Percents are hard

Some really bad science reporting from the BBC. They report on a new study finding the incidence of diagnosed coeliac disease increasing (and decreasing incidence of dermatitis herpetiformis, though this doesn’t rate a mention) in the UK. Diagnoses have gone up from 5.2 to 19.1 per 100,000 in about 20 years, which they attribute to increased awareness. Except, they don’t say what that is 100,000 of. You have to go back to the original article to see that it is person-years, and that they are talking about incidence, and not prevalence (in technical parlance); they use the word “rate”, which is pretty ambiguous, and commonly used — particularly in everyday speech — to refer to prevalence. If you read it casually — and, despite being a borderline expert in the subject, I misread it at first myself —  you might think they mean that 19 in 100,000 of the population of Britain suffers from coeliac; that would be about 12,000 people, hardly enough to explain the condition’s cultural prominence (and prominent placement on the BBC website). In fact, they estimate that about 150,000 have diagnosed CD in the UK.

As if aiming maximally to compound the confusion, they quote one of the authors saying

“This [increase] is a diagnostic phenomenon, not an incidence phenomenon. It is exactly what we had anticipated.”

In the article they (appropriately) refer to the rate of diagnosis as incidence, but here they say it’s not about “incidence”.

To make matters worse, they continue with this comment:

Previous studies have suggested around 1% of the population would test positive for the condition – but the data from this study suggests only 0.25% are diagnosed.

I think that normally, if you say “only x% are diagnosed” is meant relative to the number of cases; here it would mean 0.25% of the 1%. But, in fact, they mean to compare the 0.25% of the population who are diagnosed with the 1% who actually suffer from the disease.

More Hockey Statisticks

I wrote last week about my surprising response to two books about the public conflicts over palaeoclimatology. Whereas I expected to find myself sympathising with the respected scientist Michael Mann, I found both authors equally repellant — both are smug and self-absorbed, both write crudely — and had most sympathy with Steven McIntyre, the former mining engineer who stars in Andrew Montford’s book. Fundamentally, I found that Mann’s own account made him seem like just the sort of arrogant senior scientist I have occasionally had to deal with as a statistician, one who is outraged that anyone outside his close circle would want to challenge his methodology.

A pair of long comments on the post underlined my impression of the cultish behaviour of people who have gotten enmeshed in the struggle over climate change, on both sides. The commenter writes:

I would suggest that McIntyre’s work went out of its way to try to cast doubt on Mann’s research, and in that process created as many errors of its own. Montford’s book takes that dubious effort and magnifies it for the purposes of attacking climate change science in general by vilifying a single piece of research by a single researcher.

I have to say, Montford’s effort has been highly effective. In one lecture I saw, given by Dr Richard Alley, he recounted being in Washington speaking to a science committee where one high level member stated, “Well, we know all this climate change stuff is based on a fraudulent Hockey Stick graph.”

I’m sure [Andrew] Montford appreciates your piece here perpetuating that position.

I don’t know exactly what Montford’s “effort” is. Certainly, in his book he has little to say about the rest of climate science, but what he does have to say can hardly give any impression other than that the “hockey stick” is a small part of palaeoclimatology, and that palaeoclimatology is a small part of climate research. He never accuses Mann or anyone else of fraud in his book, although he is unyielding and close to hysterical in imputing incompetence to Mann and some of his closest collaborators.

As for McIntyre’s work going “out of its way to try to cast doubt”, this hardly seems different to me than the usual way scientists are motivated. It’s no different than the comments about “getting rid of the Mediaeval Warm Period”, that Montford is obsessed with, as evidence of scientific corruption. I was never bothered by that comment, or any of the comments that came out of the disgraceful email hack of the Climatic Research Unit, because I understand that scientists rarely launch an investigation without any preconceptions. It’s perfectly plausible — even likely — that climate researchers would have had a strong gut feeling that this warm period was much less substantial than it had seemed, but were casting about for a way to prove the point. The trick here is to have a rigorous methodology that won’t bend to your preconceptions. The same way, McIntyre had a gut feeling that the climate was much more variable in the past than the mainstream researchers wanted to believe, and he set about proving his point by trying to find the flaws in their methodology.

The fact that later studies ended up confirming the broad outlines of Mann’s picture, and disproving McIntyre’s intuition does not make his critique any the less serious or important. And it doesn’t make Mann’s efforts to portray all of his opponents as villains any less unsavoury. And his efforts to present scientific defensiveness as high principle do a disservice to science in general, and to climate science more specifically.

The commenter describes Mann’s self-righteous refusal to provide essential materials for McIntyre’s attempts to re-evaluate his work as a natural response to ” the levels to which “skeptics” are willing to go. It may seem absurd, but I think that is only because the levels they go to are so outrageous.” Except that it looks to me as though Mann’s stonewalling came first. Maybe that’s wrong, but again, if so, he doesn’t seem to think anyone has a right to expect evidence of the fact.

Mann comes across in his own book as a manipulator who would like to tar all of his opponents with the outrageous actions that some have committed. He accuses McIntyre of “intimidation” without considering it necessary to provide any shred of evidence. The portion of their correspondence quoted by Montford obviously doesn’t show anything beyond occasional exasperation at Mann’s stonewalling. Obviously there could be more to it, but Mann seems so persuaded of his own saintliness that his bare assertion of his own pure motives — and of the correctness of his methodology — ought to persuade every reader. And so convinced of the objectivity of his friends and colleagues that merely quoting their statements in his defence should suffice.

Science is science, but many climate scientists have (quite rightly) decided that the implications of what they have learned demand political action. They can’t then express horror when others blend their scientific inquiry with a political agenda.

Hippie science

There are two books I’ve read sort of recently, From Counterculture to Cyberculture by Fred Turner and How the Hippies Saved Physics by David Kaiser, that supplement each other as a picture of how antimaterialistic culture of the SF Bay area in the late 1960s through mid-1970s produced a lot of nonsense, but also hugely important new impulses in hard technical fields. Silicon Valley grew out of an ethos of DIY back-to-the-earth-ism (hence the “Homebrew Computer Club”), while the Fundamental Fysiks Group at Lawrence Berkeley Lab, took the energy of enthusiasm for parapsychology and mysticism, and channeled it into revival of an inquisitive style of physics that rediscovered entanglement and Bell’s Theorem, and laid the groundwork for quantum cryptography and quantum information science.

Data-mining for Cthulhu

I don’t ordinarily repost what other people have written, but this post by The Atlantic‘s Alexis Madrigal is so beautiful that I feel the need to copy it. It really just consists of juxtaposing the buzzword Big Data with this quote from H. P. Lovecraft — one that I was already familiar with, but had never exactly put into this context. It is the famous opening of The Call of Cthulhu:

The most merciful thing in the world, I think, is the inability of the human mind to correlate all its contents. We live on a placid island of ignorance in the midst of black seas of infinity, and it was not meant that we should voyage far. The sciences, each straining in its own direction, have hitherto harmed us little; but some day the piecing together of dissociated knowledge will open up such terrifying vistas of reality, and of our frightful position therein, that we shall either go mad from the revelation or flee from the deadly light into the peace and safety of a new dark age.

Safety of a new dark age. Hmm. If only I could turn that into a grant proposal…

A thoughtful politician

I was at the concluding conference today for the New Dynamics of Ageing research programme in London, and one of the talks was by David Willetts, the Minister of State for Universities and Science.

I won’t speak for his general politics — even if I knew how much of the policy of his ministry he is responsible for — but I was impressed with his thoughtfulness. He wasn’t academic, but he showed a nimble ability to deploy concepts from science and philosophy in response to questions, and a willingness to think on his feet that is far from the stereotype of the cautious time-serving politician.

One thing that impressed me was his answer to a somewhat vague and mundane question about ageism, and what we can do about it. It would have been easy to answer to give a conventionally pious answer, saying that we all need to recognise the contributions of blah blah blah. Instead, he spoke about the problem of increasing segregation by age in British society, related it to nurseries being more inclined to separate 2-year-olds from 3-year-olds, and concluded by saying that teenagers are at least as likely to be stereotyped and discriminated against as the elderly. I think this is true, and hardly a politically safe position to take.

In response to a question about adult learning he drew a contrast between “Calvinist education” (not quite predestination or reprobationism, but he seemed to mean more that everything is determined in the first few years) and neural plasticity. He said, “The large hippocampus of a London taxi driver isn’t because people with large hippocampus become taxi drivers.” Not a highly original point, one that I’m sure is made in any number of popular science books, but he clearly had mastered the outlines of this science, and was able to weave it in with policy considerations on the fly.

Cool nerds

An interesting article by Carl Wilson (apparently the start of a month-long series) in Slate looks at the word “cool” in its past and current incarnations. It’s a lot more readable and to the point than jazz critic Ted Gioia’s fundamentally trivial book The Birth and Death of the Cool, but I found myself hung up on his comment

 You’d be unlikely to use other decades-old slang—groovy or rad or fly—to endorse any current cultural object, at least with a straight face, but somehow cool remains evergreen.

As it happens, I was just recently having a conversation about the word nerd. I have a very clear memory that when the ’50s nostalgia wave broke in the mid-1970s (so I was about 8 years old), I encountered the word in TV programs like Happy Days as an antiquated idiom. I had never heard anyone use the word, and I associated it with my parents’ childhoods. When I was a student the prevailing word for someone too bookish to be cool (such as myself) was weenie. As late as 1993, according to an OED citation, Scientific American felt the need to explain

 ‘Nerd’..is movie shorthand for scientists, engineers and assorted technical types who play chess, perhaps, or the violin.

And I remember encountering the word again in the self-righteous name of the Society of Nerds and Geeks (SONG), an undergraduate club that popped up at Harvard about 1989 (when I was a graduate student in mathematics). This was a self-conscious attempt to co-opt these words, which at the time were exclusively terms of abuse, along the lines of the way what was formerly the sexual invert community, or whatever, renamed itself gay, and later queer. Harvard mathematics graduate student Leonid Fridman, who advised the club, published an op-ed on Jan 11, 1990 in the NY Times arguing that the popular disdain for the brainy and bookish would put the US at a disadvantage in competing with its economic and military competitors. (Remember, this was still the Cold War.) The article concluded with this plea:

Until the words “nerd” and “geek” become terms of approbation and not derision, we do not stand a chance.

This dream has come to fulfilment more than could have been imagined in the linguistic sense, but my impression is that there has been little change in the effective social status of academically-inclined American youth. Fridman’s NY Times op-ed is mysteriously unfindable in the Times online archive, so I have copied the text below: Continue reading “Cool nerds”

Macho science: Deflowering virgin nature

I was listening to BBC radio this morning, which I rarely do, because I find it generally dull. A scientist named Mark Lythgoe was being interviewed, director of the Centre for Advanced Biomedical Imaging at University College London, and an enthusiastic mountain climber. The interviewer asked — inevitably — about the connection between mountain-climbing and science. The answer was almost archaically macho, in what it said both about science and about mountain climbing. It wasn’t anything about planning or co-operation, or the beauty or peace of nature, not evening about pushing yourself to your limits. No, it was about deflowering virgin territory.

There is a very special moment when you stand on a part of this earth that no one else has ever stood on, and look out on a view that no one else has seen… That’s the same as when someone calls you up from the lab with an image that no one else has seen before… The hairs stand up on the back of your neck.

I don’t know of any better argument against the narrow British approach to education — where a scientist will never read a book after age 16 — than that through exposure to the humanities a certain percentage of scientists would recognise deflowering virgin nature as an embarrassing 19th century cliché. Some might acquire enough of a familiarity with how to think about human matters — about society and gender and nature — with a sophistication to match the overweening self-confidence that their scientific expertise tends to impart.

He also presented what was supposed to be an example of the brilliant eclecticism of his institute (and himself), a collaboration with a biologist to study homing pigeons. He says that there was a theory that pigeons have magnetite in their beaks or brains that orient them with respect to the Earth’s magnetic field. So they developed a brand new imaging technology that could make refined images of the distribution of magnetite in the beaks and brains, and found — there is no magnetite. Brilliant! Except, isn’t it a huge waste of time and effort to develop refined imaging technologies, without first figuring out (by, I don’t know, grinding up the beaks and doing some chemical tests)? Maybe I’m missing something — maybe that wasn’t possible for some reason that he was too busy talking about his drive for success to explain — or maybe I just don’t sufficiently appreciate big science and IMPACT.

The mistimed death clock: How much time do I have left?

Someone has set up a macabre “death clock“, a web site where individuals can enter a few personal statistics — birthdate, sex, smoking status, and general level of optimism, and it will calculate a “personal date of death”, together with an ominous clock ticking down the seconds remaining in your life. (For Americans, ethnic group is a hugely significant predictor, but I’m not surprised that they leave this out. Ditto for family income.) It’s supposed to be a sharp dose of reality, I suppose, except that it’s nonsense.

Not because no one knows the day or the hour, though that is true, but because the author has built into the calculator a common but elementary misconception about life expectancy, namely, that we lose a year of expected remaining life for every year that we live. Thus, when I enter my data the clock tells me that I am expected to die on August 6 2042. If I move my birthdate back* by 10 years — making myself 10 years older — my date of death moves back by the same amount, to August 6 2032. If I tell it I was born in 1936 it tells me that my time has already run out, which is obviously absurd.

In fact, every year that you live, you lose 1 year, but gain a proportion a remainder equivalent to the probability that you might have died. Thus, a 46-year-old US man has expected remaining lifespan 33.21 years. He has probability 0.00365 of dying in the next year; if he makes it through that year and reaches his 47th birthday, his expected remaining lifespan is (33.21-1)+.00365 x 32.21 = 32.33 years.** So he’s only lost 0.88 years off his remaining lifespan. In this way, it’s actually possible to have more expected remaining lifespan at an older age than at a younger, if the mortality rate is high enough. Thus, if we go back to 1933 mortality rates, the expected lifespan at birth was 59.2 years. But a 1-year-old, having made it through the 6.5% infant mortality, now has 62.3 years remaining on average.

This is another way of expressing the well-known but still often not-sufficiently-appreciated impact of infant mortality on life expectancy. The life-expectancy at birth for US males is 76.4 years. But that obviously doesn’t mean that everyone keels over 5 months into their 77th year. 60% of the newborn males are expected to live past this age, and a 77-year-old man has 10 remaining years on average.

Of course, these are all what demographers call “period” life expectancies, based on the mortality rates experienced in the current year, and pretending that these mortality rates will continue into the future. Based on the experience of the past two centuries we expect the mortality rates to continue to fall, in which case the true average lifespans for people currently alive — the “cohort life expectancies” will exceed these period calculations — but there is no way to know. If an asteroid hits the earth tomorrow and wipes out all life on earth, this period calculation will be rendered nugatory (but there will be no one left to point that out. Hah!) The true average lifespan of the infants born this year will not be known until well into the 22nd century. Or, if Aubrey de Grey is right, not until the 32nd century.

* Or is it moving my birthdate forward by 10 years when I make it 10 years earlier? Reasonable people disagree on this point! And there’s interesting research on the habits of mind that lead one to choose the metaphor of the stationary self with time streaming past me, or the self moving like a river through a background of time.

** Actually, it’s (33.21-1)/(1-.00365)

Dawkins’ faulty taxonomy

Science enthusiast Richard Dawkins is always good for a laugh, even if the laughter sometimes curdles at his anti-Catholic and anti-Muslim bigotry, and his inclination to minimise the the significance of child rape when it serves the interests of the former. He has recently published on Twitter the comment

All the world’s Muslims have fewer Nobel Prizes than Trinity College, Cambridge. They did great things in the Middle Ages, though.

There are all kinds of comments one could make about this, and many have, but what I find most striking is the utter failure of logic in the area that is closest to his area of purported expertise, which is not religion or sociology, but taxonomy. To a statistician, this comparison seems risible. Not only are Muslim and Member of Trinity College not comparable categories (I hope Professor Dawkins won’t get the vapours when I mention that they are not even mutually exclusive), but even if they were, Dawkins seems to be suggesting that the difference in NPF (Nobel Prize Frequency) between the devotees of Muhammed and of the Cambridge Trinity are due to negative selection by Islam, whereas another observer might suspect that there is some form of positive selection by Trinity College.

To put it baldly, you don’t need a Nobel Prize to get a post at Trinity College, but it doesn’t hurt. For example the most recent Trinity College Nobel Prize went to Venkatraman Ramakrishnan, who had a nearly 30-year scientific career before joining Trinity College.

A more valid comparison would ask, why does Trinity College, Cambridge boast so many more nobel laureates (32) than the comparably sized Trinity College, Oxford. (2, by my count from this list).  Is it the vitiating effect of Oxford’s high-church Anglicanism? Or is it that Dawkins cherry-picked one of the wealthiest, most exclusive academic institutions, one most concentrated on exactly the sorts of subjects that attract Nobel prizes? Why have Scandinavian authors received so many Nobel Prizes in Literature? Religion? Climate? Reindeer?

I leave the resolution of these questions to the skeptical reader. Those who are interested in a more amusing version of Dawkinsian taxonomy can have a look at Borges’s essay “John Wilkins’ Analytical Language“. Borges describes an imaginary ancient Chinese encyclopedia, Celestial Emporium of Benevolent Knowledge that divides up all animals into the following categories:

Continue reading “Dawkins’ faulty taxonomy”

Research impact and road construction

I’ve been interested in the turn of government funders of scientific research in several countries — in particular, US, UK, and Canada — to target research spending likely to have high economic benefit. I’ve commented here on Canadian developments, and satirised UK impact obsession here (though I actually think the UK bureaucracy has done a fairly good job at diverting the ill-informed government rhetorical pressure into less harmful directions). Lawrence Krauss, writing in Slate, has pulled together some of these recent developments with some interesting commentary.

One interesting analogy has recently occurred to me: Scientific research is a public good, like roads. I’m no expert on transportation policy, but my impression is that when transportation plans are laid, when they decide to invest the necessary capital in widening this highway, or paving that cowpath, the political decision-makers don’t devote a lot of energy to questioning whether it’s really productive for people to be travelling along this route, whether people going from A to B (and back) is actually going to provide economic benefits. The arguments usually stop at the evidence that people are travelling that route, that the current roads are congested, and so on. Experience has shown that efficient transportation infrastructure promotes economic growth and general public welfare, and government should provide people with the means to get where they want to go reasonably quickly and safely, without needing to micromanage exactly why everyone wants to go wherever it is they want to go.

Similarly, experience shows that thriving scientific research promotes economic growth, and public welfare, and we should invest in making it thrive. Where should we invest? We should look where the traffic is going, and not ask why it is going there.

This is not quite as straightforward as the road-building problem, because we do want to distinguish between high-quality research and low-quality research, but even a certain amount of boring, non-paradigm-breaking, grey-skies research can play an important part in keeping the scientific enterprise healthy. Making this distinction is the job of peer-review, and maybe it needs to be done differently, but I would contend that trying to slather on another layer of “impact” evaluation is not going to make the process or the research more productive.