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Finally! A way to analyse NHS data from 17 million people

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July 9, 2020 - 11:06am

There’s a new paper out in Nature, led by Ben Goldacre of Bad Science fame, which is really interesting. It’s been available in preprint for a month, but it has just been properly published.

For starters, it’s interesting because it looks at causes of death among Covid patients, and confirms, for instance, higher rates of death among black and Asian patients that can’t be fully explained by pre-existing conditions. It also found a muddy and confusing picture when it comes to smoking and Covid. Current smokers seem to do better than non-smokers, but this is complicated by the fact that some non-smokers will be former smokers who have quit because of smoking-related disease.

When the researchers accounted for that, the protective effect seemed to disappear.

(This is a really interesting problem called collider bias. The study controlled for lung disease; comparing smokers with lung disease to never-smokers and former smokers with lung disease, and smokers without lung disease to never-smokers etc without. But of course smoking causes lung disease! So by controlling for it, you’re removing the exact thing you’re looking for. An analogy: If you looked at whether obesity shortens life, but controlled for whether someone has diabetes, you might find that it doesn’t very much, because obesity often kills people by giving them diabetes.)

But what makes it really interesting is not so much for its findings but for its size — 17 million subjects — which is possible because of its innovative methods. In Britain, we have an incredible scientific resource: a centrally controlled health system which in theory gives researchers access to data of the entire population.

In reality, it’s not so easy, because a lot of that data, even if pseudonymised, can be used to identify patients; so there are lots of vitally necessary safeguards which make it hard to share it for research purposes.

The Goldacre et al. study gets around that by letting the data stay exactly where it is. They developed software which could be given to the local NHS trusts that kept the data; the analysis was then done in-house. The raw, identifiable data stays with the trusts; the more high-level summaries are available for other researchers. The more abstract the summary, the less sensitive it is, and more widely it’s made available.

It’s also all completely open-source, so anyone can download, use, or check the code behind the OpenSAFELY system that runs it; and, Goldacre points out to me, it “essentially forces” everyone who wants to use it for their own research to similarly share their code, which is sadly necessary sometimes.

As Goldacre says in this more in-depth examination, it would be completely unthinkable to share the data of 40% of the UK population in the traditional, download-a-dataset-and-run-analyses way. But by breaking it apart like this, doing it in-house, and making the more abstracted versions available, he and his team were able to get access to 17 million people’s data without compromising their privacy. The findings haven’t shown us anything wildly surprising, but that’s not the point; the point is this is a way of making full use of one of the British health system’s most powerful scientific advantages.


Tom Chivers is a science writer. His second book, How to Read Numbers, is out now.

TomChivers

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Adrian Smith
Adrian Smith
4 years ago

Slavery was not a British invention – it was the way things were done by powerful civilisations. Slaves built the pyramids, Slaves built Rome. I am not claiming it was right, just that was the way it was. All once great nations were built on the back of captured labour from weaker nations. Anglo Saxons women and children were sold into slavery by the Norse and Dane invaders of Alfred the Great’s time and as that tide turned, Danish and Norse women and children were sold into slavery by Anglo Saxons. If there needs to be a study of historic slavery then do a complete job of it.

So what will replace the Rhodes statue? What replaced the country named after him aka the bread basket of Africa now one of the poorest nations that struggles to feed itself? Perhaps the Rhodes statue should be replaced by one of Robert Mugabe.

northwestcarpenter
northwestcarpenter
4 years ago
Reply to  Adrian Smith

Killing myself with laughter over here. And yet if BLM suggests it who would be surprised?

Barbara Cleverly
Barbara Cleverly
4 years ago

The statue of Rhodes has a flimsy
protection. It is attached to the facade of a grade II* historic building. Historic England tell me that, after consultation with them, the final decision on removal will fall to the Oxford City Council. Make what you will of that.

Stephen Follows
Stephen Follows
4 years ago

I know Scrabble rewards spelling rather than meaning, but surely you mean ‘distracts’, not ‘detracts’?

Jeffrey Shaw
Jeffrey Shaw
4 years ago

Extra points for that. the author may have to change the title of his book when it goes to a second printing.

Brian Dorsley
Brian Dorsley
4 years ago

‘Detracts’ fits well here too.

Dave Weeden
Dave Weeden
4 years ago

Detracts seems absolutely right to me. Unherd’s subeditors (if they even exist) may have problems with the spelling of people’s surnames, but they use words correctly.

Jeffrey Shaw
Jeffrey Shaw
4 years ago

“….they find the kingdom of God in the minutes of the last meeting.” That is a brilliant observation relating to the C of E. The church has become a parody of itself and worse yet – it believes itself to be on some righteous path. In reality, its relationship to Christianity has been reduced to occasional coincidence. In North America, the Church has become something of a social club, predominantly homosexual, complete with dress-up vestments.

Jeffrey Shaw
Jeffrey Shaw
4 years ago

By and large i stop reading whenever an author invokes the thoughts of Naomi Klein.

Robin Lambert
Robin Lambert
4 years ago

London needs Another Central London Concert Venue .With Greedy development of Earls Court ..There is only Small venues like Shepherds bush empire, Cadogan hall….Actually employ British Architecs,Workforce for a Change..

Robin Lambert
Robin Lambert
4 years ago

If you see MOST ex Colonial countries now,especially in Africa they are dictatorships and Places Like Rwanda,South Sudan ,Nigeria characterised by Genocide, Famine,War and Muslim terrorists like Boca harim….Whilst not endorsing all colonial countries, Uk did try to put in Place, Parliaments and judicial system…

Caz
Caz
4 years ago

Thank you for this. It is reassuring to read such a reasoned, analytical argument against the divisive construct of ‘cultural appropriation’. If only it would be read by those who prefer to jump on the ‘woke’ bandwagon than look objectively at and learn more about the issue.

sublime5456
sublime5456
4 years ago

interesting points I will pursue later. I would argue that some subjects are better suited for decolonisation, such as Psychology and some Social Sciences. For example, much of Psychology is based on European perspectives. And, moreover, those of minority ethnicity are under represented as participants. We know that many prinicples of behaviour developed through Psychology studies are thought to be universal across humans while others are culturally and historically placed. As such, we have seen that papers from black and white scholars (and I concede I ahve only read about this in journal articles and texts) have been rejected when making conclusions about black participants tests of intelligence, for example (as far back as 1930 through to 1980s, for example) during schooling because they did not have white participants as a control group ignoring the specific cultural contexts of such studies being studies. I am unaware of any paper (and welcome pointers from other readers) that has been rejected based on majority white participants for not having black or other ethnicity control groups – white, perhaps being extreme here in my opinon, appears the deafault way of being in these studies about behaviour. A particularly infamous paper on such issues is by Henrich et al in 2010 on WEIRD participants. I would welcome more acknowledgement of scientific racism and black scholarship in mainstream social science and psychology, as scientific racism, implicit or explicit is easier to identify currently and historically in Psychology, in my opinion. But as you point out, decolonisation might be an uneccessary activity to pursue in other disciplines – and at risk of contradicting myself, some sub-disciplines in Psychology. This is how I have come to understand the current situation around decolonisation with specific reference to more ambiguous categories of study and theories in social sciences than we see in natural sciences with clearer tangible categories of its subjec matter (that is rocks and atome versus attitudes and surveys about behaviour).

Dougie Undersub
Dougie Undersub
4 years ago
Reply to  sublime5456

Most research in the field of experimental psychology uses American college students as subjects. So, if you want to reduce cultural bias you’ll have to change the entry procedures of American colleges.

opn
opn
4 years ago

It is no mistake that S. Cuthbert’s reaction to being made Bishop of Lindisfarne was to take himself off to the Inner Farne, far out in the German Ocean, so that he could pray for his people better.

K Sheedy
K Sheedy
4 years ago

Very clever approach. Great potential for value using NHS data. And other applications are possible.

A Spetzari
A Spetzari
4 years ago

Ben Goldacre’s Bad Science should be compulsory reading in schools/colleges.

Chris Milburn
Chris Milburn
4 years ago

Great article, as a doc with a hard science (physics/math) background, it is great to see a difficult subject explained in an understandable way.

Dougie Undersub
Dougie Undersub
4 years ago

I dont like to say I told you so but this approach was painfully obvious to me as soon the row about access to NHS data by Google etc hit the media. Researchers don’t need to have the data in house to run queries on it.

Dougie Undersub
Dougie Undersub
4 years ago

I always enjoy reading your stuff, Mary, and I was enjoying this until you got a bit lazy. Which continents’ inhabitants, exactly, did the British Victorians enslave?

Simon Forde
Simon Forde
4 years ago

I hear very little of late about the earlier English involvement in the human slave trade. As Bede writes in Bk II, chapter 1 of the History of the English People:

Nor must we pass by in silence the story of the blessed Gregory, handed down to us by the tradition of our ancestors, which explains his earnest care for the salvation of our nation. It is said that one day, when some merchants had lately arrived at Rome, many things were exposed for sale in the market place, and much people resorted thither to buy: Gregory himself went with the rest, and saw among other wares some boys put up for sale, of fair complexion, with pleasing countenances, and very beautiful hair. When he beheld them, he asked, it is said, from what region or country they were brought? and was told, from the island of Britain, and that the inhabitants were like that in appearance. He again inquired whether those islanders were Christians, or still involved in the errors of paganism, and was informed that they were pagans. Then fetching a deep sigh from the bottom of his heart, “Alas! what pity,” said he, “that the author of darkness should own men of such fair countenances; and that with such grace of outward form, their minds should be void of inward grace.” He therefore again asked, what was the name of that nation? and was answered, that they were called Angles. “Right,” said he, “for they have an angelic face, and it is meet that such should be co-heirs with the Angels in heaven. What is the name of the province from which they are brought?” It was replied, that the natives of that province were called Deiri.

andrewlukecolquhoun
andrewlukecolquhoun
4 years ago

Like a holy Rory Stewart

Michael Whittock
Michael Whittock
4 years ago

“Yet if England is one day to be re-evangelised it will be because of the power of lonely places like this”. This could do with unpacking. I’m assuming it’s a call for Christians, especially leaders to become more deeply prayerful and reflective which retreats to quiet places can enable. The evangelisation of Britain will only take place when God acts in judgement and grace in people’s lives causing them to be open to the Gospel of Jesus Christ, and that requires faithful persevering prayer on the part of the Church. Christian leaders need to sink their spiritual roots ever deeper into God for spiritual resources and sustenance for the task. Occasional visits to lonely places are conducive, but I prefer the Highlands of Scotland in the steps of St.Columba than the Essex salt flats.
“Financial pressures stimulates panicky initiatives with inviting sounding names”. Why is it that the Church has such dire pressure? It is because churchpeople do not give enough. Why do they not give enough? Because they have not been taught the Biblical principles of giving. Where that does happen churches tend to flourish and find themselves subsidising struggling churches where there is often no vision, mission or growth. Also these flourishing churches apparently stimulate (not by financial pressure but by commitment to evangelism) “panicky missionary initiatives with inviting sounding names” like Alpha, Messy Church and other types of Fresh Expressions. These and other ministries such as imaginative and contextual evangelism in baptisms,weddings and funerals are the main reasons why there is any meaningful church growth in the Church of England.
“You may believe that this “professionalisation” is a good thing- but it is extraordinary that the church has been transformed by it with very little reflection on its virtues”. The professionalisation of the Church began in the 2nd.century when the functions of the bishops,
presbyters and deacons were gradually defined. The growing and flourishing churches embrace those distinctions but also work hard at encouraging every member ministry believing that every church member has gifts and anointing from God for particular ministries in and through the church.
It’s easy to be critical of the administration of the Church. Those involved in its bureaucracy see themselves as serving the Church, and of course they do. Otherwise,amongst other things, the clergy wouldn’t receive their stipends and have their free houses maintained.

David Brewer
David Brewer
4 years ago

The whole question is absurd. Words written down are not obscene or offensive in themselves. The word ‘n****r’ in isolation does not degrade anybody. There needs to be some context. A Scrabble board is isolated from the real world.

As a side note, I also disagree with the idea that a serious Scrabble player should be uninterested in meaning. Getting the most points might be the aim of the game, but some combinations are more elegant than others, and the beauty of a word or combination of words increases with a knowledge of the meaning of the words. (Many great athletes are admired for their artistry as much as for their victories.) It is a pity that the rules of Scrabble don’t at least require players to have to show they understand the meaning of a word by giving a definition or a suitable sentence containing the word when challenged. There could be a bonus score if the challenge is met.

David Brewer
David Brewer
4 years ago

The whole question is absurd. Words written down are not obscene or offensive in themselves. When used in isolation, racial and other epithets, blasphemous words, and common words for bodily functions and body parts do not do not degrade anybody. There needs to be some context. A Scrabble board is isolated from the real world.

As a side note, I also disagree with the idea that a serious Scrabble player should be uninterested in meaning. Getting the most points might be the aim of the game, but some combinations are more elegant than others, and the beauty of a word or combination of words increases with a knowledge of the meaning of the words. (Many great athletes are admired for their artistry as much as for their victories.) It is a pity that the rules of Scrabble don’t at least require players to have to show they understand the meaning of a word by giving a definition or a suitable sentence containing the word when challenged. There could be a bonus score if the challenge is met.

Jean Redpath
Jean Redpath
4 years ago

The smoking finding is very important to South Africa, where government has banned the sale of tobacco and related products ostensibly as a Covid-19 prevention-and-seriousness reduction strategy, for the duration of lockdown – 100+ days and counting.

I understand how the authors try to explain away the findings, but essentially what the results seem to say, if you already have lung disease (possibly from smoking), then you are better off in relation Covid-19 if you keep smoking.