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The Biology of Politics: What Makes a Liberal or a Conservative? - TIME Healthland - 0 views

healthland.time.com/...akes-a-liberal-or-conservative Biology Politics
shared by Weiye Loh on 21 Dec 10 - No Cached
  • There are aspects of our lives that we like to think are totally under our control — political affiliation is certainly one of them. But a growing field of researchers asserts that there may be some biology underpinning our liberal or conservative bent.
  • this sort of theory doesn't sit well with some onlookers. Hibbing describes himself as "kicked around" because of his research: "People are usually pretty proud of their political beliefs," he says. "They think they're rational responses to the world around them, so to come along and say maybe there are these predispositions that you're not even aware of ... that doesn't really go down all that well."
  • "On the left, people don't like to think that maybe people aren't fully malleable," he says. "On the right, it's that these are a bunch of liberal academics trying to show that conservatives are genetically or physiologically flawed."
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  • Both sides are anxious to see how the field of the biology of politics will be viewed in 50 years — if it has indeed been lumped in with pseudosciences like phrenology or if it has become a new platform for widespread, interdisciplinary study. Meanwhile, the fascination — and vitriol — will likely remain. "The notion of where political ideology comes from has never been contested," says Bruce Bimber, a professor at University of California, Santa Barbara, who tackles this topic in graduate seminars. "It's always been a settled assumption that it is the product of socialization and life experience, and this research has come along saying, 'Wait a minute, wait a minute. We might have had this partly wrong all along.'"
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Editorial Policies - 0 views

www.arjournals.com/...index.php Science Academic Journal Academic Research
shared by Weiye Loh on 21 Feb 11 - Cached
  • More than 60% of the experiments fail to produce results or expected discoveries. From an objective point of view, this high percentage of “failed “ research generates high level pieces of knowledge. Generally, all these experiments have not been published anywhere as they have been considered useless for our research target. The objective of “The All Results Journals: Biology” focuses on recovering and publishing these valuable pieces of information in Biology. These key experiments must be considered vital for the development of science. They  are the catalyst for a real science-based empirical knowledge.
  • The All Results Journals: Biology is an online journal that publishes research articles after a controlled peer review. All articles will be published, without any barriers to access, immediately upon acceptance.
  • Every single contribution submitted to The All Results Journals and selected for a peer-review will be sent to, at least, one reviewer, though usually could be sent to two or more independent reviewers, selected by the editors and sometimes by more if further advice is required (e.g., on statistics or on a particular technique). Authors are welcome to suggest suitable independent reviewers and may also request the journal to exclude certain individuals or laboratories.
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  • The journal will cover negative (or “secondary”) experiments coming from all disciplines of Biology (Botany, Cell Biology, Genetics, Ecology, Microbiology, etc). An article in The All Results Journals should be created to show the failed experiments tuning methods or reactions. Articles should present experimental discoveries, interpret their significance and establish perspective with respect to earlier work of the author. It is also advisable to cite the work where the experiments has already been tuned and published.
  • Weiye Loh on 21 Feb 11
     
    More than 60% of the experiments fail to produce results or expected discoveries. From an objective point of view, this high percentage of "failed " research generates high level pieces of knowledge. Generally, all these experiment
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Science, Strong Inference -- Proper Scientific Method - 0 views

256.com/...strong_inference.html Science Statistics Media Representation Methodolatry Falsifiability
shared by Weiye Loh on 20 Mar 11 - No Cached
  • 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.
  • Weiye Loh on 20 Mar 11
     
    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.
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Rationally Speaking: Evolution as pseudoscience? - 0 views

rationallyspeaking.blogspot.com/...volution-as-pseudoscience.html Evolution Pseudo-Science Science Biology Philosophy Dermacation
shared by Weiye Loh on 16 Apr 11 - No Cached
  • I have been intrigued by an essay by my colleague Michael Ruse, entitled “Evolution and the idea of social progress,” published in a collection that I am reviewing, Biology and Ideology from Descartes to Dawkins (gotta love the title!), edited by Denis Alexander and Ronald Numbers.
  • Ruse's essay in the Alexander-Numbers collection questions the received story about the early evolution of evolutionary theory, which sees the stuff that immediately preceded Darwin — from Lamarck to Erasmus Darwin — as protoscience, the immature version of the full fledged science that biology became after Chuck's publication of the Origin of Species. Instead, Ruse thinks that pre-Darwinian evolutionists really engaged in pseudoscience, and that it took a very conscious and precise effort on Darwin’s part to sweep away all the garbage and establish a discipline with empirical and theoretical content analogous to that of the chemistry and physics of the time.
  • Ruse’s somewhat surprising yet intriguing claim is that “before Charles Darwin, evolution was an epiphenomenon of the ideology of [social] progress, a pseudoscience and seen as such. Liked by some for that very reason, despised by others for that very reason.”
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  • Ruse asserts that many serious intellectuals of the late 18th and early 19th century actually thought of evolution as pseudoscience, and he is careful to point out that the term “pseudoscience” had been used at least since 1843 (by the physiologist Francois Magendie)
  • Indeed, the link between evolution and the idea of human social-cultural progress was very strong before Darwin, and was one of the main things Darwin got rid of.
  • The encyclopedist Denis Diderot was typical in this respect: “The Tahitian is at a primary stage in the development of the world, the European is at its old age. The interval separating us is greater than that between the new-born child and the decrepit old man.” Similar nonsensical views can be found in Lamarck, Erasmus, and Chambers, the anonymous author of The Vestiges of the Natural History of Creation, usually considered the last protoscientific book on evolution to precede the Origin.
  • On the other side of the divide were social conservatives like the great anatomist George Cuvier, who rejected the idea of evolution — according to Ruse — not as much on scientific grounds as on political and ideological ones. Indeed, books like Erasmus’ Zoonomia and Chambers’ Vestiges were simply not much better than pseudoscientific treatises on, say, alchemy before the advent of modern chemistry.
  • people were well aware of this sorry situation, so much so that astronomer John Herschel referred to the question of the history of life as “the mystery of mysteries,” a phrase consciously adopted by Darwin in the Origin. Darwin set out to solve that mystery under the influence of three great thinkers: Newton, the above mentioned Herschel, and the philosopher William Whewell (whom Darwin knew and assiduously frequented in his youth)
  • Darwin was a graduate of the University of Cambridge, which had also been Newton’s home. Chuck got drilled early on during his Cambridge education with the idea that good science is about finding mechanisms (vera causa), something like the idea of gravitational attraction underpinning Newtonian mechanics. He reflected that all the talk of evolution up to then — including his grandfather’s — was empty, without a mechanism that could turn the idea into a scientific research program.
  • The second important influence was Herschel’s Preliminary Discourse on the Study of Natural Philosophy, published in 1831 and read by Darwin shortly thereafter, in which Herschel sets out to give his own take on what today we would call the demarcation problem, i.e. what methodology is distinctive of good science. One of Herschel’s points was to stress the usefulness of analogical reasoning
  • Finally, and perhaps most crucially, Darwin also read (twice!) Whewell’s History of the Inductive Sciences, which appeared in 1837. In it, Whewell sets out his notion that good scientific inductive reasoning proceeds by a consilience of ideas, a situation in which multiple independent lines of evidence point to the same conclusion.
  • the first part of the Origin, where Darwin introduces the concept of natural selection by way of analogy with artificial selection can be read as the result of Herschel’s influence (natural selection is the vera causa of evolution)
  • the second part of the book, constituting Darwin's famous “long argument,” applies Whewell’s method of consilience by bringing in evidence from a number of disparate fields, from embryology to paleontology to biogeography.
  • What, then, happened to the strict coupling of the ideas of social and biological progress that had preceded Darwin? While he still believed in the former, the latter was no longer an integral part of evolution, because natural selection makes things “better” only in a relative fashion. There is no meaningful sense in which, say, a large brain is better than very fast legs or sharp claws, as long as you still manage to have dinner and avoid being dinner by the end of the day (or, more precisely, by the time you reproduce).
  • Ruse’s claim that evolution transitioned not from protoscience to science, but from pseudoscience, makes sense to me given the historical and philosophical developments. It wasn’t the first time either. Just think about the already mentioned shift from alchemy to chemistry
  • Of course, the distinction between pseudoscience and protoscience is itself fuzzy, but we do have what I think are clear examples of the latter that cannot reasonably be confused with the former, SETI for one, and arguably Ptolemaic astronomy. We also have pretty obvious instances of pseudoscience (the usual suspects: astrology, ufology, etc.), so the distinction — as long as it is not stretched beyond usefulness — is interesting and defensible.
  • It is amusing to speculate which, if any, of the modern pseudosciences (cryonics, singularitarianism) might turn out to be able to transition in one form or another to actual sciences. To do so, they may need to find their philosophically and scientifically savvy Darwin, and a likely bet — if history teaches us anything — is that, should they succeed in this transition, their mature form will look as different from the original as chemistry and alchemy. Or as Darwinism and pre-Darwinian evolutionism.
  • Darwin called the Origin "one long argument," but I really do think that recognizing that the book contains (at least) two arguments could help to dispel that whole "just a theory" canard. The first half of the book is devoted to demonstrating that natural selection is the true cause of evolution; vera causa arguments require proof that the cause's effect be demonstrated as fact, so the second half of the book is devoted to a demonstration that evolution has really happened. In other words, evolution is a demonstrable fact and natural selection is the theory that explains that fact, just as the motion of the planets is a fact and gravity is a theory that explains it.
  • Cryogenics is the study of the production of low temperatures and the behavior of materials at those temperatures. It is a legitimate branch of physics and has been for a long time. I think you meant 'cryonics'.
  • The Singularity means different things to different people. It is uncharitable to dismiss all "singularitarians" by debunking Kurzweil. He is low hanging fruit. Reach for something higher.
  • Weiye Loh on 16 Apr 11
     
    "before Charles Darwin, evolution was an epiphenomenon of the ideology of [social] progress, a pseudoscience and seen as such. Liked by some for that very reason, despised by others for that very reason."
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Open science: a future shaped by shared experience | Education | The Observer - 0 views

www.guardian.co.uk/...ience-shared-research-internet Open Source Science
shared by Weiye Loh on 25 May 11 - No Cached
  • one day he took one of these – finding a mathematical proof about the properties of multidimensional objects – and put his thoughts on his blog. How would other people go about solving this conundrum? Would somebody else have any useful insights? Would mathematicians, notoriously competitive, be prepared to collaborate? "It was an experiment," he admits. "I thought it would be interesting to try."He called it the Polymath Project and it rapidly took on a life of its own. Within days, readers, including high-ranking academics, had chipped in vital pieces of information or new ideas. In just a few weeks, the number of contributors had reached more than 40 and a result was on the horizon. Since then, the joint effort has led to several papers published in journals under the collective pseudonym DHJ Polymath. It was an astonishing and unexpected result.
  • "If you set out to solve a problem, there's no guarantee you will succeed," says Gowers. "But different people have different aptitudes and they know different tricks… it turned out their combined efforts can be much quicker."
  • There are many interpretations of what open science means, with different motivations across different disciplines. Some are driven by the backlash against corporate-funded science, with its profit-driven research agenda. Others are internet radicals who take the "information wants to be free" slogan literally. Others want to make important discoveries more likely to happen. But for all their differences, the ambition remains roughly the same: to try and revolutionise the way research is performed by unlocking it and making it more public.
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  • Jackson is a young bioscientist who, like many others, has discovered that the technologies used in genetics and molecular biology, once the preserve of only the most well-funded labs, are now cheap enough to allow experimental work to take place in their garages. For many, this means that they can conduct genetic experiments in a new way, adopting the so-called "hacker ethic" – the desire to tinker, deconstruct, rebuild.
  • The rise of this group is entertainingly documented in a new book by science writer Marcus Wohlsen, Biopunk (Current £18.99), which describes the parallels between today's generation of biological innovators and the rise of computer software pioneers of the 1980s and 1990s. Indeed, Bill Gates has said that if he were a teenager today, he would be working on biotechnology, not computer software.
  • open scientists suggest that it doesn't have to be that way. Their arguments are propelled by a number of different factors that are making transparency more viable than ever.The first and most powerful change has been the use of the web to connect people and collect information. The internet, now an indelible part of our lives, allows like-minded individuals to seek one another out and share vast amounts of raw data. Researchers can lay claim to an idea not by publishing first in a journal (a process that can take many months) but by sharing their work online in an instant.And while the rapidly decreasing cost of previously expensive technical procedures has opened up new directions for research, there is also increasing pressure for researchers to cut costs and deliver results. The economic crisis left many budgets in tatters and governments around the world are cutting back on investment in science as they try to balance the books. Open science can, sometimes, make the process faster and cheaper, showing what one advocate, Cameron Neylon, calls "an obligation and responsibility to the public purse".
  • "The litmus test of openness is whether you can have access to the data," says Dr Rufus Pollock, a co-founder of the Open Knowledge Foundation, a group that promotes broader access to information and data. "If you have access to the data, then anyone can get it, use it, reuse it and redistribute it… we've always built on the work of others, stood on the shoulders of giants and learned from those who have gone before."
  • moves are afoot to disrupt the closed world of academic journals and make high-level teaching materials available to the public. The Public Library of Science, based in San Francisco, is working to make journals more freely accessible
  • it's more than just politics at stake – it's also a fundamental right to share knowledge, rather than hide it. The best example of open science in action, he suggests, is the Human Genome Project, which successfully mapped our DNA and then made the data public. In doing so, it outflanked J Craig Venter's proprietary attempt to patent the human genome, opening up the very essence of human life for science, rather than handing our biological information over to corporate interests.
  • the rise of open science does not please everyone. Critics have argued that while it benefits those at either end of the scientific chain – the well-established at the top of the academic tree or the outsiders who have nothing to lose – it hurts those in the middle. Most professional scientists rely on the current system for funding and reputation. Others suggest it is throwing out some of the most important elements of science and making deep, long-term research more difficult.
  • Open science proponents say that they do not want to make the current system a thing of the past, but that it shouldn't be seen as immutable either. In fact, they say, the way most people conceive of science – as a highly specialised academic discipline conducted by white-coated professionals in universities or commercial laboratories – is a very modern construction.It is only over the last century that scientific disciplines became industrialised and compartmentalised.
  • open scientists say they don't want to throw scientists to the wolves: they just want to help answer questions that, in many cases, are seen as insurmountable.
  • "Some people, very straightforwardly, said that they didn't like the idea because it undermined the concept of the romantic, lone genius." Even the most dedicated open scientists understand that appeal. "I do plan to keep going at them," he says of collaborative projects. "But I haven't given up on solitary thinking about problems entirely."
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Skepticblog » The Value of Vertigo - 1 views

skepticblog.org/...the-value-of-vertigo Kuhn Creationism
shared by Weiye Loh on 03 Sep 10 - Cached
  • But Ruse’s moment of vertigo is not as surprising as it may appear. Indeed, he put effort into achieving this immersion: “I am atypical, I took about three hours to go through [the creation museum] but judging from my students most people don’t read the material as obsessively as I and take about an hour.” Why make this meticulous effort, when he could have dismissed creationism’s well-known scientific problems from the parking lot, or from his easy chair at home?
  • According to Ruse, the vertiginous “what if?” feeling has a practical value. After all, it’s easy to find problems with a pseudoscientific belief; what’s harder is understanding how and why other people believe. “It is silly just to dismiss this stuff as false,” Ruse argues (although it is false, and although Ruse has fought against “this stuff” for decades). “A lot of people believe Creationism so we on the other side need to get a feeling not just for the ideas but for the psychology too.”
  • Weiye Loh on 03 Sep 10
     
    In June of 2009, philosopher of biology Michael Ruse took a group of grad students to the Answers in Genesis Creation Museum in Kentucky (and also some mainstream institutions) as part of a course on how museums present science. In a critical description of his visit, Ruse reflected upon "the extent to which the Creationist museum uses modern science to its own ends, melding it in seamlessly with its own Creationist message." Continental drift, the Big Bang, and even natural selection are all presented as evidence in support of Young Earth cosmology and flood geology. While immersing himself in the museum's pitch, Ruse wrote, Just for one moment about half way through the exhibit…I got that Kuhnian flash that it could all be true - it was only a flash (rather like thinking that Freudianism is true or that the Republicans are right on anything whatsoever) but it was interesting nevertheless to get a sense of how much sense this whole display and paradigm can make to people.
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Genome Biology | Full text | A Faustian bargain - 0 views

genomebiology.com/138 Education Humanities Political Economy
shared by Weiye Loh on 03 Dec 10 - No Cached
  • on October 1st, you announced that the departments of French, Italian, Classics, Russian and Theater Arts were being eliminated. You gave several reasons for your decision, including that 'there are comparatively fewer students enrolled in these degree programs.' Of course, your decision was also, perhaps chiefly, a cost-cutting measure - in fact, you stated that this decision might not have been necessary had the state legislature passed a bill that would have allowed your university to set its own tuition rates. Finally, you asserted that the humanities were a drain on the institution financially, as opposed to the sciences, which bring in money in the form of grants and contracts.
  • I'm sure that relatively few students take classes in these subjects nowadays, just as you say. There wouldn't have been many in my day, either, if universities hadn't required students to take a distribution of courses in many different parts of the academy: humanities, social sciences, the fine arts, the physical and natural sciences, and to attain minimal proficiency in at least one foreign language. You see, the reason that humanities classes have low enrollment is not because students these days are clamoring for more relevant courses; it's because administrators like you, and spineless faculty, have stopped setting distribution requirements and started allowing students to choose their own academic programs - something I feel is a complete abrogation of the duty of university faculty as teachers and mentors. You could fix the enrollment problem tomorrow by instituting a mandatory core curriculum that included a wide range of courses.
  • the vast majority of humanity cannot handle freedom. In giving humans the freedom to choose, Christ has doomed humanity to a life of suffering.
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  • in Dostoyevsky's parable of the Grand Inquisitor, which is told in Chapter Five of his great novel, The Brothers Karamazov. In the parable, Christ comes back to earth in Seville at the time of the Spanish Inquisition. He performs several miracles but is arrested by Inquisition leaders and sentenced to be burned at the stake. The Grand Inquisitor visits Him in his cell to tell Him that the Church no longer needs Him. The main portion of the text is the Inquisitor explaining why. The Inquisitor says that Jesus rejected the three temptations of Satan in the desert in favor of freedom, but he believes that Jesus has misjudged human nature.
  • I'm sure the budgetary problems you have to deal with are serious. They certainly are at Brandeis University, where I work. And we, too, faced critical strategic decisions because our income was no longer enough to meet our expenses. But we eschewed your draconian - and authoritarian - solution, and a team of faculty, with input from all parts of the university, came up with a plan to do more with fewer resources. I'm not saying that all the specifics of our solution would fit your institution, but the process sure would have. You did call a town meeting, but it was to discuss your plan, not let the university craft its own. And you called that meeting for Friday afternoon on October 1st, when few of your students or faculty would be around to attend. In your defense, you called the timing 'unfortunate', but pleaded that there was a 'limited availability of appropriate large venue options.' I find that rather surprising. If the President of Brandeis needed a lecture hall on short notice, he would get one. I guess you don't have much clout at your university.
  • As for the argument that the humanities don't pay their own way, well, I guess that's true, but it seems to me that there's a fallacy in assuming that a university should be run like a business. I'm not saying it shouldn't be managed prudently, but the notion that every part of it needs to be self-supporting is simply at variance with what a university is all about.
  • You seem to value entrepreneurial programs and practical subjects that might generate intellectual property more than you do 'old-fashioned' courses of study. But universities aren't just about discovering and capitalizing on new knowledge; they are also about preserving knowledge from being lost over time, and that requires a financial investment.
  • what seems to be archaic today can become vital in the future. I'll give you two examples of that. The first is the science of virology, which in the 1970s was dying out because people felt that infectious diseases were no longer a serious health problem in the developed world and other subjects, such as molecular biology, were much sexier. Then, in the early 1990s, a little problem called AIDS became the world's number 1 health concern. The virus that causes AIDS was first isolated and characterized at the National Institutes of Health in the USA and the Institute Pasteur in France, because these were among the few institutions that still had thriving virology programs. My second example you will probably be more familiar with. Middle Eastern Studies, including the study of foreign languages such as Arabic and Persian, was hardly a hot subject on most campuses in the 1990s. Then came September 11, 2001. Suddenly we realized that we needed a lot more people who understood something about that part of the world, especially its Muslim culture. Those universities that had preserved their Middle Eastern Studies departments, even in the face of declining enrollment, suddenly became very important places. Those that hadn't - well, I'm sure you get the picture.
  • one of your arguments is that not every place should try to do everything. Let other institutions have great programs in classics or theater arts, you say; we will focus on preparing students for jobs in the real world. Well, I hope I've just shown you that the real world is pretty fickle about what it wants. The best way for people to be prepared for the inevitable shock of change is to be as broadly educated as possible, because today's backwater is often tomorrow's hot field. And interdisciplinary research, which is all the rage these days, is only possible if people aren't too narrowly trained. If none of that convinces you, then I'm willing to let you turn your institution into a place that focuses on the practical, but only if you stop calling it a university and yourself the President of one. You see, the word 'university' derives from the Latin 'universitas', meaning 'the whole'. You can't be a university without having a thriving humanities program. You will need to call SUNY Albany a trade school, or perhaps a vocational college, but not a university. Not anymore.
  • I started out as a classics major. I'm now Professor of Biochemistry and Chemistry. Of all the courses I took in college and graduate school, the ones that have benefited me the most in my career as a scientist are the courses in classics, art history, sociology, and English literature. These courses didn't just give me a much better appreciation for my own culture; they taught me how to think, to analyze, and to write clearly. None of my sciences courses did any of that.
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Synthetic life special edition (Practical Ethics) - 0 views

www.practicalethicsnews.com/...etic-life-special-edition.html Bioethics news
shared by Weiye Loh on 23 May 10 - Cached
  • Weiye Loh on 23 May 10
     
    Synthetic Biology/ Synthetic life. 
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Cancer resembles life 1 billion years ago, say astrobiologists - microbiology, genomics... - 0 views

www.lifescientist.com.au/..._years_ago_say_astrobiologists Cancer Evolution Life
shared by Weiye Loh on 17 Feb 11 - No Cached
  • astrobiologists, working with oncologists in the US, have suggested that cancer resembles ancient forms of life that flourished between 600 million and 1 billion years ago.
  • Read more about what this discovery means for cancer research.
  • The genes that controlled the behaviour of these early multicellular organisms still reside within our own cells, managed by more recent genes that keep them in check.It's when these newer controlling genes fail that the older mechanisms take over, and the cell reverts to its earlier behaviours and grows out of control.
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  • The new theory, published in the journal Physical Biology, has been put forward by two leading figures in the world of cosmology and astrobiology: Paul Davies, director of the Beyond Center for Fundamental Concepts in Science, Arizona State University; and Charles Lineweaver, from the Australian National University.
  • According to Lineweaver, this suggests that cancer is an atavism, or an evolutionary throwback.
  • In the paper, they suggest that a close look at cancer shows similarities with early forms of multicellular life.
  • “Unlike bacteria and viruses, cancer has not developed the capacity to evolve into new forms. In fact, cancer is better understood as the reversion of cells to the way they behaved a little over one billion years ago, when humans were nothing more than loose-knit colonies of only partially differentiated cells. “We think that the tumours that develop in cancer patients today take the same form as these simple cellular structures did more than a billion years ago,” he said.
  • One piece of evidence to support this theory is that cancers appear in virtually all metazoans, with the notable exception of the bizarre naked mole rat."This quasi-ubiquity suggests that the mechanisms of cancer are deep-rooted in evolutionary history, a conjecture that receives support from both paleontology and genetics," they write.
  • the genes that controlled this early multi-cellular form of life are like a computer operating system's 'safe mode', and when there are failures or mutations in the more recent genes that manage the way cells specialise and interact to form the complex life of today, then the earlier level of programming takes over.
  • Their notion is in contrast to a prevailing theory that cancer cells are 'rogue' cells that evolve rapidly within the body, overcoming the normal slew of cellular defences.
  • However, Davies and Lineweaver point out that cancer cells are highly cooperative with each other, if competing with the host's cells. This suggests a pre-existing complexity that is reminiscent of early multicellular life.
  • cancers' manifold survival mechanisms are predictable, and unlikely to emerge spontaneously through evolution within each individual in such a consistent way.
  • The good news is that this means combating cancer is not necessarily as complex as if the cancers were rogue cells evolving new and novel defence mechanisms within the body.Instead, because cancers fall back on the same evolved mechanisms that were used by early life, we can expect them to remain predictable, thus if they're susceptible to treatment, it's unlikely they'll evolve new ways to get around it.
  • If the atavism hypothesis is correct, there are new reasons for optimism," they write.
  • Weiye Loh on 17 Feb 11
     
    Feature: Inside DNA vaccines bioMD makes a bid for Andrew Forest's Allied Medical and Coridon Alexion acquires technology for MoCD therapy More > Most Popular Media Releases Cancer resembles life 1 billion years ago, say astrobiologists Feature: The challenge of a herpes simplex vaccine Feature: Proteomics power of pawpaw bioMD makes a bid for Andrew Forest's Allied Medical and Coridon Immune system boosting hormone might lead to HIV cure Biotechnology Directory Company Profile Check out this company's profile and more in the Biotechnology Directory! Biotechnology Directory Find company by name Find company by category Latest Jobs Senior Software Developer / Java Analyst Programm App Support Developer - Java / J2ee Solutions Consultant - VIC Technical Writer Product Manager (Fisheye/Crucible)   BUYING GUIDES Portable Multimedia Players Digital Cameras Digital Video Cameras LATEST PRODUCTS HTC Wildfire S Android phone (preview) Panasonic LUMIX DMC-GH2 digital camera HTC Desire S Android phone (preview) Qld ICT minister Robert Schwarten retires Movie piracy costs Aus economy $1.37 billion in 12 months: AFACT Wireless smartphones essential to e-health: CSIRO Aussie outsourcing CRM budgets to soar in 2011: Ovum Federal government to evaluate education revolution targets Business continuity planning - more than just disaster recovery Proving the value of IT - Part one 5 open source security projects to watch In-memory computing Information security in 2011 EFA shoots down 'unproductive' AFACT movie piracy study In Pictures: IBM hosts Galactic dinner Emerson Network Power launches new infrastructure solutions Consumers not smart enough for smartphones? Google one-ups Apple online media subscription service M2M offerings expand as more machines go online India cancels satellite spectrum deal after controversy Lenovo profit rises in Q3 on strong PC sales in China Taiwan firm to supply touch sensors to Samsung HP regains top position in India's PC market Copyright 20
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11.01.97 - Misconceptions about the causes of cancer lead to skewed priorities and wast... - 0 views

berkeley.edu/...11_01_97a.html Pollution Cancer Policy Science Risk
shared by Weiye Loh on 09 Apr 11 - No Cached
  • One of the big misconceptions is that artificial chemicals such as pesticides have a lot to do with human cancer, but that's just not true," says Bruce N. Ames, professor of biochemistry and molecular biology at the University of California at Berkeley and co-author of a new review of what is known about environmental pollution and cancer. "Nevertheless, it's conventional wisdom and society spends billions on this each year." "We consume more carcinogens in one cup of coffee than we get from the pesticide residues on all the fruits and vegetables we eat in a year," he adds.
  • there may be many excellent reasons for cleaning up pollution of our air, water and soil, the researchers say, prevention of cancer is not one of them.
  • "The problem is that lifestyle changes are tough," says Gold, director of the Carcinogenic Potency Project at UC Berkeley's National Institute for Environmental Health Sciences Center and a senior scientist in the cell and molecular biology division at Lawrence Berkeley National Laboratory. "But by targeting pesticide residues as a major problem, we risk making fruits and vegetables more expensive and indirectly increasing cancer risks, especially among the poor."
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  • Whereas 99.9 percent of all the chemicals we ingest are natural, 78 percent of the chemicals tested are synthetic. So when more than half of all synthetic chemicals are found to cause cancer in rodents, it's not surprising that people link cancer with synthetic chemicals. But of the natural chemicals in our diet that have been tested in animals, half also cause cancer, Gold says.
  • "We need to recognize that there are far more carcinogens in the natural world than in the synthetic world, and go after the important things, such as lifestyle change."
  • Misconception: Cancer rates are soaring. In fact, the researchers say, if lung cancer due to smoking is excluded, overall cancer deaths in the U.S. have declined 16 percent since 1950.
  • Misconception: Reducing pesticide residues is an effective way to prevent diet-related cancer. Because fruits and vegetables are of major importance in reducing cancer, the unintended effect of requiring expensive efforts to reduce the amount of pesticides remaining on fruits and vegetables will be to increase their cost. This will lead to an increase in cancer among low income people who no longer will be able to afford to eat them.
  • Misconception: Human exposures to carcinogens and other potential hazards are primarily due to synthetic chemicals. Americans actually eat about 10,000 times more natural pesticides from fruits and vegetables than synthetic pesticide residues on food. Natural pesticides are chemicals that plants produce to defend themselves against fungi, insects, and other predators. And half of all natural pesticides tested in rodents turn out to be rodent carcinogens. In addition, we consume many other carcinogens in foods because of the chemicals produced in cooking. In a single cup of roasted coffee, for example, the natural chemicals known to be rodent carcinogens are about equal in weight to an entire year's work of synthetic pesticide residues.
  • Misconception: Cancer risks to humans can be assessed by standard high-dose animal cancer tests. In cancer tests, animals are given very high, nearly toxic doses. The effect on humans at lower doses is extrapolated from these results, as if the relationship were a straight line from high dose to low dose. However, the fact that half of all chemicals tested, whether natural or synthetic, turn out to cause cancer in rodents implies that this is an artifact of using high doses. High doses of any chemical can chronically kill cells and wound tissue, a risk factor for cancer . "Our conclusion is that the scientific evidence shows that there are high-dose effects," Ames says. "But even though government regulatory agencies recognize this, they still decide which synthetic chemicals to regulate based on linear extrapolation of high dose cancer tests in animals."
  • Misconception: Synthetic chemicals pose greater carcinogenic hazards than natural chemicals. Naturally occurring carcinogens represent an enormous background compared to the low-dose exposures to residues of synthetic chemicals such as pesticides, the researchers conclude. These results call for a reevaluation of whether animal cancer tests are really useful guides for protecting the public against minor hypothetical risks.
  • Misconception: The toxicology of synthetic chemicals is different from that of natural chemicals. No evidence exists for this, but the assumption could lead to unfortunate tradeoffs between natural and synthetic pesticides. Recently, for example, when a new variety of highly insect-resistant celery was introduced on a farm, the workers handling the celery developed rashes when they were exposed to sunlight. The pest-resistant celery turned out to contain almost eight times more natural pesticide in the form of psoralens -- chemicals known to cause cancer and genetic mutations -- than common celery.
  • Misconception: Pesticides and other synthetic chemicals are disrupting human hormones. Claims that synthetic chemicals with hormonal activity contribute to cancer and reduced sperm count ignore the fact that natural chemicals have hormone-like activity millions of times greater than do traces of synthetic chemicals. Rather, lifestyle -- lack of exercise, obesity, alcohol use and reproductive history -- are known to lead to marked changes in hormone levels in the body.
  • Misconception: Regulating low, hypothetical risks advances public health. Society -- primarily the private sector -- will spend an estimated $140 billion to comply with environmental regulations this year, according to projections by the Environmental Protection Agency. Much of this is aimed at reducing low-level human exposure to chemicals solely because they are rodent carcinogens, despite the fact that this rationale is flawed. Our improved ability to detect even minuscule concentrations of chemicals makes regulation even more expensive.
  • Weiye Loh on 09 Apr 11
     
    BERKELEY -- Despite a lack of convincing evidence that pollution is an important cause of human cancer, this misconception drives government policy today and results in billions of dollars spent to clean up minuscule amounts of synthetic chemicals, say two UC Berkeley researchers.
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Rationally Speaking: A pluralist approach to ethics - 0 views

rationallyspeaking.blogspot.com/...ralist-approach-to-ethics.html Ethics Pluralism
shared by Weiye Loh on 07 May 11 - No Cached
  • The history of Western moral philosophy includes numerous attempts to ground ethics in one rational principle, standard, or rule. This narrative stretches back 2,500 years to the Greeks, who were interested mainly in virtue ethics and the moral character of the person. The modern era has seen two major additions. In 1785, Immanuel Kant introduced the categorical imperative: act only under the assumption that what you do could be made into a universal law. And in 1789, Jeremy Bentham proposed utilitarianism: work toward the greatest happiness of the greatest number of people (the “utility” principle).
  • Many people now think projects to build a reasonable and coherent moral system are doomed. Still, most secular and religious people reject the alternative of moral relativism, and have spent much ink criticizing it (among my favorite books on the topic is Moral Relativism by Stephen Lukes). The most recent and controversial work in this area comes from Sam Harris. In The Moral Landscape, Harris argues for a morality based on (a science of) well-being and flourishing, rather than religious dogma.
  • I am interested in another oft-heard criticism of Harris’ book, which is that words like “well-being” and “flourishing” are too general to form any relevant basis for morality. This criticism has some force to it, as these certainly are somewhat vague terms. But what if “well-being” and “flourishing” were to be used only as a starting point for a moral framework? These concepts would still put us on a better grounding than religious faith. But they cannot stand alone. Nor do they need to.
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  • 1. The harm principle bases our ethical considerations on other beings’ capacity for higher-level subjective experience. Human beings (and some animals) have the potential — and desire — to experience deep pleasure and happiness while seeking to avoid pain and suffering. We have the obligation, then, to afford creatures with these capacities, desires and relations a certain level of respect. They also have other emotional and social interests: for instance, friends and families concerned with their health and enjoyment. These actors also deserve consideration.
  • 2. If we have a moral obligation to act a certain way toward someone, that should be reflected in law. Rights theory is the idea that there are certain rights worth granting to people with very few, if any, caveats. Many of these rights were spelled out in the founding documents of this country, the Declaration of Independence (which admittedly has no legal pull) and the Constitution (which does). They have been defended in a long history of U.S. Supreme Court rulings. They have also been expanded on in the U.N.’s 1948 Universal Declaration of Human Rights and in the founding documents of other countries around the world. To name a few, they include: freedom of belief, speech and expression, due process, equal treatment, health care, and education.
  • 3. While we ought to consider our broader moral efforts, and focus on our obligations to others, it is also important to place attention on our quality as moral agents. A vital part of fostering a respectable pluralist moral framework is to encourage virtues, and cultivate moral character. A short list of these virtues would include prudence, justice, wisdom, honesty, compassion, and courage. One should study these, and strive to put these into practice and work to be a better human being, as Aristotle advised us to do.
  • most people already are ethical pluralists. Life and society are complex to navigate, and one cannot rely on a single idea for guidance. It is probably accurate to say that people lean more toward one theory, rather than practice it to the exclusion of all others. Of course, this only describes the fact that people think about morality in a pluralistic way. But the outlined approach is supported, sound reasoning — that is, unless you are ready to entirely dismiss 2,500 years of Western moral philosophy.
  • Weiye Loh on 07 May 11
     
    while each ethical system discussed so far has its shortcomings, put together they form a solid possibility. One system might not be able to do the job required, but we can assemble a mature moral outlook containing parts drawn from different systems put forth by philosophers over the centuries (plus some biology, but that's Massimo's area). The following is a rough sketch of what I think a decent pluralist approach to ethics might look like.
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Hermits and Cranks: Lessons from Martin Gardner on Recognizing Pseudoscientists: Scient... - 0 views

www.scientificamerican.com/article.cfm Science Pseudo-Science
shared by Weiye Loh on 09 Jul 10 - Cached
  • In 1950 Martin Gardner published an article in the Antioch Review entitled "The Hermit Scientist," about what we would today call pseudoscientists.
  • there has been some progress since Gardner offered his first criticisms of pseudoscience. Now largely antiquated are his chapters on believers in a flat Earth, a hollow Earth, Atlantis and Lemuria, Alfred William Lawson, Roger Babson, Trofim Lysenko, Wilhelm Reich and Alfred Korzybski. But disturbingly, a good two thirds of the book's contents are relevant today, including Gardner's discussions of homeopathy, naturopathy, osteopathy, iridiagnosis (reading the iris of the eye to deter- mine bodily malfunctions), food faddists, cancer cures and other forms of medical quackery, Edgar Cayce, the Great Pyramid's alleged mystical powers, handwriting analysis, ESP and PK (psychokinesis), reincarnation, dowsing rods, eccentric sexual theories, and theories of group racial differences.
  • The "hermit scientist," a youthful Gardner wrote, works alone and is ignored by mainstream scientists. "Such neglect, of course, only strengthens the convictions of the self-declared genius."
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  • Even then Gardner was bemoaning that some beliefs never seem to go out of vogue, as he recalled an H. L. Mencken quip from the 1920s: "Heave an egg out of a Pullman window, and you will hit a Fundamentalist almost anywhere in the U.S. today." Gardner cautions that when religious superstition should be on the wane, it is easy "to forget that thousands of high school teachers of biology, in many of our southern states, are still afraid to teach the theory of evolution for fear of losing their jobs." Today creationism has spread northward and mutated into the oxymoronic form of "creation science."
  • the differences between science and pseudoscience. On the one extreme we have ideas that are most certainly false, "such as the dianetic view that a one-day-old embryo can make sound recordings of its mother's conversation." In the borderlands between the two "are theories advanced as working hypotheses, but highly debatable because of the lack of sufficient data." Of these Gardner selects a most propitious propitious example: "the theory that the universe is expanding." That theory would now fall at the other extreme end of the spectrum, where lie "theories al- most certainly true, such as the belief that the Earth is round or that men and beasts are distant cousins."
  • How can we tell if someone is a scientific crank? Gardner offers this advice: (1) "First and most important of these traits is that cranks work in almost total isolation from their colleagues." Cranks typically do not understand how the scientific process operates—that they need to try out their ideas on colleagues, attend conferences and publish their hypotheses in peer-reviewed journals before announcing to the world their startling discovery. Of course, when you explain this to them they say that their ideas are too radical for the conservative scientific establishment to accept.
  • (2) "A second characteristic of the pseudo-scientist, which greatly strengthens his isolation, is a tendency toward paranoia," which manifests itself in several ways: (1) He considers himself a genius. (2) He regards his colleagues, without exception, as ignorant blockheads....(3) He believes himself unjustly persecuted and discriminated against. The recognized societies refuse to let him lecture. The journals reject his papers and either ignore his books or assign them to "enemies" for review. It is all part of a dastardly plot. It never occurs to the crank that this opposition may be due to error in his work....(4) He has strong compulsions to focus his attacks on the greatest scientists and the best-established theories. When Newton was the outstanding name in physics, eccentric works in that science were violently anti-Newton. Today, with Einstein the father-symbol of authority, a crank theory of physics is likely to attack Einstein....(5) He often has a tendency to write in a complex jargon, in many cases making use of terms and phrases he himself has coined.
  • "If the present trend continues," Gardner concludes, "we can expect a wide variety of these men, with theories yet unimaginable, to put in their appearance in the years immediately ahead. They will write impressive books, give inspiring lectures, organize exciting cults. They may achieve a following of one—or one million. In any case, it will be well for ourselves and for society if we are on our guard against them."
  • Weiye Loh on 09 Jul 10
     
    May 23, 2010 | 31 comments Hermits and Cranks: Lessons from Martin Gardner on Recognizing Pseudoscientists Fifty years ago Gardner launched the modern skeptical movement. Unfortunately, much of what he wrote about is still current today By Michael Shermer   
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Study: Airport Security Should Stop Racial Profiling | Smart Journalism. Real Solutions... - 0 views

www.miller-mccune.com/...al-profiling-doesnt-work-25725 Discrimination Racism Terrorism
shared by Weiye Loh on 02 Dec 10 - No Cached
  • Plucking out of line most of the vaguely Middle Eastern-looking men at the airport for heightened screening is no more effective at catching terrorists than randomly sampling everyone. It may even be less effective. Press stumbled across this counterintuitive concept — sometimes the best way to find something is not to weight it by probability — in the unrelated context of computational biology. The parallels to airport security struck him when a friend mentioned he was constantly being pulled out of line at the airport.
  • Racial profiling, in other words, doesn’t work because it devotes heightened resources to innocent people — and then devotes those resources to them repeatedly even after they’ve been cleared as innocent the first time. The actual terrorists, meanwhile, may sneak through while Transportation Security Administration agents are focusing their limited attention on the wrong passengers.
  • Press tested the theory in a series of probability equations (the ambitious can check his math here and here).
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  • Sampling based on profiling is mathematically no more effective than uniform random sampling. The optimal equation, rather, turns out to be something called “square-root sampling,” a compromise between the other two methods.
  • “Crudely,” Press writes of his findings in the journal Significance, if certain people are “nine times as likely to be the terrorist, we pull out only three times as many of them for special checks. Surprisingly, and bizarrely, this turns out to be the most efficient way of catching the terrorist.”
  • Square-root sampling, though, still represents a kind of profiling, and, Press adds, not one that could be realistically implemented at airports today. Square-root sampling only works if the profile probabilities are accurate in the first place — if we are able to say with mathematical certainty that some types of people are “nine times as likely to be the terrorist” compared to others. TSA agents in a crowded holiday terminal making snap judgments about facial hair would be far from this standard. “The nice thing about uniform sampling is there’s nothing to be inaccurate about, you don’t need any data, it never can be worse than you expect,” Press said. “As soon as you use profile probabilities, if the profile probabilities are just wrong, then the strong profiling just does worse than the random sampling.”
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Rationally Speaking: The sorry state of higher education - 0 views

rationallyspeaking.blogspot.com/...state-of-higher-education.html Education Plagiarism Humanities Political Economy
shared by Weiye Loh on 03 Dec 10 - No Cached
  • two disconcerting articles crossed my computer screen, both highlighting the increasingly sorry state of higher education, though from very different perspectives. The first is “Ed Dante’s” (actually a pseudonym) piece in the Chronicle of Higher Education, entitled The Shadow Scholar. The second is Gregory Petsko’s A Faustian Bargain, published of all places in Genome Biology.
  • There is much to be learned by educators in the Shadow Scholar piece, except the moral that “Dante” would like us to take from it. The anonymous author writes:“Pointing the finger at me is too easy. Why does my business thrive? Why do so many students prefer to cheat rather than do their own work? Say what you want about me, but I am not the reason your students cheat.
  • The point is that plagiarism and cheating happen for a variety of reasons, one of which is the existence of people like Mr. Dante and his company, who set up a business that is clearly unethical and should be illegal. So, pointing fingers at him and his ilk is perfectly reasonable. Yes, there obviously is a “market” for cheating in higher education, and there are complex reasons for it, but he is in a position similar to that of the drug dealer who insists that he is simply providing the commodity to satisfy society’s demand. Much too easy of a way out, and one that doesn’t fly in the case of drug dealers, and shouldn’t fly in the case of ghost cheaters.
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  • As a teacher at the City University of New York, I am constantly aware of the possibility that my students might cheat on their tests. I do take some elementary precautionary steps
  • Still, my job is not that of the policeman. My students are adults who theoretically are there to learn. If they don’t value that learning and prefer to pay someone else to fake it, so be it, ultimately it is they who lose in the most fundamental sense of the term. Just like drug addicts, to return to my earlier metaphor. And just as in that other case, it is enablers like Mr. Dante who simply can’t duck the moral blame.
  • n open letter to the president of SUNY-Albany, penned by molecular biologist Gregory Petsko. The SUNY-Albany president has recently announced the closing — for budgetary reasons — of the departments of French, Italian, Classics, Russian and Theater Arts at his university.
  • Petsko begins by taking on one of the alleged reasons why SUNY-Albany is slashing the humanities: low enrollment. He correctly points out that the problem can be solved overnight at the stroke of a pen: stop abdicating your responsibilities as educators and actually put constraints on what your students have to take in order to graduate. Make courses in English literature, foreign languages, philosophy and critical thinking, the arts and so on, mandatory or one of a small number of options that the students must consider in order to graduate.
  • But, you might say, that’s cheating the market! Students clearly don’t want to take those courses, and a business should cater to its customers. That type of reasoning is among the most pernicious and idiotic I’ve ever heard. Students are not clients (if anything, their parents, who usually pay the tuition, are), they are not shopping for a new bag or pair of shoes. They do not know what is best for them educationally, that’s why they go to college to begin with. If you are not convinced about how absurd the students-as-clients argument is, consider an analogy: does anyone with functioning brain cells argue that since patients in a hospital pay a bill, they should be dictating how the brain surgeon operates? I didn’t think so.
  • Petsko then tackles the second lame excuse given by the president of SUNY-Albany (and common among the upper administration of plenty of public universities): I can’t do otherwise because of the legislature’s draconian cuts. Except that university budgets are simply too complicated for there not to be any other option. I know this first hand, I’m on a special committee at my own college looking at how to creatively deal with budget cuts handed down to us from the very same (admittedly small minded and dysfunctional) New York state legislature that has prompted SUNY-Albany’s action. As Petsko points out, the president there didn’t even think of involving the faculty and staff in a broad discussion of how to deal with the crisis, he simply announced the cuts on a Friday afternoon and then ran for cover. An example of very poor leadership to say the least, and downright hypocrisy considering all the talk that the same administrator has been dishing out about the university “community.”
  • Finally, there is the argument that the humanities don’t pay for their own way, unlike (some of) the sciences (some of the time). That is indubitably true, but irrelevant. Universities are not businesses, they are places of higher learning. Yes, of course they need to deal with budgets, fund raising and all the rest. But the financial and administrative side has one goal and one goal only: to provide the best education to the students who attend that university.
  • That education simply must include the sciences, philosophy, literature, and the arts, as well as more technical or pragmatic offerings such as medicine, business and law. Why? Because that’s the kind of liberal education that makes for an informed and intelligent citizenry, without which our democracy is but empty talk, and our lives nothing but slavery to the marketplace.
  • Maybe this is not how education works in the US. I thought that general (or compulsory) education (ie. up to high school) is designed to make sure that citizens in a democratic country can perform their civil duties. A balanced and well-rounded education, which includes a healthy mixture of science and humanities, is indeed very important for this purpose. However, college-level education is for personal growth and therefore the person must have a large say about what kind of classes he or she chooses to take. I am disturbed by Massimo's hospital analogy. Students are not ill. They don't go to college to be cured, or to be good citizens. They go to college to learn things that *they* want to learn. Patients are passive. Students are not.I agree that students typically do not know what kind of education is good for them. But who does?
  • students do have a saying in their education. They pick their major, and there are electives. But I object to the idea that they can customize their major any way they want. That assumes they know what the best education for them is, they don't. That's the point of education.
  • The students are in your class to get a good grade, any learning that takes place is purely incidental. Those good grades will look good on their transcript and might convince a future employer that they are smart and thus are worth paying more.
  • I don't know what the dollar to GPA exchange rate is these days, but I don't doubt that there is one.
  • Just how many of your students do you think will remember the extensive complex jargon of philosophy more than a couple of months after they leave your classroom?
  • and our lives nothing but slavery to the marketplace.We are there. Welcome. Where have you been all this time? In a capitalistic/plutocratic society money is power (and free speech too according to the supreme court). Money means a larger/better house/car/clothing/vacation than your neighbor and consequently better mating opportunities. You can mostly blame the women for that one I think just like the peacock's tail.
  • If a student of surgery fails to learn they might maim, kill or cripple someone. If an engineer of airplanes fails to learn they might design a faulty aircraft that fails and kills people. If a student of chemistry fails to learn they might design a faulty drug with unintended and unfortunate side effects, but what exactly would be the harm if a student of philosophy fails to learn Aristotle had to say about elements or Plato had to say about perfect forms? These things are so divorced from people's everyday activities as to be rendered all but meaningless.
  • human knowledge grows by leaps and bounds every day, but human brain capacity does not, so the portion of human knowledge you can personally hold gets smaller by the minute. Learn (and remember) as much as you can as fast as you can and you will still lose ground. You certainly have your work cut out for you emphasizing the importance of Thales in the Age of Twitter and whatever follows it next year.
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Arsenic bacteria - a post-mortem, a review, and some navel-gazing | Not Exactly Rocket ... - 0 views

blogs.discovermagazine.com/...a-review-and-some-navel-gazing Journalism Ethics Science Biology
shared by Weiye Loh on 11 Dec 10 - No Cached
  • 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.
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Science Warriors' Ego Trips - The Chronicle Review - The Chronicle of Higher Education - 0 views

chronicle.com/...65186 Science Philosophy
shared by Weiye Loh on 06 May 10 - Cached
  • 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.
  • Weiye Loh on 06 May 10
     
    April 25, 2010 Science Warriors' Ego Trips
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The Decline Effect and the Scientific Method : The New Yorker - 0 views

www.newyorker.com/...101213fa_fact_lehrer Truth Science Evidence Data
shared by Weiye Loh on 05 Jan 11 - No Cached
  • 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.
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The Mysterious Decline Effect | Wired Science | Wired.com - 0 views

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  • 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.
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Rationally Speaking: The problem of replicability in science - 0 views

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  • The problem of replicability in science from xkcdby Massimo Pigliucci
  • In recent months much has been written about the apparent fact that a surprising, indeed disturbing, number of scientific findings cannot be replicated, or when replicated the effect size turns out to be much smaller than previously thought.
  • Arguably, the recent streak of articles on this topic began with one penned by David Freedman in The Atlantic, and provocatively entitled “Lies, Damned Lies, and Medical Science.” In it, the major character was John Ioannidis, the author of some influential meta-studies about the low degree of replicability and high number of technical flaws in a significant portion of published papers in the biomedical literature.
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  • As Freedman put it in The Atlantic: “80 percent of non-randomized studies (by far the most common type) turn out to be wrong, as do 25 percent of supposedly gold-standard randomized trials, and as much as 10 percent of the platinum-standard large randomized trials.” Ioannidis himself was quoted uttering some sobering words for the medical community (and the public at large): “Science is a noble endeavor, but it’s also a low-yield endeavor. I’m not sure that more than a very small percentage of medical research is ever likely to lead to major improvements in clinical outcomes and quality of life. We should be very comfortable with that fact.”
  • Julia and I actually addressed this topic during a Rationally Speaking podcast, featuring as guest our friend Steve Novella, of Skeptics’ Guide to the Universe and Science-Based Medicine fame. But while Steve did quibble with the tone of the Atlantic article, he agreed that Ioannidis’ results are well known and accepted by the medical research community. Steve did point out that it should not be surprising that results get better and better as one moves toward more stringent protocols like large randomized trials, but it seems to me that one should be surprised (actually, appalled) by the fact that even there the percentage of flawed studies is high — not to mention the fact that most studies are in fact neither large nor properly randomized.
  • The second big recent blow to public perception of the reliability of scientific results is an article published in The New Yorker by Jonah Lehrer, entitled “The truth wears off.” Lehrer also mentions Ioannidis, but the bulk of his essay is about findings in psychiatry, psychology and evolutionary biology (and even in research on the paranormal!).
  • In these disciplines there are now several documented cases of results that were initially spectacularly positive — for instance the effects of second generation antipsychotic drugs, or the hypothesized relationship between a male’s body symmetry and the quality of his genes — that turned out to be increasingly difficult to replicate over time, with the original effect sizes being cut down dramatically, or even disappearing altogether.
  • As Lehrer concludes at the end of his article: “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.”
  • None of this should actually be particularly surprising to any practicing scientist. If you have spent a significant time of your life in labs and reading the technical literature, you will appreciate the difficulties posed by empirical research, not to mention a number of issues such as the fact that few scientists ever actually bother to replicate someone else’s results, for the simple reason that there is no Nobel (or even funded grant, or tenured position) waiting for the guy who arrived second.
  • n the midst of this I was directed by a tweet by my colleague Neil deGrasse Tyson (who has also appeared on the RS podcast, though in a different context) to a recent ABC News article penned by John Allen Paulos, which meant to explain the decline effect in science.
  • Paulos’ article is indeed concise and on the mark (though several of the explanations he proposes were already brought up in both the Atlantic and New Yorker essays), but it doesn’t really make things much better.
  • Paulos suggests that one explanation for the decline effect is the well known statistical phenomenon of the regression toward the mean. This phenomenon is responsible, among other things, for a fair number of superstitions: you’ve probably heard of some athletes’ and other celebrities’ fear of being featured on the cover of a magazine after a particularly impressive series of accomplishments, because this brings “bad luck,” meaning that the following year one will not be able to repeat the performance at the same level. This is actually true, not because of magical reasons, but simply as a result of the regression to the mean: extraordinary performances are the result of a large number of factors that have to line up just right for the spectacular result to be achieved. The statistical chances of such an alignment to repeat itself are low, so inevitably next year’s performance will likely be below par. Paulos correctly argues that this also explains some of the decline effect of scientific results: the first discovery might have been the result of a number of factors that are unlikely to repeat themselves in exactly the same way, thus reducing the effect size when the study is replicated.
  • nother major determinant of the unreliability of scientific results mentioned by Paulos is the well know problem of publication bias: crudely put, science journals (particularly the high-profile ones, like Nature and Science) are interested only in positive, spectacular, “sexy” results. Which creates a powerful filter against negative, or marginally significant results. What you see in science journals, in other words, isn’t a statistically representative sample of scientific results, but a highly biased one, in favor of positive outcomes. No wonder that when people try to repeat the feat they often come up empty handed.
  • A third cause for the problem, not mentioned by Paulos but addressed in the New Yorker article, is the selective reporting of results by scientists themselves. This is essentially the same phenomenon as the publication bias, except that this time it is scientists themselves, not editors and reviewers, who don’t bother to submit for publication results that are either negative or not strongly conclusive. Again, the outcome is that what we see in the literature isn’t all the science that we ought to see. And it’s no good to argue that it is the “best” science, because the quality of scientific research is measured by the appropriateness of the experimental protocols (including the use of large samples) and of the data analyses — not by whether the results happen to confirm the scientist’s favorite theory.
  • The conclusion of all this is not, of course, that we should throw the baby (science) out with the bath water (bad or unreliable results). But scientists should also be under no illusion that these are rare anomalies that do not affect scientific research at large. Too much emphasis is being put on the “publish or perish” culture of modern academia, with the result that graduate students are explicitly instructed to go for the SPU’s — Smallest Publishable Units — when they have to decide how much of their work to submit to a journal. That way they maximize the number of their publications, which maximizes the chances of landing a postdoc position, and then a tenure track one, and then of getting grants funded, and finally of getting tenure. The result is that, according to statistics published by Nature, it turns out that about ⅓ of published studies is never cited (not to mention replicated!).
  • “Scientists these days tend to keep up the 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. ... We speak piously of taking measurements and making small studies that will ‘add another brick to the temple of science.’ Most such bricks lie around the brickyard.”
    • Weiye Loh
      Weiye Loh on 05 Jan 11
       
      Written by John Platt in a "Science" article published in 1964
  • Most damning of all, however, is the potential effect that all of this may have on science’s already dubious reputation with the general public (think evolution-creation, vaccine-autism, or climate change)
  • “If we don’t tell the public about these problems, then we’re no better than non-scientists who falsely claim they can heal. If the drugs don’t work and we’re not sure how to treat something, why should we claim differently? Some fear that there may be less funding because we stop claiming we can prove we have miraculous treatments. But if we can’t really provide those miracles, how long will we be able to fool the public anyway? The scientific enterprise is probably the most fantastic achievement in human history, but that doesn’t mean we have a right to overstate what we’re accomplishing.”
  • Joseph T. Lapp said... But is any of this new for science? Perhaps science has operated this way all along, full of fits and starts, mostly duds. How do we know that this isn't the optimal way for science to operate?My issues are with the understanding of science that high school graduates have, and with the reporting of science.
    • Weiye Loh
      Weiye Loh on 05 Jan 11
       
      It's the media at fault again.
  • What seems to have emerged in recent decades is a change in the institutional setting that got science advancing spectacularly since the establishment of the Royal Society. Flaws in the system such as corporate funded research, pal-review instead of peer-review, publication bias, science entangled with policy advocacy, and suchlike, may be distorting the environment, making it less suitable for the production of good science, especially in some fields.
  • Remedies should exist, but they should evolve rather than being imposed on a reluctant sociological-economic science establishment driven by powerful motives such as professional advance or funding. After all, who or what would have the authority to impose those rules, other than the scientific establishment itself?
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Religion: Faith in science : Nature News - 0 views

www.nature.com/...470323a.html Science Religion Faith Funding Academic Academic Research
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  • The Templeton Foundation claims to be a friend of science. So why does it make so many researchers uneasy?
  • With a current endowment estimated at US$2.1 billion, the organization continues to pursue Templeton's goal of building bridges between science and religion. Each year, it doles out some $70 million in grants, more than $40 million of which goes to research in fields such as cosmology, evolutionary biology and psychology.
  • however, many scientists find it troubling — and some see it as a threat. Jerry Coyne, an evolutionary biologist at the University of Chicago, Illinois, calls the foundation "sneakier than the creationists". Through its grants to researchers, Coyne alleges, the foundation is trying to insinuate religious values into science. "It claims to be on the side of science, but wants to make faith a virtue," he says.
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  • But other researchers, both with and without Templeton grants, say that they find the foundation remarkably open and non-dogmatic. "The Templeton Foundation has never in my experience pressured, suggested or hinted at any kind of ideological slant," says Michael Shermer, editor of Skeptic, a magazine that debunks pseudoscience, who was hired by the foundation to edit an essay series entitled 'Does science make belief in God obsolete?'
  • The debate highlights some of the challenges facing the Templeton Foundation after the death of its founder in July 2008, at the age of 95.
  • With the help of a $528-million bequest from Templeton, the foundation has been radically reframing its research programme. As part of that effort, it is reducing its emphasis on religion to make its programmes more palatable to the broader scientific community. Like many of his generation, Templeton was a great believer in progress, learning, initiative and the power of human imagination — not to mention the free-enterprise system that allowed him, a middle-class boy from Winchester, Tennessee, to earn billions of dollars on Wall Street. The foundation accordingly allocates 40% of its annual grants to programmes with names such as 'character development', 'freedom and free enterprise' and 'exceptional cognitive talent and genius'.
  • Unlike most of his peers, however, Templeton thought that the principles of progress should also apply to religion. He described himself as "an enthusiastic Christian" — but was also open to learning from Hinduism, Islam and other religious traditions. Why, he wondered, couldn't religious ideas be open to the type of constructive competition that had produced so many advances in science and the free market?
  • That question sparked Templeton's mission to make religion "just as progressive as medicine or astronomy".
  • Early Templeton prizes had nothing to do with science: the first went to the Catholic missionary Mother Theresa of Calcutta in 1973.
  • By the 1980s, however, Templeton had begun to realize that fields such as neuroscience, psychology and physics could advance understanding of topics that are usually considered spiritual matters — among them forgiveness, morality and even the nature of reality. So he started to appoint scientists to the prize panel, and in 1985 the award went to a research scientist for the first time: Alister Hardy, a marine biologist who also investigated religious experience. Since then, scientists have won with increasing frequency.
  • "There's a distinct feeling in the research community that Templeton just gives the award to the most senior scientist they can find who's willing to say something nice about religion," says Harold Kroto, a chemist at Florida State University in Tallahassee, who was co-recipient of the 1996 Nobel Prize in Chemistry and describes himself as a devout atheist.
  • Yet Templeton saw scientists as allies. They had what he called "the humble approach" to knowledge, as opposed to the dogmatic approach. "Almost every scientist will agree that they know so little and they need to learn," he once said.
  • Templeton wasn't interested in funding mainstream research, says Barnaby Marsh, the foundation's executive vice-president. Templeton wanted to explore areas — such as kindness and hatred — that were not well known and did not attract major funding agencies. Marsh says Templeton wondered, "Why is it that some conflicts go on for centuries, yet some groups are able to move on?"
  • Templeton's interests gave the resulting list of grants a certain New Age quality (See Table 1). For example, in 1999 the foundation gave $4.6 million for forgiveness research at the Virginia Commonwealth University in Richmond, and in 2001 it donated $8.2 million to create an Institute for Research on Unlimited Love (that is, altruism and compassion) at Case Western Reserve University in Cleveland, Ohio. "A lot of money wasted on nonsensical ideas," says Kroto. Worse, says Coyne, these projects are profoundly corrupting to science, because the money tempts researchers into wasting time and effort on topics that aren't worth it. If someone is willing to sell out for a million dollars, he says, "Templeton is there to oblige him".
  • At the same time, says Marsh, the 'dean of value investing', as Templeton was known on Wall Street, had no intention of wasting his money on junk science or unanswerables such as whether God exists. So before pursuing a scientific topic he would ask his staff to get an assessment from appropriate scholars — a practice that soon evolved into a peer-review process drawing on experts from across the scientific community.
  • Because Templeton didn't like bureaucracy, adds Marsh, the foundation outsourced much of its peer review and grant giving. In 1996, for example, it gave $5.3 million to the American Association for the Advancement of Science (AAAS) in Washington DC, to fund efforts that work with evangelical groups to find common ground on issues such as the environment, and to get more science into seminary curricula. In 2006, Templeton gave $8.8 million towards the creation of the Foundational Questions Institute (FQXi), which funds research on the origins of the Universe and other fundamental issues in physics, under the leadership of Anthony Aguirre, an astrophysicist at the University of California, Santa Cruz, and Max Tegmark, a cosmologist at the Massachusetts Institute of Technology in Cambridge.
  • But external peer review hasn't always kept the foundation out of trouble. In the 1990s, for example, Templeton-funded organizations gave book-writing grants to Guillermo Gonzalez, an astrophysicist now at Grove City College in Pennsylvania, and William Dembski, a philosopher now at the Southwestern Baptist Theological Seminary in Fort Worth, Texas. After obtaining the grants, both later joined the Discovery Institute — a think-tank based in Seattle, Washington, that promotes intelligent design. Other Templeton grants supported a number of college courses in which intelligent design was discussed. Then, in 1999, the foundation funded a conference at Concordia University in Mequon, Wisconsin, in which intelligent-design proponents confronted critics. Those awards became a major embarrassment in late 2005, during a highly publicized court fight over the teaching of intelligent design in schools in Dover, Pennsylvania. A number of media accounts of the intelligent design movement described the Templeton Foundation as a major supporter — a charge that Charles Harper, then senior vice-president, was at pains to deny.
  • Some foundation officials were initially intrigued by intelligent design, Harper told The New York Times. But disillusionment set in — and Templeton funding stopped — when it became clear that the theory was part of a political movement from the Christian right wing, not science. Today, the foundation website explicitly warns intelligent-design researchers not to bother submitting proposals: they will not be considered.
  • Avowedly antireligious scientists such as Coyne and Kroto see the intelligent-design imbroglio as a symptom of their fundamental complaint that religion and science should not mix at all. "Religion is based on dogma and belief, whereas science is based on doubt and questioning," says Coyne, echoing an argument made by many others. "In religion, faith is a virtue. In science, faith is a vice." The purpose of the Templeton Foundation is to break down that wall, he says — to reconcile the irreconcilable and give religion scholarly legitimacy.
  • Foundation officials insist that this is backwards: questioning is their reason for being. Religious dogma is what they are fighting. That does seem to be the experience of many scientists who have taken Templeton money. During the launch of FQXi, says Aguirre, "Max and I were very suspicious at first. So we said, 'We'll try this out, and the minute something smells, we'll cut and run.' It never happened. The grants we've given have not been connected with religion in any way, and they seem perfectly happy about that."
  • John Cacioppo, a psychologist at the University of Chicago, also had concerns when he started a Templeton-funded project in 2007. He had just published a paper with survey data showing that religious affiliation had a negative correlation with health among African-Americans — the opposite of what he assumed the foundation wanted to hear. He was bracing for a protest when someone told him to look at the foundation's website. They had displayed his finding on the front page. "That made me relax a bit," says Cacioppo.
  • Yet, even scientists who give the foundation high marks for openness often find it hard to shake their unease. Sean Carroll, a physicist at the California Institute of Technology in Pasadena, is willing to participate in Templeton-funded events — but worries about the foundation's emphasis on research into 'spiritual' matters. "The act of doing science means that you accept a purely material explanation of the Universe, that no spiritual dimension is required," he says.
  • It hasn't helped that Jack Templeton is much more politically and religiously conservative than his father was. The foundation shows no obvious rightwards trend in its grant-giving and other activities since John Templeton's death — and it is barred from supporting political activities by its legal status as a not-for-profit corporation. Still, many scientists find it hard to trust an organization whose president has used his personal fortune to support right-leaning candidates and causes such as the 2008 ballot initiative that outlawed gay marriage in California.
  • Scientists' discomfort with the foundation is probably inevitable in the current political climate, says Scott Atran, an anthropologist at the University of Michigan in Ann Arbor. The past 30 years have seen the growing power of the Christian religious right in the United States, the rise of radical Islam around the world, and religiously motivated terrorist attacks such as those in the United States on 11 September 2001. Given all that, says Atran, many scientists find it almost impossible to think of religion as anything but fundamentalism at war with reason.
  • the foundation has embraced the theme of 'science and the big questions' — an open-ended list that includes topics such as 'Does the Universe have a purpose?'
  • Towards the end of Templeton's life, says Marsh, he became increasingly concerned that this reaction was getting in the way of the foundation's mission: that the word 'religion' was alienating too many good scientists.
  • The peer-review and grant-making system has also been revamped: whereas in the past the foundation ran an informal mix of projects generated by Templeton and outside grant seekers, the system is now organized around an annual list of explicit funding priorities.
  • The foundation is still a work in progress, says Jack Templeton — and it always will be. "My father believed," he says, "we were all called to be part of an ongoing creative process. He was always trying to make people think differently." "And he always said, 'If you're still doing today what you tried to do two years ago, then you're not making progress.'" 
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