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Ewan Birney

@ewanbirney

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

Ewan Birney

@ewanbirney

25 Oct

There are a variety of ultimately “don’t worry about the trajectory of COVID in the UK arguments” from mainly right wing commentators that are either plain wrong or missing the point for me. A list and key rebuttal arguments:

1. Observed cases are false positives due to higher testing levels. Plain wrong - false positives exist but they are at a low level and managed well by the system.

2. COVID as a disease has replaced influenza as the winter virus and should be handled in the same “tolerate elderly deaths” way. Wrong in that the death rate and other long term disease is far higher. Influenza levels have dropped due to the measures to stop infection generally

Read 12 tweets

Ewan Birney

@ewanbirney

24 Oct

Taking stock of COVID in October - for followers, in particular journalists. My scope is broadly across Europe, with a particular focus in the UK.

Context: I am an expert in one area - human genetics; I have broad data science / data analysis skills; I know experts from virus genomics, testing, infectious epidemiology and clinical trials; I am someone who deals with uncertainty by aiming to gain more knowledge.

I have one major conflict of interest in that I am a long established consultant to a company (Oxford Nanopore) that makes a new SARS_CoV_2 test. It's not so relevant in this thread, but it's worth knowing if you are reading stuff from me for the first time.

Read 36 tweets

Ewan Birney

@ewanbirney

23 Oct

For my American colleagues - I don't have a vote and I have enough respect for democracy to realise that reasonable people can disagree with my opinion - but I urge you to above all vote and, if I was American, my vote would be clearly for Joe Biden

I say this as someone who had exposure to American politics in a nicer time, when "bleeding heart Republicans" and "fiscally conservative Democrats" could hammer out compromises that pushed cities, states and the country forward.

America has flaws, some feel very deep and increasingly raw such as the long journey to a new America that respects all its people inside it, and can truly leave racism in the past. Just bridging that divide alone would mean if I was American, I would vote for Biden

Read 7 tweets

Ewan Birney

@ewanbirney

4 Oct

My two endless complaints on grant reviewing (a) funding agencies, stop with the insane multiple assessment axes. There are perhaps two or three (science vision/excellence, feasibility, competition) and some yes/nos (ethics, data management etc). Focus on overall narrative

(b) Authors; please please do a power calculation, however light and talk about it. *I* am doing back of envelope power calculation on your grants because you haven't done it and *I am sure* you would do a better power calculation than me.

A reminder - power calculations are not a guarantee things will work out. But it means you can't just pretend you will get an answer with (...give me strength...) 4 vs 4 mice.

Read 5 tweets

Ewan Birney

@ewanbirney

4 Oct

A primer (journalists, part written for you) on false positives and why you should (a) know about them but (b) feel confident the system does the right thing for them in a SARS CoV2 world.

False positives is when someone who does not have the thing of interest (in this case, "SARS CoV2 infection") is reported positive by a test. When one does things at the scale of 100,000s, *everything* has a false positive rate, the question is do you understand it+manage it

Just to make this confusing there are different types of false positive for any test, this included. There are samples swaps/tracking errors (very rare but not 0) - this flips a sample in the system, and one of the flips is positive. There is lab contamination (again super rare)>

Read 24 tweets

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