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Weiye Loh

From Abstract to News Release to Story, a Tilt to the 'Front-Page Thought' - NYTimes.com - 0 views

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    "In the post on research on extreme rainfall and warming, Gavin Schmidt, the NASA climate scientist and Real Climate blogger, described the misinterpretation of some paper abstracts as mainly reflecting a cultural divide: "Here we show" statements are required by Nature and Science to clearly lay out the point of the paper. If you don't include it, they will write it in. The caveats/uncertainties/issues all come later. I think the confusion is more cultural than anything. No one at Nature or Science or any of the authors in any subject think that uncertainties are zero, but they require a clear statement of the point of the paper within their house style. I think that conclusion misses the reality that, particularly in the world of online communication of science, abstracts are not merely for colleagues who know the shorthand, but have different audiences who'll have different ways of interpreting phrases such as "here we show.""
Weiye Loh

Science scorned : Nature : Nature Publishing Group - 0 views

  • There is a growing anti-science streak on the American right that could have tangible societal and political impacts on many fronts — including regulation of environmental and other issues and stem-cell research.
  • The right-wing populism that is flourishing in the current climate of economic insecurity echoes many traditional conservative themes, such as opposition to taxes, regulation and immigration. But the Tea Party and its cheerleaders, who include Limbaugh, Fox News television host Glenn Beck and Sarah Palin (who famously decried fruitfly research as a waste of public money), are also tapping an age-old US political impulse — a suspicion of elites and expertise.
  • Denialism over global warming has become a scientific cause célèbre within the movement. Limbaugh, for instance, who has told his listeners that “science has become a home for displaced socialists and communists”, has called climate-change science “the biggest scam in the history of the world”. The Tea Party's leanings encompass religious opposition to Darwinian evolution and to stem-cell and embryo research — which Beck has equated with eugenics. The movement is also averse to science-based regulation, which it sees as an excuse for intrusive government. Under the administration of George W. Bush, science in policy had already taken knocks from both neglect and ideology. Yet President Barack Obama's promise to “restore science to its rightful place” seems to have linked science to liberal politics, making it even more of a target of the right.
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  • US citizens face economic problems that are all too real, and the country's future crucially depends on education, science and technology as it faces increasing competition from China and other emerging science powers.
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    Science Scorned  The anti-science strain pervading the right wing in the United States is the last thing the country needs in a time of economic challenge.
Weiye Loh

Open Letter to Richard Dawkins: Why Are You Still In Denial About Group Selection? : Ev... - 0 views

  • Dear Richard, I do not agree with the cynical adage "science progresses--funeral by funeral", but I fear that it might be true in your case for the subject of group selection.
  • Edward Wilson was misunderstanding kin selection as far back as Sociobiology, where he treated it as a subset of group selection ... Kin selection is not a subset of group selection, it is a logical consequence of gene selection. And gene selection is (everything that Nowak et al ought to mean by) 'standard natural selection' theory: has been ever since the neo-Darwinian synthesis of the 1930s.
  • I do not agree with the Nowak et al. article in every respect and will articulate some of my disagreements in subsequent posts. For the moment, I want to stress how alone you are in your statement about group selection. Your view is essentially pre-1975, a date that is notable not only for the publication of Sociobiology but also a paper by W.D. Hamilton, one of your heroes, who correctly saw the relationship between kin selection and group selection thanks to the work of George Price. Ever since, knowledgeable theoretical biologists have known that inclusive fitness theory includes the logic of multilevel selection, which means that altruism is selectively disadvantageous within kin groups and evolves only by virtue of groups with more altruists contributing more to the gene pool than groups with fewer altruists. The significance of relatedness is that it clusters the genes coding for altruistic and selfish behaviors into different groups.
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  • Even the contemporary theoretical biologists most critical of multilevel selection, such as Stuart West and Andy Gardner, acknowledge what you still deny. In an earlier feature on group selection published in Nature, Andy Gardner is quoted as saying "Everyone agrees that group selection occurs"--everyone except you, that is.
  • You correctly say that gene selection is standard natural selection theory. Essentially, it is a popularization of the concept of average effects in population genetics theory, which averages the fitness of alternative genes across all contexts to calculate what evolves in the total population. For that reason, it is an elementary mistake to regard gene selection as an alternative to group selection. Whenever a gene evolves in the total population on the strength of group selection, despite being selectively disadvantageous within groups, it has the highest average effect compared to the genes that it replaced. Please consult the installment of my "Truth and Reconciliation for Group Selection" series titled "Naïve Gene Selectionism" for a refresher course. While you're at it, check out the installment titled "Dawkins Protests--Too Much".
  • The Nowak et al. article includes several critiques of inclusive fitness theory that need to be distinguished from each other. One issue is whether inclusive fitness theory is truly equivalent to explicit models of evolution in multi-group populations, or whether it makes so many simplifying assumptions that it restricts itself to a small region of the parameter space. A second issue is whether benefiting collateral kin is required for the evolution of eusociality and other forms of prosociality. A third issue is whether inclusive fitness theory, as understood by the average evolutionary biologist and the general public, bears any resemblance to inclusive fitness theory as understood by the cognoscenti.
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    Open Letter to Richard Dawkins: Why Are You Still In Denial About Group Selection?
Weiye Loh

Rationally Speaking: Some animals are more equal than others - 0 views

  • society's answer to the question “Is it acceptable to hurt animals for our pleasure?” isn't always “No.” Odds are that most of the people who objected to the dog fighting and crush videos are frequent consumers of meat, milk, and eggs from industrialized farms. And the life of an animal in a typical industrialized farm is notoriously punishing. Many spend their lives in cages so confining they can barely move; ammonia fumes burn their eyes; their beaks or tails are chopped off to prevent them from biting each other out of stress; and the farm's conditions make many of them so sick or weak that they die in their cages or on the way to slaughter. As a society, however, we apparently believe that the pleasure we get from eating those animals makes their suffering worth it.
  • many people will object that eating animals isn’t a matter of pleasure at all, but of the need for sustenance. While that may have been true for our ancestors who survived by hunting wild animals, I don’t think it has much relevance to our current situation. First, it's questionable whether we actually do need to eat animal products in order to be healthy; the American Dietetic Association has given the thumbs up to vegetarian and even vegan diets. But even if you believe that some amount of animal product consumption is medically necessary, we could still buy from farms that raise their livestock much more humanely. It would cost more, but we could always compensate by cutting back on other luxuries, or simply by eating less meat. By any reasonable estimate, Americans could cut their meat consumption drastically with no ill effects on their health (and likely with many positive effects). Buying the sheer amount of meat that Americans do, at the low prices made possible by industrialized farms, is a luxury that can’t be defended with a “need for sustenance” argument. It’s about pleasure — the pleasure of eating more meat than strictly necessary for health, and the pleasure of saving money that can then be spent on other things we enjoy.
  • there are several reasons why people regard consumers of industrial farming differently than consumers of crush videos and dogfighting. The first has to do with the types of animals involved: pigs, cows, and chickens simply aren't as cute as dogs, bunnies, and kittens. I don't know how many people would explicitly cite that as the reason they're willing to inflict suffering on the former and not the latter, but it seems to play a role, even if people won't admit as much. People who have no qualms about a pig spending its life in a small, dark crate would nevertheless be outraged if a dog were treated in the same way.
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  • Cuteness is a pretty silly criterion by which to assign moral status, though. It's not as if unappealing animals are less intelligent or less sensitive to pain.
  • And if you have any trouble seeing the absurdity of basing moral judgments on cuteness, it helps to try out the principle in other contexts. (Is it worse to abuse a cute child than an ugly one?)
  • But I think the biggest reason that different examples of hurting animals for pleasure elicit different reactions from people is not about the types of animals involved, but about the types of pleasure.
  • One objective difference people might cite is the fact that a desire to eat meat is “natural” while a desire to watch kittens being crushed is not. Which is true, in the sense that our species did evolve to eat meat while a fetish for crushing kittens is an aberration. But using naturalness as a criterion for moral rightness is a dubious move. First, it seems rather arbitrary, from a logical perspective, which is why it's often referred to as the naturalistic fallacy. And second, it would justify some pretty unsavory “natural” urges, like rape and tribalism, while prohibiting other “unnatural” urges, like the desire to wear clothing or to refrain from having children.
  • The closest thing that I can find to a morally relevant distinction between industrial farming, dogfighting, and crush videos is this: While it’s true that all three acts cause animal suffering in order to give people pleasure, the nature of that tradeoff differs. The consumers of crush videos and dogfighting are taking pleasure in the suffering itself, whereas the consumers of industrially-farmed meat are taking pleasure in the meat that was produced by the suffering. From a purely harm-based perspective, the moral calculus is the same: the animal suffers so that you can experience pleasure. But the degree of directness of that tradeoff makes a difference in how we perceive your character. Someone whose motive is “I enjoy seeing another creature suffer” seems more evil than someone whose motive is “I want a tasty meal,” even if both people cause the same amount of suffering.
  • And I can certainly understand why people would want to call a crush video enthusiast more “evil” than a person who buys meat from industrial farms, because of the difference in their motivations. That's a reasonable way to define evilness. But in that case we're left with the fact that a person's evilness may be totally unrelated to the amount of harm she causes; and that, in fact, some of the greatest harm may be caused by people whose motivations seem unobjectionable to us. Apathy, denial, conformity; none of these inspire the same outrage as sadism, but they've caused some pretty horrible outcomes. And if you believe that it's wrong to make animals suffer for our pleasure, but you reserve your moral condemnation only for cases that viscerally upset you, like dogfighting or crush videos, then you're falling prey to the trap that Isaac Asimov famously warned us against: “Never let your sense of morals prevent you from doing what is right.”
Weiye Loh

Sociologist Harry Collins poses as a physicist. - By Jon Lackman - Slate Magazine - 0 views

  • British sociologist Harry Collins asked a scientist who specializes in gravitational waves to answer seven questions about the physics of these waves. Collins, who has made an amateur study of this field for more than 30 years but has never actually practiced it, also answered the questions himself. Then he submitted both sets of answers to a panel of judges who are themselves gravitational-wave researchers. The judges couldn't tell the impostor from one of their own. Collins argues that he is therefore as qualified as anyone to discuss this field, even though he can't conduct experiments in it.
  • The journal Nature predicted that the experiment would have a broad impact, writing that Collins could help settle the "science wars of the 1990s," "when sociologists launched what scientists saw as attacks on the very nature of science, and scientists responded in kind," accusing the sociologists of misunderstanding science. More generally, it could affect "the argument about whether an outsider, such as an anthropologist, can properly understand another group, such as a remote rural community." With this comment, Nature seemed to be saying that if a sociologist can understand physics, then anyone can understand anything.
  • It will be interesting to see if Collins' results can indeed be repeated in different situations. Meanwhile, his experiment is plenty interesting in itself. Just one of the judges succeeded in distinguishing Collins' answers from those of the trained experts. One threw up his hands. And the other seven declared Collins the physicist. He didn't simply do as well as the trained specialist—he did better, even though the test questions demanded technical answers. One sample answer from Collins gives you the flavor: "Since gravitational waves change the shape of spacetime and radio waves do not, the effect on an interferometer of radio waves can only be to mimic the effects of a gravitational wave, not reproduce them." (More details can be found in this paper Collins wrote with his collaborators.)
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  • To be sure, a differently designed experiment would have presented more difficulty for Collins. If he'd chosen questions that involved math, they would have done him in
  • But many scientists consider themselves perfectly qualified to discuss topics for which they lack the underlying mathematical skills, as Collins noted when I talked to him. "You can be a great physicist and not know any mathematics," he said.
  • So, if Collins can talk gravitational waves as well as an insider, who cares if he doesn't know how to crunch the numbers? Alan Sokal does. The New York University physicist is famous for an experiment a decade ago that seemed to demonstrate the futility of laymen discussing science. In 1996, he tricked the top humanities journal Social Text into publishing as genuine scholarship a totally nonsensical paper that celebrated fashionable literary theory and then applied it to all manner of scientific questions. ("As Lacan suspected, there is an intimate connection between the external structure of the physical world and its inner psychological representation qua knot theory.") Sokal showed that, with a little flattery, laymen could be induced to swallow the most ridiculous of scientific canards—so why should we value their opinions on science as highly as scientists'?
  • Sokal doesn't think Collins has proved otherwise. When I reached him this week, he acknowledged that you don't need to practice science in order to understand it. But he maintains, as he put it to Nature, that in many science debates, "you need a knowledge of the field that is virtually, if not fully, at the level of researchers in the field," in order to participate. He elaborated: Say there are two scientists, X and Y. If you want to argue that X's theory was embraced over Y's, even though Y's is better, because the science community is biased against Y, then you had better be able to read and evaluate their theories yourself, mathematics included (or collaborate with someone who can). He has a point. Just because mathematics features little in the work of some gravitational-wave physicists doesn't mean it's a trivial part of the subject.
  • Even if Collins didn't demonstrate that he is qualified to pronounce on all of gravitational-wave physics, he did learn more of the subject than anyone may have thought possible. Sokal says he was shocked by Collins' store of knowledge: "He knows more about gravitational waves than I do!" Sokal admitted that Collins was already qualified to pronounce on a lot, and that with a bit more study, he would be the equal of a professional.
Weiye Loh

Where Science Meets Politics « Alan Colmes' Liberaland - 0 views

  • The New York Times series on the risks of natural gas highlights this problem.More than a quarter-century of efforts by some lawmakers and regulators to force the federal government to police the industry better have been thwarted, as E.P.A. studies have been repeatedly narrowed in scope and important findings have been removed.
  • if, as the article indicates, Republicans from gas drilling states and even the EPA are suppressing research into the dangerous side effects of natural gas extraction to encourage its us at the expense of fuels that are worse for climate change, then it is making a serious mistake. Better to understand the dangers of natural gas drilling, compare them to the benefits of natural gas vs. coal and oil for climate change, and regulate accordingly.
Weiye Loh

Science, Strong Inference -- Proper Scientific Method - 0 views

  • Scientists these days tend to keep up a polite fiction that all science is equal. Except for the work of the misguided opponent whose arguments we happen to be refuting at the time, we speak as though every scientist's field and methods of study are as good as every other scientist's and perhaps a little better. This keeps us all cordial when it comes to recommending each other for government grants.
  • Why should there be such rapid advances in some fields and not in others? I think the usual explanations that we tend to think of - such as the tractability of the subject, or the quality or education of the men drawn into it, or the size of research contracts - are important but inadequate. I have begun to believe that the primary factor in scientific advance is an intellectual one. These rapidly moving fields are fields where a particular method of doing scientific research is systematically used and taught, an accumulative method of inductive inference that is so effective that I think it should be given the name of "strong inference." I believe it is important to examine this method, its use and history and rationale, and to see whether other groups and individuals might learn to adopt it profitably in their own scientific and intellectual work. In its separate elements, strong inference is just the simple and old-fashioned method of inductive inference that goes back to Francis Bacon. The steps are familiar to every college student and are practiced, off and on, by every scientist. The difference comes in their systematic application. Strong inference consists of applying the following steps to every problem in science, formally and explicitly and regularly: Devising alternative hypotheses; Devising a crucial experiment (or several of them), with alternative possible outcomes, each of which will, as nearly is possible, exclude one or more of the hypotheses; Carrying out the experiment so as to get a clean result; Recycling the procedure, making subhypotheses or sequential hypotheses to refine the possibilities that remain, and so on.
  • On any new problem, of course, inductive inference is not as simple and certain as deduction, because it involves reaching out into the unknown. Steps 1 and 2 require intellectual inventions, which must be cleverly chosen so that hypothesis, experiment, outcome, and exclusion will be related in a rigorous syllogism; and the question of how to generate such inventions is one which has been extensively discussed elsewhere (2, 3). What the formal schema reminds us to do is to try to make these inventions, to take the next step, to proceed to the next fork, without dawdling or getting tied up in irrelevancies.
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  • It is clear why this makes for rapid and powerful progress. For exploring the unknown, there is no faster method; this is the minimum sequence of steps. Any conclusion that is not an exclusion is insecure and must be rechecked. Any delay in recycling to the next set of hypotheses is only a delay. Strong inference, and the logical tree it generates, are to inductive reasoning what the syllogism is to deductive reasoning in that it offers a regular method for reaching firm inductive conclusions one after the other as rapidly as possible.
  • "But what is so novel about this?" someone will say. This is the method of science and always has been, why give it a special name? The reason is that many of us have almost forgotten it. Science is now an everyday business. Equipment, calculations, lectures become ends in themselves. How many of us write down our alternatives and crucial experiments every day, focusing on the exclusion of a hypothesis? We may write our scientific papers so that it looks as if we had steps 1, 2, and 3 in mind all along. But in between, we do busywork. We become "method- oriented" rather than "problem-oriented." We say we prefer to "feel our way" toward generalizations. We fail to teach our students how to sharpen up their inductive inferences. And we do not realize the added power that the regular and explicit use of alternative hypothesis and sharp exclusion could give us at every step of our research.
  • A distinguished cell biologist rose and said, "No two cells give the same properties. Biology is the science of heterogeneous systems." And he added privately. "You know there are scientists, and there are people in science who are just working with these over-simplified model systems - DNA chains and in vitro systems - who are not doing science at all. We need their auxiliary work: they build apparatus, they make minor studies, but they are not scientists." To which Cy Levinthal replied: "Well, there are two kinds of biologists, those who are looking to see if there is one thing that can be understood and those who keep saying it is very complicated and that nothing can be understood. . . . You must study the simplest system you think has the properties you are interested in."
  • At the 1958 Conference on Biophysics, at Boulder, there was a dramatic confrontation between the two points of view. Leo Szilard said: "The problems of how enzymes are induced, of how proteins are synthesized, of how antibodies are formed, are closer to solution than is generally believed. If you do stupid experiments, and finish one a year, it can take 50 years. But if you stop doing experiments for a little while and think how proteins can possibly be synthesized, there are only about 5 different ways, not 50! And it will take only a few experiments to distinguish these." One of the young men added: "It is essentially the old question: How small and elegant an experiment can you perform?" These comments upset a number of those present. An electron microscopist said. "Gentlemen, this is off the track. This is philosophy of science." Szilard retorted. "I was not quarreling with third-rate scientists: I was quarreling with first-rate scientists."
  • Any criticism or challenge to consider changing our methods strikes of course at all our ego-defenses. But in this case the analytical method offers the possibility of such great increases in effectiveness that it is unfortunate that it cannot be regarded more often as a challenge to learning rather than as challenge to combat. Many of the recent triumphs in molecular biology have in fact been achieved on just such "oversimplified model systems," very much along the analytical lines laid down in the 1958 discussion. They have not fallen to the kind of men who justify themselves by saying "No two cells are alike," regardless of how true that may ultimately be. The triumphs are in fact triumphs of a new way of thinking.
  • the emphasis on strong inference
  • is also partly due to the nature of the fields themselves. Biology, with its vast informational detail and complexity, is a "high-information" field, where years and decades can easily be wasted on the usual type of "low-information" observations or experiments if one does not think carefully in advance about what the most important and conclusive experiments would be. And in high-energy physics, both the "information flux" of particles from the new accelerators and the million-dollar costs of operation have forced a similar analytical approach. It pays to have a top-notch group debate every experiment ahead of time; and the habit spreads throughout the field.
  • Historically, I think, there have been two main contributions to the development of a satisfactory strong-inference method. The first is that of Francis Bacon (13). He wanted a "surer method" of "finding out nature" than either the logic-chopping or all-inclusive theories of the time or the laudable but crude attempts to make inductions "by simple enumeration." He did not merely urge experiments as some suppose, he showed the fruitfulness of interconnecting theory and experiment so that the one checked the other. Of the many inductive procedures he suggested, the most important, I think, was the conditional inductive tree, which proceeded from alternative hypothesis (possible "causes," as he calls them), through crucial experiments ("Instances of the Fingerpost"), to exclusion of some alternatives and adoption of what is left ("establishing axioms"). His Instances of the Fingerpost are explicitly at the forks in the logical tree, the term being borrowed "from the fingerposts which are set up where roads part, to indicate the several directions."
  • ere was a method that could separate off the empty theories! Bacon, said the inductive method could be learned by anybody, just like learning to "draw a straighter line or more perfect circle . . . with the help of a ruler or a pair of compasses." "My way of discovering sciences goes far to level men's wit and leaves but little to individual excellence, because it performs everything by the surest rules and demonstrations." Even occasional mistakes would not be fatal. "Truth will sooner come out from error than from confusion."
  • Nevertheless there is a difficulty with this method. As Bacon emphasizes, it is necessary to make "exclusions." He says, "The induction which is to be available for the discovery and demonstration of sciences and arts, must analyze nature by proper rejections and exclusions, and then, after a sufficient number of negatives come to a conclusion on the affirmative instances." "[To man] it is granted only to proceed at first by negatives, and at last to end in affirmatives after exclusion has been exhausted." Or, as the philosopher Karl Popper says today there is no such thing as proof in science - because some later alternative explanation may be as good or better - so that science advances only by disproofs. There is no point in making hypotheses that are not falsifiable because such hypotheses do not say anything, "it must be possible for all empirical scientific system to be refuted by experience" (14).
  • The difficulty is that disproof is a hard doctrine. If you have a hypothesis and I have another hypothesis, evidently one of them must be eliminated. The scientist seems to have no choice but to be either soft-headed or disputatious. Perhaps this is why so many tend to resist the strong analytical approach and why some great scientists are so disputatious.
  • Fortunately, it seems to me, this difficulty can be removed by the use of a second great intellectual invention, the "method of multiple hypotheses," which is what was needed to round out the Baconian scheme. This is a method that was put forward by T.C. Chamberlin (15), a geologist at Chicago at the turn of the century, who is best known for his contribution to the Chamberlain-Moulton hypothesis of the origin of the solar system.
  • Chamberlin says our trouble is that when we make a single hypothesis, we become attached to it. "The moment one has offered an original explanation for a phenomenon which seems satisfactory, that moment affection for his intellectual child springs into existence, and as the explanation grows into a definite theory his parental affections cluster about his offspring and it grows more and more dear to him. . . . There springs up also unwittingly a pressing of the theory to make it fit the facts and a pressing of the facts to make them fit the theory..." "To avoid this grave danger, the method of multiple working hypotheses is urged. It differs from the simple working hypothesis in that it distributes the effort and divides the affections. . . . Each hypothesis suggests its own criteria, its own method of proof, its own method of developing the truth, and if a group of hypotheses encompass the subject on all sides, the total outcome of means and of methods is full and rich."
  • The conflict and exclusion of alternatives that is necessary to sharp inductive inference has been all too often a conflict between men, each with his single Ruling Theory. But whenever each man begins to have multiple working hypotheses, it becomes purely a conflict between ideas. It becomes much easier then for each of us to aim every day at conclusive disproofs - at strong inference - without either reluctance or combativeness. In fact, when there are multiple hypotheses, which are not anyone's "personal property," and when there are crucial experiments to test them, the daily life in the laboratory takes on an interest and excitement it never had, and the students can hardly wait to get to work to see how the detective story will come out. It seems to me that this is the reason for the development of those distinctive habits of mind and the "complex thought" that Chamberlin described, the reason for the sharpness, the excitement, the zeal, the teamwork - yes, even international teamwork - in molecular biology and high- energy physics today. What else could be so effective?
  • Unfortunately, I think, there are other other areas of science today that are sick by comparison, because they have forgotten the necessity for alternative hypotheses and disproof. Each man has only one branch - or none - on the logical tree, and it twists at random without ever coming to the need for a crucial decision at any point. We can see from the external symptoms that there is something scientifically wrong. The Frozen Method, The Eternal Surveyor, The Never Finished, The Great Man With a Single Hypothcsis, The Little Club of Dependents, The Vendetta, The All-Encompassing Theory Which Can Never Be Falsified.
  • a "theory" of this sort is not a theory at all, because it does not exclude anything. It predicts everything, and therefore does not predict anything. It becomes simply a verbal formula which the graduate student repeats and believes because the professor has said it so often. This is not science, but faith; not theory, but theology. Whether it is hand-waving or number-waving, or equation-waving, a theory is not a theory unless it can be disproved. That is, unless it can be falsified by some possible experimental outcome.
  • the work methods of a number of scientists have been testimony to the power of strong inference. Is success not due in many cases to systematic use of Bacon's "surest rules and demonstrations" as much as to rare and unattainable intellectual power? Faraday's famous diary (16), or Fermi's notebooks (3, 17), show how these men believed in the effectiveness of daily steps in applying formal inductive methods to one problem after another.
  • Surveys, taxonomy, design of equipment, systematic measurements and tables, theoretical computations - all have their proper and honored place, provided they are parts of a chain of precise induction of how nature works. Unfortunately, all too often they become ends in themselves, mere time-serving from the point of view of real scientific advance, a hypertrophied methodology that justifies itself as a lore of respectability.
  • We speak piously of taking measurements and making small studies that will "add another brick to the temple of science." Most such bricks just lie around the brickyard (20). Tables of constraints have their place and value, but the study of one spectrum after another, if not frequently re-evaluated, may become a substitute for thinking, a sad waste of intelligence in a research laboratory, and a mistraining whose crippling effects may last a lifetime.
  • Beware of the man of one method or one instrument, either experimental or theoretical. He tends to become method-oriented rather than problem-oriented. The method-oriented man is shackled; the problem-oriented man is at least reaching freely toward that is most important. Strong inference redirects a man to problem-orientation, but it requires him to be willing repeatedly to put aside his last methods and teach himself new ones.
  • anyone who asks the question about scientific effectiveness will also conclude that much of the mathematizing in physics and chemistry today is irrelevant if not misleading. The great value of mathematical formulation is that when an experiment agrees with a calculation to five decimal places, a great many alternative hypotheses are pretty well excluded (though the Bohr theory and the Schrödinger theory both predict exactly the same Rydberg constant!). But when the fit is only to two decimal places, or one, it may be a trap for the unwary; it may be no better than any rule-of-thumb extrapolation, and some other kind of qualitative exclusion might be more rigorous for testing the assumptions and more important to scientific understanding than the quantitative fit.
  • Today we preach that science is not science unless it is quantitative. We substitute correlations for causal studies, and physical equations for organic reasoning. Measurements and equations are supposed to sharpen thinking, but, in my observation, they more often tend to make the thinking noncausal and fuzzy. They tend to become the object of scientific manipulation instead of auxiliary tests of crucial inferences.
  • Many - perhaps most - of the great issues of science are qualitative, not quantitative, even in physics and chemistry. Equations and measurements are useful when and only when they are related to proof; but proof or disproof comes first and is in fact strongest when it is absolutely convincing without any quantitative measurement.
  • you can catch phenomena in a logical box or in a mathematical box. The logical box is coarse but strong. The mathematical box is fine-grained but flimsy. The mathematical box is a beautiful way of wrapping up a problem, but it will not hold the phenomena unless they have been caught in a logical box to begin with.
  • Of course it is easy - and all too common - for one scientist to call the others unscientific. My point is not that my particular conclusions here are necessarily correct, but that we have long needed some absolute standard of possible scientific effectiveness by which to measure how well we are succeeding in various areas - a standard that many could agree on and one that would be undistorted by the scientific pressures and fashions of the times and the vested interests and busywork that they develop. It is not public evaluation I am interested in so much as a private measure by which to compare one's own scientific performance with what it might be. I believe that strong inference provides this kind of standard of what the maximum possible scientific effectiveness could be - as well as a recipe for reaching it.
  • The strong-inference point of view is so resolutely critical of methods of work and values in science that any attempt to compare specific cases is likely to sound but smug and destructive. Mainly one should try to teach it by example and by exhorting to self-analysis and self-improvement only in general terms
  • one severe but useful private test - a touchstone of strong inference - that removes the necessity for third-person criticism, because it is a test that anyone can learn to carry with him for use as needed. It is our old friend the Baconian "exclusion," but I call it "The Question." Obviously it should be applied as much to one's own thinking as to others'. It consists of asking in your own mind, on hearing any scientific explanation or theory put forward, "But sir, what experiment could disprove your hypothesis?"; or, on hearing a scientific experiment described, "But sir, what hypothesis does your experiment disprove?"
  • It is not true that all science is equal; or that we cannot justly compare the effectiveness of scientists by any method other than a mutual-recommendation system. The man to watch, the man to put your money on, is not the man who wants to make "a survey" or a "more detailed study" but the man with the notebook, the man with the alternative hypotheses and the crucial experiments, the man who knows how to answer your Question of disproof and is already working on it.
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    There is so much bad science and bad statistics information in media reports, publications, and shared between conversants that I think it is important to understand about facts and proofs and the associated pitfalls.
Weiye Loh

Major reform for climate body : Nature News - 0 views

  • The first major test of these changes will be towards the end of this year, with the release of a report assessing whether climate change is increasing the likelihood of extreme weather events. Despite much speculation, there is scant scientific evidence for such a link — particularly between climate warming, storm frequency and economic losses — and the report is expected to spark renewed controversy. "It'll be interesting to see how the IPCC will handle this hot potato where stakes are high but solid peer-reviewed results are few," says Silke Beck, a policy expert at the Helmholtz Centre for Environmental Research in Leipzig, Germany.
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    A new conflict-of-interest policy will require all IPCC officials and authors to disclose financial and other interests relevant to their work (Pachauri had been harshly criticized in 2009 for alleged conflicts of interest.) The meeting also adopted a detailed protocol for addressing errors in existing and future IPCC reports, along with guidelines to ensure that descriptions of scientific uncertainties remain consistent across reports. "This is a heartening and encouraging outcome of the review we started one year ago," Pachauri told Nature. "It will strengthen the IPCC and help restore public trust in the climate sciences."
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Roger Pielke Jr.'s Blog: Neville Nicholls on Australia's Extreme Rainfall - 0 views

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    The record La Niña event was the fundamental cause of the heavy rains and floods, ie it was a natural fluctuation of the climate system. There may be a global warming signal enhancing this natural variability, but if so then this effect has been quite subtle, at least thus far
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U. of California Tries Just Saying No to Rising Journal Costs - Research - The Chronicl... - 0 views

  • Nature proposed to raise the cost of California's license for its journals by 400 percent next year. If the publisher won't negotiate, the letter said, the system may have to take "more drastic actions" with the help of the faculty. Those actions could include suspending subscriptions to all of the Nature Group journals the California system buys access to—67 in all, including Nature.
  • faculty would also organize "a systemwide boycott" of Nature's journals if the publisher does not relent. The voluntary boycott would "strongly encourage" researchers not to contribute papers to those journals or review manuscripts for them. It would urge them to resign from Nature's editorial boards and to encourage similar "sympathy actions" among colleagues outside the University of California system.
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Op-Ed Columnist - The Moral Naturalists - NYTimes.com - 0 views

  • Moral naturalists, on the other hand, believe that we have moral sentiments that have emerged from a long history of relationships. To learn about morality, you don’t rely upon revelation or metaphysics; you observe people as they live.
  • By the time humans came around, evolution had forged a pretty firm foundation for a moral sense. Jonathan Haidt of the University of Virginia argues that this moral sense is like our sense of taste. We have natural receptors that help us pick up sweetness and saltiness. In the same way, we have natural receptors that help us recognize fairness and cruelty. Just as a few universal tastes can grow into many different cuisines, a few moral senses can grow into many different moral cultures.
  • Paul Bloom of Yale noted that this moral sense can be observed early in life. Bloom and his colleagues conducted an experiment in which they showed babies a scene featuring one figure struggling to climb a hill, another figure trying to help it, and a third trying to hinder it. At as early as six months, the babies showed a preference for the helper over the hinderer. In some plays, there is a second act. The hindering figure is either punished or rewarded. In this case, 8-month-olds preferred a character who was punishing the hinderer over ones being nice to it.
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  • This illustrates, Bloom says, that people have a rudimentary sense of justice from a very early age. This doesn’t make people naturally good. If you give a 3-year-old two pieces of candy and ask him if he wants to share one of them, he will almost certainly say no. It’s not until age 7 or 8 that even half the children are willing to share. But it does mean that social norms fall upon prepared ground. We come equipped to learn fairness and other virtues.
  • If you ask for donations with the photo and name of one sick child, you are likely to get twice as much money than if you had asked for donations with a photo and the names of eight children. Our minds respond more powerfully to the plight of an individual than the plight of a group.
  • If you are in a bad mood you will make harsher moral judgments than if you’re in a good mood or have just seen a comedy. As Elizabeth Phelps of New York University points out, feelings of disgust will evoke a desire to expel things, even those things unrelated to your original mood. General fear makes people risk-averse. Anger makes them risk-seeking.
  • People who behave morally don’t generally do it because they have greater knowledge; they do it because they have a greater sensitivity to other people’s points of view.
  • The moral naturalists differ over what role reason plays in moral judgments. Some, like Haidt, believe that we make moral judgments intuitively and then construct justifications after the fact. Others, like Joshua Greene of Harvard, liken moral thinking to a camera. Most of the time we rely on the automatic point-and-shoot process, but occasionally we use deliberation to override the quick and easy method.
  • For people wary of abstract theorizing, it’s nice to see people investigating morality in ways that are concrete and empirical. But their approach does have certain implicit tendencies. They emphasize group cohesion over individual dissent. They emphasize the cooperative virtues, like empathy, over the competitive virtues, like the thirst for recognition and superiority. At this conference, they barely mentioned the yearning for transcendence and the sacred, which plays such a major role in every human society. Their implied description of the moral life is gentle, fair and grounded. But it is all lower case. So far, at least, it might not satisfy those who want their morality to be awesome, formidable, transcendent or great.
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    The Moral Naturalists By DAVID BROOKS Published: July 22, 2010
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Mystery and Evidence - NYTimes.com - 0 views

  • a very natural way for atheists to react to religious claims: to ask for evidence, and reject these claims in the absence of it. Many of the several hundred comments that followed two earlier Stone posts “Philosophy and Faith” and “On Dawkins’s Atheism: A Response,” both by Gary Gutting, took this stance. Certainly this is the way that today’s “new atheists”  tend to approach religion. According to their view, religions — by this they mean basically Christianity, Judaism and Islam and I will follow them in this — are largely in the business of making claims about the universe that are a bit like scientific hypotheses. In other words, they are claims — like the claim that God created the world — that are supported by evidence, that are proved by arguments and tested against our experience of the world. And against the evidence, these hypotheses do not seem to fare well.
  • But is this the right way to think about religion? Here I want to suggest that it is not, and to try and locate what seem to me some significant differences between science and religion
  • To begin with, scientific explanation is a very specific and technical kind of knowledge. It requires patience, pedantry, a narrowing of focus and (in the case of the most profound scientific theories) considerable mathematical knowledge and ability. No-one can understand quantum theory — by any account, the most successful physical theory there has ever been — unless they grasp the underlying mathematics. Anyone who says otherwise is fooling themselves.
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  • Religious belief is a very different kind of thing. It is not restricted only to those with a certain education or knowledge, it does not require years of training, it is not specialized and it is not technical. (I’m talking here about the content of what people who regularly attend church, mosque or synagogue take themselves to be thinking; I’m not talking about how theologians interpret this content.)
  • while religious belief is widespread, scientific knowledge is not. I would guess that very few people in the world are actually interested in the details of contemporary scientific theories. Why? One obvious reason is that many lack access to this knowledge. Another reason is that even when they have access, these theories require sophisticated knowledge and abilities, which not everyone is capable of getting.
  • most people aren’t deeply interested in science, even when they have the opportunity and the basic intellectual capacity to learn about it. Of course, educated people who know about science know roughly what Einstein, Newton and Darwin said. Many educated people accept the modern scientific view of the world and understand its main outlines. But this is not the same as being interested in the details of science, or being immersed in scientific thinking.
  • This lack of interest in science contrasts sharply with the worldwide interest in religion. It’s hard to say whether religion is in decline or growing, partly because it’s hard to identify only one thing as religion — not a question I can address here. But it’s pretty obvious that whatever it is, religion commands and absorbs the passions and intellects of hundreds of millions of people, many more people than science does. Why is this? Is it because — as the new atheists might argue — they want to explain the world in a scientific kind of way, but since they have not been properly educated they haven’t quite got there yet? Or is it because so many people are incurably irrational and are incapable of scientific thinking? Or is something else going on?
  • Some philosophers have said that religion is so unlike science that it has its own “grammar” or “logic” and should not be held accountable to the same standards as scientific or ordinary empirical belief. When Christians express their belief that “Christ has risen,” for example, they should not be taken as making a factual claim, but as expressing their commitment to what Wittgenstein called a certain “form of life,” a way of seeing significance in the world, a moral and practical outlook which is worlds away from scientific explanation.
  • This view has some merits, as we shall see, but it grossly misrepresents some central phenomena of religion. It is absolutely essential to religions that they make certain factual or historical claims. When Saint Paul says “if Christ is not risen, then our preaching is in vain and our faith is in vain” he is saying that the point of his faith depends on a certain historical occurrence.
  • Theologians will debate exactly what it means to claim that Christ has risen, what exactly the meaning and significance of this occurrence is, and will give more or less sophisticated accounts of it. But all I am saying is that whatever its specific nature, Christians must hold that there was such an occurrence. Christianity does make factual, historical claims. But this is not the same as being a kind of proto-science. This will become clear if we reflect a bit on what science involves.
  • The essence of science involves making hypotheses about the causes and natures of things, in order to explain the phenomena we observe around us, and to predict their future behavior. Some sciences — medical science, for example — make hypotheses about the causes of diseases and test them by intervening. Others — cosmology, for example — make hypotheses that are more remote from everyday causes, and involve a high level of mathematical abstraction and idealization. Scientific reasoning involves an obligation to hold a hypothesis only to the extent that the evidence requires it. Scientists should not accept hypotheses which are “ad hoc” — that is, just tailored for one specific situation but cannot be generalized to others. Most scientific theories involve some kind of generalization: they don’t just make claims about one thing, but about things of a general kind. And their hypotheses are designed, on the whole, to make predictions; and if these predictions don’t come out true, then this is something for the scientists to worry about.
  • Religions do not construct hypotheses in this sense. I said above that Christianity rests upon certain historical claims, like the claim of the resurrection. But this is not enough to make scientific hypotheses central to Christianity, any more than it makes such hypotheses central to history. It is true, as I have just said, that Christianity does place certain historical events at the heart of their conception of the world, and to that extent, one cannot be a Christian unless one believes that these events happened. Speaking for myself, it is because I reject the factual basis of the central Christian doctrines that I consider myself an atheist. But I do not reject these claims because I think they are bad hypotheses in the scientific sense. Not all factual claims are scientific hypotheses. So I disagree with Richard Dawkins when he says “religions make existence claims, and this means scientific claims.”
  • Taken as hypotheses, religious claims do very badly: they are ad hoc, they are arbitrary, they rarely make predictions and when they do they almost never come true. Yet the striking fact is that it does not worry Christians when this happens. In the gospels Jesus predicts the end of the world and the coming of the kingdom of God. It does not worry believers that Jesus was wrong (even if it causes theologians to reinterpret what is meant by ‘the kingdom of God’). If Jesus was framing something like a scientific hypothesis, then it should worry them. Critics of religion might say that this just shows the manifest irrationality of religion. But what it suggests to me is that that something else is going on, other than hypothesis formation.
  • Religious belief tolerates a high degree of mystery and ignorance in its understanding of the world. When the devout pray, and their prayers are not answered, they do not take this as evidence which has to be weighed alongside all the other evidence that prayer is effective. They feel no obligation whatsoever to weigh the evidence. If God does not answer their prayers, well, there must be some explanation of this, even though we may never know it. Why do people suffer if an omnipotent God loves them? Many complex answers have been offered, but in the end they come down to this: it’s a mystery.
  • Science too has its share of mysteries (or rather: things that must simply be accepted without further explanation). But one aim of science is to minimize such things, to reduce the number of primitive concepts or primitive explanations. The religious attitude is very different. It does not seek to minimize mystery. Mysteries are accepted as a consequence of what, for the religious, makes the world meaningful.
  • Religion is an attempt to make sense of the world, but it does not try and do this in the way science does. Science makes sense of the world by showing how things conform to its hypotheses. The characteristic mode of scientific explanation is showing how events fit into a general pattern.
  • Religion, on the other hand, attempts to make sense of the world by seeing a kind of meaning or significance in things. This kind of significance does not need laws or generalizations, but just the sense that the everyday world we experience is not all there is, and that behind it all is the mystery of God’s presence. The believer is already convinced that God is present in everything, even if they cannot explain this or support it with evidence. But it makes sense of their life by suffusing it with meaning. This is the attitude (seeing God in everything) expressed in George Herbert’s poem, “The Elixir.” Equipped with this attitude, even the most miserable tasks can come to have value: Who sweeps a room as for Thy laws/ Makes that and th’ action fine.
  • None of these remarks are intended as being for or against religion. Rather, they are part of an attempt (by an atheist, from the outside) to understand what it is. Those who criticize religion should have an accurate understanding of what it is they are criticizing. But to understand a world view, or a philosophy or system of thought, it is not enough just to understand the propositions it contains. You also have to understand what is central and what is peripheral to the view. Religions do make factual and historical claims, and if these claims are false, then the religions fail. But this dependence on fact does not make religious claims anything like hypotheses in the scientific sense. Hypotheses are not central. Rather, what is central is the commitment to the meaningfulness (and therefore the mystery) of the world.
  • while religious thinking is widespread in the world, scientific thinking is not. I don’t think that this can be accounted for merely in terms of the ignorance or irrationality of human beings. Rather, it is because of the kind of intellectual, emotional and practical appeal that religion has for people, which is a very different appeal from the kind of appeal that science has. Stephen Jay Gould once argued that religion and science are “non-overlapping magisteria.” If he meant by this that religion makes no factual claims which can be refuted by empirical investigations, then he was wrong. But if he meant that religion and science are very different kinds of attempt to understand the world, then he was certainly right.
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    Mystery and Evidence By TIM CRANE
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MacIntyre on money « Prospect Magazine - 0 views

  • MacIntyre has often given the impression of a robe-ripping Savonarola. He has lambasted the heirs to the principal western ethical schools: John Locke’s social contract, Immanuel Kant’s categorical imperative, Jeremy Bentham’s utilitarian “the greatest happiness for the greatest number.” Yet his is not a lone voice in the wilderness. He can claim connections with a trio of 20th-century intellectual heavyweights: the late Elizabeth Anscombe, her surviving husband, Peter Geach, and the Canadian philosopher Charles Taylor, winner in 2007 of the Templeton prize. What all four have in common is their Catholic faith, enthusiasm for Aristotle’s telos (life goals), and promotion of Thomism, the philosophy of St Thomas Aquinas who married Christianity and Aristotle. Leo XIII (pope from 1878 to 1903), who revived Thomism while condemning communism and unfettered capitalism, is also an influence.
  • MacIntyre’s key moral and political idea is that to be human is to be an Aristotelian goal-driven, social animal. Being good, according to Aristotle, consists in a creature (whether plant, animal, or human) acting according to its nature—its telos, or purpose. The telos for human beings is to generate a communal life with others; and the good society is composed of many independent, self-reliant groups.
  • MacIntyre differs from all these influences and alliances, from Leo XIII onwards, in his residual respect for Marx’s critique of capitalism.
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  • MacIntyre begins his Cambridge talk by asserting that the 2008 economic crisis was not due to a failure of business ethics.
  • he has argued that moral behaviour begins with the good practice of a profession, trade, or art: playing the violin, cutting hair, brick-laying, teaching philosophy.
  • In other words, the virtues necessary for human flourishing are not a result of the top-down application of abstract ethical principles, but the development of good character in everyday life.
  • After Virtue, which is in essence an attack on the failings of the Enlightenment, has in its sights a catalogue of modern assumptions of beneficence: liberalism, humanism, individualism, capitalism. MacIntyre yearns for a single, shared view of the good life as opposed to modern pluralism’s assumption that there can be many competing views of how to live well.
  • In philosophy he attacks consequentialism, the view that what matters about an action is its consequences, which is usually coupled with utilitarianism’s “greatest happiness” principle. He also rejects Kantianism—the identification of universal ethical maxims based on reason and applied to circumstances top down. MacIntyre’s critique routinely cites the contradictory moral principles adopted by the allies in the second world war. Britain invoked a Kantian reason for declaring war on Germany: that Hitler could not be allowed to invade his neighbours. But the bombing of Dresden (which for a Kantian involved the treatment of people as a means to an end, something that should never be countenanced) was justified under consequentialist or utilitarian arguments: to bring the war to a swift end.
  • MacIntyre seeks to oppose utilitarianism on the grounds that people are called on by their very nature to be good, not merely to perform acts that can be interpreted as good. The most damaging consequence of the Enlightenment, for MacIntyre, is the decline of the idea of a tradition within which an individual’s desires are disciplined by virtue. And that means being guided by internal rather than external “goods.” So the point of being a good footballer is the internal good of playing beautifully and scoring lots of goals, not the external good of earning a lot of money. The trend away from an Aristotelian perspective has been inexorable: from the empiricism of David Hume, to Darwin’s account of nature driven forward without a purpose, to the sterile analytical philosophy of AJ Ayer and the “demolition of metaphysics” in his 1936 book Language, Truth and Logic.
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    The influential moral philosopher Alasdair MacIntyre has long stood outside the mainstream. Has the financial crisis finally vindicated his critique of global capitalism?
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Arsenic bacteria - a post-mortem, a review, and some navel-gazing | Not Exactly Rocket ... - 0 views

  • t was the big news that wasn’t. Hyperbolic claims about the possible discovery of alien life, or a second branch of life on Earth, turned out to be nothing more than bacteria that can thrive on arsenic, using it in place of phosphorus in their DNA and other molecules. But after the initial layers of hype were peeled away, even this extraordinar
  • This is a chronological roundup of the criticism against the science in the paper itself, ending with some personal reflections on my own handling of the story (skip to Friday, December 10th for that bit).
  • Thursday, December 2nd: Felisa Wolfe-Simon published a paper in Science, claiming to have found bacteria in California’s Mono Lake that can grow using arsenic instead of phosphorus. Given that phosphorus is meant to be one of six irreplaceable elements, this would have been a big deal, not least because the bacteria apparently used arsenic to build the backbones of their DNA molecules.
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  • In my post, I mentioned some caveats. Wolfe-Simon isolated the arsenic-loving strain, known as GFAJ-1, by growing Mono Lake bacteria in ever-increasing concentrations of arsenic while diluting out the phosphorus. It is possible that the bacteria’s arsenic molecules were an adaptation to the harsh environments within the experiment, rather than Mono Lake itself. More importantly, there were still detectable levels of phosphorus left in the cells at the end of the experiment, although Wolfe-Simon claimed that the bacteria shouldn’t have been able to grow on such small amounts.
  • signs emerged that NASA weren’t going to engage with the criticisms. Dwayne Brown, their senior public affairs officer, highlighted the fact that the paper was published in one of the “most prestigious scientific journals” and deemed it inappropriate to debate the science using the same media and bloggers who they relied on for press coverage of the science. Wolfe-Simon herself tweeted that “discussion about scientific details MUST be within a scientific venue so that we can come back to the public with a unified understanding.”
  • Jonathan Eisen says that “they carried out science by press release and press conference” and “are now hypocritical if they say that the only response should be in the scientific literature.” David Dobbs calls the attitude “a return to pre-Enlightenment thinking”, and rightly noted that “Rosie Redfield is a peer, and her blog is peer review”.
  • Chris Rowan agreed, saying that what happens after publication is what he considers to be “real peer review”. Rowan said, “The pre-publication stuff is just a quality filter, a check that the paper is not obviously wrong – and an imperfect filter at that. The real test is what happens in the months and years after publication.”Grant Jacobs and others post similar thoughts, while Nature and the Columbia Journalism Review both cover the fracas.
  • Jack Gilbert at the University of Chicago said that impatient though he is, peer-reviewed journals are the proper forum for criticism. Others were not so kind. At the Guardian, Martin Robbins says that “at almost every stage of this story the actors involved were collapsing under the weight of their own slavish obedience to a fundamentally broken… well… ’system’” And Ivan Oransky noted that NASA failed to follow its own code of conduct when announcing the study.
  • Dr Isis said, “If question remains about the voracity of these authors findings, then the only thing that is going to answer that doubt is data.  Data cannot be generated by blog discussion… Talking about digging a ditch never got it dug.”
  • it is astonishing how quickly these events unfolded and the sheer number of bloggers and media outlets that became involved in the criticism. This is indeed a brave new world, and one in which we are all the infamous Third Reviewer.
  • I tried to quell the hype around the study as best I could. I had the paper and I think that what I wrote was a fair representation of it. But, of course, that’s not necessarily enough. I’ve argued before that journalists should not be merely messengers – we should make the best possible efforts to cut through what’s being said in an attempt to uncover what’s actually true. Arguably, that didn’t happen although to clarify, I am not saying that the paper is rubbish or untrue. Despite the criticisms, I want to see the authors respond in a thorough way or to see another lab attempt replicate the experiments before jumping to conclusions.
  • the sheer amount of negative comment indicates that I could have been more critical of the paper in my piece. Others have been supportive in suggesting that this was more egg on the face of the peer reviewers and indeed, several practicing scientists took the findings on face value, speculating about everything from the implications for chemotherapy to whether the bacteria have special viruses. The counter-argument, which I have no good retort to, is that peer review is no guarantee of quality, and that writers should be able to see through the fog of whatever topic they write about.
  • my response was that we should expect people to make reasonable efforts to uncover truth and be skeptical, while appreciating that people can and will make mistakes.
  • it comes down to this: did I do enough? I was certainly cautious. I said that “there is room for doubt” and I brought up the fact that the arsenic-loving bacteria still contain measurable levels of phosphorus. But I didn’t run the paper past other sources for comment, which I typically do it for stories that contain extraordinary claims. There was certainly plenty of time to do so here and while there were various reasons that I didn’t, the bottom line is that I could have done more. That doesn’t always help, of course, but it was an important missed step. A lesson for next time.
  • I do believe that it you’re going to try to hold your profession to a higher standard, you have to be honest and open when you’ve made mistakes yourself. I also think that if you cover a story that turns out to be a bit dodgy, you have a certain responsibility in covering the follow-up
  • A basic problem with is the embargo. Specifically that journalists get early access, while peers – other specialists in the field – do not. It means that the journalist, like yourself, can rely only on the original authors, with no way of getting other views on the findings. And it means that peers can’t write about the paper when the journalists (who, inevitably, do a positive-only coverage due to the lack of other viewpoints) do, but will be able to voice only after they’ve been able to digest the paper and formulate a response.
  • No, that’s not true. The embargo doens’t preclude journalists from sending papers out to other authors for review and comment. I do this a lot and I have been critical about new papers as a result, but that’s the step that I missed for this story.
Weiye Loh

Nature Journal Editors are Well-Meaning and Insightful « Medical Writing, Edi... - 0 views

  • Myths addressed include gaming impact factor, kowtowing to big names, using only a small clique of reviewers per discipline, and allowing a single spiteful reviewer to derail a submission.
  • but one wonders the long-term outcome of these papers and whether reveiwers whose recommendations were ignored (particularly if there was consensus, unbeknownst to them, among the reviewers against publication) were inclined to accept more Nature manuscripts for review, having had their time, effort, and expertise discounted by an editor’s prerogative.
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Science Warriors' Ego Trips - The Chronicle Review - The Chronicle of Higher Education - 0 views

  • By Carlin Romano Standing up for science excites some intellectuals the way beautiful actresses arouse Warren Beatty, or career liberals boil the blood of Glenn Beck and Rush Limbaugh. It's visceral.
  • A brave champion of beleaguered science in the modern age of pseudoscience, this Ayn Rand protagonist sarcastically derides the benighted irrationalists and glows with a self-anointed superiority. Who wouldn't want to feel that sense of power and rightness?
  • You hear the voice regularly—along with far more sensible stuff—in the latest of a now common genre of science patriotism, Nonsense on Stilts: How to Tell Science From Bunk (University of Chicago Press), by Massimo Pigliucci, a philosophy professor at the City University of New York.
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  • it mixes eminent common sense and frequent good reporting with a cocksure hubris utterly inappropriate to the practice it apotheosizes.
  • According to Pigliucci, both Freudian psychoanalysis and Marxist theory of history "are too broad, too flexible with regard to observations, to actually tell us anything interesting." (That's right—not one "interesting" thing.) The idea of intelligent design in biology "has made no progress since its last serious articulation by natural theologian William Paley in 1802," and the empirical evidence for evolution is like that for "an open-and-shut murder case."
  • Pigliucci offers more hero sandwiches spiced with derision and certainty. Media coverage of science is "characterized by allegedly serious journalists who behave like comedians." Commenting on the highly publicized Dover, Pa., court case in which U.S. District Judge John E. Jones III ruled that intelligent-design theory is not science, Pigliucci labels the need for that judgment a "bizarre" consequence of the local school board's "inane" resolution. Noting the complaint of intelligent-design advocate William Buckingham that an approved science textbook didn't give creationism a fair shake, Pigliucci writes, "This is like complaining that a textbook in astronomy is too focused on the Copernican theory of the structure of the solar system and unfairly neglects the possibility that the Flying Spaghetti Monster is really pulling each planet's strings, unseen by the deluded scientists."
  • Or is it possible that the alternate view unfairly neglected could be more like that of Harvard scientist Owen Gingerich, who contends in God's Universe (Harvard University Press, 2006) that it is partly statistical arguments—the extraordinary unlikelihood eons ago of the physical conditions necessary for self-conscious life—that support his belief in a universe "congenially designed for the existence of intelligent, self-reflective life"?
  • Even if we agree that capital "I" and "D" intelligent-design of the scriptural sort—what Gingerich himself calls "primitive scriptural literalism"—is not scientifically credible, does that make Gingerich's assertion, "I believe in intelligent design, lowercase i and lowercase d," equivalent to Flying-Spaghetti-Monsterism? Tone matters. And sarcasm is not science.
  • The problem with polemicists like Pigliucci is that a chasm has opened up between two groups that might loosely be distinguished as "philosophers of science" and "science warriors."
  • Philosophers of science, often operating under the aegis of Thomas Kuhn, recognize that science is a diverse, social enterprise that has changed over time, developed different methodologies in different subsciences, and often advanced by taking putative pseudoscience seriously, as in debunking cold fusion
  • The science warriors, by contrast, often write as if our science of the moment is isomorphic with knowledge of an objective world-in-itself—Kant be damned!—and any form of inquiry that doesn't fit the writer's criteria of proper science must be banished as "bunk." Pigliucci, typically, hasn't much sympathy for radical philosophies of science. He calls the work of Paul Feyerabend "lunacy," deems Bruno Latour "a fool," and observes that "the great pronouncements of feminist science have fallen as flat as the similarly empty utterances of supporters of intelligent design."
  • It doesn't have to be this way. The noble enterprise of submitting nonscientific knowledge claims to critical scrutiny—an activity continuous with both philosophy and science—took off in an admirable way in the late 20th century when Paul Kurtz, of the University at Buffalo, established the Committee for the Scientific Investigation of Claims of the Paranormal (Csicop) in May 1976. Csicop soon after launched the marvelous journal Skeptical Inquirer
  • Although Pigliucci himself publishes in Skeptical Inquirer, his contributions there exhibit his signature smugness. For an antidote to Pigliucci's overweening scientism 'tude, it's refreshing to consult Kurtz's curtain-raising essay, "Science and the Public," in Science Under Siege (Prometheus Books, 2009, edited by Frazier)
  • Kurtz's commandment might be stated, "Don't mock or ridicule—investigate and explain." He writes: "We attempted to make it clear that we were interested in fair and impartial inquiry, that we were not dogmatic or closed-minded, and that skepticism did not imply a priori rejection of any reasonable claim. Indeed, I insisted that our skepticism was not totalistic or nihilistic about paranormal claims."
  • Kurtz combines the ethos of both critical investigator and philosopher of science. Describing modern science as a practice in which "hypotheses and theories are based upon rigorous methods of empirical investigation, experimental confirmation, and replication," he notes: "One must be prepared to overthrow an entire theoretical framework—and this has happened often in the history of science ... skeptical doubt is an integral part of the method of science, and scientists should be prepared to question received scientific doctrines and reject them in the light of new evidence."
  • Pigliucci, alas, allows his animus against the nonscientific to pull him away from sensitive distinctions among various sciences to sloppy arguments one didn't see in such earlier works of science patriotism as Carl Sagan's The Demon-Haunted World: Science as a Candle in the Dark (Random House, 1995). Indeed, he probably sets a world record for misuse of the word "fallacy."
  • To his credit, Pigliucci at times acknowledges the nondogmatic spine of science. He concedes that "science is characterized by a fuzzy borderline with other types of inquiry that may or may not one day become sciences." Science, he admits, "actually refers to a rather heterogeneous family of activities, not to a single and universal method." He rightly warns that some pseudoscience—for example, denial of HIV-AIDS causation—is dangerous and terrible.
  • But at other points, Pigliucci ferociously attacks opponents like the most unreflective science fanatic
  • He dismisses Feyerabend's view that "science is a religion" as simply "preposterous," even though he elsewhere admits that "methodological naturalism"—the commitment of all scientists to reject "supernatural" explanations—is itself not an empirically verifiable principle or fact, but rather an almost Kantian precondition of scientific knowledge. An article of faith, some cold-eyed Feyerabend fans might say.
  • He writes, "ID is not a scientific theory at all because there is no empirical observation that can possibly contradict it. Anything we observe in nature could, in principle, be attributed to an unspecified intelligent designer who works in mysterious ways." But earlier in the book, he correctly argues against Karl Popper that susceptibility to falsification cannot be the sole criterion of science, because science also confirms. It is, in principle, possible that an empirical observation could confirm intelligent design—i.e., that magic moment when the ultimate UFO lands with representatives of the intergalactic society that planted early life here, and we accept their evidence that they did it.
  • "As long as we do not venture to make hypotheses about who the designer is and why and how she operates," he writes, "there are no empirical constraints on the 'theory' at all. Anything goes, and therefore nothing holds, because a theory that 'explains' everything really explains nothing."
  • Here, Pigliucci again mixes up what's likely or provable with what's logically possible or rational. The creation stories of traditional religions and scriptures do, in effect, offer hypotheses, or claims, about who the designer is—e.g., see the Bible.
  • Far from explaining nothing because it explains everything, such an explanation explains a lot by explaining everything. It just doesn't explain it convincingly to a scientist with other evidentiary standards.
  • A sensible person can side with scientists on what's true, but not with Pigliucci on what's rational and possible. Pigliucci occasionally recognizes that. Late in his book, he concedes that "nonscientific claims may be true and still not qualify as science." But if that's so, and we care about truth, why exalt science to the degree he does? If there's really a heaven, and science can't (yet?) detect it, so much the worse for science.
  • Pigliucci quotes a line from Aristotle: "It is the mark of an educated mind to be able to entertain a thought without accepting it." Science warriors such as Pigliucci, or Michael Ruse in his recent clash with other philosophers in these pages, should reflect on a related modern sense of "entertain." One does not entertain a guest by mocking, deriding, and abusing the guest. Similarly, one does not entertain a thought or approach to knowledge by ridiculing it.
  • Long live Skeptical Inquirer! But can we deep-six the egomania and unearned arrogance of the science patriots? As Descartes, that immortal hero of scientists and skeptics everywhere, pointed out, true skepticism, like true charity, begins at home.
  • Carlin Romano, critic at large for The Chronicle Review, teaches philosophy and media theory at the University of Pennsylvania.
  •  
    April 25, 2010 Science Warriors' Ego Trips
Weiye Loh

The Decline Effect and the Scientific Method : The New Yorker - 0 views

  • On September 18, 2007, a few dozen neuroscientists, psychiatrists, and drug-company executives gathered in a hotel conference room in Brussels to hear some startling news. It had to do with a class of drugs known as atypical or second-generation antipsychotics, which came on the market in the early nineties.
  • the therapeutic power of the drugs appeared to be steadily waning. A recent study showed an effect that was less than half of that documented in the first trials, in the early nineteen-nineties. Many researchers began to argue that the expensive pharmaceuticals weren’t any better than first-generation antipsychotics, which have been in use since the fifties. “In fact, sometimes they now look even worse,” John Davis, a professor of psychiatry at the University of Illinois at Chicago, told me.
  • Before the effectiveness of a drug can be confirmed, it must be tested and tested again. Different scientists in different labs need to repeat the protocols and publish their results. The test of replicability, as it’s known, is the foundation of modern research. Replicability is how the community enforces itself. It’s a safeguard for the creep of subjectivity. Most of the time, scientists know what results they want, and that can influence the results they get. The premise of replicability is that the scientific community can correct for these flaws.
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  • But now all sorts of well-established, multiply confirmed findings have started to look increasingly uncertain. It’s as if our facts were losing their truth: claims that have been enshrined in textbooks are suddenly unprovable. This phenomenon doesn’t yet have an official name, but it’s occurring across a wide range of fields, from psychology to ecology. In the field of medicine, the phenomenon seems extremely widespread, affecting not only antipsychotics but also therapies ranging from cardiac stents to Vitamin E and antidepressants: Davis has a forthcoming analysis demonstrating that the efficacy of antidepressants has gone down as much as threefold in recent decades.
  • the effect is especially troubling because of what it exposes about the scientific process. If replication is what separates the rigor of science from the squishiness of pseudoscience, where do we put all these rigorously validated findings that can no longer be proved? Which results should we believe? Francis Bacon, the early-modern philosopher and pioneer of the scientific method, once declared that experiments were essential, because they allowed us to “put nature to the question.” But it appears that nature often gives us different answers.
  • At first, he assumed that he’d made an error in experimental design or a statistical miscalculation. But he couldn’t find anything wrong with his research. He then concluded that his initial batch of research subjects must have been unusually susceptible to verbal overshadowing. (John Davis, similarly, has speculated that part of the drop-off in the effectiveness of antipsychotics can be attributed to using subjects who suffer from milder forms of psychosis which are less likely to show dramatic improvement.) “It wasn’t a very satisfying explanation,” Schooler says. “One of my mentors told me that my real mistake was trying to replicate my work. He told me doing that was just setting myself up for disappointment.”
  • In private, Schooler began referring to the problem as “cosmic habituation,” by analogy to the decrease in response that occurs when individuals habituate to particular stimuli. “Habituation is why you don’t notice the stuff that’s always there,” Schooler says. “It’s an inevitable process of adjustment, a ratcheting down of excitement. I started joking that it was like the cosmos was habituating to my ideas. I took it very personally.”
  • The most likely explanation for the decline is an obvious one: regression to the mean. As the experiment is repeated, that is, an early statistical fluke gets cancelled out. The extrasensory powers of Schooler’s subjects didn’t decline—they were simply an illusion that vanished over time. And yet Schooler has noticed that many of the data sets that end up declining seem statistically solid—that is, they contain enough data that any regression to the mean shouldn’t be dramatic. “These are the results that pass all the tests,” he says. “The odds of them being random are typically quite remote, like one in a million. This means that the decline effect should almost never happen. But it happens all the time!
  • this is why Schooler believes that the decline effect deserves more attention: its ubiquity seems to violate the laws of statistics. “Whenever I start talking about this, scientists get very nervous,” he says. “But I still want to know what happened to my results. Like most scientists, I assumed that it would get easier to document my effect over time. I’d get better at doing the experiments, at zeroing in on the conditions that produce verbal overshadowing. So why did the opposite happen? I’m convinced that we can use the tools of science to figure this out. First, though, we have to admit that we’ve got a problem.”
  • In 2001, Michael Jennions, a biologist at the Australian National University, set out to analyze “temporal trends” across a wide range of subjects in ecology and evolutionary biology. He looked at hundreds of papers and forty-four meta-analyses (that is, statistical syntheses of related studies), and discovered a consistent decline effect over time, as many of the theories seemed to fade into irrelevance. In fact, even when numerous variables were controlled for—Jennions knew, for instance, that the same author might publish several critical papers, which could distort his analysis—there was still a significant decrease in the validity of the hypothesis, often within a year of publication. Jennions admits that his findings are troubling, but expresses a reluctance to talk about them publicly. “This is a very sensitive issue for scientists,” he says. “You know, we’re supposed to be dealing with hard facts, the stuff that’s supposed to stand the test of time. But when you see these trends you become a little more skeptical of things.”
  • the worst part was that when I submitted these null results I had difficulty getting them published. The journals only wanted confirming data. It was too exciting an idea to disprove, at least back then.
  • the steep rise and slow fall of fluctuating asymmetry is a clear example of a scientific paradigm, one of those intellectual fads that both guide and constrain research: after a new paradigm is proposed, the peer-review process is tilted toward positive results. But then, after a few years, the academic incentives shift—the paradigm has become entrenched—so that the most notable results are now those that disprove the theory.
  • Jennions, similarly, argues that the decline effect is largely a product of publication bias, or the tendency of scientists and scientific journals to prefer positive data over null results, which is what happens when no effect is found. The bias was first identified by the statistician Theodore Sterling, in 1959, after he noticed that ninety-seven per cent of all published psychological studies with statistically significant data found the effect they were looking for. A “significant” result is defined as any data point that would be produced by chance less than five per cent of the time. This ubiquitous test was invented in 1922 by the English mathematician Ronald Fisher, who picked five per cent as the boundary line, somewhat arbitrarily, because it made pencil and slide-rule calculations easier. Sterling saw that if ninety-seven per cent of psychology studies were proving their hypotheses, either psychologists were extraordinarily lucky or they published only the outcomes of successful experiments. In recent years, publication bias has mostly been seen as a problem for clinical trials, since pharmaceutical companies are less interested in publishing results that aren’t favorable. But it’s becoming increasingly clear that publication bias also produces major distortions in fields without large corporate incentives, such as psychology and ecology.
  • While publication bias almost certainly plays a role in the decline effect, it remains an incomplete explanation. For one thing, it fails to account for the initial prevalence of positive results among studies that never even get submitted to journals. It also fails to explain the experience of people like Schooler, who have been unable to replicate their initial data despite their best efforts
  • an equally significant issue is the selective reporting of results—the data that scientists choose to document in the first place. Palmer’s most convincing evidence relies on a statistical tool known as a funnel graph. When a large number of studies have been done on a single subject, the data should follow a pattern: studies with a large sample size should all cluster around a common value—the true result—whereas those with a smaller sample size should exhibit a random scattering, since they’re subject to greater sampling error. This pattern gives the graph its name, since the distribution resembles a funnel.
  • The funnel graph visually captures the distortions of selective reporting. For instance, after Palmer plotted every study of fluctuating asymmetry, he noticed that the distribution of results with smaller sample sizes wasn’t random at all but instead skewed heavily toward positive results.
  • Palmer has since documented a similar problem in several other contested subject areas. “Once I realized that selective reporting is everywhere in science, I got quite depressed,” Palmer told me. “As a researcher, you’re always aware that there might be some nonrandom patterns, but I had no idea how widespread it is.” In a recent review article, Palmer summarized the impact of selective reporting on his field: “We cannot escape the troubling conclusion that some—perhaps many—cherished generalities are at best exaggerated in their biological significance and at worst a collective illusion nurtured by strong a-priori beliefs often repeated.”
  • Palmer emphasizes that selective reporting is not the same as scientific fraud. Rather, the problem seems to be one of subtle omissions and unconscious misperceptions, as researchers struggle to make sense of their results. Stephen Jay Gould referred to this as the “shoehorning” process. “A lot of scientific measurement is really hard,” Simmons told me. “If you’re talking about fluctuating asymmetry, then it’s a matter of minuscule differences between the right and left sides of an animal. It’s millimetres of a tail feather. And so maybe a researcher knows that he’s measuring a good male”—an animal that has successfully mated—“and he knows that it’s supposed to be symmetrical. Well, that act of measurement is going to be vulnerable to all sorts of perception biases. That’s not a cynical statement. That’s just the way human beings work.”
  • One of the classic examples of selective reporting concerns the testing of acupuncture in different countries. While acupuncture is widely accepted as a medical treatment in various Asian countries, its use is much more contested in the West. These cultural differences have profoundly influenced the results of clinical trials. Between 1966 and 1995, there were forty-seven studies of acupuncture in China, Taiwan, and Japan, and every single trial concluded that acupuncture was an effective treatment. During the same period, there were ninety-four clinical trials of acupuncture in the United States, Sweden, and the U.K., and only fifty-six per cent of these studies found any therapeutic benefits. As Palmer notes, this wide discrepancy suggests that scientists find ways to confirm their preferred hypothesis, disregarding what they don’t want to see. Our beliefs are a form of blindness.
  • John Ioannidis, an epidemiologist at Stanford University, argues that such distortions are a serious issue in biomedical research. “These exaggerations are why the decline has become so common,” he says. “It’d be really great if the initial studies gave us an accurate summary of things. But they don’t. And so what happens is we waste a lot of money treating millions of patients and doing lots of follow-up studies on other themes based on results that are misleading.”
  • In 2005, Ioannidis published an article in the Journal of the American Medical Association that looked at the forty-nine most cited clinical-research studies in three major medical journals. Forty-five of these studies reported positive results, suggesting that the intervention being tested was effective. Because most of these studies were randomized controlled trials—the “gold standard” of medical evidence—they tended to have a significant impact on clinical practice, and led to the spread of treatments such as hormone replacement therapy for menopausal women and daily low-dose aspirin to prevent heart attacks and strokes. Nevertheless, the data Ioannidis found were disturbing: of the thirty-four claims that had been subject to replication, forty-one per cent had either been directly contradicted or had their effect sizes significantly downgraded.
  • The situation is even worse when a subject is fashionable. In recent years, for instance, there have been hundreds of studies on the various genes that control the differences in disease risk between men and women. These findings have included everything from the mutations responsible for the increased risk of schizophrenia to the genes underlying hypertension. Ioannidis and his colleagues looked at four hundred and thirty-two of these claims. They quickly discovered that the vast majority had serious flaws. But the most troubling fact emerged when he looked at the test of replication: out of four hundred and thirty-two claims, only a single one was consistently replicable. “This doesn’t mean that none of these claims will turn out to be true,” he says. “But, given that most of them were done badly, I wouldn’t hold my breath.”
  • the main problem is that too many researchers engage in what he calls “significance chasing,” or finding ways to interpret the data so that it passes the statistical test of significance—the ninety-five-per-cent boundary invented by Ronald Fisher. “The scientists are so eager to pass this magical test that they start playing around with the numbers, trying to find anything that seems worthy,” Ioannidis says. In recent years, Ioannidis has become increasingly blunt about the pervasiveness of the problem. One of his most cited papers has a deliberately provocative title: “Why Most Published Research Findings Are False.”
  • The problem of selective reporting is rooted in a fundamental cognitive flaw, which is that we like proving ourselves right and hate being wrong. “It feels good to validate a hypothesis,” Ioannidis said. “It feels even better when you’ve got a financial interest in the idea or your career depends upon it. And that’s why, even after a claim has been systematically disproven”—he cites, for instance, the early work on hormone replacement therapy, or claims involving various vitamins—“you still see some stubborn researchers citing the first few studies that show a strong effect. They really want to believe that it’s true.”
  • scientists need to become more rigorous about data collection before they publish. “We’re wasting too much time chasing after bad studies and underpowered experiments,” he says. The current “obsession” with replicability distracts from the real problem, which is faulty design. He notes that nobody even tries to replicate most science papers—there are simply too many. (According to Nature, a third of all studies never even get cited, let alone repeated.)
  • Schooler recommends the establishment of an open-source database, in which researchers are required to outline their planned investigations and document all their results. “I think this would provide a huge increase in access to scientific work and give us a much better way to judge the quality of an experiment,” Schooler says. “It would help us finally deal with all these issues that the decline effect is exposing.”
  • Although such reforms would mitigate the dangers of publication bias and selective reporting, they still wouldn’t erase the decline effect. This is largely because scientific research will always be shadowed by a force that can’t be curbed, only contained: sheer randomness. Although little research has been done on the experimental dangers of chance and happenstance, the research that exists isn’t encouraging
  • John Crabbe, a neuroscientist at the Oregon Health and Science University, conducted an experiment that showed how unknowable chance events can skew tests of replicability. He performed a series of experiments on mouse behavior in three different science labs: in Albany, New York; Edmonton, Alberta; and Portland, Oregon. Before he conducted the experiments, he tried to standardize every variable he could think of. The same strains of mice were used in each lab, shipped on the same day from the same supplier. The animals were raised in the same kind of enclosure, with the same brand of sawdust bedding. They had been exposed to the same amount of incandescent light, were living with the same number of littermates, and were fed the exact same type of chow pellets. When the mice were handled, it was with the same kind of surgical glove, and when they were tested it was on the same equipment, at the same time in the morning.
  • The premise of this test of replicability, of course, is that each of the labs should have generated the same pattern of results. “If any set of experiments should have passed the test, it should have been ours,” Crabbe says. “But that’s not the way it turned out.” In one experiment, Crabbe injected a particular strain of mouse with cocaine. In Portland the mice given the drug moved, on average, six hundred centimetres more than they normally did; in Albany they moved seven hundred and one additional centimetres. But in the Edmonton lab they moved more than five thousand additional centimetres. Similar deviations were observed in a test of anxiety. Furthermore, these inconsistencies didn’t follow any detectable pattern. In Portland one strain of mouse proved most anxious, while in Albany another strain won that distinction.
  • The disturbing implication of the Crabbe study is that a lot of extraordinary scientific data are nothing but noise. The hyperactivity of those coked-up Edmonton mice wasn’t an interesting new fact—it was a meaningless outlier, a by-product of invisible variables we don’t understand. The problem, of course, is that such dramatic findings are also the most likely to get published in prestigious journals, since the data are both statistically significant and entirely unexpected. Grants get written, follow-up studies are conducted. The end result is a scientific accident that can take years to unravel.
  • This suggests that the decline effect is actually a decline of illusion.
  • While Karl Popper imagined falsification occurring with a single, definitive experiment—Galileo refuted Aristotelian mechanics in an afternoon—the process turns out to be much messier than that. Many scientific theories continue to be considered true even after failing numerous experimental tests. Verbal overshadowing might exhibit the decline effect, but it remains extensively relied upon within the field. The same holds for any number of phenomena, from the disappearing benefits of second-generation antipsychotics to the weak coupling ratio exhibited by decaying neutrons, which appears to have fallen by more than ten standard deviations between 1969 and 2001. Even the law of gravity hasn’t always been perfect at predicting real-world phenomena. (In one test, physicists measuring gravity by means of deep boreholes in the Nevada desert found a two-and-a-half-per-cent discrepancy between the theoretical predictions and the actual data.) Despite these findings, second-generation antipsychotics are still widely prescribed, and our model of the neutron hasn’t changed. The law of gravity remains the same.
  • Such anomalies demonstrate the slipperiness of empiricism. Although many scientific ideas generate conflicting results and suffer from falling effect sizes, they continue to get cited in the textbooks and drive standard medical practice. Why? Because these ideas seem true. Because they make sense. Because we can’t bear to let them go. And this is why the decline effect is so troubling. Not because it reveals the human fallibility of science, in which data are tweaked and beliefs shape perceptions. (Such shortcomings aren’t surprising, at least for scientists.) And not because it reveals that many of our most exciting theories are fleeting fads and will soon be rejected. (That idea has been around since Thomas Kuhn.) The decline effect is troubling because it reminds us how difficult it is to prove anything. We like to pretend that our experiments define the truth for us. But that’s often not the case. Just because an idea is true doesn’t mean it can be proved. And just because an idea can be proved doesn’t mean it’s true. When the experiments are done, we still have to choose what to believe.
Weiye Loh

The Mysterious Decline Effect | Wired Science | Wired.com - 0 views

  • Question #1: Does this mean I don’t have to believe in climate change? Me: I’m afraid not. One of the sad ironies of scientific denialism is that we tend to be skeptical of precisely the wrong kind of scientific claims. In poll after poll, Americans have dismissed two of the most robust and widely tested theories of modern science: evolution by natural selection and climate change. These are theories that have been verified in thousands of different ways by thousands of different scientists working in many different fields. (This doesn’t mean, of course, that such theories won’t change or get modified – the strength of science is that nothing is settled.) Instead of wasting public debate on creationism or the rhetoric of Senator Inhofe, I wish we’d spend more time considering the value of spinal fusion surgery, or second generation antipsychotics, or the verity of the latest gene association study. The larger point is that we need to be a better job of considering the context behind every claim. In 1952, the Harvard philosopher Willard Von Orman published “The Two Dogmas of Empiricism.” In the essay, Quine compared the truths of science to a spider’s web, in which the strength of the lattice depends upon its interconnectedness. (Quine: “The unit of empirical significance is the whole of science.”) One of the implications of Quine’s paper is that, when evaluating the power of a given study, we need to also consider the other studies and untested assumptions that it depends upon. Don’t just fixate on the effect size – look at the web. Unfortunately for the denialists, climate change and natural selection have very sturdy webs.
  • biases are not fraud. We sometimes forget that science is a human pursuit, mingled with all of our flaws and failings. (Perhaps that explains why an episode like Climategate gets so much attention.) If there’s a single theme that runs through the article it’s that finding the truth is really hard. It’s hard because reality is complicated, shaped by a surreal excess of variables. But it’s also hard because scientists aren’t robots: the act of observation is simultaneously an act of interpretation.
  • (As Paul Simon sang, “A man sees what he wants to see and disregards the rest.”) Most of the time, these distortions are unconscious – we don’t know even we are misperceiving the data. However, even when the distortion is intentional it’s still rarely rises to the level of outright fraud. Consider the story of Mike Rossner. He’s executive director of the Rockefeller University Press, and helps oversee several scientific publications, including The Journal of Cell Biology.  In 2002, while trying to format a scientific image in Photoshop that was going to appear in one of the journals, Rossner noticed that the background of the image contained distinct intensities of pixels. “That’s a hallmark of image manipulation,” Rossner told me. “It means the scientist has gone in and deliberately changed what the data looks like. What’s disturbing is just how easy this is to do.” This led Rossner and his colleagues to begin analyzing every image in every accepted paper. They soon discovered that approximately 25 percent of all papers contained at least one “inappropriately manipulated” picture. Interestingly, the vast, vast majority of these manipulations (~99 percent) didn’t affect the interpretation of the results. Instead, the scientists seemed to be photoshopping the pictures for aesthetic reasons: perhaps a line on a gel was erased, or a background blur was deleted, or the contrast was exaggerated. In other words, they wanted to publish pretty images. That’s a perfectly understandable desire, but it gets problematic when that same basic instinct – we want our data to be neat, our pictures to be clean, our charts to be clear – is transposed across the entire scientific process.
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  • One of the philosophy papers that I kept on thinking about while writing the article was Nancy Cartwright’s essay “Do the Laws of Physics State the Facts?” Cartwright used numerous examples from modern physics to argue that there is often a basic trade-off between scientific “truth” and experimental validity, so that the laws that are the most true are also the most useless. “Despite their great explanatory power, these laws [such as gravity] do not describe reality,” Cartwright writes. “Instead, fundamental laws describe highly idealized objects in models.”  The problem, of course, is that experiments don’t test models. They test reality.
  • Cartwright’s larger point is that many essential scientific theories – those laws that explain things – are not actually provable, at least in the conventional sense. This doesn’t mean that gravity isn’t true or real. There is, perhaps, no truer idea in all of science. (Feynman famously referred to gravity as the “greatest generalization achieved by the human mind.”) Instead, what the anomalies of physics demonstrate is that there is no single test that can define the truth. Although we often pretend that experiments and peer-review and clinical trials settle the truth for us – that we are mere passive observers, dutifully recording the results – the actuality of science is a lot messier than that. Richard Rorty said it best: “To say that we should drop the idea of truth as out there waiting to be discovered is not to say that we have discovered that, out there, there is no truth.” Of course, the very fact that the facts aren’t obvious, that the truth isn’t “waiting to be discovered,” means that science is intensely human. It requires us to look, to search, to plead with nature for an answer.
Weiye Loh

FT.com / FT Magazine - A disastrous truth - 0 views

  • Every time a disaster strikes, some environmentalists blame it on climate change. “It’s been such a part of the narrative of the public and political debate, particularly after Hurricane Katrina,” Roger Pielke Jr, an expert on the politics of climate change at the University of Colorado, told me.
  • But nothing in the scientific literature indicates that this is true. A host of recent peer-reviewed studies agree: there’s no evidence that climate change has increased the damage from natural disasters. Most likely, climate change will make disasters worse some day, but not yet.
  • Laurens Bouwer, of Amsterdam’s Vrije Universiteit, has recently reviewed 22 “disaster loss studies” and concludes: “Anthropogenic climate change so far has not had a significant impact on losses from natural disasters.”
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  • Eric Neumayer and Fabian Barthel of the London School of Economics found likewise in their recent “global analysis” of natural disasters.
  • in his book The Climate Fix: What Scientists and Politicians Won’t Tell You About Global Warming, Pielke writes that there’s no upward trend in the landfalls of tropical cyclones. Even floods in Brisbane aren’t getting worse – just check out the city’s 19th-century floods. Pielke says the consensus of peer-reviewed research on this point – that climate change is not yet worsening disasters – is as strong as any consensus in climate science.
  • It’s true that floods and hurricanes do more damage every decade. However, that’s because ever more people, owning ever more “stuff”, live in vulnerable spots.
  • When it comes to preventing today’s disasters, the squabble about climate change is just a distraction. The media usually has room for only one environmental argument: is climate change happening? This pits virtually all climate scientists against a band of self-taught freelance sceptics, many of whom think the “global warming hoax” is a ruse got up by 1960s radicals as a trick to bring in socialism. (I know, I get the sceptics’ e-mails.) Sometimes in this squabble, climate scientists are tempted to overstate their case, and to say that the latest disaster proves that the climate is changing. This is bad science. It also gives the sceptics something dubious to attack. Better to ignore the sceptics, and have more useful debates about disasters and climate change – which, for now, are two separate problems.
Weiye Loh

Learn to love uncertainty and failure, say leading thinkers | Edge question | Science |... - 0 views

  • Being comfortable with uncertainty, knowing the limits of what science can tell us, and understanding the worth of failure are all valuable tools that would improve people's lives, according to some of the world's leading thinkers.
  • he ideas were submitted as part of an annual exercise by the web magazine Edge, which invites scientists, philosophers and artists to opine on a major question of the moment. This year it was, "What scientific concept would improve everybody's cognitive toolkit?"
  • the public often misunderstands the scientific process and the nature of scientific doubt. This can fuel public rows over the significance of disagreements between scientists about controversial issues such as climate change and vaccine safety.
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  • Carlo Rovelli, a physicist at the University of Aix-Marseille, emphasised the uselessness of certainty. He said that the idea of something being "scientifically proven" was practically an oxymoron and that the very foundation of science is to keep the door open to doubt.
  • "A good scientist is never 'certain'. Lack of certainty is precisely what makes conclusions more reliable than the conclusions of those who are certain: because the good scientist will be ready to shift to a different point of view if better elements of evidence, or novel arguments emerge. Therefore certainty is not only something of no use, but is in fact damaging, if we value reliability."
  • physicist Lawrence Krauss of Arizona State University agreed. "In the public parlance, uncertainty is a bad thing, implying a lack of rigour and predictability. The fact that global warming estimates are uncertain, for example, has been used by many to argue against any action at the present time," he said.
  • however, uncertainty is a central component of what makes science successful. Being able to quantify uncertainty, and incorporate it into models, is what makes science quantitative, rather than qualitative. Indeed, no number, no measurement, no observable in science is exact. Quoting numbers without attaching an uncertainty to them implies they have, in essence, no meaning."
  • Neil Gershenfeld, director of the Massachusetts Institute of Technology's Centre for Bits and Atoms wants everyone to know that "truth" is just a model. "The most common misunderstanding about science is that scientists seek and find truth. They don't – they make and test models," he said.
  • Building models is very different from proclaiming truths. It's a never-ending process of discovery and refinement, not a war to win or destination to reach. Uncertainty is intrinsic to the process of finding out what you don't know, not a weakness to avoid. Bugs are features – violations of expectations are opportunities to refine them. And decisions are made by evaluating what works better, not by invoking received wisdom."
  • writer and web commentator Clay Shirky suggested that people should think more carefully about how they see the world. His suggestion was the Pareto principle, a pattern whereby the top 1% of the population control 35% of the wealth or, on Twitter, the top 2% of users send 60% of the messages. Sometimes known as the "80/20 rule", the Pareto principle means that the average is far from the middle.It is applicable to many complex systems, "And yet, despite a century of scientific familiarity, samples drawn from Pareto distributions are routinely presented to the public as anomalies, which prevents us from thinking clearly about the world," said Shirky. "We should stop thinking that average family income and the income of the median family have anything to do with one another, or that enthusiastic and normal users of communications tools are doing similar things, or that extroverts should be only moderately more connected than normal people. We should stop thinking that the largest future earthquake or market panic will be as large as the largest historical one; the longer a system persists, the likelier it is that an event twice as large as all previous ones is coming."
  • Kevin Kelly, editor-at-large of Wired, pointed to the value of negative results. "We can learn nearly as much from an experiment that does not work as from one that does. Failure is not something to be avoided but rather something to be cultivated. That's a lesson from science that benefits not only laboratory research, but design, sport, engineering, art, entrepreneurship, and even daily life itself. All creative avenues yield the maximum when failures are embraced."
  • Michael Shermer, publisher of the Skeptic Magazine, wrote about the importance of thinking "bottom up not top down", since almost everything in nature and society happens this way.
  • But most people don't see things that way, said Shermer. "Bottom up reasoning is counterintuitive. This is why so many people believe that life was designed from the top down, and why so many think that economies must be designed and that countries should be ruled from the top down."
  • Roger Schank, a psychologist and computer scientist, proposed that we should all know the true meaning of "experimentation", which he said had been ruined by bad schooling, where pupils learn that scientists conduct experiments and if we copy exactly what they did in our high school labs we will get the results they got. "In effect we learn that experimentation is boring, is something done by scientists and has nothing to do with our daily lives."Instead, he said, proper experiments are all about assessing and gathering evidence. "In other words, the scientific activity that surrounds experimentation is about thinking clearly in the face of evidence obtained as the result of an experiment. But people who don't see their actions as experiments, and those who don't know how to reason carefully from data, will continue to learn less well from their own experiences than those who do
  • Lisa Randall, a physicist at Harvard University, argued that perhaps "science" itself would be a useful concept for wider appreciation. "The idea that we can systematically understand certain aspects of the world and make predictions based on what we've learned – while appreciating and categorising the extent and limitations of what we know – plays a big role in how we think.
  • "Many words that summarise the nature of science such as 'cause and effect', 'predictions', and 'experiments', as well as words that describe probabilistic results such as 'mean', 'median', 'standard deviation', and the notion of 'probability' itself help us understand more specifically what this means and how to interpret the world and behaviour within it."
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