Tag: Indian Council of Medical Research

• In conversation with Sree Srinivasan

  On May 1, I was hosted on a webinar by the American journalist Sree Srinivasan, along with Anna Isaac of The News Minute and Arunabh Saikia of Scroll.in. As part of his daily show on the COVID-19 crisis, hosted by Scroll.in, Srinivasan hosts a few people working in different areas, and they all chat about what they’re doing and how they’re dealing with everything that’s going on for about an hour. However, our episode, the 50th of the series, was a double feature: the first 60 minutes was a conversation among us journalists, and for the next 50 minutes or so, Srinivasan had on Aseem Chhabra to discuss the lives and work of Irrfan Khan and Rishi Kapoor, who had passed away a few days earlier. The full video is available to view here as well as is embedded below.

  I also transcribed the portion of the video where I spoke for two reasons. First, because I’d like to remember what I said, and writing helps me do that. Second, I’m a lousy speaker because I constantly lose my train of thought, and often swallow words that I really should have spoken out loud, often rendering what I’m saying difficult to piece together. So by preparing a transcript, pasted below, I can both clarify what I meant in the video as well as remember what I thought, not just what I said.

  How would you grade Indian journalism at the moment, in these last two months, in terms of coverage of the COVID-19 pandemic?

  The mainstream English press has been doing okay, I guess, but even then to paint it all with the same brush is very difficult because there are also very different stories to cover at a time like this. For example, many social and political issues are being covered well by specific publications. Some others are addressing different aspects of this.

  In fact, if I had to pick out one aspect that I could say we’re not doing enough about is in terms of the science itself. The coronavirus outbreak is a crisis, and a large part of it is rooted in health issues, in scientific issues – much like climate change, antimicrobial resistance, etc. A lot of journalists are doing a good job of covering how this outbreak has impacted our society, our economy, etc. but there’s actually very little going into understanding how the virus really works or how epidemiologists or virologists do what they do.

  One easy example is this business of testing kits. There’s a lot of controversy now about the serological tests that ICMR procured, probably at inflated prices, are not very accurate. The thing is, whenever you’re in a crisis like this and somebody’s rapidly developing kits – testing kits or ventilators or anything like that – there is always going to be a higher error rate.

  Also, no test is 100% perfect. Every test is error-prone, including false positives and false negatives. But in this rush to make sure everything is covered, most of what is being elided – at least among organisations that are taking the trouble – is the science itself [of how tests are developed, why the errors are unavoidable, etc.]. That’s a significant blindspot.

  But on the positive side of it, there is also a heightened awareness now of the need to understand how science works. We’ve been seeing this at The Wire, I don’t know if it applies to other organisations: there is a sort of demand… the engagement with science stories has increased. We’re using this opportunity to push out these stories, but the thing is we’re also hoping that once this pandemic ends and the crisis passes, this appreciation for science will continue, especially among journalists.

  Apart from this, I don’t want to attempt any grading.

  What is your reaction to the value of data journalism at this time?

  The value of charts has been great, and there are lots of charts out there right now, projecting or contrasting different data-points. Just a few days ago we published a piece with something like 60 charts discussing the different rates of testing and positivity in all of India’s states.

  But the problem with these charts – and there is a problem, that needs to be acknowledged – is that they tend to focus the conversation on the data itself. The issue with that is that they miss ground realities. [I’m not accusing the charts of stealing the attention so much as giving the impression, or supporting the takeaway, that the numbers being shown are all that matter.]

  While data journalism is very important, especially in terms of bringing sense to the lots of numbers floating about, [it also feeds problematic narratives about how numbers are all that matter.] I recently watched this short clip on Twitter in which a bunch of people were crowded at a quarantine centre in Allahabad fighting for food. There was very little food available and I think they were daily-wage labourers. I think there is a lot being said about the value and virtues of data journalism and visualisations but I don’t think there is much being said at all – but definitely needs to be – about how data can’t ever describe the full picture.

  Especially in India, and we’ve seen this recently with the implementation of the Aadhaar programme as well: even if your success rate with something is as high as 99%, 1% of India’s population is still millions of people [and it’s no coincidence that they already belong to the margins of society.] And this is something I’ve thus far not seen data stories capture. Numbers are good to address the big picture but they’ve been effectively counterproductive during this crisis in terms of distracting from the ground stories. [So even the best charts can only become the best stories if they’re complemented with some reporting.]

  The Wire compiled a list of books to read during the lockdown, with recommendations by its staff. You recommended Dune by Frank Herbert. Why?

  Dune to me was an obvious choice for [three] reasons. One is that Dune is set on a planet where you already see life in extremes, especially with the tribe of the Fremen, who play an important role in the plot. What really stayed with me about that book was its sort of mystic environmentalism, about how humans and nature are connected. The book explores this in a long-winded way, but that’s something we’ve seen a lot of these days in terms of zoonoses – [pathogens] that jump from animals to humans.

  There’s also a lot of chatter these days about killing bats because they host coronaviruses. But all of that is rubbish. Humans are very deeply responsible for this crisis we’ve brought on ourselves in many ways.

  This also alludes to what Anna Isaac mentioned earlier: what do you mean by normal? Yes, life probably will return to normal in India’s green zones next week, but the thing is, once this crisis ends, there’s still climate change, antimicrobial resistance and environmental degradation awaiting us that will bring on more epidemics and pandemics. Ecologists who have written for us have discussed this concept called ‘One Health’, where you don’t just discuss your health in terms of your body or your immediate environment but also in terms of your wider environment – at the ecosystem level.

  Dune I think is a really good example of sci-fi that captures such an idea. And Dune is also special because it’s sci-fi, which helps us escape from our reality better, because sci-fi is both like and unlike.

  The third reason it’s special is because the movie adaptation is coming out later this year, so it’s good to be ready. 😀

  [When asked for closing remarks…]

  When I started out being a journalist, I was quite pissed off that there wasn’t much going on in terms of the science coverage in India. So my favourite stories to write in the last eight years I’ve been a journalist have been about making a strong point about a lot of knowledge being out there in the world that seems like it’s not of immediate benefit or use [but is knowledge – and therefore worth knowing – nonetheless]. That’s how I started off being a science journalist.

  My forte is writing about high-energy physics and astrophysics. Those are the stories I’ve really enjoyed covering and that’s the sort of thing that’s also lacking at the moment in the Indian journalism landscape – and that’s also the sort of coverage of science news we wanted to bring into the pandemic.

  Here, I should mention that The Wire is trying to build what we hope will be the country’s first fully reader-funded, independent science news website. We launched it in February. We really want to put something together like the Scientific American of India. You can support that by donating at thewire.in/support. This is really a plea to support us to go after stories that we haven’t seen many others cover in India at the moment.

  Right now, most stories are about the coronavirus outbreak but as we go ahead, we’d like to focus more and more on two areas: science/society and pure research, stuff that we’re finding out but not talking about probably because we think it’s of no use to us [but really that’s true only because we haven’t zoomed out enough].

  2020.05.04

• ‘Science alone triumphs’: A skeptic annotates

  An article entitled ‘Science alone triumphs: Providing a true picture of the world, only science can help India against coronavirus’, penned by a Jayant Sinha, appeared on the Times of India‘s editorials page on April 8, 2020. My annotated reading of the article follows…

  

  As the coronavirus continues its deadly spread around the world, it is only science that protects us. Many different scientists and experts are responding to the global challenge…

  A sweeping statement that suggests whatever science can protect for us are the only things worth protecting. Obvious exceptions include social security, access to food and other essential supplies, protection against discrimination and stigma, and of course individual rights. The author quite likely does not intend to imply that one’s biological safety is more important than any of these other attributes, but that’s what the words imply.

  … Their deep technical expertise, honed through years of education and practice, keeps us from falling into the abyss.

  A bit too florid but okay.

  Ultimately, it is the practice of science – developing new ideas, testing them against hard evidence, replicating them successfully, scaling them up, and then further improving them through honest feedback – that drives all of them.

  It’s quite heartening to have a lawmaker acknowledge these aspects of the scientific method, esp. a member of the Bharatiya Janata Party, but these exact are also curious at this time. The Indian Council of Medical Research has allowed frontline health workers to consume hydroxychloroquine as a prophylactic against COVID-19 with flimsy (if that) evidence to support the drug’s efficacy and safety. Where are the tests, leave alone the replication studies?

  This is the quintessential scientific method, the unrelenting search for truth.

  More than 99% of the article’s readers are unlikely to notice a difference between the scientific method and the search for truths (I prefer using the plural), but it exists: the scientific method is a way to acquire new knowledge about the natural universe. The nature of the quest depends on the practitioner – the scientist.

  What science tells us about coronavirus infections has reached everyone. People are wearing masks, washing their hands, and avoiding crowds. Yet most people I meet are stumped by questions such as: What is a virus? How does it actually spread? How does your body fight the coronavirus? Why do some people die from the virus? This indeed is the great paradox of our times.

  Truly!

  Even as science becomes more vital, fewer and fewer people understand and appreciate it. As a child who loved science, as a young man trained in engineering, and as a technocrat who believes in analytical reasoning and hard evidence, I find this hard to accept.

  I’m not sure if the author means he does not understand why this paradoxical engagement with science persists but I have some ideas:

  1. Science is becoming increasingly more specialised, and a lot of what we learn from the cutting edge these days cannot be communicated to anyone without at least 18 years of education.
  2. Most people think they understand science when they really mean they’re familiar with its commonest precepts and scientists’ pronouncements. Their knowledge is still only based on faith: that, for example, the new coronavirus spreads rapidly but not why so, freeing them to use scientific knowledge in unscientific narratives.

  (Reason: because the virus’s spike proteins have evolved to establish stronger bonds with the ACE2 receptor protein produced by cells in the respiratory tract, compared to the spike proteins of the closely related SARS virus, as well as the ability to attach, albeit less strongly, to another protein – furin – produced by all cells in the body.)

  To change this state of affairs, we must focus on four key areas. … We are afflicted by too much quackery and superstition.

  Is this article really a dog-whistle? The author is the BJP MP from Hazaribagh (Jharkhand) so there is some comfort – no matter how fleeting – that the BJP is not completely devoid of appreciation for science. However, I’m curious how often the author has brought these issues up with other BJP lawmakers, including the prime minister himself, who have frequently issued a stream of nonsense that undermines a scientific understanding of the world. The answer wouldn’t affect what we should or shouldn’t take away from this piece, but this not uncommon practice of speaking sense in some fora but shutting up in others is annoying, especially when the speaker wields some power.

  … Of course, mythology has immense power to shape people’s beliefs, but it must be acknowledged that it is only science that can solve our material problems.

  Well said… I think. Can’t be a 100% sure.

  While there is certainly much wisdom in age-old practices, it is primarily because there is a genuine scientifically proven cause-and-effect relationship that underlies these practices.

  No. Specifically, causality – nor any of the properties we associate with modern science – is not a precondition for traditional wisdom, beliefs and rituals, nor is it meaningful to attempt to validate such wisdom, beliefs and rituals using filters developed to qualify scientific theories of the natural universe. Science and tradition (in many contexts) are born of and seek to fulfil different purposes. Additionally, science alone does not empower – traditional practices do as well (look no further than tribal groups that have been stewarding many of India’s forests for centuries) – and science abandoned by the guiding hand of social forces has often become an instrument of disempowerment.

  … In short, we would all be much better off if we shifted some of our time and resources away from blind faith and towards a better scientific understanding of the world.

  This is very true. Faith has its place in the world (more so than some might like to acknowledge); outside this finite domain, however, it’s a threat.

  Second, our children must learn honestly about science. There is no ‘Western’ concept of science taught in schools which should then be negated at home. Science is universal – just look up the path-breaking research conducted by SN Bose, or CV Raman, or S Chandrasekhar. The pure scientific truth that they discovered holds true everywhere, even in the deep cosmos.

  💯 A diversity in the choice of names (by gender or by caste, for example) would have been better.

  Teachers and parents must tell children that science is the pursuit of truth and provides a true picture of the world.

  As the children grow up, can we encourage our teachers and parents to communicate more nuanced ideas of what science is and why it was invented?

  … We should not demand obedience from our children, rather we should encourage them to probe all that we do. …

  Again, is this article really a dog-whistle?

  Third, we must revere our scientists and technologists.

  Never revere another human. Never assume anyone is closed off to (constructive) criticism, particularly when they deserve it. Obviously there’s a time and place (including absurd advice like “don’t berate a surgeon in the middle of a surgery”), but when such opportunities arise don’t let reverence stop you.

  It is through their efforts that we flourish today.

  Brian Josephson won the Nobel Prize for physics in 1973 for predicting the Josephson effect but he also supported the “water memory” hypothesis that claimed to make sense of homeopathic remedies. Giving scientists the keys to running the world is not guaranteed to produce the desired results.

  … Even our start-up culture tends to value the business celebrity, not so much the tech nerd. …

  The author is probably thinking of celebrity tech nerds, the Bezoses and the Jobses. “Nerds” and “geeks” in general have become more popular and their culture more socially and commercially profitable.

  Billions of dollars of wealth has been created by writing great code, developing insanely good products, creating clever new financial solutions, and establishing entirely new scientific approaches. …

  Many of these “insanely good products” have also progressively eroded democracy. To quote Jacob Silverman in The Baffler (at length, hoping Silverman doesn’t mind):

  The fundamental underlying problem is the system of economic exchange we’re dealing with, which is sometimes called surveillance capitalism. It’s surveillance capitalism that, by tracking and monetizing the basic informational content of our lives, has fueled the spectacular growth of social media and other networked services in the last fifteen years. Personal privacy has been annihilated, and power and money have concentrated in the hands of whoever owns the most sophisticated machine to collect and parse consumer data. Because of the logic of network effects—according to which services increase in value and utility as more people use them—a few strong players have consolidated their control over the digital economy and show little sign of surrendering it.

  It wasn’t supposed to be this way. For years, tech executives and data scientists maintained the pose that a digital economy run almost exclusively on the parsing of personal data and sensitive information would not only be competitive and fair but would somehow lead to a more democratic society. Just let Facebook and Google, along with untold other players large and small, tap into the drip-drip of personal data following you around the internet, and in return you’ll get free personalized services and—through an alchemy that has never been adequately explained—a more democratized public sphere.

  While these promises provided the ideological ballast for the tech revolution of the last decade or two, they turned out to be horribly wrong. There is nothing neutral, much less emancipatory, about our technological systems or the data sloshing through them. They record and shape the world in powerful, troubling ways. The recent clutch of stories, including in the New York Times and the Guardian, about Cambridge Analytica, the favored data firm of the Trump campaign, provides a humbling example of how personal data can be used to manipulate voter populations. This essential truth has been known at least since 2012, when a University of California-San Diego study found that a few nudges on Facebook appreciably increased voter turnout. From there, it’s only a small jump to isolating and bombarding millions of potential Trump voters with customized appeals, as Cambridge Analytica did.

  In the final analysis, the author’s association of “scientific approaches” with technological triumphalism is just a very good reminder that “scientific approaches” don’t have morals built-in.

  Finally, we must massively strengthen our scientific institutions. … The hard work of science gets done in these places and they must be among the best in the world. …

  Without specifying how ‘best’ or even ‘better’ needs to be measured, the task of strengthening institutes is at risk of being hijacked by the single-minded pursuit of better scores on ranking tables.

  … Our best diaspora scientists should be provided generous support to come back to India and set up their research labs. Top scientific institutions must be granted the autonomy to govern themselves, hire the best faculty, attract great students from around the world, and pursue the best research. …

  I once picked a fight with a scientist after he submitted a piece arguing that the Government of India should improve the supply of masks and other PPE to tame India’s tuberculosis burden. He couldn’t understand why I was opposed to publishing the piece, insisting he was “saying the rights things – the things that need to be said.” Here’s the thing: no one disagrees, and the dialogue has in fact moved leaps and bounds ahead. So while it may be the right thing to say, I’m not sure it needs to be said – much less deserves a thousand words. Put differently: You’re a minister, try moving the needle!

  To that end, I have introduced a private members bill to grant IIM-level autonomy to the IITs that have been selected as institutions of eminence.

  Okay… Is this what the article was about: to build support for your Bill? According to PRS, fewer than 4% of private members’ Bills were even discussed during the 14th Lok Sabha (i.e. Modi’s first term as prime minister). Why not build support within the party and introduce it as a government Bill?

  Our civilisation is marked by its unending quest for knowledge, … The Mundaka Upanishad enlightens us: Satyameva Jayate – Truth alone triumphs. Our republic is based on this eternal principle. …

  Seriously, STAHP. 😂

  2020.04.12

• On India’s path to community transmission

  There’s a virus out there among many, many viruses that’s caught the world’s attention. This virus came into existence somewhere else, it doesn’t matter where, and developed a mutation at some point that allowed it to do what it needs to do inside the body of one specific kind of animal: Homo sapiens. And once it enters one Homo sapiens, it takes advantage of its new surroundings to produce more copies of itself. Then, its offspring wait for the animal to cough or sneeze – acts originally designed to expel irritating substances – to exit their current home and hopefully enter a new one. There, these viruses go through the same cycle of reproduction and expulsion, and so forth.

  This way, the virus has infected over 210,000 people in the last hundred days or so. Some people’s bodies have been so invaded by the virus that their immune systems weren’t able to fight it off, and they – nearly 9,000 of them – succumbed to it.

  Thus far, the virus has reportedly invaded the bodies of at least 282 people in India. There’s no telling how the virus will dissipate through the rest of the population – if it needs to – except by catching people who have the virus early, separating them from the rest of the population for long enough to ensure they don’t have and/or transmit the virus or, if they do, providing additional treatment, and finally reintegrating them with the general population.

  But as the virus spreads among more and more people, it’s going to become harder and harder to tell how every single new patient got their particular infection. Ultimately, a situation is going to arise wherein too many people have the virus for public-health officials to be able to say how exactly the virus got to them. The WHO calls this phase ‘community transmission’.

  India is a country of over 1.3 billion people, and is currently on the cusp of what the Indian Council of Medical Research (ICMR) has called ‘stage 3’ – the advent of community transmission. It’s impossible to expect a developing country as big and as densely populated as India to begin testing all 1.3 billion Indians for the virus as soon as there is news of the virus having entered the national border because the resource cost required to undertake such an exercise is extremely high, well beyond what India can generally afford. However, this doesn’t mean Indians are screwed.

  Instead of testing every Indian, ICMR took a different route. Consider the following example: there’s a population of red flecks randomly interspersed with yellow flecks. You need to choose a small subset of flecks from this grid (shown below) such that checking for the number of yellow flecks in the subset gives you a reliable idea of the number of yellow flecks overall.

  The ideal subset would be the whole set, of course, so there is one more catch: you have a fixed amount of money to figure out the correct answer (as well as for a bunch of other activities), so it’s in your best interests to keep the subset as small as possible. In effect, you need to balance the tension between two important demands: getting to a more accurate answer while spending less.

  

  Similarly, ICMR assumed that the virus is randomly distributed in the Indian population, and decided to divide the population into different groups, for example by their relative proximity to a testing centre. That is, each testing centre would correspond to the group of all people who live closer to that testing centre than any other. Then, ICMR would pick a certain number of people from each group, collect their nasal and throat samples and send it to the corresponding labs for tests.

  Say group size equals 100. For a Bernoulli random variable with unknown probability p, if no events occur in n independent trials, the maximum value of p (at 95% confidence) is approximately 3/n. In our case, n = 100 and p at 95% confidence is 3/100, which is 3%. Since this is the upper bound, it means less than 3% of the population has the ‘event’ which didn’t occur in n trials – which in our case is the event of ‘testing positive’. Do note, this is what is safe to say; it’s not what may actually be happening on the ground. So by increasing the sample size n as much as possible, ICMR can ascertain with higher and higher confidence as to whether the corresponding group has community transmission or not.

  Thus far, ICMR has said there is no community transmission in India based on these calculations. Independent experts have been reluctant to take its word, however, because while ICMR has publicised what the sample size and the number of positives are, there is very little information about two other things.

  First: we don’t know how ICMR selected the samples that it did for testing. While the virus’s distribution in the population can be considered to be random, especially if community transmission is said to have commenced, the selection of samples needs to have an underlying logic. What is that logic?

  Second: we don’t know the group sizes. It’s important for the sample size to be proportionate to the group size. So without knowing what the group size underlying each sample is, it becomes impossible to tell if ICMR is doing its job right.

  On March 17, one ICMR scientist said that some testing centres had admitted fewer people with COVID-19-like symptoms and the source of whose infections was unknown (i.e. community transmission) than the size of the sample chosen from their corresponding group. She was suggesting that ICMR’s choice of samples from each group was large enough to not overlook community transmission. To translate in terms of the example above: she was saying ICMR’s subset size was big enough to catch at least one yellow fleck – and didn’t.

  As it happens, on March 20, ICMR announced that it would begin testing for a potential type of community-transmission cases even though its sampling exercise had produced 1,020 negative results in 1,020 samples (distributed across 51 testing centres).

  The reasons for this are yet unclear but suggests that ICMR suspects there is community transmission of the virus in the country even though its methods – which ICMR has always stood by – haven’t found evidence of such transmission. This in turn prompts the following question: why not test for all types of community transmission? The answer is the same as before: ICMR has limited resources but at the same time has been tasked with discovering how many yellow flecks are there in the total population.

  The virus is not an intelligent creature. In fact, it’s extremely primitive. Each virus is in its essence a packet of chemical reactions, and when each reaction happens depends on a combination of internal and external conditions. Other than this, the virus does not harbour any intentions or aspirations. It simply responds to stimuli that it cannot manipulate or affect in any way.

  The overarching implication is that beyond how good the virus is at spreading from person to person, a pandemic is what it is because of human interactions, and because of human adaptation and mitigation systems. And as more and more people get infected, and their groups verge towards the WHO’s definition of ‘community transmission’, the virus’s path through the population becomes less and less obvious, but at the same time a greater depth of transmission opens the path to better epidemiological modelling.

  When such transmission happens in a country like India, the body responsible for keeping the people safe – whether the Union health ministry, ICMR or any other entity – faces the same challenge that ICMR did. This is also why direct comparisons of India’s and South Korea’s testing strategies are difficult to justify, especially of the number of people tested per million: India has nearly 26-times as many people but spends 11.5-times less on healthcare per capita.

  At the same time, ICMR isn’t making it easy for anyone – least of all itself – when it doesn’t communicate properly, and leaves itself open to criticism, which in turn chips away at its authority and trustworthiness in a time as testing as this. Demonetisation taught us very well that a strategy is only as good as its implementation.

  But on the flip side, it wouldn’t be amiss to make a distinction here: between testing enough to get a sense of the virus’s prevalence in the population – in order to guide further action and policy – and the fact that the low expenditure on public healthcare is always going to incentivise India to skew towards a sampling strategy instead of an alternative that requires mass-testing. ICMR and the Union health ministry haven’t inspired confidence on the first count but it’s important to ensure criticism of the former doesn’t spillover into criticism of the latter as well.

  Anyway, the corresponding sampling strategy is going to have to be based on a logic. Why? Because while the resources for the virus to spread exist abundantly in nature (in the form of humans), the human response to containing the spread requires resources that humans find hard to get. Against the background of this disparity, sampling, testing and treatment logics – such as Italy’s brutal triaging policy – help us choose better sampling strategies; predict approximately how many people will need to be quarantined in the near future; prepare our medical supplies; recruit the requisite number of health workers; stockpile important drugs; prepare for economic losses; issue rules of social conduct for the people; and so forth.

  A logic could even help anticipate (or perpetuate, depending on your appetite for cynicism) ‘leakages’ arising due to, say, caste or class issues. Think of it like trying to draw a circle with only straight lines of a fixed length: with 200 strokes, you could technically draw a polygon with 200 sides that looks approximately like a circle – but it will still have some discernible edges and vertices that won’t exactly map on a circle, leaving a small part of the latter out. Similarly, using a properly designed technique that can predict which person might get infected and who might not can still catch a large number of people – but the technique won’t catch all of them.

  One obvious way to significantly improve the technique’s efficacy as it stands is to account for the fact that more than half of all Indians are treated at private hospitals whereas you can be tested for COVID-19 only at a government facility, and not all VRDLs receive samples from all private hospitals in their respective areas.

  Ultimately, the officials who devise the logics must be expected to justify how the combination of all logics can – even if only on paper – uncover most, if not all, cases of the virus’s infection in India.

  2020.03.22