Ewan Birney Profile picture
Oct 3, 2020 16 tweets 3 min read Read on X
For COVID watchers, in particular journalists, a primer (again) to get you through what - best case - will be a bumpy month and could possibly be going the wrong way on the numbers.
(Context: I am an expert on one area - human genetics/genomics; I am one-step-away from experts in other areas; I have one substantial COI on testing in that I'm a long established consultant to Oxford Nanopore which has made a new COVID test)
I will keep banging this drum - your (and government's) solid ground is hospitalisations and random sampled surveys (REACT and ONS in the UK; I think there are equivalent in France and Germany; could French and German pros respond. I don't think there is a regularly one in Spain)
Not only do daily numbers go up and down due to all sorts of reporting fluctuations (it is super hard to do this; don't confuse an easy to use/download website into making you think it is easy to even get the numbers) but also testing strategy is now broadening out
For example, there is more asymptomatic testing (healthcare workers, care home workers, universities) though at different cadences. The presence of more back tracing (enhanced tracing in UK speak) means opportunities for targetted local asymptomatic testing.
Asymptomatic testing is ideally closing the gap between estimated cases (from surveys etc) to known (with isolation etc). In contrast, testing capacity and logistics issues (people unable to get a test) means tests are being rationed or prioritised in often changing ways.
In this case, it is perfectly possible lower case numbers reported on a day is about a change in capacity/logistics and how that interacts with previous test seeking behviours (mandated or encouraged).
So - where possible - stick to your solid ground, and say wisely "we will have to wait for the next ONS survey".
Some other things which I think don't get enough attention in the UK context:
1. Northern Ireland. Because the surveys often don't reach there we have a less rounded dataset there, but the case data does not look like it is going the right way.
2. The regionality of UK rise in cases, and the regionality of control (North West is a big region, and you want to get inside of Bolton/Liverpool/St Helens etc). Frustratingly having argued you should know your solid ground, you have to go off case levels numbers here.
3. Contact tracing - these are the hard yards of infectious epidemiology both in call centres who know what they are doing and also house-to-house in high areas. I am now at a two-steps-away expertise zone from this, but lots of hard work to do well here.
4. Isolation support and isolation compliance. It is a key part to this phase and there is no point testing and contact tracing if the action is not there. Again, I think working this out from London/Hampshire zoom calls is not the same as a Manchester/Newcastle perspective
How many people isolate? Changing their behaviour alot is probably as important as "not seeing anyone at all" - but what do people actually do? For the people who do less, why is it in a "how do we make this work for everyone" way?
I'm afraid my understanding of French, German and Italian contact tracing and isolation is poor, beyond that Germany really seems to do it well (Go Germany!) and I think Italy has really improved from March (Go Italy). French feels, from afar, similar to UK.
Spanish is always super-complex because here there is no "Spainish" way - there are the regional health regions with plenty of variance in approach; also makes understanding it from the outside super-tricky. I hope Madrid and other hot areas in Spain get it under control.

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More from @ewanbirney

Oct 13
So @JeremyFarrar asked for an "explainer thread" on Noble Prizes in Chemistry around AlphaFold and Protein design, so here goes.
First off, this is an old problem. It starts with observations in the 1950s/1960s, leading to a Noble Prize in 1972 to Anfinsen, Moore and Stein where in particular Anfinsen convincingly shows that the particular sequence of amino acids in a protein determines its 3D structure
Just to visualise this; think of amino acid chain as different sorts of beads on a string. The beads come in 20 types - some type like to stick to other types; some types like to be hidden away from water; some are small and some are large. A protein is somewhere around 50 beads
Read 46 tweets
Sep 3
Great to see this paper out by @D_Westergaard and colleagues - including myself - leveraging the just jaw-droppingly good combination of the Danish pedigree data (across the entire country!) and their highly detailed EHR. nature.com/articles/s4146…
This is pedigree based genetics - the correlation of phenotypes (in this case diagnoses of diseases) - as was done in the 1910s - formalised by RA Fischer and S. Wright from ideas at the turn of the 20th Cent.
This concept of the correlation of phenotype to pedigree predates the identification of DNA as molecular mechanism for inheritance - this is old school genetics updated in the modern age.
Read 24 tweets
Sep 1
One of the more depressing things re-engaging on social media is the undercurrent of pseudo-scientific racism which continues to pop up with exciting data rich plots, often lots of maths and just lots of class A bullshit justifying tired anti-woke (but just ol' fashioned racist)
I'm not going to amplify the crappy threads/blogs/messages forwarded to me, but I do want to arm my followers with the most cogent arguments against this if this does come up in conversation around you.
First off, humans are a super-young species - we exploded out of Africa very quickly and although lots of the details we still don't know (and the science changes quickly) it's pretty clear we adapted to the changing environment main by behaviour
Read 27 tweets
Jul 24
A reminder ( it’s an evergreen topic) - humans are a genetically undiverse species - we exploded out Africa in a heartbeat of evolutionary time and we predominantly adapted to the multitude of environments by our behaviour, passing that knowledge down culturally in groups
Although there are genetic adaptations to some environments- eg lack of sunlight (fair skin), regular milk consumption (lactase persistence) or reduced sweat for humid environments (less sweat pores and thicker hair) these have two features
Firstly these adaptions are sparse in the context of the genome - its small regions which do this
Read 8 tweets
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

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