Ads on The Wire Science

Sometime this week, but quite likely tomorrow, advertisements will begin appearing on The Wire Science. The Wire‘s, and by extension The Wire Science‘s, principal source of funds is donations from our readers. We also run ads as a way to supplement this revenue; they’re especially handy to make up small shortfalls in monthly donations. Even so, many of these ads look quite ugly – individually, often with a garish choice of colours, but more so all together, by the very fact that they’re advertisements, representing a business model often rightly blamed for the dilution of good journalism published on the internet.

But I offer all of these opinions as caveats because I’m quite looking forward to having ads on The Wire Science. At least one reason must be obvious: while The Wire‘s success itself, for being an influential and widely read, respected and shared publication that runs almost entirely on readers’ donations, is inspiring, The Wire Science as a niche publication focusing on science, health and the environment (in its specific way) has a long way to go before it can be fully reader funded. This is okay if only because it’s just six months old – and The Wire got to its current pride of place after more than four years, with six major sections and millions of loyal readers.

As things stand, The Wire Science receives its funds as a grant of sorts from The Wire (technically, it’s a section with a subdomain). We don’t yet have a section-wise breakdown of where on the site people donate from, so while The Wire Science also solicits donations from readers (at the bottom of every article), it’s perhaps best to assume it doesn’t funnel much. Against this background, the fact that The Wire Science will run ads from this week is worth celebrating for two reasons: 1. that it’s already a publication where ads are expected to bring in a not insubstantial amount of money, and 2. that a part of this money will be reinvested in The Wire Science.

I’m particularly excited about reason no. 1. Yes, ads suck, but I think that’s truer in the specific context of ads being the principal source of funds – when editors are subordinated to business managers and editorial decisions serve the bottomline. But our editorial standards won’t be diluted by the presence of ads because of ads’ relative contribution to our revenue mix. (I admit that psychologically it’s going to take some adjusting.) The Wire Science is already accommodated in The Wire‘s current outlay, which means ad revenue is opportunistic, and an opportunity in itself to commission an extra story now and then, get more readers to the site and have a fraction of them donate.

I hope you’ll be able to see it the same way, and skip the ad-blocker if you can. πŸ™‚

Eight years

On June 1 last year, I wrote:

Today, I complete seven years of trying to piece together a picture of what journalism is and where I fit in.

Today, I begin my ninth year as a journalist. I’m happy to report I’m not so confused this time round, if only because in the intervening time, two things have taken shape that have allowed me to channel my efforts and aspirations better, leaving less room for at least some types of uncertainty.

The first is The Wire Science, which was born as an idea around August 2019 and launched as a separate website in February 2020. From The Wire‘s point of view, the vision backing the product is “to build a constituency for science journalism – of contributors as well as readers – and drive a science journalism ecosystem.”

For me, this is in addition an opportunity to publish high-quality science writing that breaks away from the instrumental narratives that dominate most journalistic science pieces in India today.

The second thing that took shape was our readers’ and supporters’ appreciation for The Wire‘s work in general. I like to think we’re slowly breaking even on this front, indicating that we’re doing something right.

On these notes of focus, progress and hope – even though the last 12 months have been terrible in many ways – I must say I do look forward to the next 12 months. I’m sure lots of things are going to go wrong, just as they’ve been going wrong, but for once it also feels like there are going to be meaningful opportunities to do something about them.

For coronavirus claims, there is a world between true and false

In high school, you must have learnt about Boolean algebra, possibly the most fascinating kind of algebra for its deceptive ease and simplicity. But thanks to its foundations in computer science, Boolean algebra – at least as we it learnt in school – is fixated with ‘true’ and ‘false’ states but not with the state of ‘don’t know’ that falls in between. This state may not have many applications as regards the functioning of logic gates but in the real world, it is quite important, especially when the truth threatens to be spun out of control.

Amitabh Bachchan recently published a video in which he delivered a monologue claiming that when a fly alights on human faeces containing traces of the new coronavirus, flies off and then alights on some food, the food could also be contaminated by the same virus. The Wire Science commissioned a fact-check from Dr Deepak Natarajan, a reputed (and thankfully opinionated) cardiologist in New Delhi. In his straightforward article, Dr Natarajan presents evidence from peer-reviewed papers to argue that while we know the new coronavirus does enter the faeces of an infected person, we don’t know anything about whether the virus remains viable, or capable of precipitating an infection. Second, we know nothing of the participation of flies either.

The thing to remember here is that, during a panic – or in a pre-panic situation that constantly threatens to devolve into a panic – society as such has an unusually higher uptake capacity for information that confirms their biases irrespective of whether it is true. This property, so to speak, amplifies the importance of ‘not knowing’.

Thanks to scientism, there is a common impression among many experts and most non-experts that science has, or could have, the answers to all questions that could ever be asked. So when a scientist says she does not know something, there is a pronounced tendency among some groups of people – particularly, if not entirely, those who may not be scientistic themselves but believe science itself is scientistic – to assume the lack of an answer means the absence of an answer. That is, to think “If the scientist does not have an answer, then the science does not have an answer”, rather than “If the scientist does not have an answer, then the science does not have an answer yet” or even “If the scientist does not have an answer yet, she could have an answer later“.

This response at a time of panic or pre-panic forces almost all information to be classified as either ‘true’ or ‘false’, precluding the agency science still retains to move towards a ‘true’ or ‘false’ conclusion and rendering their truth-value to be a foregone conclusion. That is, we need evidence to say if something is true – but we also need to understand that saying something is ‘not true’ without outright saying it is ‘false’ is an important state of the truth itself.

It also forces the claimant to be more accountable. Here is one oversimplified but nonetheless illustrative example: When only ‘true’ and ‘false’ exist, any new bit of information has a 50% chance of being in one bin or the other. But when ‘not true/false’ or ‘don’t know’ is in the picture, new information has only a 33% chance of assuming one of the truth values. Further, the only truth value based on which people should be allowed to claim something is true is ‘true’. ‘False’ has never been good enough but ‘don’t know’ is not good enough either, which means that before we subject a claim to a test, it has a 66% chance of being ‘not true’.

Amitabh Bachchan’s mistake was to conflate ‘don’t know’ and ‘true’ without considering the possibility of ‘not true’, and has thus ended up exposing his millions of followers on Twitter to claims that are decidedly not true. As Dr Natarajan said, silence has never been more golden.

Another controversy, another round of blaming preprints

On February 1, Anand Ranganathan, the molecular biologist more popular as a columnist for Swarajya, amplified a new preprint paper from scientists at IIT Delhi that (purportedly) claims the Wuhan coronavirus’s (2019 nCoV’s) DNA appears to contain some genes also found in the human immunodeficiency virus but not in any other coronaviruses. Ranganathan also chose to magnify the preprint paper’s claim that the sequences’ presence was “non-fortuitous”.

To be fair, the IIT Delhi group did not properly qualify what they meant by the use of this term, but this wouldn’t exculpate Ranganathan and others who followed him: to first amplify with alarmist language a claim that did not deserve such treatment, and then, once he discovered his mistake, to wonder out loud about whether such “non-peer reviewed studies” about “fast-moving, in-public-eye domains” should be published before scientific journals have subjected them to peer-review.

The more conservative scientist is likely to find ample room here to revive the claim that preprint papers only promote shoddy journalism, and that preprint papers that are part of the biomedical literature should be abolished entirely. This is bullshit.

The ‘print’ in ‘preprint’ refers to the act of a traditional journal printing a paper for publication after peer-review. A paper is designated ‘preprint’ if it hasn’t undergone peer-review yet, even though it may or may not have been submitted to a scientific journal for consideration. To quote from an article championing the use of preprints during a medical emergency, by three of the six cofounders of medRxiv, the preprints repository for the biomedical literature:

The advantages of preprints are that scientists can post them rapidly and receive feedback from their peers quickly, sometimes almost instantaneously. They also keep other scientists informed about what their colleagues are doing and build on that work. Preprints are archived in a way that they can be referenced and will always be available online. As the science evolves, newer versions of the paper can be posted, with older historical versions remaining available, including any associated comments made on them.

In this regard, Ranganathan’s ringing the alarm bells (with language like “oh my god”) the first time he tweeted the link to the preprint paper without sufficiently evaluating the attendant science was his decision, and not prompted by the paper’s status as a preprint. Second, the bioRxiv preprint repository where the IIT Delhi document showed up has a comments section, and it was brimming with discussion within minutes of the paper being uploaded. More broadly, preprint repositories are equipped to accommodate peer-review. So if anyone had looked in the comments section before tweeting, they wouldn’t have had reason to jump the gun.

Third, and most important: peer-review is not fool-proof. Instead, it is a legacy method employed by scientific journals to filter legitimate from illegitimate research and, more recently, higher quality from lower quality research (using ‘quality’ from the journals’ oft-twisted points of view, not as an objective standard of any kind).

This framing supports three important takeaways from this little scandal.

A. Much like preprint repositories, peer-reviewed journals also regularly publish rubbish. (Axiomatically, just as conventional journals also regularly publish the outcomes of good science, so do preprint repositories; in the case of 2019 nCoV alone, bioRxiv, medRxiv and SSRN together published at least 30 legitimate and noteworthy research articles.) It is just that conventional scientific journals conduct the peer-review before publication and preprint repositories (and research-discussion platforms like PubPeer), after. And, in fact, conducting the review after allows it to be continuous process able to respond to new information, and not a one-time event that culminates with the act of printing the paper.

But notably, preprint repositories can recreate journals’ ability to closely control the review process and ensure only experts’ comments are in the fray by enrolling a team of voluntary curators. The arXiv preprint server has been successfully using a similar team to carefully eliminate manuscripts advancing pseudoscientific claims. So as such, it is easier to make sure people are familiar with the preprint and post-publication review paradigm than to take advantage of their confusion and call for preprint papers to be eliminated altogether.

B. Those who support the idea that preprint papers are dangerous, and argue that peer-review is a better way to protect against unsupported claims, are by proxy advocating for the persistence of a knowledge hegemony. Peer-review is opaque, sustained by unpaid and overworked labour, and dispenses the same function that an open discussion often does at larger scale and with greater transparency. Indeed, the transparency represents the most important difference: since peer-review has traditionally been the demesne of journals, supporting peer-review is tantamount to designating journals as the sole and unquestionable arbiters of what knowledge enters the public domain and what doesn’t.

(Here’s one example of how such gatekeeping can have tragic consequences for society.)

C. Given these safeguards and perspectives, and as I have written before, bad journalists and bad comments will be bad irrespective of the window through which an idea has presented itself in the public domain. There is a way to cover different types of stories, and the decision to abdicate one’s responsibility to think carefully about the implications of what one is writing can never have a causal relationship with the subject matter. The Times of India and the Daily Mail will continue to publicise every new paper discussing whatever coffee, chocolate and/or wine does to the heart, and The Hindu and The Wire Science will publicise research published in preprint papers because we know how to be careful and of the risks to protect ourselves against.

By extension, ‘reputable’ scientific journals that use pre-publication peer-review will continue to publish many papers that will someday be retracted.

An ongoing scandal concerning spider biologist Jonathan Pruitt offers a useful parable – that journals don’t always publish bad science due to wilful negligence or poor peer-review alone but that such failures still do well to highlight the shortcomings of the latter. A string of papers the work on which Pruitt led were found to contain implausible data in support of some significant conclusions. Dan Bolnick, the editor of The American Naturalist, which became the first journal to retract Pruitt’s papers that it had published, wrote on his blog on January 30:

I want to emphasise that regardless of the root cause of the data problems (error or intent), these people are victims who have been harmed by trusting data that they themselves did not generate. Having spent days sifting through these data files I can also attest to the fact that the suspect patterns are often non-obvious, so we should not be blaming these victims for failing to see something that requires significant effort to uncover by examining the data in ways that are not standard for any of this. … The associate editor [who Bolnick tasked with checking more of Pruitt’s papers] went as far back as digging into some of Pruitt’s PhD work, when he was a student with Susan Riechert at the University of Tennessee Knoxville. Similar problems were identified in those data… Seeking an explanation, I [emailed and then called] his PhD mentor, Susan Riechert, to discuss the biology of the spiders, his data collection habits, and his integrity. She was shocked, and disturbed, and surprised. That someone who knew him so well for many years could be unaware of this problem (and its extent), highlights for me how reasonable it is that the rest of us could be caught unaware.

Why should we expect peer-review – or any kind of review, for that matter – to be better? The only thing we can do is be honest, transparent and reflexive.