Ewan Birney Profile picture
Oct 1, 2020 7 tweets 1 min read Read on X
Today was a good day for the UK COVID numbers; The solid(er) ground of the REACT survey indicates slow growth of this set of infections (along with other things - see my thread) + the testing system capacity is up and turn around time is back(ish) to summer levels.
This is a tribute to the public health (both local+national) in the North West and North East, the forbearance of the people living in these lockdown regions and, for testing, the hard work of Pillar1 + Pillar2. Total respect for everyone involved.
*however*
Pausing / plateauing growth is a fragile situation; one would like to suppress the virus down to at least some lower levels *and* we have more contact pattern changes to feed in with universities and also a severe risk of temperature+ weather changing how transmission rates.
Plus, I'd highlight that Northern Ireland (Derry) and Glasgow look less controlled to my amateur eyes at the moment. We are going to have, best case, a slightly edgy month watching numbers I hope bump down. I bet it will be bumpy.
On the future positive side, the testing capacity build out is not done yet - more to come I suspect (and promised!); the App has probably not been fully used; more focus on the fine details of back-tracing with action (a long standing drum I beat!) and supporting isolation.
To navigate numbers, remember the solid ground is the REACT survey, the ONS survey and hospitalisations. Other daily numbers are complex to pull apart (even for the pros) and full of complex reporting lags, biology lags and also ascertainment issues.

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More from @ewanbirney

Apr 2
A short, personal thread on what is odd about other cultures when interacting with Brits, and then also what I think is odd about Brits when interacting with other cultures - highly, highly personal, but from >30 years working internationally.
German+Dutch do not have to preface a challenge with "I think you might have missed something..." or some other British-style softening up. It is entirely fine - indeed polite/shows respect - just come out "you are wrong because X,Y" - this directness is surprising for a Brit.
Northern (Protestant/river/Prussian) Germans are very different from Southern (Catholic, Mountain+Forest) Germans. Don't confuse them. External stereotypes of Germans (in particular in Britain) is a weird mixture of both and you have to untangle this.
Read 20 tweets
Feb 20
The publication of the whole genomes from the US @AllofUsResearch cohort is great to see, but the choice of how to represent an overview of the genetic relationships has (rightly) drawn controversy, in particular how the concepts of ethnicity and race are mapped to it.
This is not in bad faith - the AllofUs cohort should be applauded in its diversity push and much of the but it is an illustration of the messiness of genetics and the inability to represent our complex relationships in any 2D space. Longer thread below>>
A reminder that genetics (the variation in DNA sequence passed down from your parents, +their parents etc) and race or ethnicity (a box people tick on surveys or on census) are quite different concepts, strongly linked only by visible features which are genetic, eg, skin colour
Read 28 tweets
Jan 19
Next monday is 4 hours of preliminary grant reviews - a necessary but intense part of being a scientist who goes through peer review is being the reviewer. As ever, I am rather amazed by scientists who make simple mistakes in their proposals. My thoughts for a good proposal:
For me as a reviewer you need to convince me of 4 major things. >>
1. Is the problem important/interesting? 2. What has changed in the last ~five years that means an important/interesting problem can now be tackled? 3. Can you actually perform the science? Is it likely to fail? 4. Why are you one of the best people in the world to do this?
Read 18 tweets
Dec 10, 2023
It is a dark, drizzly december sunday in London and I've just read yet another depressing thread of someone reaching for genetics to justify racism and superiority to themselves. It is deeply wrong, but such a recurrent thread worth both dismantling+ understanding the attraction
Let's dismantle first; although a feature of ethnicity/race is skin colour and other visible features, and although these have strong genetic components, counter-intutively for most people, ethnicity is *not* a good predictor for genetics
(certain manipulations of genetic information are reasonable predictors of ethnicity in a single country setting but the reverse is not true; the genetic space is far more high dimensional than these crude ethnicity labels, and it all breaks down when you go global)
Read 25 tweets
May 21, 2023
Here is the slightly cheesy montage for the great #nanoporeconf for 2023 - and, with a reminder of my conflict of interest - I am a longestablished paid consultant for Oxford Nanopore and a shareholder - here are my thoughts on the conference.
For long time nanopore scientists -and I am definitely one of those- one can definitely both plot progress London Calling conference (on the Thames in London) both in terms of what the company presents as near and long horizon+how the plenary speakers use and talk about nanopore
From the company side, much of this was giving a roadmap of key software and flow cells; the R10 flow cells (which is a distinct step up in quality) are now routine; what is not yet is high yield duplex which has being moving from Oxford to Alpha to broader Beta testers.
Read 34 tweets
May 21, 2023
My friend and economics/ markets guru @felixmwmartin commenting on super human AI and all too human market behaviour - on the money that AI will transform many things (science included - it has started in earnest) but also more broadly in the economy
Economics and biology are closer in data science than you might think - in particular micro economics and observational human biology aka epidemiology. Plenty of differences but lots of overlap as well, eg biased sampling, many hidden confounders, clearly correlated variables
A deeper issue is the need to understand causality / intervention- if I enacted this policy or provided this drug what would happen next. Finding the golden causal threads in the tangled Gordian knot (hairball?) of correlation is a common challenge shared by biology+economics
Read 6 tweets

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