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Before reproducibility must come preproducibility

by reestheskin on 10/02/2020

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This is an article by Philip Stark in Nature published awhile back. I like it.

In 1992, philosopher Karl Popper wrote: “Science may be described as the art of systematic oversimplification — the art of discerning what we may with advantage omit.” What may be omitted depends on the discipline.

You can say this another way: all experiments do violence to the natural world. We always want to cleave at the joints. But doing so may lead to error.

In 1992, philosopher Karl Popper wrote: “Science may be described as the art of systematic oversimplification — the art of discerning what we may with advantage omit.” What may be omitted depends on the discipline. Results that generalize to all universes (or perhaps do not even require a universe) are part of mathematics. Results that generalize to our Universe belong to physics. Results that generalize to all life on Earth underpin molecular biology. Results that generalize to all mice are murine biology. And results that hold only for a particular mouse in a particular lab in a particular experiment are arguably not science.

Science should be ‘show me’, not ‘trust me’; it should be ‘help me if you can’, not ‘catch me if you can’. If I publish an advertisement for my work (that is, a paper long on results but short on methods) and it’s wrong, that makes me untrustworthy. If I say: “here’s my work” and it’s wrong, I might have erred, but at least I am honest.

In medicine we have particular problems. Repeating experiments in model organisms is often possible whereas in man things are much harder. There is an awful lot of published medical research that is not a reliable guide to action.

Before reproducibility must come preproducibility

On one word after another

by reestheskin on 28/01/2020

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Well, I doubt if any readers of these scribblings will be shocked. After all TIJABP. But this piece by the editor of PNAS wonders if the day of meaningful editing is over. I hope not. Looking backwards over my several hundred papers, the American Journal of Human Genetics was the most rigorous and did the most to improve our manuscript.

On a subject no one wants to read about (about which no one wants to read?) | PNAS

“Communication” remains in the vocabulary of scientific publishing—for example, as a category of manuscript (“Rapid Communications”) and as an element of a journal name (Nature Communications)—not as a vestigial remnant but as a vital part of the enterprise. The goal of communicating effectively is also why grammar, with its arcane, baffling, or even irritating “rules,” continues to matter. With the rise of digital publishing, attendant demands for economy and immediacy have diminished the role of copyeditor. The demands are particularly acute in journalism. As The New York Times editorial board member Lawrence Downs (4) lamented, “…in that world of the perpetual present tense—post it now, fix it later, update constantly—old-time, persnickety editing may be a luxury…. It will be an artisanal product, like monastery honey and wooden yachts.” Scientific publishing is catching up to journalism in this regard.

We are not of this world

This is from Larry Page of Google (quoted in “The Age of Surveillance Capitalism: The Fight for a Human Future at the New Frontier of Power” by Shoshana Zuboff)

CEO Page surprised a convocation of developers in 2013 by responding to questions from the audience, commenting on the “negativity” that hampered the firm’s freedom to “build really great things” and create “interoperable” technologies with other companies: “Old institutions like the law and so on aren’t keeping up with the rate of change that we’ve caused through technology. . . . The laws when we went public were 50 years old. A law can’t be right if it’s 50 years old, like it’s before the internet.” When asked his thoughts on how to limit “negativity” and increase “positivity,” Page reflected, “Maybe we should set aside a small part of the world . . . as technologists we should have some safe places where we can try out some new things and figure out what is the effect on society, what’s the effect on people, without having to deploy kind of into the normal world.

As for his comments on safe spaces, I agree. There are plenty of empty planets left.

I wish I had said that..

A comment on an article:

With reference to Janan Ganesh’s column (“What the US lost when the Berlin Wall fell”, November 7). This is such a clever line.

“It is as though hatred obeys the first law of thermodynamics. Like energy, it can be transferred but never destroyed.

This apropos the US right’s shifting from the Soviet Union to immigration and climate. I’m trying to figure out how to work it into my own stuff. Full credit, of course.

Link

Term of the day

Negative egalitarianism (also known as jealousy)

Richard Gombrich

We need a science of the night

by reestheskin on 03/01/2020

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One-third of everyone employed in London, 1.6 million people, work at night.

In 2018, at least 8,855 people slept rough on the streets of London, a 140% increase over the past decade, with similar trends globally.

We need a science of the night

Finnish lessons

by reestheskin on 19/12/2019

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No, not Pasi Salberg, but cognate.

But idealists now have another international beacon of social mobility: long live the Finnish dream, in which a 34-year-old woman who once worked in a shop can become prime minister.

“I am extremely proud of Finland. Here a poor family’s child can educate themselves and achieve their goals in life. A cashier can become even a prime minister,” tweeted Sanna Marin

Meanwhile back in the UK as the FT rightly comments:

..egregious examples of rigging the game endure: on being rejected by the voters, Zac Goldsmith is to be elevated to the House of Lords, from where he will carry on as a minister in the government of Boris Johnson, also an Etonian from a high-profile family.

Looking in envy at Finland’s social mobility pin-up PM | Financial Times

On not being the Queen of Sciences

by reestheskin on 16/12/2019

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“If biology is difficult, it is because of the bewildering number and variety of things one must hold in one’s head”.
John Maynard Smith (1977).

Leo Szilard recalled, that when he did physics he could lounge in the bath for hours and hours, just thinking. Once he moved into biology things were never the same: he was always having to get out to check some annoying fact. Dermatology is worse, trust me.

Even the human world is queerer than I can imagine

The world is indeed very strange and common sense not much of a guide. Facts, my dear boy, facts…

link

Fiction, apparently.

“…what he read was clear proof of an Anglo-American covert operation already in the planning stage with the dual aim of undermining the social democratic institutions of the European Union and dismantling our international trading tariffs…In the post-Brexit era Britain will be desperate for increased trade with America. America will accommodate Britain’s needs, but only on terms. One such term will be a joint covert operation to obtain by persuasion — bribery and blackmail not excluded — officials, parliamentarians and opinionmakers of the European Establishment. Also to disseminate fake news on a large scale in order to aggravate existing differences between member states of the Union”

Agent Running in the Field, John le Carré

Knowing more than we can see

by reestheskin on 05/12/2019

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I spent near on ten years thinking about automated skin cancer detection. There are various approaches you might use — cyborg human/machine hybrids were my personal favourite — but we settled on more standard machine learning approaches. Conceptually what you need is straightforward: data to learn from, and ways to lever the historical data to the future examples. The following quote is apposite.

One is that, for all the advances in machine learning, machines are still not very good at learning. Most humans need a few dozen hours to master driving. Waymo’s cars have had over 10m miles of practice, and still fall short. And once humans have learned to drive, even on the easy streets of Phoenix, they can, with a little effort, apply that knowledge anywhere, rapidly learning to adapt their skills to rush-hour Bangkok or a gravel-track in rural Greece.

Driverless cars are stuck in a jam – Autonomous vehicles

You see exactly the same thing with skin cancer. With a relatively small number of examples, you can train (human) novices to be much better than most doctors. By contrast, with the machines you need literally hundreds and thousands of examples. Even when you start with large databases, as you parse the diagnostic groups, you quickly find out that for many ‘types’ you have only a few examples to learn from. The rate limiting factor becomes acquiring mega-databases cheaply. The best way to do this is to change data acquisition from a ‘research task’ to a matter of grabbing data that was collected routinely for other purposes (there is a lot of money in digital waste — ask Google).

Noam Chomsky had a few statements germane to this and much else that gets in the way of such goals (1).

Plato’s problem: How can we know so much when the evidence is do slight.

Orwell’s problem: How do we remain so ignorant when the evidence is so overwhelming.

(1): Noam Chomsky: Ideas and Ideals, Cambridge University Press, (1999). Neil Smith.

Books

We commonly think of books as containers of ideas or wrapping for literature, but they can be understood in other ways—as if they were blood cells carrying oxygen through a body politic or data points as infinite as stars in the sky. Books lead lives of their own, and they intersect with our lives in ways we have only begun to understand.

Best Sellers by the Bargeload | by Robert Darnton | The New York Review of Books

A job for life

In the essay “Telling,” he describes the upsetting case of the director of a hospital who, struck down by Alzheimer’s, is admitted to his own hospital. He behaves as if he were still running it, until one day by chance he picks up his own chart. “That’s me,” he says, recognizing his name on the cover. Inside, he reads “Alzheimer’s disease” and weeps. In the same hospital a former janitor is admitted; he too is convinced that he is still working there. He is given harmless tasks to perform; one day he dies of a sudden heart attack “without perhaps ever realising that he had been anything but a janitor with a lifetime of loyal work behind him.”

Truth, Beauty, and Oliver Sacks | by Simon Callow | The New York Review of Books

My mother, a nurse, took on such imagined roles when she too was demented and in a care home.

Writings from the margins

by reestheskin on 28/11/2019

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I was back in Dublin a few weeks ago for a family celebration. Then last night — on C4 I think— I was listening to an interview with Fintan O’Toole. Something stirred and below are two quotes from Brian Friel: the context may be Brexit, the reality is something much more.

As a character in Translations says, describing his own fading Gaelic world, “a civilisation can be imprisoned in a linguistic contour which no longer matches the landscape of fact”.

 

To remember everything is a form of madness,” warns one of Friel’s characters.

(1) Brexit, the UK and Ireland: a dialogue of the deaf | Financial Times

Dark matters.

by reestheskin on 21/11/2019

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Frank Davidoff had a telling phrase about clinical expertise. He likened it to “Dark Matter”. Dark Matter makes up most of the universe, but we know very little about it. In the clinical arena I have spent a lot of time reading and thinking about ‘expertise’,  without developing any grand unifying themes of my own worth sharing. But we live in a world where ‘expertise’ in many domains is under assault, and I have no wise thoughts to pull together what is happening. I do however like (as ever) some nice phrases from Paul Graham. I can’t see any roadmap here just perspectives and shadows.

When experts are wrong, it’s often because they’re experts on an earlier version of the world.

any

Instead of trying to point yourself in the right direction, admit you have no idea what the right direction is, and try instead to be super sensitive to the winds of change.

How to Be an Expert in a Changing World

Bullshit (of the world-class variety)

by reestheskin on 12/11/2019

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Andrew Wathey its chairman [of the UK Standing Committee for Quality Assessment] and vice-chancellor of Northumbria University, said: “The UK delivers world-class education to students from all nations. It is therefore right that the sector commits to ensuring that the value of these world-class qualifications is maintained over time in line with the expectations of the UK Quality Code for Higher Education.”

Universities agree more openness on degree marking guidelines | Financial Times

The language betrays all you need to know: spoken by somebody who clearly has no idea what UK higher education once stood for, or who has any sympathy or understanding of the academic ideal. Will the last person who leaves please turn off the ….

Thought of the day

by reestheskin on 11/11/2019

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That, across human experience, in all places and at all times, only one or two societies have unwound concentrations of income and wealth as great as [those that] plague the US today without losing in war to a foreign foe or succumbing to a domestic revolution.

Interview with Daniel Markovits

THE, 31-10-2019

Sensing the future.

by reestheskin on 05/11/2019

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We are not a great power and never will be again. We are a great nation but if we continue to behave like a great power we shall soon cease to be a great nation.

Sir Henry Tizard, 1949.

Quoted in the LRB by Ian Gilmore (reprinted 7-11-2019)

What every (good) fly half knows

by reestheskin on 24/10/2019

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“If I can predict what you are going to think of pretty much any problem, it is likely that you will be wrong on stuff. [speaking of certain other economists]….they are very predictable

Lunch with the FT: Esther Duflo | Financial Times

When capitalisms collide

by reestheskin on 22/10/2019

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The future of capitalism is out of the hands of those who spend their time thinking about it.

Not too dissimilar to medicine, either: discuss…..

When capitalisms collide

That was then

by reestheskin on 22/10/2019

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The world has problems, as the old saying puts it, but universities have departments.

Well not any more, I would add.

The Puzzle of Economic Progress by Diane Coyle – Project Syndicate

Invention: good and bad

by reestheskin on 21/10/2019

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The history of innovation is littered with examples of new technologies causing unintended harm. As cultural theorist Paul Virilio said, “When you invent the ship, you also invent the shipwreck.”

Big Tobacco, war and politics

by reestheskin on 11/10/2019

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Tobacco killed an estimated 100 million people in the twentieth century. Without radical action, it is projected to kill around one billion in the twenty-first.

Big Tobacco, war and politics

Monday morning blues

by reestheskin on 07/10/2019

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“Change? Change? Aren’t things bad enough as they are?”

Response (attributed to Robert Gascoyne-Cecil, 3rd Marquess of Salisbury)

“I have wasted a lot of time living”

John Gray on Michael Oakeshott

He would have found the industrial-style intellectual labour that has entrenched itself in much of academic life over the past twenty-odd years impossible to take seriously. He wrote for himself and anyone else who might be interested; it is unlikely that anyone working in a university today could find the freedom or leisure that are needed to produce a volume such as this. Writing in 1967, Oakeshott laments, ‘I have wasted a lot of time living.’ Perhaps so, but as this absorbing selection demonstrates, he still managed to fit in a great deal of thinking.

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Send in the clown

But what lies ahead for Johnson in those uncharted waters? His best joke was not meant to be one. In November 2016 he claimed that “Brexit means Brexit and we are going to make a titanic success of it.” In this weirdly akratic moment of British history, most of those who support Johnson actually know very well that Brexit is the Titanic and that his evasive actions will be of no avail. But if the ship is going down anyway, why not have some fun with Boris on the upper deck? There is a fatalistic end-of-days pleasure in the idea of Boris doing his Churchill impressions while the iceberg looms ever closer. When things are too serious to be contemplated in sobriety, send in the clown.

The Ham of Fate | by Fintan O’Toole | The New York Review of Books

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What is science for: dangerous thoughts.

The quote below was from a piece in the Lancet by Richard Horton.

Reading [Bertrand]Russell today is a resonant experience. Existential fears surround us. Yet today seems a long way from the dream of Enlightenment. Modern science is a brutally competitive affair. It is driven by incentives to acquire money (research funding), priority (journal publication), and glory (prizes and honours). Science’s metrics of success embed these motivations deep in transnational scientific cultures. At The Lancet, while we resist the idea that Impact Factors measure our achievements, we are not naive enough to believe that authors do not judge us by those same numbers. It is hard not to capitulate to a narrow range of indicators that has come to define success and failure. Science, once a powerful force to overturn orthodoxy, has created its own orthodoxies that diminish the possibility of creative thought and experiment. At this moment of planetary jeopardy, perhaps it is time to rethink and restate the purpose of science.

Offline: What is science for? – The Lancet

I am just musing on this. We like to think that ‘freedom’ was necessary for a modern wealthy state. We are not so certain, now. We used to think that certain freedoms of expression underpinned the scientific revolution. We are having doubts about this, too. Maybe it is possible to have atom bombs and live in a cesspool of immorality. Oops…

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Living in Scot itchland

Genital scabies was, to the English, “Scotch itch,” and Scotland was “Itch-land.” The pox was the Spanish or Neapolitan Disease to the French; the French Disease to the Spanish, English, and Germans; the Polish Disease to the Russians; the Portuguese Disease to the Japanese. Captain Cook was chagrined to learn that it was called the British Disease in Tahiti as, in so many words, it was in Ireland: in Ulysses the Citizen, a rabid Irish nationalist, mocks Leopold Bloom’s reference to British civilization: “Their syphilisation you mean.”

Vile Bodies | by Fintan O’Toole | The New York Review of Books

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Sunday in Lisbon

“Catholicism imbued a spirit of rebellion and the ghost of faith.”

Well, I get that, too. In a review of Bruce Springsteen’s biography in the Economist.

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Chadgrind lives on

I have had of all people a historian tell me that science is a collection of facts, and his voice had not even the ironic rasp of one filing-cabinet reproving another.

Jacob Bronowski | Science and Human Values

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