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.
At the moment the main tools are improving the end-to-end operation of Test-Trace-Isolate (as ever, very easy to tweet, far harder to do, and the system is as good as its weakest link) and broader regional or national NPIs
Again, in a pandemic it is far far better to go in hard early, get control and then take away restrictions once control is re-established. In the majority of England we don't have clear control of viral transmission and we are likely at health-care unsustainable levels.
I don't envy the people who either generate the advice here how to chart the way forwards nor the people who take the decisions.

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More from @ewanbirney

1 Nov
There are debates - important debates - to have in these COVID times, but there are some either stupid debates or misguided in my view debates. Here's my list with brief rejoinders.
1. False positives on tests are grossly inflating the number of cases. Straightforwardly they are not; the system understands false positives, goes to a lot of length to prevent them, and, acknowledging that they can never be 0, carefully models them in analysis.
2. "Hard" Stratify and Shield (or segmentation) is a solution. By "Hard" I mean placing all the at risk people in entirely COVID "safe" environments (extremely low risk of infection) and then having the remaining people at low risk live normal lives, and get the infection.
Read 24 tweets
1 Nov
It is somewhat hard to know which strand on England's November lockdown to pick apart - a large number of people in the press (and twitter) are commenting ("hot takes" in the US parlance) - most heat and not so much light.
Yesterday, before the announcement, I tweeted on this here:
Read 17 tweets
1 Nov
Can we have a ban of the use the definite article “the” with science ? Unpack to at least one level to be clear “we need to heed the dire warnings of the coronavirus infection modellers” or “we cannot ignore the impact of change in weather patterns”
“The science” implies certainty when science rarely has it (but parts of science can have high confidence - lack of complete certainty does *not* mean no very confident view) and it often socially placed science as an actor in other societal debates
Ie, rather than societal debates accepting shared facts +understanding, poking and asking questions of the science, some people think of science being allied with their point of view, often spilling over from the “understanding the world” bit to the “and so what do we do” bit
Read 6 tweets
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
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).
Read 16 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

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