Environment

Does this sound familiar ?

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The science community is now closing in on an example of scientific fraud at Duke University. The story sounds awfully familiar.

ANIL POTTI, Joseph Nevins and their colleagues at Duke University in Durham, North Carolina, garnered widespread attention in 2006. They reported in the New England Journal of Medicine that they could predict the course of a patient’s lung cancer using devices called expression arrays, which log the activity patterns of thousands of genes in a sample of tissue as a colourful picture. A few months later, they wrote in Nature Medicine that they had developed a similar technique which used gene expression in laboratory cultures of cancer cells, known as cell lines, to predict which chemotherapy would be most effective for an individual patient suffering from lung, breast or ovarian cancer.
 
At the time, this work looked like a tremendous advance for personalised medicine—the idea that understanding the molecular specifics of an individual’s illness will lead to a tailored treatment.

This would be an incredible step forward in chemotherapy. Sensitivity to anti-tumor drugs is the holy grail of chemotherapy.

Unbeknown to most people in the field, however, within a few weeks of the publication of the Nature Medicine paper a group of biostatisticians at the MD Anderson Cancer Centre in Houston, led by Keith Baggerly and Kevin Coombes, had begun to find serious flaws in the work.
 
Dr Baggerly and Dr Coombes had been trying to reproduce Dr Potti’s results at the request of clinical researchers at the Anderson centre who wished to use the new technique. When they first encountered problems, they followed normal procedures by asking Dr Potti, who had been in charge of the day-to-day research, and Dr Nevins, who was Dr Potti’s supervisor, for the raw data on which the published analysis was based—and also for further details about the team’s methods, so that they could try to replicate the original findings.

The raw data is always the place that any analysis of another’s work must begin.

Dr Potti and Dr Nevins answered the queries and publicly corrected several errors, but Dr Baggerly and Dr Coombes still found the methods’ predictions were little better than chance. Furthermore, the list of problems they uncovered continued to grow. For example, they saw that in one of their papers Dr Potti and his colleagues had mislabelled the cell lines they used to derive their chemotherapy prediction model, describing those that were sensitive as resistant, and vice versa. This meant that even if the predictive method the team at Duke were describing did work, which Dr Baggerly and Dr Coombes now seriously doubted, patients whose doctors relied on this paper would end up being given a drug they were less likely to benefit from instead of more likely.

In other words, the raw data was a mess. The results had to be random.

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Historical footnotes to game theory

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[ cross-posted from Zenpundit — philosophy, psychology, history, game theory, dilemma, commons cooperation, analogy, 9/11 ]

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I have an interest in game theory that is much like my interest in music: I can’t play, but I can whistle. And so it is that I’ve substituted curiosity about the history of the thing, and whatever analogical patterns I can discern there, for any actual ability at the thing itself.

Somewhere in my analogy-collector’s mind, then, I have these two quotes, cut from the living tissue of their writer’s thoughts, and prepped fpor contemplation. I find them, in retrospect, quite remarkable.

Jean-Jacques Rousseau, in On the Inequality among Mankind, wrote:

Such was the manner in which men might have insensibly acquired some gross idea of their mutual engagements and the advantage of fulfilling them, but this only as far as their present and sensible interest required; for as to foresight they were utter strangers to it, and far from troubling their heads about a distant futurity, they scarce thought of the day following. Was a deer to be taken? Every one saw that to succeed he must faithfully stand to his post; but suppose a hare to have slipped by within reach of any one of them, it is not to be doubted but he pursued it without scruple, and when he had seized his prey never reproached himself with having made his companions miss theirs.

And David Hume, in A Treatise of Human Nature:

Your corn is ripe today; mine will be so tomorrow. ‘Tis profitable for us both that I shou’d labour with you today, and that you shou’d aid me tomorrow. I have no kindness for you, and know that you have as little for me. I will not, therefore, take any pains on your account; and should I labour with you on my account, I know I shou’d be disappointed, and that I shou’d in vain depend upon your gratitude. Here then I leave you to labour alone: You treat me in the same manner. The seasons change; and both of us lose our harvests for want of mutual confidence and security.

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Those two, I believe, are fairly well known – I was delighted the other day to run across a third sample for my collection. William James, in The Will to Believe, writes:

Wherever a desired result is achieved by the co-operation of many independent persons, its existence as a fact is a pure consequence of the precursive faith in one another of those immediately concerned. A government, an army, a commercial system, a ship, a college, an athletic team, all exist on this condition, without which not only is nothing achieved, but nothing is even attempted. A whole train of passengers (individually brave enough) will be looted by a few highwaymen, simply because the latter can count on one another, while each passenger fears that if he makes a movement of resistance, he will be shot before any one else backs him up. If we believed that the whole car-full would rise at once with us, we should each severally rise, and train-robbing would never even be attempted.

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The first two quotes are of interest as showing the forms that an idea which will later be mathematized can take. They are, if you like, precursors of game theoretic constructs, although neither Hume nor Rousseau appears to be mentioned in von Neumann and Morgenstern‘s Theory of Games and Economic Behavior.

The third, I think, is even more interesting.. Consider the eerie and heroic “fulfillment” of that third paragraph if read “as prophecy” – in this account from the 9/11 Commission Report of the events on United Flight 93:

During at least five of the passengers’ phone calls, information was shared about the attacks that had occurred earlier that morning at the World Trade Center. Five calls described the intent of passengers and surviving crew members to revolt against the hijackers. According to one call, they voted on whether to rush the terrorists in an attempt to retake the plane. They decided, and acted. At 9:57, the passenger assault began. Several passengers had terminated phone calls with loved ones in order to join the revolt. One of the callers ended her message as follows:

“Everyone’s running up to first class. I’ve got to go. Bye.” The cockpit voice recorder captured the sounds of the passenger assault muffled by the intervening cockpit door.

Yesterday’s highwayman is today’s hijacker, yesterday’s train is today’s plane…

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If there’s anything to be learned here, it’s not a novel way of protecting trains or aircraft from passengers of malicious intent —

It’s that there’s a subtle thread running from something akin to instinct that’s also close to unspoken common sense, surfacing for a moment in the writings of thoughtful individuals, leading on occasion to the formulation of exact mathematical principles — but also (i) available, (ii) in the human repertoire, (iii) to be acted upon, (iv) cooperatively, (v) as required, (vi) via the medium of human common interest, (vii) which provides the resultant trust.

Which may in turn offer some reason for hope — for a humanity in various forms of communal distress…

UBL and the African elephant

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[ cross-posted from Zenpundit — UBL, global warming, elephants, and Al-Shabaab ]
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“Natives with ivory tusks, Dar Es Salaam, Tanganyika” ca 1900, LOC

I’d like to quietly propose a few dots or data points…

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Alex Shoumatoff has a fine article titled “Agony and Ivory”, in Vanity Fair:

The riverbank is littered with elephant dung. Andrea kicks apart one of the boluses, and it is full of big, hard-shelled seeds — Pandanus, Drypetes, and Gambeya. A new study has found that forest elephants are essential to central Africa’s forests for tree-seed dispersal. They can carry heavy seeds like these (which wouldn’t get very far on their own) in their gut for 50 miles before voiding them. Another study measures the rapid, prodigious growth of the forest trees and concludes that central Africa is the second-most-important equatorial sink for atmospheric carbon after the Amazon, so elephants are important for controlling global warming, on top of everything else.

Here is Shaykh Usama bin Laden, in his radio message “The Way to Save the Earth” from As-Sahab Media:

This is a message to the whole world about those who cause climate change and its dangers — intentionally or unintentionally — and what we must do. Talk of climate change isn’t extravagant speculation: it is a tangible fact which is not diminished by its being muddled by some greedy heads of major corporations. The effects of global warming have spread to all continents of the world. Drought, desertification and sands are advancing on one front, while on another front, torrential floods and huge storms the likes of which only used to be seen once every few decades now reoccur every few years.

From UBL’s perspective, this is clearly a moral issue:

First, the corruption of the climate stems from the corruption of hearts and deeds, and there is a close relationship between the two types of corruption.

And here’s Shoumatoff again, on the situation in Kenya:

A few weeks ago, two poachers were killed and a ranger was wounded in a firefight in Meru National Park. Al-Shabaab, the Islamist youth militia which is in league with al-Qaeda and controls most of Somalia, has been coming over the border and killing elephants in Arawale National Reserve. Ivory, like the blood diamonds of other African conflicts, is funding many rebel groups in Africa, and Kenya, K.W.S. director Julius Kipng’etich told me, “is in the unenviable position of sharing over 1,700 kilometers of border with three countries with civil wars that are awash with firearms: Somalia, Ethiopia, and Sudan.” Nothing less than a full-scale military operation is going to stop the poaching in the north.

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Now, as EM Forster suggested, Only connect!

Let’s Not Forget This

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Steven Chu, Obama’s astonishingly arrogant (Nobel-prize-winning!) energy secretary, defends the Edison-bulb ban:

We are taking away a choice that continues to let people waste their own money.

Read the PowerLine post at the link, and continue to the Mark Steyn post….Steyn is, as usual, in fine form. But I’m mainly posting this because we need to remember Chu’s comment at election time, to be added to the very long list of statements and actions that show just how disconnected this administration is from traditional American ideas of liberty. I don’t think most Americans yet understand just how extreme this disconnect is, and we need to help ensure that it is made visible.

This is an administration, as I’ve noted before, that is comprised of two kinds of people: theorists and agitators. They do not value individual freedom, and they are not interested in problem-solving.

“Carbon” is not a synonym for “CO2”

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…any more than “hydrogen” is a synonym for “H2O.”

Senator Barbara Boxer (D-CA) seems a little confused on this point.

I’ve noticed quite a few people, in various debates about environmental matters, referring to “carbon” as generically a bad thing. Some of them are probably just using it as a shorthand for carbon dioxide, in order to save syllables or characters—others, though, really do seem to think that the discussion is about some sinister product of the Industrial Revolution, rather than the natural compound that they exhale with every breath and that is required for the growth of plants. Maybe they think it’s about carbon particulates.

The situation isn’t helped by various corporations which, when promoting their products/technologies on environmental grounds, now almost always talk about how they reduce carbon, or at best carbon dioxide, rather than talking about reductions in real air pollution in the form of mercury, sulfur dioxide, etc. The terms “carbon” and “carbon dioxide” are now generally being used as shorthand for atmospheric Bad Things.

Returning to Boxer, the levels of her ignorance and demagoguery are astonishing–but we should not forget also her amazing arrogance and self-centeredness.