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On that 'Last Word on Nothing' post

A post published on the Last Word On Nothing blog yesterday has been creating quite the stir on Twitter. Excerpt:

While I can appreciate that this is an important scientific discovery, I still have a hard time mustering excitement over gravitational waves. I would not have read these articles had I not embarked on this experiment. And I wanted to stop reading some of these articles as I was conducting the experiment. Space is not my thing. I don’t think it ever will be, at least not without a concerted effort on my part to get a basic handle on physics and astronomy. …

Physics writers, this is how you nab the physics haters — human emotion. You can explain gravitational waves using the cleanest, clearest, most eloquent words that exist — and you should! — but I want the story of the scientists in all their messy, human glory.

Cassandra Willyard, the post’s author, was writing about the neutron-star collision announcement from LIGO. Many of those who are dissing the point the post is making are saying that Willyard is vilifying the ‘school’ of science writing that focuses on the science itself over its relationship with the human condition. I think she’s only expressing her personal opinion (as the last line in the excerpt suggests) – so the levels of indignation that has erupted in some pockets of the social media over these opinions suggests Willyard may have touched off some nerves.

I myself belong to the school that prefers to excite science readers over the science itself over its human/humanist/humanitarian aspects. In the words of Tracy, who wrote them as a comment on Willyard’s post,

So many amazing things happen in this universe without a human noticing it, reflecting on it, understanding it, being central to it. So many wondrous mysteries abound despite the ego. The human story is just one of billions.

And I will concede from personal experience that it’s quite difficult as a result to sell such stories to one’s editors as well as readers. I’ve written about this many times before, e.g. here; edited excerpt:

I couldn’t give less of a fuck for longer pieces, especially because they’re all the same: they’re concerned with science that is deemed to be worthy of anyone’s attention because it is affecting us directly. And I posit that they’ve kept us from recognising an important problem with science journalism in the country: it is becoming less and less concerned with the science itself; what has been identified as successful science journalism is simply a discussion – no matter how elaborate and/or nuanced – of how science impacts us. Instead, I’d love to read a piece reported over 5,000 words about molecules, experiments, ideas. It should be okay to want to write only about particle physics because that’s all I’m interested in reading. Okay to want to write only about this even if I don’t have any strength to hope that QCD will save lives, that Feynman diagrams will help repeal AFSPA, that the LHC will accelerate India’s economic growth, that the philosophies of fundamental particles will lead to the legalisation of same-sex marriage. I haven’t been presented with any evidence whatsoever to purchase my faith in the possibility that the obscurities of particle physics will help humans in any way other than to enlighten them, that there is neither reward nor sanction in anxiously bookending every articulation of wonder with the hope that we will find a way to profit from all of our beliefs, discoveries and perceptions.

For many people in this ‘school’, this fight is almost personal because it’s arduous and requires tremendous conviction, will and resilience on one’s part to see coverage of such kind through. In this scenario, to have a science writer come forward and say “I won’t write about this science because I don’t understand this science” can be quite dispiriting. It’s a science writer’s job to disentangle some invention, discovery or whatever and then communicate it to those who are interested in knowing more about it. So when Willyard writes in her post that “The day I write about a neutron star collision is the day hell will freeze over” – it’s a public abdication of an important responsibility, and arguably one of the most complicated responsibilities in journalism in the Information Age thanks to its fiercely non-populist nature.

(Such a thing happened recently with Natalie Wolchover as well. Her words – written against topological physics – were more disappointing to come across because Wolchover writes very good physics pieces for Quanta. And while she apologised for the “flippancy” of her tweet shortly after, saying that she’d been in a hurry at 5.45 am, that’s precisely the sort of sentiment that shouldn’t receive wider coverage without the necessary qualifications. So my thanks to Chad Orzel for the thread he published in response.)

However, it must be acknowledged that the suggestion Willyard makes (in the second paragraph of the excerpt) is quite on point. To have to repeatedly pander to the human condition in one way or another when in fact you think the science in and of itself is incredibly cool can become frustrating over time – but this doesn’t mean that a fundamental disconnect between writers like me and the statistically average science reader out there doesn’t exist. If I’m to get her attention, then I’ve found from experience that one must begin with the humans of science and then flow on to the science itself. As Alice Bell recommends here, you start upstream and go downstream. And once you’ve lured them in, you can begin to discuss the science more freely.

(PS: Some areas of Twitter have gone nuts, claiming Willyard shouldn’t be called a science journalist. I’m making no such judgment call. To be clear, I’m only criticising a peer’s words. I still consider Willyard to be a science journalist – though my fingers cry as I type this because it’s so embarrassing to have to spell it out – and possibly a good one at that going by her willingness to introspect.)

Featured image credit: Pexels/pixabay.

Oct 19, 2017
Hair conditioners and immortality

I’m not a fan of cosmetic products whatsoever. The most I use is a bar of soap, a bottle of shampoo, a smaller bottle of coconut oil and the occasional earbud. Maybe a bottle of deodorant when I’ve been out in the sun overlong. But recently, when I made a trip to Delhi, more than one person noticed that I don’t moisturise and suggested that I do. I wasn’t embarrassed because my anti-cosmetics line is, or was, one of principle: they’re unnecessary products of the consumerist culture. Look no further than the hair conditioner: there’s no reason shampoos can’t be chemically engineered to condition one’s hair as well – but no. Two products means double the revenue, especially if they can be marketed and sold together.

However, the advice about moisturising struck me. While it is redundant in Chennai (especially for me; I grew up in the city and have skin used to high humidity and naturally oily hair), moisturisers are almost mandatory to have healthy skin in Delhi. The national capital has dry weather all year round except during the monsoon spell, around July. During summers, hot, dry winds blow through the city, transforming it into a Bessemer converter. During winters, cold, dry winds move like sludge through the air, cracking skin everywhere in minutes. So from this perspective, what could be overkill in Chennai is a necessity in Delhi.

This in turn recalls a more important and consequential distinction that has occasionally surfaced in anti-vaccination propaganda, among other contexts. Humans live much longer today than they did, say, 500 years ago because we invented antibiotics in the intervening period – and we as a species accomplish more in a single generation today than we did ever before in history as a result. But are antibiotics cosmetic? The answer would be a ready ‘no’ if humans had some sort of moral obligation to live longer. But do we?

What will simplify this consideration is acknowledging that the obligation we do have is to improve the quality of life. Thanks to antibiotic prescriptions, we spend fewer hours in a lifetime tending to diseases, and we lose fewer years to disabilities. However, not all kinds/forms of medication are dedicated to making us live better lives. For example, a study published in March 2017 by researchers from the University of New South Wales announced the discovery of a cellular mechanism the manipulation of which slowed down, and even eliminated, ageing in mice. The researchers said that human trials are set to begin later this year. Notwithstanding any negative outcomes during the trials, will the introduction of an anti-ageing drug in the market be equivalent to the introduction of a new hair conditioner? In other words, the question is whether increased human lifespan is equivalent to, or even a subset of, a better quality of life.

The UNSW team isn’t alone in its pursuit. While it had found a way to improve cells’ ability to repair their DNA in case of damage, a research group from the Mayo Clinic College of Medicine, Minnesota, claimed in 2016 that they could make mice live longer by causing such problem cells to self-destruct. Peter de Kezier, a scientist at the Erasmus University Medical Centre, the Netherlands, had told The Guardian at the time: “Maybe when you get to 65 you’ll go every five years for your anti-senescence shot in the clinic. You’ll go for your rejuvenation shot.”

In the same year, a group from the Salk Institute in California announced that it had slowed ageing in mice by 30% by replacing the problem cells with pluripotent stem cells. The group’s leader Juan Carlos Izpisua Belmonte had said, “We believe that this approach will not lead to immortality. There are probably still limits that we will face in terms of complete reversal of ageing. Our focus is not only extension of lifespan but most importantly health-span.” I assume by ‘health-span’ he means the number of years lived in good health – and this is interesting.

All these anti-ageing studies have one thing in common: they started out trying to eliminate age-related diseases, and now are pursuing anti-ageing therapies as a way to eliminate those diseases. So should such therapies become commonplace, they will improve the quality of life by making us less susceptible to those diseases. But this is not the same as walking into a clinic once every five years for an anti-senescence shot or a rejuvenation shot just to live longer. The latter feels less principled, probably because it will shape up to be more of an enhancement of the quantity of life than of the quality of life. The ones having lived for longer as a result will also have been those who could afford all those shots.

In other words, it sounds just like hair conditioner.

Featured image credit: tookapic/pixabay.

Oct 18, 2017
Confused thoughts on embargoes

Seventy! That’s how many observatories around the world turned their antennae to study the neutron-star collision that LIGO first detected. So I don’t know why the LIGO Collaboration, and Nature, bothered to embargo the announcement and, more importantly, the scientific papers of the LIGO-Virgo collaboration as well as those by the people at all these observatories. That’s a lot of people and many of them leaked the neutron-star collision news on blogs and on Twitter. Madness. I even trawled through arΧiv to see if I could find preprint copies of the LIGO papers. Nope; it’s all been removed.

Embargoes create hype from which journals profit. Everyone knows this. Instead of dumping the data along with the scientific articles as soon as they’re ready, journals like Nature, Science and others announce that the information will all be available at a particular time on a particular date. And between this announcement and the moment at which the embargo lifts, the journal’s PR team fuels hype surrounding whatever’s being reported. This hype is important because it generates interest. And if the information promises to be good enough, the interest in turn creates ‘high pressure’ zones on the internet – populated by those people who want to know what’s going on.

Search engines and news aggregators like Google and Facebook are sensitive to the formation of these high-pressure zones and, at the time of the embargo’s lifting, watch out for news publications carrying the relevant information. And after the embargo lifts, thanks to the attention already devoted by the aggregators, news websites are transformed into ‘low pressure’ zones into which the aggregators divert all the traffic. It’s like the moment a giant information bubble goes pop! And the journal profits from all of this because, while the bubble was building, the journal’s name is everywhere.

In short: embargoes are a traffic-producing opportunity for news websites because they create ‘pseudo-cycles of news’, and an advertising opportunity for journals.

But what’s in it for someone reporting on the science itself? And what’s in it for the consumers? And, overall, am I being too vicious about the idea?

For science reporters, there’s the Ingelfinger rule promulgated by the New England Journal of Medicine in 1969. It states that the journal will not publish any papers with results that have been previously published elsewhere and/or whose authors have not discussed the results with the media. NEJM defended the rule by claiming it was to keep their output fresh and interesting as well as to prevent scientists from getting carried away by the implications of their own research (NEJM’s peer-review process would prevent that, they said). In the end, the consumers would receive scientific information that has been thoroughly vetted.

While the rule makes sense from the scientists’ point of view, it doesn’t from the reporters’. A good science reporter, having chosen to cover a certain paper, will present the paper to an expert unaffiliated with the authors and working in the same area for her judgment. This is a form of peer-review that is extraneous to the journal publishing the paper. Second: a pro-embargo argument that’s been advanced is that embargoes alert science reporters to papers of importance as well as give them time to write a good story on it.

I’m conflicted about this. Embargoes, and the attendant hype, do help science reporters pick up on a story they might’ve missed out on, to capitalise on the traffic potential of a new announcement that may not be as big as it becomes without the embargo. Case in point: today’s neutron-star collision announcement. At the same time, science reporters constantly pick up on interesting research that is considered old/stale or that wasn’t ever embargoed and write great stories about them. Case in point: almost everything else.

My perspective is coloured by the fact that I manage a very small science newsroom at The Wire. I have a very finite monthly budget (equal to about what someone working eight hours a day and five days a week would make in two months on the US minimum wage) using which I’ve to ensure that all my writers – who are all freelancers – provide both the big picture of science in that month as well as the important nitty-gritties. Embargoes, for me, are good news because it helps me reallocate human and financial resources for a story well in advance and make The Wire‘s presence felt on the big stage when the curtain lifts. Rather, even if I can’t make it on time to the moment the curtain lifts, I’ve still got what I know for sure is good story on my hands.

A similar point was made by Kent Anderson when he wrote about eLife‘s media policy, which said that the journal would not be enforcing the Ingelfinger rule, over at The Scholarly Kitchen:

By waiving the Ingelfinger rule in its modernised and evolved form – which still places a premium on embargoes but makes pre-publication communications allowable as long as they don’t threaten the news power – eLife is running a huge risk in the attention economy. Namely, there is only so much time and attention to go around, and if you don’t cut through the noise, you won’t get the attention. …

Like it or not, but press embargoes help journals, authors, sponsors, and institutions cut through the noise. Most reporters appreciate them because they level the playing field, provide time to report on complicated and novel science, and create an effective overall communication scenario for important science news. Without embargoes and coordinated media activity, interviews become more difficult to secure, complex stories may go uncovered because they’re too difficult to do well under deadline pressures, and coverage becomes more fragmented.

What would I be thinking if I had a bigger budget and many full-time reporters to work with? I don’t know.

On Embargo Watch in July this year, Ivan Oransky wrote about how an editor wasn’t pleased with embargoes because “staffers had been pulled off other stories to make sure to have this one ready by the original embargo”. I.e., embargoes create deadlines that are not in your control; they create deadlines within which everyone, over time, tends to do the bare minimum (“as much as other publications will do”) so they can ride the interest wave and move on to other things – sometimes not revisiting this story again even. In a separate post, Oransky briefly reviewed a book against embargoes by Vincent Kiernan, a noted critic of the idea:

In his book, Embargoed Science, Kiernan argues that embargoes make journalists lazy, always chasing that week’s big studies. They become addicted to the journal hit, afraid to divert their attention to more original and enterprising reporting because their editors will give them grief for not covering that study everyone else seems to have covered.

Alice Bell wrote a fantastic post in 2010 about how to overcome such tendencies: by newsrooms redistributing their attention on science to both upstream and downstream activities. But more than that, I don’t think lethargic news coverage can be explained solely by the addiction to embargoes. A good editor should keep stirring the pot – should keep her journalists moving on good stories, particularly of the kind no one wants to talk about, report on it and play it up. So, while I’m hoping that The Wire‘s coverage of the neutron-star collision discovery is a hit, I’ve also got great pieces coming this week about solar flares, open-access publishing, the health effects of ******** mining and the conservation of sea snakes.

I hope time will provide some clarity.

Featured image credit: Free-Photos/pixabay.

Oct 16, 2017
Neutron stars

When the hype for the announcement of the previous GW detection was ramping up, I had a feeling LIGO was about to announce the detection of a neutron-star collision. It wasn’t to be – but in my excitement, I’d written a small part of the article. I’m sharing it below. I’d also recommend reading this post: The Secrets of How Planets Form.

Stars die. Sometimes, when that happens, their outer layers explode into space in a supernova. Their inner layers collapse inwards under the gravity of their own weight in a violent rush. If the starstuff can be packed dense enough, the collapse produces a blackhole – a volume of space where the laws of quantum mechanics and relativity break down and the particles of matter are plunged into a monumental identity crisis. However, if the dying star wasn’t heavy enough when it blew up, then the inward rush will create a very, very, very dense object – but not a blackhole: a neutron star.

Neutron stars are the densest objects in the universe that astronomers can observe. The only things we know are denser than them are blackholes.

You’d think observed means ‘saw’, but what is ‘seeing’ but the light – a form of electromagnetic energy – from an event reaching our eyes? We can’t directly ‘see’ blackholes collide because the collision doesn’t release any electromagnetic energy. So astronomers have built a special kind of eyes – called gravitational wave detectors – that can observe ripples of gravitational energy that the collision lets loose.

The Laser Interferometer Gravitational-wave Detector (LIGO) we already know about. Its twin eyes, located in Washington and Louisiana, US, have detected three blackhole-blackhole collisions thus far. Two of the scientists who helped build it are hot favourites to win the Nobel Prize for physics next week. The other set of eyes involved in the last find is Virgo, a detector in Italy.

You’ve been told that blackholes are freaks of nature. Heavy objects bend spacetime around themselves. Blackholes are freaks because they step it up: they fold it. They’re so heavy that when spacetime bends around them, it goes all the way around and becomes a three-dimensional loop. Thus, a blackhole traps one patch of the cosmos around a vanishingly small heart of darkness. Even light, if it comes close enough, becomes trapped in this loop and can never escape. This is why astronomers can’t observe blackholes directly, and use gravitational-wave detectors instead.

But neutron stars they can observe. They’re exactly what their names suggest: a ball of neutrons. And neutrons experience a force of nature called the strong nuclear force, and it can be 100,000 billion billion billion times stronger than gravity. This makes neutron stars extremely dense and altogether incredibly heavy as well. On their surface, a classic can of Coke will weigh 355,000 billion tonnes, a thousand-times heavier than all the humans on Earth combined.

Sometimes, a neutron star is ravaged by a powerful magnetic field. This field focuses charged particles on the neutron star’s surface into a tight beam of radiation shooting off into space. If the orb is also spinning, then this beam of radiation sweeps through space like the light from a lighthouse sweeps over the sea near it. Such neutron stars are called pulsars.

Oct 16, 2017
Drama along the line of sight

TIL one reason some of us are so dejected and furious at the TV when in, a cricket match being telecast live, a fielder appears to miss catching the ball even though it looks like he easily could have. A.k.a. why my grandpa loses his shit when M.S. Dhoni won’t chase a ball that has spun past his gloves and is racing towards the boundary. (If you don’t follow cricket, here’s a primer.)

When the bowler runs up to the wicket to bowl a ball, the camera focuses on the batsman, but the frame is set to capture everything from the umpire’s position in the foreground to the back-most man on the slip cordon (the line of fielders standing adjacent to the wicketkeeper) in the background.

However, the camera that’s recording this is located far from the pitch itself, down the ground and beyond the boundary line, at least 270-300 feet from the batsman (according to Law 19.1 of ICC Test Match Playing Conditions). This results in an effect called foreshortening. When the camera has a long line of sight, distances along the line of slight are shrunk by more than distances across the line of sight. For example, in the screenshot above, the pitch is 66 feet long and the wicketkeeper is standing almost 26 feet behind the batsman.

However, onscreen, the ball to be bowled is going to appear as if it’s going to travel 20 or so feet to the batsman and the 10 or so feet to the wicketkeeper. On a cognitive level, viewers are also unmindful of the foreshortening for two reasons: they used to it, and because the ball bowled (by Bhuvaneshwar Kumar, above) is going to move at 120-140 km/hr.

At the same time, foreshortening is going to make it appear as if it’s moving at a slower speed. Broadcasting channels employ on-ground radar to track the speed of the ball and display the number almost immediately after it’s bowled, so foreshortening could arguably dull our sense of how high these speeds are as well.

However, the contrast between shortening along the line of sight versus across the line of sight isn’t very evident in a cricket broadcast because the distances are of comparable magnitudes. Instead, consider the Cassini probe shot of the Jovian moons Epimetheus (lower left) and Janus shown below. Without accounting for foreshortening, it would appear as if the moons are close to each other. However, at the time this image was taken, Janus, on the right, was 40,000 km behind Epimetheus.

Credit: NASA/JPL/Space Science Institute

In the same vein, foreshortening is a common confounding factor when natural terrain is scanned from space.

Axiomatically, painters and graphic artists use foreshortening to imply depth in the viewer’s eye and also suggest an ‘appropriate’ viewing angle. Frescoes created in the 15th century were among the first to use foreshortening to provide an illusion of depth on two-dimensional surfaces. A famous example is Andrea Mantegna’s Lamentation of Christ, created c. 1480. Thanks to the effect being in play, Jesus’s body is angled towards the viewer (along the line of slight), drawing attention to this chest, abdomen, genitals and the holes in his hands and feet.

Credit: Wikimedia Commons

Finally, foreshortening is held to be an essential compositional feature of millennials’ most ubiquitous creation: the selfies. The American art critic Jerry Saltz wrote for Vulture magazine in January 2014,

Maybe the first significant twentieth-century pre-selfie is M.C. Escher’s 1935 lithograph Hand With Reflecting Sphere. Its strange compositional structure is dominated by the artist’s distorted face, reflected in a convex mirror held in his hand and showing his weirdly foreshortened arm. It echoes the closeness, shallow depth, and odd cropping of modern selfies. In another image, which might be called an allegory of a selfie, Escher rendered a hand drawing another hand drawing the first hand. It almost says, “What comes first, the self or the selfie?” My favorite proto-selfie is Parmigianino’s 1523–24 Self-Portrait in a Convex Mirror, seen on the title page of this story. All the attributes of the selfie are here: the subject’s face from a bizarre angle, the elongated arm, foreshortening, compositional distortion, the close-in intimacy. As the poet John Ashbery wrote of this painting (and seemingly all good selfies), “the right hand / Bigger than the head, thrust at the viewer / And swerving easily away, as though to protect what it advertises.”

Oct 12, 2017
By the way: the Chekhov’s gun and the science article

“If in the first act you have hung a pistol on the wall, then in the following one it should be fired. Otherwise don’t put it there.” (source)

This is the principle of the Chekhov’s gun: that all items within a narrative must contribute to the overarching narrative itself, and those that don’t should be removed. This is very, very true of the first two Harry Potter books, where J.K. Rowling includes seemingly random bits of information in the first half of each book that, voila, suddenly reappear during the climax in important ways. (Examples: Quirrell’s turban and the Whomping Willow). Thankfully, Rowling’s writing improves significantly from the third book, where the Chekhov’s guns are more subtly introduced, and don’t always stay out of sight before being revived for the grand finale.

However, does the Chekhov’s gun have a place in a science article?

Most writers, editors and readers (I suspect) would reply in the affirmative. The more a bit of science communication stays away from redundancy, the better. Why introduce a term if it’s not going to be reused, or if it won’t contribute to the reader understanding what a writer has set out to explain? This is common-sensical. But my concern is about introducing information deftly embedded in the overarching narrative but which does not play any role in further elucidating the writer’s overall point.

Consider this example: I’m explaining a new research paper that talks about how a bunch of astronomers used a bunch of cool techniques to identify the properties of a distant star. While what is entirely novel about the paper is the set of techniques, I also include two lines about how the telescopes the astronomers used to make their observations operate using a principle called long baseline interferometry. And a third line about why each telescope is equipped with an atomic clock.

Now, I have absolutely no need to mention the phrases ‘long baseline interferometry’ and ‘atomic clocks’ in the piece. I can make my point just as well without them. However, to me it seems like a good opportunity to communicate to – and not just inform – the reader about interesting technologies, an opportunity I may not get again. But a professional editor (again, I suspect) would argue that if I’m trying to make a point and I know what that point is, I should just make that. That, like a laser pointer, I should keep my arguments focused and coherent.

I’m not sure I would agree. A little bit of divergence is okay, maybe even desirable at times.

Yes, I’m aware that editors working on stories that are going to be printed, and/or are paying per word, would like to keep things as concisely pointy as possible. And yes, I’m aware that including something that needn’t be included risks throwing the reader off, that we ought to minimise risk at all times. Finally, yes, I’m aware that digressing off into rivulets of information also forces the writer to later segue back into the narrative river, and that may not be elegant.

Of these three arguments (that I’ve been able to think of; if you have others, please feel free to let me know), the first one alone has the potential to be non-negotiable. The other two are up to the writer and the editor: if she or they can tuck away little gems of trivia without disrupting the story’s flow, why not? I for one would love to discover them, to find out about connections – scientific, technological or otherwise – in the real world that frequently find expression only with the prefix of a “by the way, did you know…”.

Featured image credit: DariuszSankowski/pixabay.

Oct 11, 2017
Before seeing, there are the ways of imaging

When May-Britt Moser, Edvard Moser and John O’Keefe were awarded the 2014 Nobel Prize for physiology and medicine “for their discoveries of cells that constitute a positioning system in the brain”, there was a noticeable uptick in the number of articles on similar subjects in the popular as well as scientific literature in the following months. The same thing happened with the sciences Nobel Prizes in subsequent years, and I suspect it will be the same this year with cryo-electron microscopy (cryoEM) as well. And I’d like to ride this wave.

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It has often been that the Nobel Prizes for physiology/medicine (a.k.a. ~ for biology) and for chemistry have awarded advancements in chemistry and biology, respectively. This year, however, the chemistry prize was more physics. Joachim Frank, Jacques Dubochet and Richard Henderson – three biologists – were on a quest to make the tool that they were using to explore structural biology more powerful, more efficient. So Frank invented computational techniques; Dubochet invented a new way to prepare the sample; and Henderson used them both deftly to prove their methods worked.

Since then, cryoEM has come a long way but the improvisations hence have only been more sophisticated versions of what Frank, Dubochet and Henderson first demonstrated … except for one component: the microscope’s electronics.

Just the way human eyes are primed to detect photons of a certain wavelength, extract the information encoded in them, convert that into an electric signal and send it to the brain for processing, a cryoEM uses electrons. A wave can be scattered by objects in its path that are of size comparable to the wave’s wavelength. So electrons, which have a shorter wavelength than photons, can be used to probe smaller distances. A cryoEM fires a tight, powerful beam of electrons into the specimen. Parts of the specimen scatter the electrons into a detector on the microscope. The detector ‘reads’ how the electrons have changed and delivers that information to a computer. This happens repeatedly as electron beams are fired at different copies of the specimen oriented at random angles. A computer then puts together a high-resolution 3D image of the specimen using all the detector data. In this scheme of things: a technological advancement in 2012 significantly improved the cryoEM’s imaging abilities. It was called the direct electron detector, developed to substitute the charged couple device (CCD).

The simplest imaging system known to humans is the photographic film, which uses a surface of composed of certain chemical substances that are sensitive visible light. When the surface is exposed to a frame, say a painting, the photons reflected by the painting impinge on the surface. The substances therein then ‘record’ the information carried by the photons in the form of a photograph. A CCD employs a surface of metal-oxide semiconductors (MOS). A semiconductor relies on the behaviour of electric charge on either side of a special junction: an interface of dissimilar materials to which impurities have been added such that one layer is rich in electrons (n) and the other, poor (p). The junction will now either conduct electricity or not depending on how a voltage is applied across it. Anyway: when a photon impinges on the MOS, the latter releases an electron (thanks to the photoelectric effect) that is then moved through the device to an area where it can be manipulated to contribute to one pixel of the image.

(Note: When I write ‘one photon’ or ‘one electron’, I don’t mean one exactly. Various uncertainties, including Heisenberg’s, prevail in quantum mechanics and it’s unreasonable to assume humans can manipulate particles one at a time. My use of the singular is only illustrative. At the same time, I hope you will pause to appreciate – later in this post – how close to the singular we’ve been able to get.)

CCDs can produce images quickly and with high contrast even in low light. However, they have an important disadvantage. CCDs have a lower detective quantum efficiency than photographic films at higher spatial frequencies. Detective quantum efficiency is a measure of how well a detector – like the film or a CCD – can record an image when the signal to noise ratio is higher. For example, when you’re getting a dental X-ray done to understand how your teeth look below the gums, your mouth is bombarded with X-ray photons that penetrate the gums but don’t penetrate the teeth. The more such photons there are, the better the image of your teeth. However, inundating your mouth with X-rays just to get a better picture risks damaging tissue and hurting you. This would be the case if an X-ray ‘camera’ had a CCD with a lower detective quantum efficiency. The simplest workaround would be to use an amplifier to boost the signal produced by the detector – but then this would also boost the noise.

So, in other words, CCDs have more trouble recording the finer details in an image than photographic films when there is a lot of noise coming with the incident signal. The noise can also be internally generated, such as during the process when photons are converted into electrons.

However, scientists can’t use photographic films with cryoEM instead because CCDs have other important advantages. They scan images faster, allow for easier refocusing and realignment of the object under study, and require lesser maintenance. This dilemma provided the impetus to develop the direct electron detector – effectively a CCD with better detective quantum efficiency.

Because a cryoEM is in the business of ‘seeing’ electrons, a scintillator is placed between the electrons and the CCD. When the electron hits the scintillator, the material absorbs the energy and emits a glow – in the form of a photon. This photon is then picked up by the CCD for processing. Sometimes, the incoming electron may not create a photon at exactly the location on the scintillator where it is received. Instead, it may bounce off of multiple locations, producing a splatter of photons in a larger area and creating a blur in the image.

In a direct electron detector, the scintillator is removed, forcing the CCD to directly receive and process electrons produced by the initial beam for study. Such (higher energy) electrons can damage the CCD as well as produce unnecessary signals within the system. These effects can be protected against using suitable hardware and circuit design techniques, either of which required advancements in materials science that weren’t available until recently. Even so, the eventual device itself is pretty simple in design. According to the 2009 doctoral thesis of one Liang Jin,

The device can be divided into three major regions. At the very top of the surface is the circuitry layer that has pixel transistors and photodiode as well as interconnects between all the components (metallisation layers). The middle layer is a p-epitaxial layer (about 8 to 10 µm thick) that is epitaxially grown with very low defect levels and highly doped. The rest of the 300 um silicon substrate is used mainly for mechanical support.

…

On average, a single incident electron of 200 keV will generate about 2,000 ionisation electrons in the 10 µm epitaxial layer, which is significantly larger than the noise level of the device (less than 50 electrons). Each pixel integrates the collected electrons during an exposure period and at the conclusion of a frame, the contents of the sensor array are read out, digitised and stored.

To understand the extent to which noise was reduced as a result, consider an example. In 2010, a research group led by Jean-Paul Armache of the Ludwig-Maximilians-Universität München was able to image eukaryotic ribosomes using cryoEM at a resolution of 6 angstrom (0.6 nanometers) using 1.4 million images. In 2013, a different group, led by Xiao-chen Bai of the Medical Research Council Laboratory of Molecular Biology in Cambridge, the UK, imaged the same ribosomes to 4.5 angstrom using 35,813 images. The first group used cryoEM + CCDs. The second group used cryoEM + direct detection devices.

An even newer development seeks to bring back the CCD as the detector of choice among structural biologists. In September 2017, scientists from the Femi National Accelerator Laboratory announced that they had engineered a highly optimised skipper CCD in their lab. The skipper CCD was first theorised by, among others, D.D. Wen in 1974. It’s a CCD in which the electrons released by the photons are measured multiple times – up to 4,000 times per pixel according to one study – during processing to better separate signal from noise. The same study said that, as a result, the skipper CCD’s readout noise could be reduced to 0.068 electrons per pixel. The cost for this was that from the time the CCD received the first electrons to when the processed image became available, it would be a few hours. But in a review, Michael Schirber, a corresponding editor for Physics, argues that “this could be an acceptable tradeoff for rare events, such as hypothetical dark matter particles interacting with silicon atoms”.

Featured image: Scientists using a 300kV cryo-electron microscope at the Max Planck Institute of Molecular Physiology, Dortmund. Credit: MPI Dortmund.

Oct 8, 2017
Are the papers behind this year’s Nobel Prizes in the public domain?

Note: One of my editors thought this post would work for The Wire as well, so it’s been republished there.

“… for the greatest benefit of mankind” – these words are scrawled across a banner that adorns the Nobel Prize’s homepage. They are the words of Alfred Nobel, who instituted the prizes and bequeathed his fortunes to run the foundation that awards them. The words were chosen by the prize’s awarders to denote the significance of their awardees’ accomplishments.

However, the scientific papers that first described these accomplishments in the technical literature are often not available in the public domain. They languish behind paywalls erected by the journals that publish them, that seek to cash in on their importance to the advancement of science. Many of these papers are also funded by public money, but that hasn’t deterred journals and their publishers from keeping the papers out of public reach. How then can they be for the greatest benefit of mankind?

§

I’ve listed some of the more important papers published by this year’s laureates; they describe work that earned them their respective prizes. Please remember that my choice of papers is selective; where I have found other papers that are fully accessible – or otherwise – I have provided a note. This said, I picked the papers from the scientific background document first and then checked if they were accessible, not the other way round. (If you, whoever you are, are interested in replicating my analysis but more thoroughly, be my guest; I will help you in any way I can.)

A laureate may have published many papers collectively for which he was awarded (this year’s science laureates are all male). I’ve picked the papers most proximate to their citation from the references listed in the ‘advanced scientific background’ section available for each prize on the Nobel Prize website. Among publishers, the worst offender appears – to no one’s surprise – to be Elsevier.

A paper title in green indicates it’s in the public domain; red indicates it isn’t – both on the pages of the journal itself. Some titles in red maybe available in full elsewhere, such as in university archives. The names of laureates in the papers’ citations are underlined.

Physiology/medicine

“for their discoveries of molecular mechanisms controlling the circadian rhythm”

The paywall for papers by Young and Rosbash published in Nature were lifted by the journal on the day their joint Nobel Prize was announced. Until then, they’d been inaccessible to the general public. Interestingly, both papers acknowledge funding grants from the US National Institutes of Health, a tax-funded body of the US government.

Michael Young

Restoration of circadian behavioural rhythms by gene transfer in Drosophila – Nature 312, 752 – 754 (20 December 1984); doi:10.1038/312752a0 link

Isolation of timeless by PER protein interaction: defective interaction between timeless protein and long-period mutant PERL – Gekakis, N., Saez, L., Delahaye-Brown, A.M., Myers, M.P., Sehgal, A., Young, M.W., and Weitz, C.J. (1995). Science 270, 811–815. link

Michael Rosbash

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels – Nature 343, 536 – 540 (08 February 1990); doi:10.1038/343536a0 link

The period gene encodes a predominantly nuclear protein in adult Drosophila – Liu, X., Zwiebel, L.J., Hinton, D., Benzer, S., Hall, J.C., and Rosbash, M. (1992). J Neurosci 12, 2735–2744. link

Jeffrey Hall

Molecular analysis of the period locus in Drosophila melanogaster and identification of a transcript involved in biological rhythms – Reddy, P., Zehring, W.A., Wheeler, D.A., Pirrotta, V., Hadfield, C., Hall, J.C., and Rosbash, M. (1984). Cell 38, 701–710. link

P-element transformation with period locus DNA restores rhythmicity to mutant, arrhythmic Drosophila melanogaster – Zehring, W.A., Wheeler, D.A., Reddy, P., Konopka, R.J., Kyriacou, C.P., Rosbash, M., and Hall, J.C. (1984). Cell 39, 369–376. link

Antibodies to the period gene product of Drosophila reveal diverse tissue distribution and rhythmic changes in the visual system – Siwicki, K.K., Eastman, C., Petersen, G., Rosbash, M., and Hall, J.C. (1988). Neuron 1, 141–150. link

Physics

“for decisive contributions to the LIGO detector and the observation of gravitational waves”

While results from the LIGO detector were published in peer-reviewed journals, the development of the detector itself was supported by personnel and grants from MIT and Caltech. As a result, the Nobel laureates’ more important contributions were published as a reports since archived by the LIGO collaboration and made available in the public domain.

Rainer Weiss

Quarterly progress report – R. Weiss, MIT Research Lab of Electronics 105, 54 (1972) link

The Blue Book – R. Weiss, P.R. Saulson, P. Linsay and S. Whitcomb link

Chemistry

“for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution”

The journal Cell, in which the chemistry laureates appear to have published many papers, publicised a collection after the Nobel Prize was announced. Most papers in the collection are marked ‘Open Archive’ and are readable in full. However, the papers cited by the Nobel Committee in its scientific background document don’t appear there. I also don’t know whether the papers in the collection available in full were always available in full.

Jacques Dubochet

Cryo-electron microscopy of vitrified specimens – Dubochet, J., Adrian, M., Chang, J.-J., Homo, J.-C., Lepault, J., McDowall, A. W., and Schultz, P. (1988). Q. Rev. Biophys. 21, 129-228 link

Vitrification of pure water for electron microscopy – Dubochet, J., and McDowall, A. W. (1981). J. Microsc. 124, 3-4 link

Cryo-electron microscopy of viruses – Adrian, M., Dubochet, J., Lepault, J., and McDowall, A. W. (1984). Nature 308, 32-36 link

Joachim Frank

Averaging of low exposure electron micrographs of non-periodic objects – Frank, J. (1975). Ultramicroscopy 1, 159-162 link

Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli – Radermacher, M., Wagenknecht, T., Verschoor, A., and Frank, J. (1987). J. Microsc. 146, 113-136 link

SPIDER-A modular software system for electron image processing – Frank, J., Shimkin, B., and Dowse, H. (1981). Ultramicroscopy 6, 343-357 link

Richard Henderson

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy – Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E., and Downing, K. H. (1990). J. Mol. Biol. 213, 899-929 link

The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules – Henderson, R. (1995). Q. Rev. Biophys. 28, 171-193 link (available in full here)

§

By locking the red-tagged papers behind a paywall – often impossible to breach because of the fees involved – they’re kept out of hands of less-well-funded institutions and libraries, particularly researchers in countries whose currencies have lower purchasing power. More about this here and here. But the more detestable thing with the papers listed above is that the latest of them (among the reds) was published in 1995, fully 22 years ago, and the earliest, 42 years go – both on cryo-electron microscopy. Both represent almost unforgivable durations across which to have paywalls, with the journals Nature and Cell further attempting to ride the Nobel wave for attention. It’s not clear if the papers they’ve liberated from behind the paywall will always be available for free hence either.

Read all this in the context of the Nobel Prizes not being awarded to more than three people at a time and maybe you’ll see how much of scientific knowledge is truly out of bounds of most of humankind.

Featured image credit: Pexels/pixabay.

Oct 5, 2017
Are the papers behind this year's Nobel Prizes in the public domain?

Note: One of my editors thought this post would work for The Wire as well, so it’s been republished there.

“… for the greatest benefit of mankind” – these words are scrawled across a banner that adorns the Nobel Prize’s homepage. They are the words of Alfred Nobel, who instituted the prizes and bequeathed his fortunes to run the foundation that awards them. The words were chosen by the prize’s awarders to denote the significance of their awardees’ accomplishments.

However, the scientific papers that first described these accomplishments in the technical literature are often not available in the public domain. They languish behind paywalls erected by the journals that publish them, that seek to cash in on their importance to the advancement of science. Many of these papers are also funded by public money, but that hasn’t deterred journals and their publishers from keeping the papers out of public reach. How then can they be for the greatest benefit of mankind?

§

I’ve listed some of the more important papers published by this year’s laureates; they describe work that earned them their respective prizes. Please remember that my choice of papers is selective; where I have found other papers that are fully accessible – or otherwise – I have provided a note. This said, I picked the papers from the scientific background document first and then checked if they were accessible, not the other way round. (If you, whoever you are, are interested in replicating my analysis but more thoroughly, be my guest; I will help you in any way I can.)

A laureate may have published many papers collectively for which he was awarded (this year’s science laureates are all male). I’ve picked the papers most proximate to their citation from the references listed in the ‘advanced scientific background’ section available for each prize on the Nobel Prize website. Among publishers, the worst offender appears – to no one’s surprise – to be Elsevier.

A paper title in green indicates it’s in the public domain; red indicates it isn’t – both on the pages of the journal itself. Some titles in red maybe available in full elsewhere, such as in university archives. The names of laureates in the papers’ citations are underlined.

Physiology/medicine

“for their discoveries of molecular mechanisms controlling the circadian rhythm”

The paywall for papers by Young and Rosbash published in Nature were lifted by the journal on the day their joint Nobel Prize was announced. Until then, they’d been inaccessible to the general public. Interestingly, both papers acknowledge funding grants from the US National Institutes of Health, a tax-funded body of the US government.

Michael Young

Restoration of circadian behavioural rhythms by gene transfer in Drosophila – Nature 312, 752 – 754 (20 December 1984); doi:10.1038/312752a0 link

Isolation of timeless by PER protein interaction: defective interaction between timeless protein and long-period mutant PERL – Gekakis, N., Saez, L., Delahaye-Brown, A.M., Myers, M.P., Sehgal, A., Young, M.W., and Weitz, C.J. (1995). Science 270, 811–815. link

Michael Rosbash

Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels – Nature 343, 536 – 540 (08 February 1990); doi:10.1038/343536a0 link

The period gene encodes a predominantly nuclear protein in adult Drosophila – Liu, X., Zwiebel, L.J., Hinton, D., Benzer, S., Hall, J.C., and Rosbash, M. (1992). J Neurosci 12, 2735–2744. link

Jeffrey Hall

Molecular analysis of the period locus in Drosophila melanogaster and identification of a transcript involved in biological rhythms – Reddy, P., Zehring, W.A., Wheeler, D.A., Pirrotta, V., Hadfield, C., Hall, J.C., and Rosbash, M. (1984). Cell 38, 701–710. link

P-element transformation with period locus DNA restores rhythmicity to mutant, arrhythmic Drosophila melanogaster – Zehring, W.A., Wheeler, D.A., Reddy, P., Konopka, R.J., Kyriacou, C.P., Rosbash, M., and Hall, J.C. (1984). Cell 39, 369–376. link

Antibodies to the period gene product of Drosophila reveal diverse tissue distribution and rhythmic changes in the visual system – Siwicki, K.K., Eastman, C., Petersen, G., Rosbash, M., and Hall, J.C. (1988). Neuron 1, 141–150. link

Physics

“for decisive contributions to the LIGO detector and the observation of gravitational waves”

While results from the LIGO detector were published in peer-reviewed journals, the development of the detector itself was supported by personnel and grants from MIT and Caltech. As a result, the Nobel laureates’ more important contributions were published as a reports since archived by the LIGO collaboration and made available in the public domain.

Rainer Weiss

Quarterly progress report – R. Weiss, MIT Research Lab of Electronics 105, 54 (1972) link

The Blue Book – R. Weiss, P.R. Saulson, P. Linsay and S. Whitcomb link

Chemistry

“for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution”

The journal Cell, in which the chemistry laureates appear to have published many papers, publicised a collection after the Nobel Prize was announced. Most papers in the collection are marked ‘Open Archive’ and are readable in full. However, the papers cited by the Nobel Committee in its scientific background document don’t appear there. I also don’t know whether the papers in the collection available in full were always available in full.

Jacques Dubochet

Cryo-electron microscopy of vitrified specimens – Dubochet, J., Adrian, M., Chang, J.-J., Homo, J.-C., Lepault, J., McDowall, A. W., and Schultz, P. (1988). Q. Rev. Biophys. 21, 129-228 link

Vitrification of pure water for electron microscopy – Dubochet, J., and McDowall, A. W. (1981). J. Microsc. 124, 3-4 link

Cryo-electron microscopy of viruses – Adrian, M., Dubochet, J., Lepault, J., and McDowall, A. W. (1984). Nature 308, 32-36 link

Joachim Frank

Averaging of low exposure electron micrographs of non-periodic objects – Frank, J. (1975). Ultramicroscopy 1, 159-162 link

Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli – Radermacher, M., Wagenknecht, T., Verschoor, A., and Frank, J. (1987). J. Microsc. 146, 113-136 link

SPIDER-A modular software system for electron image processing – Frank, J., Shimkin, B., and Dowse, H. (1981). Ultramicroscopy 6, 343-357 link

Richard Henderson

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy – Henderson, R., Baldwin, J. M., Ceska, T. A., Zemlin, F., Beckmann, E., and Downing, K. H. (1990). J. Mol. Biol. 213, 899-929 link

The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules – Henderson, R. (1995). Q. Rev. Biophys. 28, 171-193 link (available in full here)

§

By locking the red-tagged papers behind a paywall – often impossible to breach because of the fees involved – they’re kept out of hands of less-well-funded institutions and libraries, particularly researchers in countries whose currencies have lower purchasing power. More about this here and here. But the more detestable thing with the papers listed above is that the latest of them (among the reds) was published in 1995, fully 22 years ago, and the earliest, 42 years go – both on cryo-electron microscopy. Both represent almost unforgivable durations across which to have paywalls, with the journals Nature and Cell further attempting to ride the Nobel wave for attention. It’s not clear if the papers they’ve liberated from behind the paywall will always be available for free hence either.

Read all this in the context of the Nobel Prizes not being awarded to more than three people at a time and maybe you’ll see how much of scientific knowledge is truly out of bounds of most of humankind.

Featured image credit: Pexels/pixabay.

Oct 5, 2017
In pursuit of a nebulous metaphor…

I don’t believe in god, but if he/it/she/they existed, then his/its/her/their gift to science communication would’ve been the metaphor. Metaphors help make sense of truly unknowable things, get a grip on things so large that our minds boggle trying to comprehend them, and help writers express book-length concepts in a dozen words. Even if there is something lost in translation, as it were, metaphors help both writers and readers get a handle on something they would otherwise have struggled to.

One of my favourite expositions on the power of metaphors appeared in an article by Daniel Sarewitz, writing in Nature (readers of this blog will be familiar with the text I’m referring to). Sarewitz was writing about how nobody but trained physicists understands what the Higgs boson really is because those of us who do think we get it are only getting metaphors. The Higgs boson exists in a realm that humans cannot ever access (even Ant-Man almost died getting there), and physicists make sense of them through complicated mathematical abstractions.

Mr Wednesday makes just this point in American Gods (the TV show), when he asks his co-passenger in a flight what it is that makes them trust that the plane will fly. (Relatively) Few of us know the physics behind Newton’s laws of motion and Bernoulli’s work in fluid dynamics – but many of us believe in their robustness. In a sense, faith and metaphors keep us going and not knowledge itself because we truly know only little.

However, the ease that metaphors offer writers at such a small cost (minimised further for those writers who know how to deal with that cost) sometimes means that they’re misused or overused. Sometimes, some writers will abdicate their responsibility to stay as close to the science – and the objective truth, such as it is – as possible by employing metaphors where one could easily be avoided. My grouse of choice at the moment is this tweet by New Scientist:

The health impact of feeling lonely is equivalent to smoking 15 cigarettes a day https://t.co/h5wVErzQIx pic.twitter.com/TE3iZDanIl

— New Scientist (@newscientist) October 1, 2017

The writer has had the courtesy to use the word ‘equivalent’ but it can’t do much to salvage the sentence’s implications from the dumpster. Different people have different takeaways from the act of smoking. I think of lung and throat cancer; someone else will think of reduced lifespan; yet another person will think it’s not so bad because she’s a chain-smoker; someone will think it gives them GERD. It’s also a bad metaphor to use because the effects of smoking vary from person to person based on various factors (including how long they’ve been smoking 15 cigarettes a day for). This is why researchers studying the effects of smoking quantify not the risk but the relative risk (RR): the risk of some ailment (including reduced lifespan) relative to non-smokers in the same population.

There are additional concerns that don’t allow the smoking-loneliness congruence to be generally applicable. For example, according to a paper published in the Journal of Insurance Medicine in 2008,

An important consideration [is] the extent to which each study (a) excluded persons with pre-existing medical conditions, perhaps those due to smoking, and (b) controlled for various co-morbid factors, such as age, sex, race, education, weight, cholesterol, blood pressure, heart disease, and cancer. Studies that excluded persons with medical conditions due to smoking, or controlled for factors related to smoking (e.g., blood pressure), would be expected to find lower RRs. Conversely, studies that did not account for sufficient confounding factors (such as age or weight) might find higher RRs.

So, which of these – or any other – effects of smoking is the writer alluding to? Quoting from the New Scientist article,

Lonely people are at increased risk of “just about every major chronic illness – heart attacks, neurodegenerative diseases, cancer,” says Cole. “Just a completely crazy range of bad disease risks seem to all coalesce around loneliness.” A meta-analysis of nearly 150 studies found that a poor quality of social relationships had the same negative effect on risk of death smoking, alcohol and other well-known factors such as inactivity and obesity. “Correcting for demographic factors, loneliness increases the odds of early mortality by 26 per cent,” says Cacioppo. “That’s about the same as living with chronic obesity.”

The metaphor the writer was going for was one of longevity. Bleh.

When I searched for the provenance of this comparison (between smoking and loneliness), I landed up on two articles by the British writer George Monbiot in The Guardian, both of which make the same claim*: that smoking 15 cigarettes a day will reduce your lifespan by as much as a lifetime of loneliness. Both claims referenced a paper titled ‘Social Relationships and Mortality Risk: A Meta-analytic Review’, published in July 2010. Its ‘Discussion’ section reads:

Data across 308,849 individuals, followed for an average of 7.5 years, indicate that individuals with adequate social relationships have a 50% greater likelihood of survival compared to those with poor or insufficient social relationships. The magnitude of this effect is comparable with quitting smoking and it exceeds many well-known risk factors for mortality (e.g., obesity, physical inactivity).

In this context, there’s no doubt that the writer is referring to the benefits of smoking cessation on lifespan. However, the number ’15’ itself is missing from its text. This is presumably because, as Cacioppo – one of the scientists quoted by the New Scientist – says, loneliness can decrease your lifespan by 26%, and I assume an older study cited by the one quoted above relates it to smoking 15 cigarettes a day. So I went looking, and (two hours later) couldn’t find anything.

I don’t mean to rubbish the congruence as a result, however – far from it. I want to highlight the principal reason I didn’t find a claim that fit the proverbial glove: most studies that seek to quantify smoking-related illnesses like to keep things as specific as possible, especially the cohort under consideration. This suggests that extrapolating the ’15 cigarettes a day’ benchmark into other contexts is not a good idea, especially when the writer does not know – and the reader is not aware of – the terms of the ’15 cigarettes’ claim nor the terms of the social relationships study. For example, one study I found involved the following:

The authors investigated the association between changes in smoking habits and mortality by pooling data from three large cohort studies conducted in Copenhagen, Denmark. The study included a total of 19,732 persons who had been examined between 1967 and 1988, with reexaminations at 5- to 10-year intervals and a mean follow-up of 15.5 years. Date of death and cause of death were obtained by record linkage with nationwide registers. By means of Cox proportional hazards models, heavy smokers (≥15 cigarettes/day) who reduced their daily tobacco intake by at least 50% without quitting between the first two examinations and participants who quit smoking were compared with persons who continued to smoke heavily.

… and it presents a table of table with various RRs. Perhaps something from there can be fished out by the New Scientist writer and used carefully to suggest the comparability between smoking-associated mortality rates and the corresponding effects of loneliness…

*The figure of ’15 cigarettes’ seems to appear in conjunction with a lot of claims about smoking as well as loneliness all over the web. It seems 15 a day is the line between light and heavy smoking.

Featured image credit: skeeze/pixabay.

Oct 4, 2017