To the sea

With emails running alongside, barking for attention, we beat a retreat from London. The clamour of work was soon swamped by the heat and light and sights and sounds and smells of Barcelona, and by the newness and oldness of it all. In the evening as we wandered the narrow streets in a desultory Google search for a restaurant, the continental warmth seeped into our bodies like a muscle relaxant.

Spanish scenes

All that night and all the next day the city wrapped us in its hot bright charms. We let ourselves be taken away by the saturated colours of the Mercado de La Bouqueria, the vertiginous splendour of La Sagrada Familia, and Picasso’s singular view of our misshapen world.

Spanish scenes

La Sagrada Familia

Spanish scenes

And then we were gone, swept by the train to Cadaqués and to the sea to be with friends and family, to laugh and eat and swim and sit, and to try to remember why it is we go to work so much of the time…

Spanish scenes

…when there is all this.

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Message for my reader

For the longest time I have been meaning to get back to—ugh!—blogging. Regular readers, should any remain, will see that this is the first post of 2022. I haven’t broken any promises with the hiatus and have no excuses to make.

Empty chair

I’ve been busy. I know – who hasn’t been busy in UK academia? Nevertheless, the first half of this year was intense, with several major deadlines that left little mental spare capacity. Plus I’m not getting any younger. I think my recovery times may be lengthening – I don’t remember always being this tired at the end of every day. And then there is the wearisome effects of the ongoing disaster of UK politics, which passed through its latest crisis in this past week with the resignation of Boris Johnson. The runners are now lining up for the next one as the Conservative party leadership contest gets under way. Ho hum. Plus ça change. Perhaps age is making me more cynical. Or is it experience? Added to all this is a feeling, no doubt exacerbated by social media, that there are just too many words spewing forth into the world these days. Why add to that?

And yet, and yet, there are important things to think about. I’ve always regarded blogging as a form of thinking out loud, a discipline that forces me to do my research and get my thoughts in order on a whole range to topics. I’ve missed the rigour of that process.

So here goes, again. Though not just yet. My aim is to keep things short for now. So let me leave you with someone else’s thoughts. Here is Brandon Taylor’s substack post – apparently that’s what we call blogposts these days – on Netflix’s adaptation of Jane Austen’s Persuasion. I haven’t seen the show or read the book (yet) but I do so enjoy Taylor’s ability to write in a style that manages to be loose, funny and razor sharp.

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Books of the Year

One final look back before I turn to face 2022. Following a practice started last year, I have maintained a thread of tweet-sized reviews of the books that I read in 2021 – all of them.


The Twitter thread of the books I read in 2021. Click on the image to see the high-res version.

There are only eighteen in total, a singularly unimpressive tally – fewer even than I managed in the first year of the Covid-19 pandemic. The only thing I miss about my commute is the loss of a regular slot for reading during the working week. Although life settled into a wearisome rhythm while working from home, the time gained from not taking the bus and train into London was not recovered for reading. Clearly, I lack discipline.

Even so, there was a decent level of diversity within my 18 titles – around 36% were written by women and 31% by Black or minority ethnic authors. I like to think I’m not too old to have my mind broadened. However, only three of my reads were novels and while my non-fiction selections demonstrate — I hope — a reasonable breadth of interest, most of those are rooted in history, and scientific history at that.

So much for numbers. Quality should usually trump quantity and this year’s titles have afforded me a great deal of pleasure and insight. While I have long been a fan of Marilynne Robinson, Jack seemed to take a while to reach the deep resonances that I recall from the opening pages of Gilead, the first instalment of her Iowa novels. Zora Neale Thurston’s Their Eyes Were Watching God, written over eighty years earlier, was a fresher and more impactful encounter.

As for this year’s non-fictional forays, Obama’s A Promised Land and Power’s The Education of an Idealist both provided terrific insights into the challenge of trying to do some good in the world through politics (as did Michael Barber’s more practical tome, Accomplishment). I was also gripped by Ananyo Bhattacharya’s prodigious biography of John von Neumann (The Man from the Future) and by Spike, Jeremy Farrar’s and Anjana Ahuja’s blistering account of the Covid-19 pandemic, while Matthew Cobb’s The Idea of the Brain gave a fascinating and sobering view of our faltering attempts to understand that most precious organ.

The most important book I read this year was Shon Faye’s The Transgender Issue which brought much needed cool-headedness – and a human heart – to a topic that seems only ever to be debated in screams on social media.

But my favourite of the year has to be Ian Dunt’s How to be a Liberal, a rich and thoughtful exploration of the development of liberal thought over the past several centuries. It’s a strand of thinking that seems to be under relentless assault from the populists who have taken centre-stage for the moment, but Dunt’s book ably demonstrates that its roots run deep. So we might still hope for another flowering.

Happy new year, everyone.


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Photographs of 2021

Continuing the theme of gently exercising the writing muscle by composing posts made mostly of pictures, I present here the round-up of what I think are the best photographs that I took in the past year.


2021 has been a tad leaner than last year on the photography front because the longeurs of lockdown took a firmer hold, mentally and physically. Being confined to working from home for much of the year and having scant opportunity to travel beyond these shores might have dulled the appetite and reduced the variation the world has to offer, but looking back I find my eye isn’t quite so jaded as I feared.

There’s a small selection below but the full album of 65 photographs can be found on flickr.



Photos-of-2021 - 70


Photos-of-2021 - 72


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In the garden

What is it about living through a pandemic that has quelled the motivation to write? I suspect it may have something to do with the unstructuring of time, or rather its reduction through confinement to rhythms dulled by repetition. Whatever the reason, a quick glance through the log of posts here over the past year reveals a loss of activity – or is it a loss of discipline? I am faintly troubled by the notion but still only in a place to regard it obliquely.

Garden-Animals-2021 - 7

For now, I will take an easy way out by relying more on pictures than words. Here below are some of the birds and animals I photographed in the garden in 2021. Normally, my camera roll of the year would provide a kaleidoscope of travels, my view this twelve month has mostly relied on the local fauna for variation. I am grateful to them.

Garden-Animals-2021 - 26-28

Garden-Animals-2021 - 19

Garden-Animals-2021 - 17

Garden-Animals-2021 - 29

Garden-Animals-2021 - 15-16

Garden-Animals-2021 - 10

Garden-Animals-2021 - 14

Garden-Animals-2021 - 22
Garden-Animals-2021 - 33

The full album (31 photos) can be found on flickr.


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For my mother

Black masked, weighed down by grey grief,
We carried you into the church
To be wrung out of our sodden farewells.
But you had already gone.

It was a slow journey to that sombre altar.
In the last years the traces that bound us
Stretched and frayed
As Nature’s cruelty took hold.
We had already said the longest of goodbyes
While your mind darkened and your hands stilled.
There was time enough to remember happier days
Surrounded by grandchildren,
Bustling in a kitchen warmed by the smells of baking.

In that same kitchen you tended to us,
Your children, with the food of love.
Through laughter, anger and tears,
You were our constant consolation.

Your body spent, drained of the devotion
That bathed us all our lives,
You have departed this love-dimmed world.
But your star shines on
In every one of our hearts.



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A Reckoning with Huxley’s Legacy

Recognition and Redistribution for Imperial College’s Community

This is a guest post by my former colleague, Dr Rahma (Red) Elmahdi, in which she lays our her reaction to the Imperial College History Report, and in particular the recommendation to rename the Huxley Building. I am grateful to Red for allowing me to share her perspective.  


Red making her case in a group discussion

As a former student and member of teaching staff at Imperial College London, I was excited to finally read the Community Report from the College’s History Group, released earlier this month. Despite no longer studying at or working for the College, I consider myself a continuing member of its community, having spent over a decade (including some of my most formative years) learning, teaching and researching there, even spending five years living and working at the College as a subwarden in student halls of residence.

In the last few years of my time at Imperial, I became increasingly involved in ongoing efforts for progressive change for equity, diversity and inclusion, particularly working with Black and Minority Ethnic (BME) groups in the College to increase representation and foster a stronger sense of identity as members of the college community. Efforts such as these are usually uncontentious and considered a reflection of an institution’s commitment to improving the lot of the underrepresented groups who study and work there.

In keeping with these efforts, and following the lead of many international universities in exploring the roots of structural discrimination in their own institutions, Imperial commissioned the work to “report on the current understanding and reception of the College’s legacy and heritage in the context of its present-day mission”. Among the recommendations of the report, which was supported by two independent external Russell group advisors, was the removal of a bust of Thomas Henry Huxley (first Dean of the Royal College of Science, renowned 19th century naturalist and principal defender of Darwin’s theory of evolution) and the renaming of a building which currently bears his name. This recommendation was made because Huxley used racial divisions and hierarchical categorisation in his work that might now be called ‘racist’. Despite being only one of many recommendations put forward by the report, this stirred the most media attention and the strongest criticism of the History Group and the College as a whole. Headlines in online newspapers from across the political spectrum accused the College of giving in to wokery, erasing its history and effectively besmirching the name of one of the UK’s greatest scientists and educators who was even a known slavery abolitionist.

Making sense of the criticisms of recommendations such as this are never easy. Even for those of us who are genuinely trying to engage in our shared history with the intention of learning from the past for progressive future change, it often boils down to an issue of ‘recognition or redistribution’, to quote Nancy Fraser. After all, how can the renaming of a building or removal of a bust of a man (who most students and staff only have a vague notion of anyway) help with the challenges experienced by black and brown students today?

Speaking as a black woman, (and I think my identity matters here) I think that this has everything to do with these challenges. If Imperial does not honestly contend with its history of racism, it makes it easy for Black students and staff to continue to feel excluded, and othered in their own institution. I appreciate and value the work of the History group and take its recommendations seriously for this reason. Providing more opportunities for talented Black students to gain good degrees from a university with a history of racism, without acknowledging the deeply exclusive historic (and ongoing practices) of that university, does not allow us to move forward honestly. Therefore, I believe that between recognition and redistribution, a reckoning is necessary for reparation.

The challenge in the criticisms here can be surmised as two questions. 1) Is it morally correct for the College to continue to honour Thomas Henry Huxley (and by proxy his racist views)? 2) How do we contend with the fact that the bricks and mortar of the building (regardless of what it is called) is part of an intellectual legacy of dehumanising Black people at Imperial that cannot be undone?

I admit that the latter is far more important for both the education of all staff and students and for fostering an understanding of minority staff and students’ struggle in the correct context. We cannot change where the money to build our institution came from or what the product of the research undertaken in it has meant for the lives of countless people deemed scientifically inferior by the likes of Huxley. We can however attempt to highlight the legacy of Huxley’s work and the role Imperial has had to play in creating ‘evidence’ for racialised exploitation under empire, through the lens of those affected.

The first of my two questions is an easier one for me. The purpose of naming a building after someone is to honour that person. It is paying homage to their work, what they contributed and what they stood for. Whether that is ever a good idea is another question, and I think Gary Younge has made a very persuasive case that it isn’t. There is no one person in history who has held perfect morals by modern (and changing) standards of acceptability and so perhaps there is no use in honouring anyone with a statue, bust or by naming a building after them. Racist views however are clearly not something we should want to honour at the College “in the context of its present-day mission” and I think it is an insult to the Black people who continue to work and study in a building named after a person who was so adamant in questioning their capabilities and equality.

We all understand why the Imperial College Business School was renamed from Tanaka, so why is it so different in the context of Huxley? No one accused the College of ‘Cancelling Tanaka’ but isn’t this the same thing? We are not obliged to preserve, in reverence, the names of slavers, oppressors or racists and if we do so in the name of ‘history’, we are doing a deep disservice to those who suffered because of Huxley’s views and the work he produced. What is worse, we are contending that, at one point in time at least, racism and sexism were fine. Just because some views and actions were historically commonplace, it does not mean they were correct and they were certainly never correct in the minds of those who suffered because of them at the time (or continue to suffer because of their legacy). This line of argumentation only serves to continue to normalise sexism and racism by insisting that they were once acceptable. Acceptable to whom? Certainly not to me or to those like me who Huxley deemed inferior.

One of the more interesting and surprising critiques of the report came from Kenan Malik in an Observer article where he likened Facebook’s recent rebranding to the recommendation for renaming the Huxley building. This parallel is unhelpful for many reasons, but particularly because the arguments for maintaining the building’s name and the place of the bust essentially boil down to ‘white supremacy was normal in Victorian England’. In itself this is unimportant for Black staff and students living with Huxley’s legacy at the College today. The interests of intellectual classes of Victorian Britain fall outside of the remit of the History Group. Malik also reasons that Huxley was not as big a racist as say, 18th century slave trader Edward Colston, and that by “damning both equally as racists who do not deserve commemoration is to abandon historical evaluation for a crude mode of moral judgment”. This argument in particular misinterprets the entire notion of racial equality. Just because Huxley’s work or views did not directly subject black people to violent degradation and exploitation in an utterly dehumanising system for economic gain, does this mean that they were not racist? It is the same argument that those who misunderstand calls for equality make when they equate bigotry and racism, disregarding systemic contributors to the discrimination experienced by Black people every day.

Huxley’s contribution to scientific racism has arguably had a far more profound and longer-lasting impact on racial discrimination than slavery alone. Although Huxley disagreed with the application of his work to Social Darwinism, and was no advocate of eugenics, his belief in the deterministic significance of his system of classification of the “higher and lower races” (which he states in his essay Emancipation: Black and White), were undoubtedly significant contributors to the formalisation and normalisation of scientific racism and its subsequent applications. It would have been much harder to create and maintain systems of racial domination without the validation of scientific racism that men such as Huxley helped create and perpetuate.

Ultimately, I am not only in support of the work undertaken by the History Group but also in agreement with their recommendations. Whether or not Huxley’s name remains attached to the mathematics and computing department building, the College must actually identify, disseminate and educate on Huxley’s legacy through the lens of those harmed by his work and that is the reckoning. Without this, there can be no recognition, and the value of redistributive efforts will not be fully realised. These efforts, which include increasing access to Black students from disadvantaged backgrounds to the opportunities that an education from an institution like Imperial can provide, as well as improving retention and career progression of the existing Black staff in the College, are absolutely essential. We need both to address historic legacies of injustice.

You can’t have a true attempt at reparation of institutional discrimination without doing the uncomfortable work of explaining why it was necessary to start with, who lost out, who was exploited and who continues to be excluded as a result of scientific racism. This means exposing Huxley’s contribution to racist injustice and acknowledging how Imperial benefited from this. It is one knot among many to disentangle in the complex web of historical injustice across British society that we all remain caught up in today. But it is at least one knot less.

Red is currently a postdoctoral researcher in the Department of Clinical Medicine at the University of Aalborg, Denmark. She can be found on Twitter as @RahmaElmahdi.


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The Huxley Question

Writing in The Observer a couple of weeks ago, Kenan Malik cast a sceptical eye over a report published by the history group at Imperial College that had been asked to reflect on “the current understanding and reception of the College’s legacy and heritage in the context of its present-day mission.” Linking the report’s controversial recommendation that that the Huxley Building be renamed because of Thomas Henry Huxley’s views on race to the recent rebranding of the Facebook parent company, Malik wondered if Imperial’s historical self-examination was more of a PR front than a serious attempt to address race inequalities.


Thomas Henry Huxley – keep clear?

I have long been an admirer of Malik’s newspapers columns and books. His rigorous and thoughtful analyses of the questions thrown up by identity politics are almost unparalleled in the mainstream media and his superb book, The Quest for a Moral Compass, is one that I turn to regularly when thinking about equality. So, it is uncomfortable to find myself somewhat out of alignment with him on the Huxley question.

But I think I can illuminate the gulf between us and venture to suggest that is may not be as wide as it first appears. I should start by declaring my hand: although I am writing here in a personal capacity, I am presently the Assistant Provost for Equality, Diversity and Inclusion at Imperial College and served as an advisor to the history group alongside a diverse range of colleagues and a couple of historians who are external to the university. I have worked at Imperial College for over twenty-five years, several of which were spent in an office in the Huxley building without giving the great man a great deal of thought.

Malik raises important challenges for Imperial in his article. He cites Nancy Fraser’s warning that too often “cultural recognition displaces socio-economic redistribution as the remedy for injustice and the goal of political struggle” and goes on to ask “in what way would removing Huxley’s bust and renaming the hall improve the lives of minority students at Imperial College?”

That’s a fair question. The answer comes in part from Fraser herself. Addressing her own warning, she writes: “we should see ourselves as presented with a new intellectual and practical task: that of developing a critical theory of recognition, one which identifies and defends only those versions of the cultural politics of difference that can be coherently combined with the social politics of equality.” In essence, if I have understood correctly, Fraser is arguing that the cultural and practical impacts of inequality must be addressed together and this is the approach that, in my view, Imperial is striving to achieve. Malik has overlooked the fact that the history group report is part of a broader effort at the university to identify and dismantle barriers to race equality. This includes ambitious targets to address the under-representation of Black undergraduate students at Imperial, which is supported by substantial financial investment, and serious commitments to a slew of practical and cultural actions in support for ethnic minority staff and students (e.g. on recruitment, career progression, curriculum development) that have been developed using the Race Equality Charter (REC) framework.

The REC action plan has been worked up through lengthy and wide-ranging discussions with our community and the leadership team. These will now continue as staff, students and alumni enter into a period of dialogue on the recommendations of the history report, which will inform the College’s final decision. Together these strands of work have given the university a clearer view than ever before of the race inequalities that persist at Imperial, but it has also helped to raise awareness of the issues of race and racism right across the organisation. Ultimately, the university should be judged on the success of the actions taken to build a truly inclusive environment for staff and students.

For now, much of the discussion remains centred on Huxley, whose case raises the thorny matter of how figures from the past should be judged by modern standards. Malik rightly highlights Huxley’s scientific standing and his progressivism on many issues: he was a proponent of women’s education and avowedly anti-slavery. He revelled in taunting the white supremacists of his day even if he clearly believed in their racial superiority: “no rational man, cognisant of the facts, believes that the average negro is the equal, still less the superior, of the average white man. […] The highest places in the hierarchy of civilisation will assuredly not be within the reach of our dusky cousins.”

In Malik’s view, the recommendation to rename the Huxley building because such views “fall far short of Imperial’s modern values” is to damn Huxley “primarily as a racist”, “to warp both the past and the present” and to “abandon historical evaluation for a crude mode of moral judgement.” Respectfully, I would like to challenge that assessment.

To remove a name from a building is not to damn someone. We will remember Huxley; he is an inextricable and ineradicable part of our history. It’s just that his part in our history is more complex and has troubling resonances with members of our minority communities than we had previously appreciated – and I think we must address that. For what it’s worth, I would favour keeping the bust of Huxley within the building but in a glass case as part of a display that discusses his history and a narrative accompanying the renamed building, should that be what the College eventually decides to do.

I agree with Malik on all the difficulties that attend the evaluation of figures from history by today’s standards. But we should not discount the power of their reach into the present. Huxley is a figure I have long admired – I have even described him in a public lecture as one of my scientific heroes. I came across his views on race years ago when I read Adrian Desmond’s magnificent biography, but what strikes me now, after listening to Black colleagues and students talking about how Imperial’s honouring of Huxley impacts their sense of belonging to the university, is how little I was struck by them at the time. My Black colleagues’ views on history are inflected with the power of experience and need to be heard. As one put it pithily in questioning the argument that Huxley’s views on race cannot be judged by 21st Century standards because they were commonplace in Victorian Britain, “it does not mean they were correct (and they were certainly never correct in the minds of those who suffered because of them at the time)”.  For white men like myself and for institutions like Imperial, an honest confrontation with history must entail a letting go of power, a greater responsiveness to the legacies of European racism, and a willingness to tackle its enduring cultural and economic effects.

The aim of the university must be to present a more complete picture of its history to everyone in our community. The controversy over the proposal to rename the building has had the happy effect – thanks in part to Kenan Malik – of raising the matter for discussion in the public domain and drawing attention to aspects of Huxley’s history that have been overlooked. But no one is being cancelled here, however difficult the ongoing process of grappling with the past. Our conversation with history has sprung to new, argumentative life and this is exactly the sort of free and critical enquiry that universities were created for.

Posted in History of Science | 3 Comments

To be or not to be exceptional?

I can’t remember how I came across this video from philosopher Alain de Botton, but I feel seen.

Like many academics, I guess, I have always prized scholarly achievement. And of course, within our systems of research assessment, we are forever talking about notions of excellence and exceptionalism, spurred on by the relentless competition for jobs, grants, and admission to the ‘top’ journals, and by the powerful grip on our imaginations of the idea of the genius or hero scientist.

Increasingly, I have come to question my priorities, not only for my own quality of life, but also for the health of scholarly endeavour in general. Why do we so willingly submit, as de Botton puts it, to “the cruel absurdity of other people’s expectations”?

How might we find our way to a place where doing your job well is good enough? This question is hardly new, but it is one that many of us repeatedly fail to answer and, to me, it feels more urgent than ever.


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Books of 2020

I made what I think was a smart move at the beginning of 2020. Instead of waiting until the year’s end and then struggling to recall what I thought of the books I had read, I created a Twitter thread of one-line reviews as I completed each title. Here, finally, is the entire thread:

Books of 2020

Books of 2020 – a twitter thread. Click on the image for the high-res version.

You may find it easier to scroll through the thread on Twitter.

It has without doubt been an exceptional year. The arrival of the coronavirus pandemic in mid-March disrupted my working and commuting patterns in a major way, but it didn’t seem to create any extra time for reading. The time freed by the loss of a daily commute of at least two hours was absorbed by the expansion of the working day. I have if anything undershot my usual annual tally. No matter. It’s not a competition.

My habits did change somewhat: almost half of the twenty-one books I read were novels. Normally, I only manage three or four. I also succeeded in reading my highest ever proportion of women authors – 48%. One of these, Hilary Mantel, produced my favourite book of the year, The Mirror and the Light, the final instalment of her visceral and magisterial trilogy on Thomas Cromwell. I have already pegged her earlier novel on the French Revolution, A Place of Greater Safety, as one to tackle in 2021.

Otherwise, it is a little harder to discern the highlights. That’s not because of the books themselves. I think that is more of a reflection of the dulling effects of life during lockdown, where days without events blend into one another, the colours of life merging into a dull monotone.

But some do stand out. Oliver Morton’s The Moon: a History of the Future was that rare thing, a book of poetic non-fiction, while my first encounter with Toni Morrison in The Bluest Eye was short and sharp and cut to the heart. Brandon Taylor’s first novel, Real Life, is one of the few I’ve ever read to bring life in a laboratory to life, through the tortured isolation of its gay, black protagonist. By contrast, Kathryn Mannix’s hospice stories, With the End in Mind, brought death to life in a way that was blessedly reassuring.

Only one novel disappointed me: The Left Hand of Darkness by Ursula Le Guin. I know it is regarded by many as a classic, but I was left out in the cold by its icy, alien landscapes. Everything else provided many moments of delight and insight, words to map out the world a little more clearly than before. I am grateful to all the authors I read. But for some reason the non-fiction titles figure more sharply in my memory, so I am especially thankful to Adam Rutherford for setting out his anti-racist manifesto (How to Argue with a Racist), to Philip Ball for unpicking the entanglement of physics with Nazism (Serving the Reich), to John Ziman for delineating the boundaries of science (Real Science), to Stuart Ritchie for his accounts of how and why those boundaries are crossed (Science Fictions), to Michael Sandel for examining the underbelly of ‘merit’ (The Tyranny of Merit), and to Margaret Heffernan for charting a more human course through the complex endeavours of organisations (Uncharted: How to Map the Future Together and Wilful Blindness). 


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Photographs of 2020

My computer tells me that I took over 2,400 photographs in 2020. Here are my favourites. I’m afraid I have failed to whittle them down to fewer than seventy-five. Click on the first image, taken on a winter walk on the first of January, to go to the album on flickr.

Photos of 2020

2020 was the year of lockdown, but we still managed to get out and about on occasion.


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No, DeepMind has not solved protein folding

(Please note that this post was updated on 12th Dec 2020 – see below)

This week DeepMind has announced that, using artificial intelligence (AI), it has solved the 50-year old problem of ‘protein folding’. The announcement was made as the results were released from the 14th and latest competition on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14). The competition pits teams of computational scientists against one another to see whose method is the best at predicting the structures of protein molecules – and DeepMind’s solution, ‘AlphaFold 2’,  emerged as the clear winner.


Don’t believe everything you read in the media

There followed much breathless reporting in the media that AI can now be used to accurately predict the structures of proteins – the molecular machinery of every living thing. Previously the laborious experimental work of solving protein structures was the domain of protein crystallographers, NMR spectroscopists and cryo-electron microscopists, who worked for months and sometimes years to work out each new structure.

Should the experimentalist now all quit the lab and leave the field to Deep Mind?

No, they shouldn’t, for several reasons.

Firstly, there is no doubt that DeepMind have made a big step forward. Of all the teams competing against one another they are so far ahead of the pack that the other computational modellers may be thinking about giving up. But we are not yet at the point where we can say that protein folding is ‘solved’. For one thing, only two-thirds of DeepMind’s solutions were comparable to the experimentally determined structure of the protein. This is impressive but you have to bear in mind that they didn’t know exactly which two-thirds of their predictions were closest to correct until the comparison with experimental solutions was made.* Would you buy a satnav that was only 67% accurate?

So a dose of realism is required. It is also difficult to see right now, despite DeepMind’s impressive performance, that this will immediately transform biology.


Impressive predictions – but how do you know they’re correct?

Alphafold 2 will certainly help to advance biology. For example, as already reported, it can generate folded structure predictions that can then be used to solve experimental structures by crystallography (and probably other techniques). So this will help the science of structure determination go a bit faster in some cases.

However, despite some of the claims being made, we are not at the point where this AI tool can be used for drug discovery. For DeepMind’s structure predictions (111 in all), the average or root-mean-squared difference (RMSD) in atomic positions between the prediction and the actual structure is 1.6 Å (0.16 nm). That’s about the size of a bond-length.

That sounds pretty good but it’s not clear from DeepMind’s announcement how that number is calculated. It might be calculated only by comparing the positions of the alpha-Carbon atoms in the protein backbone – a reasonable way to estimate the accuracy of the overall fold of the protein. Or, it might be calculated over all the atomic positions, a much more rigorous test. If it is the latter, then an RMSD of 1.6 Å is an even more impressive result.

But it’s still not nearly good enough for delivering reliable insights into protein chemistry or drug design. To do that, we want to be confident of atomic positions to within a margin of around 0.3 Å. AlphaFold 2’s best prediction has an RMSD for all atoms of 0.9 Å. Many of the predictions contributing to their average of 1.6 Å will have deviations in atomic positions even greater than that. So, despite the claims, we’re not yet ready to use Alphafold 2 to create new drugs.

There are other reasons not to believe that the protein folding problem is ‘solved’. AI methods rely on learning the rules of protein folding from existing protein structures. This means that it may find it more difficult to predict the structures of proteins with folds that are not well represented in the database of solved structures.

Also, as reported in Nature, the method cannot yet reliably tackle predictions of proteins that are components of multi-protein complexes. These are among the most interesting biological entities in living things (e.g. ribosomes, ion channels, polymerases). So there is quite a large territory remaining were AlphaFold 2 cannot take us. The experimentalists, who have been successful in mapping out the structures of complexes of growing complexity, have still a lot of valuable work to do.

While all of the above is supposed to sound a note of caution to counter some of the more hyperbolic claims that have been heard in the media in recent days, I still want to emphasise my admiration for the achievements of the AlphaFold team. They have clearly made a very significant advance.

That advance will be much clearer once their peer-reviewed paper is published (we should not judge science by press releases), and once the tool is openly available to the academic community – or indeed anyone who wants to study protein structure.

Update (02 Dec, 18:43): This post was updated to provide a clearer explanation of the RMSD measures used to compare predicted and experimentally determined protein structures. I am very grateful to Prof Leonid Sazanov who pointed out some necessary corrections and additions on Twitter.

*Update (12 Dec, 15:35): Strictly this is true, but it misses the more important point that the score given to each structure prediction (GDT_TS) broadly correlates with the closeness of its match to the experimental structure. As a result, I have deleted my SatNav crack.

For a deeply informed and very measured assessment of what DeepMind has actually achieved in CASP14, please read this blogpost by Prof. Mohammed AlQuraishi who knows this territory much better than I do. His post is pretty long but you can skip the technical bits explaining how AlphaFold 2 works. He gives a very good account of the nature of DeepMind’s advance; in AlQuraishi’s view, AlphaFold 2 does represent a solution to the protein structure prediction problem, though he is careful to define what he means by a solution. He also acknowledges that there are still some significant improvements to be made to the programme, but regards these as more of an engineering challenge than a scientific one. He agrees that AlphaFold 2 won’t be used any time soon for drug design work. AlQuraishi also gives an excellent overview of the implications of this work for protein folders, structural biologists and biotechnologists in general, and offers some very interesting thoughts on the differences between DeepMind’s approach to research and that of more traditional academic groups.

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