Root Privileges

Month: December 2024

  • Rescuing superconductivity

    From a paper in Nature Reviews Physics, December 19, 2024:

    One of the forefront fields of modern superconductivity research is that on hydrides at high pressures. Over the past few years, this research has attracted considerable publicity, of which a substantial fraction has been negative. Scientific fraud has been committed and exposed, and arguments continue about specific aspects of data presented in some other papers. Among all the noise that is being generated, one might lose sight of the big-picture question of whether the field is on solid foundations or not, that is, whether high-pressure hydrides host superconductivity at all. Here, we readdress this central issue. We select and critically examine what we identify as six key papers on the topic. We have all spent substantial portions of our careers working on superconductivity, so hope that the conclusions that we reach will carry at least some weight. We also decided to include among our authorship team only people who have never worked directly on hydride superconductivity, so that our examination of the scientific facts can be as impartial as possible. We conclude that it is overwhelmingly probable that the phenomenon of hydride superconductivity is genuine.

    It’s intriguing such an exercise had to be undertaken. It’s yet another reminder that practising science isn’t simply a matter of following the facts. Science is part of the world, not separate from it, and is affected by what others think of it, especially based on perceptions of trustworthiness, self-correctability, and integrity. Self-correctability in particular went out the window the moment the holes in the Dias/Salamat saga became clear, followed by integrity. Imagine discovering a groundbreaking new natural phenomenon: usually such things revitalise fields looking for a breakthrough, but here, the field became marred by a slew of bad papers that shrunk funding opportunities and rendered young researchers trying to enter or already in the field nervous about their future.

    In fact the self-correctability and integrity issues were compounded by the actions of the journals that published the problem papers. Nature and Physical Review Letters both have submissions peer-reviewed. The process of peer review is designed to check whether the data provided match the conclusion provided, not the integrity of the data. However, the data the journals reviewed before publishing the papers was also the data independent experts reviewed to find flaws, consequently leading to the retractions. What explains this? Further, one of the papers, purporting to show superconductivity in LuNH and published in Nature in March 2023, didn’t contain enough evidence to support the conclusion, which the journal’s review missed as well. A Nature news feature reported in September that year:

    Critiques started appearing as soon as the Nature paper was published. One major line of criticism is that the Rochester team didn’t provide enough evidence to show that resistance does go to zero in its material. Dias and his colleagues state in the paper that they removed “small residual resistance” from some of their electrical measurements, but critics argue that it should not be necessary to remove background for these types of measurements, given clean readings of both a sample’s current and voltage. The problem with removing a background, says Sven Friedemann, a physicist at the University of Bristol, UK, is that it implies that the raw data do not go to zero — and therefore don’t show superconductivity.

    The same feature also quoted two scientists saying Nature’s retraction of a carbonaceous sulphur hydride paper in 2022 was “not strong enough”.

    The names of many of the authors of the review should be familiar to people who have been following the Dias/Salamat saga, including Peter Hirschfeld, Steven Kivelson, Andrew Mackenzie, and Subir Sachdev. The review reportedly began with the two possible outcomes — hydrides display superconductivity versus hydrides don’t — being equally probable and concluded in favour of the former after assessing the results reported by multiple groups. While the nominal definition of superconductivity alludes only to the fact that a material’s electrical resistance drops to zero, condensed-matter physicists perform four tests looking for different features. One is zero electrical resistance; another is that the material’s magnetisation varies through a particular pattern. On this count the reviewers assessed data from only one group, that of Mikhail Eremets & co. in 2022.

    Yet another familiar name, Jorge Hirsch, has already expressed his disapproval towards the review. “I was surprised and disappointed to see this. I speculate [they wrote] it because hydrides being superconductors would establish the validity of BCS theory, in which they firmly believe,” he told Physics. A bit of relevant background here is that Hirsch is a detractor of the popular BCS theory of superconductivity and a proponent of his own holes theory. While Physics writes that he’s already flagged some problems with the Eremets et al. paper, it doesn’t say the Eremets et al. paper raised significant doubts about the validity of his holes theory — which is to say both the study and Hirsch’s idea could be flawed rather than the study alone. Overall, if science is to remain trustworthy, scientists need to undertake exercises like this, conducting — while being seen to be conducting — impartial reviews of the prevailing evidence and considering whether it makes sense to continue working in fields beleaguered by the influence of some dishonest exponents.

    I only hope reviewers will also take a closer look at the roles journals and their misguided incentives — and the still largely blind trust the global scientific community places in them — play in sustaining scandals in science.

  • The SARS-CoV-2 red herring

    From my piece in The Hindu today:

    We don’t know where or how the virus originated. If it did in a lab, we would have to re-examine how we regulate research facilities and their safeguards and the manner of political oversight that won’t curtail research freedom. If the virus is au naturel, we would have to institute and/or expand pathogen surveillance, eliminate wildlife trafficking, and improve social security measures to ensure populations can withstand outbreaks without becoming distressed. But even as these possibilities aren’t equally likely (according to scientists I trust), the origin of SARS-CoV-2 is less important than it once was because the COVID-19 pandemic caused us to implement all these outcomes to varying degrees.

    Not many people I’ve encountered seem to harbour the view that the origins question has become irrelevant. I sincerely believe there are many things we just can’t know. They’re easier to find in science but they’re likely there in all domains. The origin of SARS-CoV-2 has become one of them. The virus could have been entirely natural or it could have been engineered in a lab. This means we need to establish a clear and straightforward genetic link between two species: SARS-CoV-2 and its ancestor, a bat coronavirus called RaTG13. We haven’t yet. Even when we do, we’ll have to find a way to prove that the evolution from the in-between species to SARS-CoV-2 was natural, not engineered. As for the second possibility, we simply need China’s cooperation whereas China hasn’t been cooperating. But as I’ve written, we’ve already done what we’d do if either of these possibilities is established without doubt. It’s time we move on.

    In fact, one thing I’ve left unsaid in the piece — mostly because of the word limit — speaks as much to the origins of the origins question as to the sort of people who continue to keep these concerns alive. (My piece itself was motivated by the US Select Subcommittee Report, a Republican-led effort that earlier this month concluded the lab-leak theory remains plausible and worthy of investigation.) The origins question is no longer about science when it’s on the big stage. Instead it’s an excuse disguised as scientific inquiry for the US to punish China. Both the US and China didn’t help the cause of working together during the COVID-19 pandemic: one reduced funding for the World Health Organisation, actively spread misinformation, and hoarded vaccines and the other limited scientific access to medical data and used it to curry favours. Now, with Donald Trump a month away from his second term as the US’s nincompoop-in-chief, the origins question is being used to set the stage for the US to smack down a challenger in the global world order.

    This hasn’t been about science for sometime. If science is why you’re interested in the origins of SARS-CoV-2, I suggest switching from either hypotheses to the eternal third possibility — “I don’t know” — while keeping in touch with scientists you trust.

  • Visual science journalism’s DNA problem

    Your left hand and right hand are mirror-images of each other. You can’t superimpose them completely even after all manner of rotations and translations. Only mirroring them works. The same thing can happen to some molecules. When two molecules are identical in every way except their geometric structure in space is such that one is a mirror-image of another, they’re said to be enantiomers. These molecules have a chirality, or handedness: like your hands, one is left-handed and the other right-handed.

    On December 3, an international group of scientists published a technical report and commentary in Science warning against work to develop “mirror life”: cells whose chiral molecules are replaced with their complementary enantiomers. To quote from the commentary:

    Our analysis suggests that mirror bacteria could broadly evade many immune defenses of humans, animals, and plants. Chiral interactions, which are central to immune recognition and activation in multicellular organisms, would be impaired with mirror bacteria. This could result in weakened immune recognition, a weakened response by innate immune systems, and (in vertebrates) limited downstream activation of adaptive immune functions. For example, experiments show that mirror proteins resist cleavage into peptides for antigen presentation and do not reliably trigger important adaptive immune responses such as the production of antibodies. We are thus concerned that the function of many vertebrate immune systems against mirror bacteria would be severely impaired. Invertebrate and plant immune systems are less well studied but appear to suffer analogous limitations.

    Given the potential for severe immune evasion, mirror bacteria might not require host-specific factors to invade hosts and cause infection. In animals (including humans), bacteria regularly cross barriers in the skin, mouth, gut, lungs, and other mucosal surfaces because of routine damage and intrinsic leakiness; mirror bacteria would be expected to do the same. In healthy animals, translocated natural-chirality bacteria are typically cleared by immune defenses. However, if the immune response against mirror bacteria is sufficiently impaired, translocated mirror bacteria might replicate within the host and establish an infection. Unchecked replication of mirror bacteria within internal tissues is likely to be deleterious to the host organism and may be lethal.

    While this is very intriguing, the report/commentary reminded me of another problem I’ve been noticing in the science journalism press, especially these days when we’re all writing and publishing more articles about genetics.

    Stock images and illustrations are an important resource both for small newsrooms that can’t hire their own designers and for all newsrooms — including those with designers — lacking the skills to create (even partially accurate) scientific visuals. Articles of science journalism about genetics require such visuals more than others because, while the subjects of these narratives are physical entities, they’re too small to be seen by the naked eye as well as whose visuals as seen through microscopes aren’t particularly visually captivating. Instead, stock images have done the trick.

    Pixabay, Getty Images, and other libraries of such assets are choc-a-bloc with 2D and 3D (or 2.5D?) illustrations of the DNA double helix. But I’ve noticed that a great number of them have a common problem — curiously, in a specific way, echoed in the objection the scientists’ group has expressed against “mirror life”: many of these illustrations show the DNA helix twisting to the left. In all our bodies, DNA virtually always twists to the right. That is, the right-handed enantiomer is what animates our bodies whereas the left-handed enantiomer is absent, but which hasn’t stopped it from dominating stock images of DNA.

    I realise most people don’t care and/or that the image is captioned to be “for representative use only”. DNA of other configurations, including a left-handed one, exist as well to be fair. And most of all, DNA’s chirality has almost never been the narrative subject. But today it is, as the scientists have so clearly articulated, and the visuals of science journalism need to buck up as well.

  • What is ONOS’s (real) problem?

    The Indian government set the country’s research community aflutter when it announced the launch of a long-awaited plan to improve research access without announcing many of its salient details as well.

    On November 25, the Ministry of Education published a press release saying the Union Cabinet had approved the plan — called ‘One Nation, One Subscription’ (ONOS) — at a total value of Rs 6,000 crore over three years. This release was so low on details as to be deeply polarising in the public sphere. In fact, its reception was only saved by its offer to bring access to prohibitively expensive research journals to students at poorly funded public colleges and universities. As speculation and debate swelled to fill the information gap, many experts unsurprisingly concluded the government shouldn’t have adopted ONOS in its current form. Their arguments were that it spent too much for too little gain, didn’t make room for open-access (OA) publishing, and had no arrangements to support domestic publishers of scholarly journals.

    But on December 11, after criticism in the press, the government organised a press conference with officials of the Department of Science & Technology, Department of Higher Education, and the office of the Principal Scientific Advisor, and they revealed many more details about ONOS — often enough to allay suspicions that ONOS was an attempt by the government to take the easiest way out of a difficult problem. The officials even acknowledged the importance of supporting domestic publishers of scholarly journals (which are likely to be more mindful of local contexts of research), rooted for changes in the way professional scholars are evaluated for promotions (to focus less on journal names and more on the quality of work), and called ONOS part of a plan to “bring about OA transformation”.

    However, after the press conference, the discussions in many OA communities (of which I am part) still indicated a significant degree of dissatisfaction. Chief among critics’ complaints was that the government’s decision to set aside Rs 150 crore per year for researchers publishing in ‘gold’ OA journals (where the publisher charges researchers to publish a paper rather than a reader to read it) was a waste. They were also unhappy about the authors of papers having to sign their copyrights over to the publishers and about the ‘lost opportunity’ to use the Rs 6,000 crore to make the ‘green’ OA publishing model (whereby researchers self-archive copies of their papers that can be availed freely) a national priority.

    Between November 25 and December 11, an important source of disgruntlement with ONOS was the scheme amounted to paying research journals a sum so researchers in the country could access their output for free, without addressing any of the issues associated with the country’s research publishing and evaluation culture. This version of ONOS effectively maintained the status quo at a small discount. But the details revealed on December 11 refocused what criticism still remained to a different form — and one that Remya Haridasan, a scientist at the PSA’s office and one of the officials present at the press conference, inadvertently captured. She said, “ONOS is not a value judgment of the subscription-based model of knowledge dissemination but an adoption of the most practical India-specific solution until a sustainable OA model is achieved globally.”

    In this paradigm, the government is simply responding to what the country’s scientists are asking for while keeping the door open to change whereas critics want the government to (help) change what it is that scientists want altogether. Put another way, the conflict now is between what a country can do in the face of a world-order that is still far from assuming a more ideal state versus what a country ought to do.

    ONOS was necessitated by subscription-based journals charging higher and higher subscription fees, over time guzzling an increasingly non-trivial fraction of the research expenditures of various countries. Yet many scientists wished to keep publishing in these journals because the world’s oldest journals belong to this group and have carefully cultivated a great reputation for themselves. A paper published in their pages ensures it is read by all scientists in that field. In fact, because these journals have also been highly picky about what they publish and there is a global competition to be featured in their pages, to be published with them has itself become a mark of success. The journals’ publishers took advantage of their products’ desirability to increase subscription fees further.

    To break the stranglehold of subscription-based journals, then, is also to break the research publishing culture wherein publishing in XYZ journals is the crowning aspiration. And this is what those who remain critical of ONOS are fighting for, and probably expected ONOS would do as well. Their contention is that rather than passively responding to whatever the country’s research community wants, the government should actively reshape what the community wants. For example, it could ensure a scientist’s career prospects in academia are not affected by the name of the journals in which they publish and only by the quality of their work. Doing so would nudge the community to favour green OA, or that’s the expectation, and move away from ‘prestige’ journals. This is the context in which the quality and resourcefulness of homegrown journals would matter as well.

    In many ways, this line of inquiry constitutes the essential criticism of ONOS, the fundamental substrate upon which more material concerns — like how its allocation will change and how it will prevent paying for already freely-available papers — stand. If we go by the press conference alone, the government has staved this criticism off for now by moving its object into the future. The “OA transformation” is the ultimate outcome one must ensure the government’s plan for ONOS achieves, otherwise what the country is prepared to do will allow subscription-based journals to flourish at the expense of our academic publishing culture.

  • Solve all our problems

    This is xkcd #1232. When it came out I remember it was to rebut a particular line of argument against NASA’s lunar and interplanetary missions — that the agency was spending large sums of money that would be better spent on “solving problems on Earth”. Considering Earth would always have problems, xkcd and others contended, we’d never be able to go to space if we had to spend all our time, money, and labours fixing them. The snark implied in #1232 was warranted.

    But recently, I saw this comic used in a different context: during a conversation (in a private group) about Elon Musk’s aggression with SpaceX and his plans to colonise the moon and visit Mars in his lifetime. Insofar as #1232 pushed back against space exploration that couldn’t by any measure subtract from public spending on socio-economic welfare and justice, it was clever and good. But in the conversation in the group, #1232 donned a new implication: of reducing any other (even minimally) legitimate criticism of the world’s plans to land probes on the moon, establish lunar bases, and start the human campaign to permanently settle the moon and of Elon Musk’s and SpaceX’s plans to being an argument about spending on space exploration subtracting from more immediately measurable pursuits.

    Two arguments come to mind that are poorly served by such flattening. First: the pace at which SpaceX has been manufacturing satellites, launching rockets, and expanding its satellite constellations is at odds with its, and our, ability to deal with the environmental footprint of these activities. Neither SpaceX nor Musk have made any provisions for the activities to be sustainable and they should asap. Doing so might slow the company down, and the company needs to stop considering this retardation to be undesirable. Yet SpaceX’s supporters have often construed any criticism of the company’s pace to be criticism of the company altogether and as the argument that its money would be better spent doing other things.

    Second: I was recently asked a curious question during a formal engagement at work. Is it ethical for India to spend so much on Gaganyaan considering we live in a world with war, violence, and poverty? Gaganyaan has so far cost the Indian government more than Rs 11,000 crore. But there are a couple underlying assumptions here, leading up to questions of the ethicality of human spaceflight, that are flawed.

    (i) The allocation of resources for various activities isn’t a zero-sum game in India. The national budget is voluminous enough for the government to fund both human spaceflight and poverty alleviation programmes. Also unlike in game theory, fractional outcomes are possible and possibly more desirable. For example, India can make great strides in its poverty alleviation programme if it diverts only 0.1% of its defence spending (Rs 6.2 lakh crore in 2024-2025) that way.

    (ii) Many of us like to believe if we don’t spend money on X, it will be available for Y. (Here, X could be ’spaceflight’ and Y could be ‘alleviating poverty’.) We don’t stop to ask whether the state will divert it to Z instead (say, ‘missiles’). If we’d like to guarantee X → Y, we need to persuade the state to rejig its existing priorities and prevent X → Z. Expecting ISRO to not pursue Gaganyaan with funds provided by the state isn’t reasonable.

    In sum, it seems like the “let’s first fix all problems on Earth” argument has become both straw man and red herring in conversations about off-world human activities whose benefits aren’t entirely clear at the moment. The real problem is of course that the benefits aren’t clear, not that the activities are happening at all, plus the belief that money spared by not performing one activity will automatically become available for the precise alternative activity we’re rooting for.

  • Keep the crap going

    Have you seen the new ads for Google Gemini?

    In one version, just as a young employee is grabbing her fast-food lunch, she notices her snooty boss get on an elevator. So she drops her sandwich, rushes to meet her just as the doors are about to close, and submits her proposal in the form of a thick dossier. The boss asks her for a 500-word summary to consume during her minute-long elevator ride. The employee turns to Google Gemini, which digests the report and spits out the gist, and which the employee regurgitates to the boss’s approval. The end.

    Isn’t this unsettling? Google isn’t alone either. In May this year, Apple released a tactless ad for its new iPad Pro. From Variety:

    The “Crush!” ad shows various creative and cultural objects — including a TV, record player, piano, trumpet, guitar, cameras, a typewriter, books, paint cans and tubes, and an arcade game machine — getting demolished in an industrial press. At the end of the spot, the new iPad Pro pops out, shiny and new, with a voiceover that says, “The most powerful iPad ever is also the thinnest.”

    After the backlash, Apple bactracked and apologised — and then produced two ads in November for its Apple Intelligence product showcasing how it could help thoughtless people continue to be thoughtless.

    The second video is additionally weird because it seems to suggest reaching all the way for an AI tool makes more sense than setting a reminder on the calendar that comes in all smartphones these days.

    And they are now joined in spirit by Google, because bosses can now expect their subordinates to Geminify their way through what could otherwise have been tedious work or just impossible to do on punishingly short deadlines — without the bosses having to think about whether their attitudes towards what they believe is reasonable to ask of their teammates need to change. (This includes a dossier of details that ultimately won’t be read.)

    If AI is going to absorb the shock that comes of someone being crappy to you, will we continue to notice that crappiness and demand they change or — as Apple and Google now suggest — will we blame ourselves for not using AI to become crappy ourselves? To quote from a previous post:

    When machines make decisions, the opportunity to consider the emotional input goes away. This is a recurring concern I’m hearing about from people working with or responding to AI in some way. … This is Anna Mae Duane, director of the University of Connecticut Humanities Institute, in The Conversation: “I fear how humans will be damaged by the moral vacuum created when their primary social contacts are designed solely to serve the emotional needs of the ‘user’.”

    The applications of these AI tools have really blossomed and millions of people around the world are using them for all sorts of tasks. But even if the ads don’t pigeonhole these tools, they reveal how their makers — Apple and Google — are thinking about what the tools bring to the table and what these tech companies believe to be their value. To Google’s credit at least, its other ads in the same series are much better (see here and here for examples), but they do need to actively cut down on supporting or promoting the idea that crappy behaviour is okay.