Yesterday I used the phrase "uptick in cases" about the REACT study - some people drew comfort here (upticks are small); other people were horrified I was giving false comfort. To be clear - the REACT study shows strong growth of Coronavirus infections in nearly all of England
I am definitely someone who has an optimism bias - it serves me well in many scenarios in science and life - and in this pandemic it is justified **in the mid to long term** : BUT *not* in the short term. Optimism biased people like me are not good decision makers in a pandemic
(we might be good data analysts; we might be good communicators; we might be good technologists in getting out of this; but optimism is a curse in the management of pandemics. I find the cross current on this really hard - the mindset that has served me well is not good here).
Back to the REACT study - like the ONS study this is the solid ground to stand on it is clear cut that transmission of the virus has grown in all areas across England, and has grown *strongly* in nearly all areas; as concerning is that the growth has moved to older age groups.
This obviously has impact on decisions. It means the current combination of high testing (testing capacity a positive in TTI system in the UK) and the Tier 2/Tier 3 scheme is not adequate in controlling the virus.
(one region, East of England, one might be able to convince yourself it is close to control, but thats 1 of 7, and given the other trajectories one *must* have a proper worst case scenario in mind where this is a timing issue.)
As well as optimism bias being a curse, the often used "keep something in your back pocket" and "see how the new things change" - or continuation bias if you prefer - is also a real issue in decision making.
For me this is as much because the risk/rewards are very asymmetrical. Downside risk here is further lack of control of the virus and *exponential* growth with a reasonable coefficient. It becomes uncontrollable (perhaps is already - one has to own all our mistakes here)
As Dr Fauci says, it is far better to be criticised for overreacting than under reacting in a pandemic.
Finally in this rather bleak thread I want to acknowledge the clear aspects that increased, population wide NPIs - call it higher Tiers, or more lockdown or whatever works to get it done - does not come "for free" - certainly not! They have serious, far reaching impacts.
It has serious consequences on lives and livelihoods and life in general. We have pretty good frameworks to navigate the awful decision tree ahead of us - whether it is Welfare economics and cost benefit analysis or "all in" health economics and QALYs.
Frustratingly we haven't done much public exploration of this decision tree probably because it is all a bit too bleak/lack of courage, +/- just higher priorities. One meta-thing to do right is to (a) have these bleak scenarios game planned in the abstract ahead of time and >>
(b) on any new pandemic have some strongly worded (perhaps even legislation?) triggers which force a future government to map out the decision tree in public.
My final two pleas after this thread. Firstly - do not envy either the people giving advice or making decisions. None of this is easy. If anyone provides an easy solution to this be very very skeptical.
Secondly - be kind and nice to the people around you - neighbours, friends, twitter followers and public. Assume best intent, even of the people you don't like or trust. It's hard I know, but this is a human vs virus thing, not left vs right, nor countries against each other.
We humans have to work as one team.

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More from @ewanbirney

31 Oct
An explainer thread (often I feel I am pitching these to journalists as much as anyone else) on COVID this month.
Context: I am an expert in one area (human genetics) with battlescars in complex data flow+analysis; I know experts in most other areas and aim to be curious about their viewpoints; I have a clear conflict of interest in that I am consultant to ONT, which makes a new COVID test
Again, worth reminding people of the overall situation; SARS_CoV_2 is an infectious virus which causes a nasty, often lethal, disease in a subset of people. It is now across the world.
Read 29 tweets
30 Oct
Coronavirus and the options for the UK government (or more accurately, each of the 4 component parts of the UK) are pretty bleak, but one good thing has been the steady increase in testing capacity (480K; 347K used) and now improvement in turn around time (more done in 48 hours)
Personally I think more can be done at the local level between "Pillar 1" (NHS) and "Pillar 2" (community testing) to help get even deeper+faster testing, but of course testing by itself doesn't solve the issues; one needs effective isolation support as well.
All this doesn't change the fact that there are a very large number of active infections across the UK, and these inevitably lead to hospitalisations, nasty disease and for older people, often death. We need to push down this infection level harder for this to be sustainable.
Read 6 tweets
29 Oct
Done a genetics, statistics, CS, image analysis or physics PhD? Want to do a postdoc? Love biology and genetics? Want to understand the limit of genetics, using genetics? Want to work internationally in UK, Germany and Japan? This postdoc is for you: embl.de/jobs/searchjob…
You will be based @emblebi which is part of the international treaty organisation @embl. This is a European science organisation; you will live in the UK but can come from any country worldwide. We work in an @ERC_Research funded synergy grant with @WittbrodtLab on Medaka fish
Medaka fish are japanese rice paddy fish, and we work closely with @Naruse_kiyoshi from NIBB in Nagoya Japan. Medaka are unique in vertebrates in that there is a protocol to inbreed individuals from the wild which is successful in around 1 in 2 attempts.
Read 14 tweets
29 Oct
ONS and REACT surveys pretty concordant and show overall uptick. I’m particularly concerned about increase in old age range in Yorks+Humber. Overall clearly England (REACT England only) not in control of the virus
There are two glimmers of positivity in my amateur reading around this very very dark cloud - the north east changed trajectory ( also shown in ONS survey) - drop mainly in young people but slow growth other age groups
The other positive is how well East of England (and south east to some extent) has suppressed the virus so far. Incidence has gone up but nothing like North West.
Read 5 tweets
25 Oct
To add to the left leaning commentators on COVID that hold water for me
Local action at public health is key. Funding and empowering local public health is a key part of the “trace” solution
The disadvantaged and poorer in society is a section of society one needs huge attention on; the economic hit is far bigger as a proportion; they often can’t “work from home” and other health complications are higher.
Read 4 tweets
25 Oct
I should do a mirror one about left wing commentators on COVID, which I have to admit I find generally more palatable. Still, here goes
1. TTI is a complete waste of money. Simply no due to the testing capacity and reasonable (but could - should - have better turn around time). Can TTI work better? Hell yes! Do some parts work now? Absolutely yes.
2. Dido Harding is unsuited to chair a health agency. Somehow people forget her chair role in NHS improvement in 2017 and her part in the NHS ecosystem/ management since then
Read 5 tweets

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