milan and Turin at the end of last year, and Bologna in January, the ISS institute said in a statement seen by AFP on Friday.

Italy’s first known native case was discovered mid-February.

The results “help to understand the start of the circulation of the virus in Italy,” the ISS said.

They also “confirm the by-now consolidated international evidence” as to the strategic function of sewer samples as an early detection tool, it added."

I seem to remember taking some stick from you, on this subject, a couple of weeks ago...

I argued against making assumptions that this is the same mutation of the virus, not that you were wrong saying it was around in the EU earlier than people thought. It's a big puzzle with missing pieces but nearly all the data still indicates the current deadly characteristics of the virus could not have been around then or we would have seen deaths in January in Italy and France.

[Offwidth]

https://www.bbc.co.uk/news/technology-53095336

Change of tack on the tracing app.

Well, Apple say they’re lying and the UK Government haven’t contacted them at all:
https://www.bbc.co.uk/news/technology-53105642

On Newsnight last night one of the developers helping Apple and Google in Europe said he tried to warn the government in April and offered help at any point as the code is open source. An offer not accepted.

Newsnight was a classic episode last night as the ongoing and very sad issues at the Tavistock were also covered in detail. It's amazing how good the show is currently, in great contrast to the main BBC news.

https://www.bbc.co.uk/iplayer/episode/m000k4f6/newsnight-18062020

[Oldmanmatt]

From Guardian live

https://www.theguardian.com/world/live/2020/jun/19/coronavirus-covid-19-live-news-update-us-questions-beijing-cluster-figures-who-vaccine-doses-latest-updates

"Researchers discovered genetic traces of Sars-CoV-2 - as the virus is officially known - in samples of waste water collected in Milan and Turin at the end of last year, and Bologna in January, the ISS institute said in a statement seen by AFP on Friday.

Italy’s first known native case was discovered mid-February.

The results “help to understand the start of the circulation of the virus in Italy,” the ISS said.

They also “confirm the by-now consolidated international evidence” as to the strategic function of sewer samples as an early detection tool, it added."

I seem to remember taking some stick from you, on this subject, a couple of weeks ago...

I argued against making assumptions that this is the same mutation of the virus, not that you were wrong saying it was around in the EU earlier than people thought. It's a big puzzle with missing pieces but nearly all the data still indicates the current deadly characteristics of the virus could not have been around then or we would have seen deaths in January in Italy and France.

Bollocks.

You said I was spreading conspiracy stories. Do I have to quote those posts? I just re-read them.
Also, the post I made about the discovery of the more infectious mutation, was an entirely separate post, several posts later, from the link I posted to the French early case article.

You were way off base then, and even further now. In fact, you called any countenance of any “early infection” line of thought, dangerous.
FFS, there is even strong circumstantial evidence of a much earlier outbreak than has yet been considered, based on a 10/12x increase, above seasonal, of hospitalised Flu cases in China in the Autumn of 2019.

I don’t know if you are aware of this, but you often come across as a bit of a slave to the “Party line” or consensus. Both politically and in matters such as this.
(That probably seems harsh and unduly personal, especially coming via the impersonal medium of a forum post. I promise, we’d get on well arguing such things over a pint, it wouldn’t be a bad tempered affair).
I’m rather combative and flit around from idea to idea, with deeply held convictions, that last for all of five seconds before I lurch off on a tangent and forget why I cared. You seem to run on tracks, that require a committee vote, ratification from the central party, authorisation forms (in triplicate) and a duly appointed (union recognised) operator to change the Points; before you can deviate. I suspect, the decoupling and turntable operations required for you to turn around completely, would be epic...

[Oldmanmatt]

This is an interesting article, with links to supporting data, about the increase (in the US) of young adult and child infection and transmission:
https://www.npr.org/sections/health-shots/2020/06/19/880912184/younger-adults-are-increasingly-testing-positive-for-coronavirus?utm_medium=40digest.7days3.20200619.carousel&utm_source=email&utm_content=&utm_campaign=campaign

[Fultonius]

Matt - I found this thought provoking. There are a fair few criticisms of their research, and it's not peer reviewed yet.

[Oldmanmatt]

Father-in-law keeps coming back to the Oxford study.
I whole heartedly embraced/embrace the “prepare for the worst, be thankful if you are wrong” philosophy, but I’ve been following this rather closely and the light has shifted, as far as I can see.

FiL (yes, I know I’ve mentioned it before) was a very senior doctor prior to retirement (he ran hospitals for the Navy). From the outset, he kept saying “this is nasty”, “this is going to kill a lot of people”, but he also kept on about the Imperial study being “worst case” and that that was “unlikely the reality”.
He was, for instance, really quite upset that we chose not to send the kids back to school, until we explained that Polly’s boss has cancer (st 4) and her continued employment requires her to shield (in effect) and given the vulnerability of my parents, it just wasn’t worth the added risk.

I’m now not convinced either way, but moderately sure the truth lies somewhere in between and acutely aware Death is not the only negative outcome from this infection, as has been widely noted.

Look at these projections and then compare them (Useful little tab on the graphs). The shapes are very similar. The US a notable exception.
https://covid19.healthdata.org/united-kingdom

I should add, my impression of the general public’s attitude to “the rules” is that, here, most no longer take it at all seriously and that has been the case for three weeks or more.
We know that on the 4th of July, most of the restrictions will be lifted. If the Times are correct, even the gyms/walls will be able to open. We are about to/are already testing the Oxford hypothesis and the results will be available by the end of July.
I actually think, we don’t really have a choice. There seems no definitive test to prove one or the other, except trying to ease and watching the signs.

[Offwidth]

Bollocks.

You said I was spreading conspiracy stories. Do I have to quote those posts? I just re-read them.
Also, the post I made about the discovery of the more infectious mutation, was an entirely separate post, several posts later, from the link I posted to the French early case article.

You were way off base then, and even further now. In fact, you called any countenance of any “early infection” line of thought, dangerous.
FFS, there is even strong circumstantial evidence of a much earlier outbreak than has yet been considered, based on a 10/12x increase, above seasonal, of hospitalised Flu cases in China in the Autumn of 2019.

I don’t know if you are aware of this, but you often come across as a bit of a slave to the “Party line” or consensus. Both politically and in matters such as this.
(That probably seems harsh and unduly personal, especially coming via the impersonal medium of a forum post. I promise, we’d get on well arguing such things over a pint, it wouldn’t be a bad tempered affair).
I’m rather combative and flit around from idea to idea, with deeply held convictions, that last for all of five seconds before I lurch off on a tangent and forget why I cared. You seem to run on tracks, that require a committee vote, ratification from the central party, authorisation forms (in triplicate) and a duly appointed (union recognised) operator to change the Points; before you can deviate. I suspect, the decoupling and turntable operations required for you to turn around completely, would be epic...

I don't understand what you mean by a party line or tracks unless that is the mainstream scientific view. Science never denies clear evidence but it doesn't use one piece to ignore everything else. The most likely explanation is the virus was around earler but mutated to become more lethal and/or spread faster. Prof Gupta's views that the virus is unchanged and the level of infection is much larger and been around much longer than the scientific establishment say is still counter to most of the evidence and encourages people not to take the virus seriously; if she is wrong, as is very likely, that is a very dangerous view.  Guess who Ian Duncan Smith was lauding to help push for 1m on the news yesterday?

On the discussion on May 6th I explicitly said others were spreading such conspiracy stories but as for you:

"I know you are not Matt but the internet is full of such wish fullfillment shit. Its a threat to everyone as such people won't care about following social distancing."

[Oldmanmatt]

An interview with a medic involved in the Dexamethasone trials.

Not wholly encouraging...😱

https://www.msn.com/en-gb/health/medical/gwynedd-doctor-behind-coronavirus-trials-terrified-of-peoples-reactions-to-lockdown-easing/ar-BB15TAvV?ocid=sf

[TobyD]

 I thought that this article is interesting, I've wondered about the obsession with modelling scenarios endlessly : https://www.newstatesman.com/politics/2020/07/government-chose-follow-wrong-science-lethal-social-and-economic-consequences

[Sidehaas]

I thought that this article is interesting, I've wondered about the obsession with modelling scenarios endlessly : https://www.newstatesman.com/politics/2020/07/government-chose-follow-wrong-science-lethal-social-and-economic-consequences

I've thought for a while the Govt and Sage has taken the wrong approach with its modelling. I actually think some of the examples that article gives are poor (eg overestimating the size of the peak - those estimates could easily have been reasonable if no action had been taken, which was what they assumed) but I agree with the general argument.

Modelling should be used to help predict how a situation might evolve and, if you don't have enough confidence in the model's absolute accuracy, it can sometimes still be used to predict the relative sensitivity of the outcome to different parameters as long as you treat the absolute numbers with pinch of salt - this is what they have tried to do with the effects of some social distancing measures.

However it's critical that theoretical models have some validation. Whenever the process isn't fully understood, a model describing it has to include coefficients or other parameters (as well as the various input assumptions) that aim to mimic the effect of the true process. This is fine if you have evidence with which to tune the coefficients until you are confident they give a reasonable outcome with a known uncertainty. However if you don't have that, all you can do is put in the numbers that give you the answer that intuitively makes the most sense. This seems to be the situation a lot of our modellers have been in. It leads to the models being biased towards what people expect from their past experience or personal intuition, regardless of whether there is actually an intent to do this. With all the different assumptions and variables involved in a complex process like Corona virus spread, different models that use slightly different coefficients will end up giving wildly different outcomes when assumptions are changed slightly, and the uncertainty bands are fairly useless.
This has been demonstrated by the fact that many of the models claiming to predict the same thing (an example springing to mind is local r value) have given estimates that are far enough apart that the 95% confidence band intervals do not overlap at all. This simply shows that some or all of the modelling is wrong and those bands cannot be trusted.

Sage's approach as far as I can discern from what Vallance et al have said seems to have been to take lots of different models and assume the best prediction is somewhere down the middle of what they all say. The problem with this is that the true answer for any particular scenario could easily be at one end of the spectrum rather than in the middle ( or even completely outside it) and also that different models will be the best in different scenarios (eg, one might better estimate the sensitivity of R to opening pubs, another might better estimate the sensitivity to travel quarantines.) Really, they were just winging it.
What should have been happening is that they should have been looking for every scrap of evidence they could find to provide some validity to those models and the assumptions and coefficients underlying them, so that they can become a more reliable decision making tool. It's possible they have been doing this. But in the meantime they should not have been being used as the primary way of making decisions. Sage should have been providing advice in a conservative manner, benchmarking it against the decisions taken by other countries and perhaps using that information also to investigate how their own modelling might differ from that in the UK. Govt should only have been using modelling to predict what a very wide range of outcomes might be to inform their planning (and I think the Nightingales was something they did right). One thing this approach would have led to was earlier lockdown when it became obvious our approach was inconsistent with almost everyone else.
Like the Swedes but fortunately in a slightly less extreme manner, our scientists seem to have been too willing to believe that if we paid enough scientists to sit around the table then our own modelling must be about right and all those other countries must be wrong. It's also arguable from the Sage minutes released that early in the pandemic they were simply too unwilling to take really difficult decisions at all without having evidence underlying their models - but what this meant in practice is that the default decision for Govt was simply not to do anything. This perhaps comes to the structural question the article raises.

Disclaimer: I know nothing about epidemiology but I work in the nuclear industry and have to make decisions about the validity and use of a lot of models of uncertain processes that have a high hazard outcome if you get it wrong.

On the subject of structural problems with Sage and the advice it provides, Nick Robinson did quite a good Political Thinking podcast with Neil Ferguson last week.

[tomtom]

As someone who has spent the last 25 years building numerical models (of how landscapes change - which I’d argue is possibly more complex) I have a lot of sympathy for what has been carried out. I’m also a bit concerned about an emerging narrative (that The article subconsciously supports) that this is a model/modellers fault - rather than those who make policy decisions based on a breadth (hopefully) of scientific views including models.

A couple of points to bear in mind first - the George Box quote “All models are wrong but some are useful” is completely correct and

Second - modelling CV19 is impossible to do accurately or precisely. Even more so 3 months ago when we knew much less about it and how it behaved in comparison to other viruses. The High levels of asymptomatic transmission - the importance of close physical indoors transmission as opposed to touch contact. The importance of individual or super spreaders. All of these are now better though still far from satisfactorily understood.

You can’t validate something you don’t fully or even partially understand - This can put you in danger of getting “the right results for the wrong reasons” aka the calibration trap.

But what you can do - and wasn’t done with the first imperial model - is carry out a full sensitivity analysis (how internal model parameters affect the outcome) and an uncertainty analysis (how variations/uncertainty in input variables can cascade through the model and affect outcomes). (Basic descriptions above caveat..).  If you have little variation in the model outcomes wrt small changes in input values/parameters you can have greater confidence in the modelled predictions.

Sorry - toddler duty is dragging me away.. edit - the above might come across a bit arsey - not meant to be - bad night etc...

[Sidehaas]

Not arsey at all. I suffer from the same toddler related problems all the time.
I disagree with some of what you said but it's probably in the weeds.

The point about accountability is important. The Govt have to be accountable for all their actions and it is certainly true that they have cocked up on several fronts. They are also ultimately responsible for ensuring that Sage and it's supporting structure and scientists are adequate to give them good advice. However when you look at the Sage minutes and what members have said publicly, is appears to be true that for at least for the first half of the pandemic to datw (I'm not sure about the undoing of lockdown yet) the Govt really did follow the scientific advice closely and the fundamental reasons for our higher than necessary infection rate were scientific rather than political. This does mean we need to learn lessons about our scientific approach thoroughly and carefully, without taking accountability for the overall picture away from Boris and co.

[Offwidth]

That's my view as well.  The CMO and CSA saying for a long time that we were 4 weeks behind Italy when the gap was clearly 2 weeks was a clear sign they were clinging to model outputs that just didn't match real data in an incredibly high risk manner. The way to deal with this is to be less secretive (allow peer review) and be conservative on responses (ie lockdown early) given the risk of unknowns on a new virus exponential growth. The modelling is what it is, those to blame are the scientific leaders who set up SAGE with too much model emphasis and too little experience in fighting viral outbreaks (as per the famous Times article) and then didn't open up their work to peer scrutiny. Then there is the clear evidence that we were working on some pessimistic assumptions that the virus could not be stopped, alongside NL and Sweden (who later complained NL and the UK started this with them, then lost their nerve). Other detailed aspects of Cygnus were also ignored or under emphasised, and Cygnus was buried for political reasons. Tens of thousands died because of our scientific and political exceptionalism. Then we need to remember we wrecked a world class Public Health system and Boris joked about handshakes and muddled messages.

https://www.theguardian.com/world/2020/jul/05/anthony-costello-world-health-organization-independent-sage-coronavirus

[tomtom]

Interesting article here in the Grauniad (of course...) musing over what will happen to Gyms when they are allowed to re-open. Some overlaps with what may happen with climbing walls I expect (though not completely)..

https://www.theguardian.com/lifeandstyle/2020/jul/07/parklife-when-gyms-reopen-will-anyone-go-back

[Offwidth]

Updates in WHO

https://www.theguardian.com/world/2020/jul/08/who-says-evidence-emerging-of-airborne-coronavirus-spread