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Showing newest posts with label science. Show older posts
Showing newest posts with label science. Show older posts

Sunday, September 12, 2010

Subway science map

Totally, incredibly, awesomely cool, in a totally geeky way.

BERJAYA
click to embiggen

The Original Post (with commentary)

Also check out the Periodic Table of Irrational Nonsense:

BERJAYA
click to embiggen

(via Ken)

Tuesday, July 27, 2010

Scientific naturalism

Tim Kowal responds to my criticism of his post chiding atheists' "intellectual procrastination":
We are certain some element or elements of a theory — a set of statements about the world — are false if the theory entails false statements about observation.
There cannot be any "true" statement about reality once one rejects the concept that truth can transcends the empirical world. You are correct that there are as many models of truth and reality as there are religions--more, even. This is a debate for the respective adherents to those models. But to reject any truth that is not empirically observable is to cut oneself off at the knees. At the very least, atheists must posit that objects in the world have causal relationships with one another, that the future will resemble the past, and so on. Religion is simply an organized, systematic way to organize these transcendental truths.

Atheists certainly don't reject causation and induction, but they don't give an account for how they can know it. They simply refuse to acknowledge the transcendental truths they rely upon. This is disingenuous.
I'm never encouraged when readers cannot read and understand simple declarative sentences in the English language. But after blogging for more than 30 months and discussing religion and philosophy on the internet for a decade, I'm rarely surprised. Much as I dislike repeating myself, I will do so. Even if it were true (which it's not) that "Atheists... don't give an account of how they can know" about causation an induction, it is necessary to acknowledge that we do not have such an account before we can begin to create one. Organizing wildly contradictory religious "models" — models that give no account of knowledge more sophisticated than an invisible sky-fairy magically putting ideas into our heads — in some systematic way and leaving the resolution of those contradictions to some vague debate on unspecified grounds just avoids beginning that search for truth. Even if atheism were to bring nothing at all to the philosophical table, it would be rational and sensible to reject religious thought and admit profound ignorance. If after millennia they are unable to give us anything at all better than magical sky-fairies and consensus by the sword, then we are rationally entitled to explicitly acknowledge we are starting from nothing at all.

But of course there is something. There were atheists before scientific naturalism, but it is no surprise that atheism has flourished under scientific naturalism, which does not just recognize the failures and vacuity of what passes for "epistemology" in religion but gives us a powerful way of explaining features of the world both gross and subtle in a more sophisticated way than invoking magic.

Even an inattentive reader should note the glaring contradiction in Kowal's comment: in almost the same breath he complains that atheists "don't give an account" of knowledge while also undermining the account we do give, i.e. empiricism. Just this discrepancy alone forces the reader to choose which of two uncomfortable interpretations is the most charitable: either Kowal is insane, he is simply too stupid to detect this rather obvious contradiction, or he is intentionally trying to deceive his readers. If he does not like the epistemic account that scientific naturalism does in fact give, let him say so: to critique an account he does not acknowledge the existence of too greatly shocks the mind of those unpracticed in religious doublethink and cognitive dissonance.

Worse yet, Kowal must reach decades back to the beginning of the 20th century (or perhaps to the middle of the 18th) to find a natural epistemology he can criticize with cognitive abilities deficient in competence or honesty.

It is simply false that modern scientific naturalism — the sort of naturalism practiced for centuries by actual scientists and explicitly described by at least some philosophers of science for decades — "reject[s] any truth that is not empirically observable." Even the most misguided of the logical positivists and naive empiricists would not have gone so far: even they admitted truths derived from an empirical foundation, even if those derived truths were themselves not empirically observable.

But of course problems with the naive empiricism of the 20th century were anticipated in the 18th by David Hume (objections that Kowal mentions without crediting Hume, an atheist). We cannot directly observe either causality or consistency over time, and much to the dismay of the naive empiricists, we cannot rigorously deduce these features of the world from the directly observable evidence. (There are a lot of other problems with logical positivism and naive empiricism, not the least of which is that the systems themselves are neither observable nor deducible from observation.)

Philosophers are little better than theologians, and it is unsurprising that anyone who reads only philosophy might think that this naive view constitutes the core of scientific thought. There are intelligent philosophers who have propounded more sophisticated concepts, but their work is buried in a mound of bullshit exceeded in scope and elaboration only by theology. The atheist criticism that finding the diamonds of theological sensibility is simply too difficult to be worth the trouble applies equally to philosophy*. Kowal's misunderstanding of scientific naturalism is excusable and correctable in a way that his "bad food and not enough of it" contradiction about the very existence of a natural epistemology is not.

*I have for various reasons decided to go to college in my old age. Despite my interest, I've rejected philosophy as a subject of academic study: the bullshit to sense ratio is too high for me to have any hope of making a meaningful contribution to anything but the edifice of bullshit itself. There is too little bullshit in science for a person to make a substantial contribution on the basis of only clarity and honesty: science demands competence, competence I lack both the time and alas! natural talent to develop. Economics and political science seem just about right: enough bullshit that an honest man of mediocre competence can make a contribution; enough sense (I hope) that the contribution can be meaningful.

Modern scientific naturalism shares two features of theology. First, both systems make guesses about how the world might be. We do not directly know the world is causal, and we cannot (as we have discovered) deduce the world is causal from what we do directly know. In order to talk about causality, we have to introduce the concept without knowledge or even any real confidence as whether it's actually true. Second, despite their protestations of universal truth, scientific naturalism and theology are dynamic: one way or another, when these systems fail to correspond to the world of experience, both actually change.

But — and this is a very substantial but indeed — from these similarities scientific naturalism departs radically from religious faith. In religious faith, our core guesses about God (and thus God's world) are upheld "come what may". Our articles of faith are utterly immune from change (until an authority changes them). Anything and everything else might change — we might even deny experience itself (who are you going to believe? the Pope God, or your lying eyes?) — but our articles of faith are immune from public criticism.

Under scientific naturalism, however, none of our guesses are immune from criticism. Everything is, at least formally, subject to change. Similarly, no authority can declare any guess as immune from change; no one requires the permission of any authority to change any part of any theory.

More importantly, a theory that predicts more (in a specific sense) is, under scientific naturalism, considered worse than a theory that predicts less. A theory that predicts that we will see an object move is worse than a theory that predicts that we will see an object move in a particular direction at a particular velocity. The first theory predicts more: our theory is consistent with observation if we see the object move up or down, left or right, fast or slow; the second theory predicts less: movement in one direction only and at one velocity only.

In contrast, it is no fault under theology if our core faith predicts more or less. God's love is equally compatible with slavery or abolition; His hatred of homosexuality equally compatible with loving gay marriage as with discord; His contempt of women equally compatible with women's demonstrable competence as with their failure; His divine creation equally compatible with life-friendly physical law as with constant miraculous intervention; His intention to create a race of beings to worship and adore Him equally compatible with a 6,000 year-old universe with the Earth at its center as with a universe of such cosmic scale and scope that all of human history is no more significant than the mold in my shower is to all of terrestrial civilization.

Our scientific naturalistic theories about the world are true because they explain and predict this world; they are valuable because they predict only this world. Theology is compatible with any old world we might find ourselves in: change the laws of physics, remove them altogether, transform billions of light years of galaxies, clusters and superclusters to a uniform distribution of a hundred stars or even lanterns in a quintessential firmament, chop scores of elements from the periodic table and rearrange them with a throw of the dice, and not one word of the vast edifice of theological bullshit created over the last ten thousand years would have to change.

Kowal admits that theology and religion lack any epistemic system. In his own words, all we can do is organize and systematize all the contradictory models and theories about the world: we can do nothing to choose between these theories other than a handwaving mention of some vague debate (a "debate" that throughout history has all too often been conducted through the media of murder, rape, slavery, torture, conquest, oppression and genocide). Indeed scientific naturalism has developed a way to choose between these models and — while Kowal complains in that we have no way to choose — he complains in the same breath that our epistemic system is fatally flawed because it does choose, and it chooses against the arrant superstitions and vacuous bullshit of theology.

When Glendower famously boasted, "I can call spirits from the vasty deep," Hotspur astutely retorted, "Why, so can I, or so can any man; But will they come when you do call for them?" Answers are easy: I can answer any question, or so can any man; but are they true? Theologians can indeed answer any question, but we suffer not from a lack of answers but from a surfeit. We know that scientific materialism can not just answer some questions, but we can know that those answers and only those answers are true. If, by applying some distinction we are left with some questions entirely unanswered, with every candidate so far rejection, that is but a small price to pay for knowing that other answers really are true. Answers are easy: we can always think up more answers and test them out.

It would of course be disingenuous or at least incomplete to extol the virtues of scientific naturalism without mentioning legitimate philosophical objections.

Science is, of course, a human endeavor, and its pursuit susceptible to the ordinary intellectual and moral vices typical of human beings. Our scientific knowledge is dependent on what we choose to study, the kinds of knowledge we choose to pursue, and our answers are dependent on the questions we choose to ask. Science is no universal panacea, a machine we can put questions into and be confident of always or even often get true answers. The best we can say about science is that sometimes it makes some distinctions. But just sometimes is incomparably better than never, and that sometimes is on the basis of ordinary logical thought and the evidence of our senses, not the pronouncements of ridiculous men in silly hats or the elimination of dissent by the sword and the prison cell.

Strictly speaking, scientific naturalism does not separate theories into true and false, it separates theories into definitely false, not definitely false and bullshit: "When you have eliminated the impossible, whatever remains, however improbable, must be the truth." We cannot know the theory of universal gravitation with the certainty we know that "there are infinitely many prime numbers" is a theorem of the axioms of arithmetic. If for this reason you don't want to label scientific naturalism as knowledge, so much worse for your view of knowledge. When you can demonstrate the truth of General Relativity or Quantum Mechanics with deductive certainty, let me know. Until then, I'll happily trade certainty of nothing for confidence in not just something but quite a lot while you play solipsistic games you could pursue without distraction if you put out your eyes and stopped up your ears.

We cannot apply scientific naturalism to scientific naturalism without circularity. But scientific naturalism as a method is not itself a theory about the world; it is simply a language game we play, a game we play not because we can somehow prove it itself is "true" but because we find it useful, a utility that — because we are uninterested in the what appears to be its the sole utility for justifying abominable behavior — that religion has never and apparently cannot provide.

Indeed it is the theologians whom we must accuse of intellectual procrastination. They have, to be sure, been diligent about providing answers, but after ten thousand years we are still waiting for them to give us a way — any way, however imperfect, that appeals not to our prejudice but our reason — to separate the the meaningful answers from the bullshit and the true answers from the false.

Saturday, July 24, 2010

Evolution is hard!

A really good article on evolution by the inestimable PZ Myers: It's more than genes, it's networks and systems:
What's left out in the 101 story, and in creationist tales, is that: evolution is about populations, so many changes go on in parallel; selectable traits are usually the product of networks of genes, so there are rarely single alleles that can be categorized as the effector of change; and genes and gene networks are plastic or responsive to the environment. All of these complications make the actual story more complicated and interesting, and also, perhaps to your surprise, make evolutionary change faster and more powerful.
If biologists can figure out this:

BERJAYA

and hundreds of other pathways like it, then there's simply no excuse for economists to complain about complexity.

Saturday, May 08, 2010

Five cheap magic tricks

5 Cheap Magic Tricks Behind Every Psychic:
  1. Don't strain credulity
  2. Stick with one trick
  3. Have more than one way to do the same trick
  4. Tell everyone they can do it
  5. Include a disclaimer

Tuesday, May 04, 2010

Selection-against

I suspect that not even evolutionary biologists pay enough attention to the fact that in any evolutionary process, selection is a fundamentally negative process. Natural selection in evolution does not select for, it selects against.

The usual narrative of evolution is that some heritable variation (such as a mutation) gives an individual a reproductive advantage. The individual's descendants inherit that advantageous variation, and because it is indeed advantageous, the variation comes to dominate the gene pool of the population. Not a bad story, and it gets the gist across, but it's missing an important component of the story: what precisely do we mean by "reproductive advantage"? The straightforward intuitive meaning isn't bad, but it misses important subtleties, especially when we want to intelligently direct evolutionary processes, such as social evolution.

A more accurate and direct narrative of evolution is that there is no selection-for, there is only selection-against. Some individuals have — for various reasons — a reproductive disadvantage; they fail to create descendants to inherit their individual variations. A specific variation can confer a reproductive advantage only indirectly, by changing the environment so that lacking the specific variation directly entails a disadvantage. A variation dominates the population's gene pool only when its competitors are selected against.

The selection-against narrative makes the creationist objection that, "If human beings are descended from monkeys, why are there still monkeys?" more obviously fallacious, A naive or superficial grasp of the selection-for narrative makes this objection plausible, but the selection-against narrative makes the answer more obvious: because nature did not select against monkeys nor did nature select against humans; nature selected against that which we do not see.

Another somewhat less naive example is Jerry Fodor and Massimo Piattelli-Palmarini's book, What Darwin Got Wrong (reviewed by Ned Block and Philip Kitcher as well as PZ Myers). I don't want to excuse the authors — they're professional intellectuals, and they shouldn't allow themselves to be misled by superficialities — but it seems clear to me that a narrative of negative selection would make their thesis more obviously incorrect.

Fodor and Piattelli-Palmarini argue that
Darwinists say that evolution is explained by the selection of phenotypic traits by environmental filters. But the effects of endogenous structure can wreak havoc with this theory. Consider the following case: traits t1 and t2 are endogenously linked in such a way that if a creature has one, it has both. Now the core of natural selection is the claim that phenotypic traits are selected for their adaptivity, that is, for their effect on fitness. But it is perfectly possible that one of two linked traits is adaptive but the other isn't; having one of them affects fitness but having the other one doesn't. So one is selected for and the other "free-rides" on it.
The follow this critique up with a deeper philosophical critique. As Block and Kitcher describe
... Fodor and Piattelli-Palmarini think that problems about selection-for are omnipresent... [b]ecause they envisage a vast space of properties and expect proponents of natural selection to discriminate among all the rivals. Not only is there a property of being-a-melanic-moth, there is also a property of being-a-melanic-moth-and-smaller-than-Manhattan. These properties are not only correlated in the world’s actual moth populations, they are correlated universally. Maybe it is impossible, even with the most rarefied genomic technology, to build a moth bigger than Manhattan. If so, the correlation between these properties could not be broken. How then could there be a sense in which one of the properties—being-a-melanic-moth—rather than the other—being-a-melanic-moth-and-smaller-than-Manhattan—caused the increased reproductive success?
Block and Kitcher would have us simply shrug off this object (nobody really cares whether nature is selecting for being-a-melanic-moth or being-a-melanic-moth-and-smaller-than-Manhattan), but even a definite error can be an opportunity to learn.

Block and Kitcher accept the narrative of selection-for, but they seem more flexible about its interpretation.
Natural selection, soberly presented, is about differential success in leaving descendants. If a variant trait (say, a long neck or reduced forelimbs) causes its bearer to have a greater number of offspring, and if the variant is heritable, then the proportion of organisms with the variant trait will increase in subsequent generations. To say that there is “selection for” a trait is thus to make a causal claim: having the trait causes greater reproductive success.
But a narrative of selection-against makes Fodor and Piattelli-Palmarini argument more obviously invalid. We don't have to distinguish between selecting for being-a-melanic-moth and being-a-melanic-moth-and-smaller-than-Manhattan, because nature is not selecting for anything. Rather, nature in this case is selecting against getting eaten by a bird (before leaving descendants). It happens to be the case that being-a-melanic-moth (or perhaps being-a-melanic-moth-and-smaller-than-Manhattan) exempted individuals from this selection-against.

Fodor and Piattelli-Palmarini philosophical critique just doesn't apply to a selection-against narrative. A selection-for narrative makes what is being selected for ambiguous; it's easy to see, however, in a selection-against narrative that nature is selecting against being-eaten-by-a-bird and being-eaten-by-a-bird-and-smaller-than-Manhattan (and being-eaten-by-a-bird-and- anything else). There's no ambiguity we have to shrug off.

If you want to understand why different outcomes occur in different evolutionary scenarios, look for differences in the negative selection pressures.

Consider three modes of negative selection in a population with a fixed food source. There's never enough food for all the individuals in the population. Some individuals will starve (before they reproduce): nature will select against those individuals and their heritable characteristics. Under ordinary circumstances, without any relevant variation, this selection is random: some individuals are just "unlucky" and don't happen to find enough food. But random selection is still selection, and over time it will from time to time happen to be the case by pure chance that all or most of the individuals with some variation will happen to starve by accident. Thus the competing variation(s) will dominate the population even though there is no causal reason why the dominant variation is "better than" the eliminated variation. Selection-for creates a mystery; selection-against provides an explanation: sometimes shit just happens; given enough time, shit will just happen.

In the second case, consider a variation that appears to provide a "reproductive advantage": individuals with this variation are faster, smarter, stronger or whatnot, and more likely to find food... specifically food that, but for their "advantage", other individuals would have eaten. This variation will (probably) dominate the population, but it will do so not because it's advantageous, but because the competing variations have become disadvantageous: individuals without the variation are disproportionally selected against.

Consider the third case: a variation that gives individuals access — even a little — to an alternative food source. In this case, the individuals have a reproductive advantage — if they fail by chance to eat the primary food source, they might not starve and be selected against — but this advantage does not create an immediate corresponding disadvantage in the rest of the population: all the food that was available to individuals without the variation is still available. The outcome in this situation is unclear precisely because we don't know what negative selection-against will actually operate: we have to look more deeply into the situation to identify how nature will select against individuals.

The selection-for narrative does not really distinguish between these situations. Why does some particular trait dominate the population? Because it was selected for. Why was it selected for? Using a selected-for narrative encourages the adaptationist fallacy: we don't know that just because a trait dominates the population it therefore confers a reproductive advantage. We can simply invert the question: the trait was selected for because it wasn't selected against, which encourages the question: why wasn't it selected against. But that's still not quite the correct question. We want to ask: what was selected against, and why? The selection-for narrative leads us down a winding mental path with many pitfalls; the selection-against narrative leads us by the nose to the correct question.

Clarity and precision are important in their own right, but there's a more compelling reason to stress the negative nature of selection in evolutionary processes. Human societies also evolve — dialectical/historical materialism is evolution — and although the low-level mechanisms obviously differ greatly (people do not transmit ideas and beliefs to their children through their DNA) the abstract mechanisms of heritable variation and negative natural selection still apply. If we are to "intelligently" affect our social evolution, we must understand how evolution actually works, and the negative character of selection becomes critically important.

UTA: I don't want to minimize the importance and subtlety of forces other than selection: e.g. mechanisms of heritability and variation as well as accidents large and small. My point is that to understand how selection operates in an evolutionary system, you have to look at what is selected against, not for.

Thursday, April 29, 2010

Political arguments

PZ Myers reviews an interesting study of political argumentation and strategy:
[W]hen you've got an argument going, and one side has the evidence but the other side has an inflexible certainty that the evidence is wrong, the inflexibles tend to distort the normal process of weighing the evidence and drawing reasonable conclusions — they suck in more uncommitted participants (called 'floaters') to their way of thinking, generating more inflexibles, strengthing [sic] the position of the anti-science side, leading to greater attraction to being wrong. The counter-strategy, suggested later in the paper, is to 'get more inflexibles' — winning over floaters so they drift over to your side has little long-term impact, it's far better to build a larger army of forceful advocates for your position.
Myers notes that the paper "is entirely theoretical, based on a mathematical model of human behavior" and therefore of limited usefulness. It's an interesting paper nonetheless, and [from the original paper]
The results she a new but disturbing light on Designing adequate strategies to eventually win public debates. To produce inflexibles in one's own side is thus critical to win a public argument whatever the rigor cost and the associated epistemological paradoxes. At odds, to focus on convincing open-minded agents is useless. In summary, when the scientific evidence is not as strong as claimed, the inflexibles rather than the data are found to drive the collective opinion of the population. Consequences on Designing adequate strategies to win a public debate are discussed.

Friday, April 09, 2010

The stupidest people on the face of the planet

Evolution, Big Bang Polls Omitted From NSF Report:
In an unusual last-minute edit that has drawn flak from the White House and science educators, a federal advisory committee omitted data on Americans' knowledge of evolution and the big bang from a key report. The data shows that Americans are far less likely than the rest of the world to accept that humans evolved from earlier species and that the universe began with a big bang.

They're not surprising findings, but the National Science Board, which oversees the National Science Foundation (NSF), says it chose to leave the section out of the 2010 edition of the biennial Science and Engineering Indicators because the survey questions used to measure knowledge of the two topics force respondents to choose between factual knowledge and religious beliefs.

Wednesday, March 03, 2010

Cargo Cult Science

[This essay has been on the web for a long time, but the various incarnations I link to keep going away. So here's the essay in its entirety. I'll take it down if Dr. Feynman's heirs or estate ask me to.]

Cargo Cult Science
by Richard Feynman

Adapted from the Caltech commencement address given in 1974.

During the Middle Ages there were all kinds of crazy ideas, such as that a piece of rhinoceros horn would increase potency. Then a method was discovered for separating the ideas--which was to try one to see if it worked, and if it didn't work, to eliminate it. This method became organized, of course, into science. And it developed very well, so that we are now in the scientific age. It is such a scientific age, in fact that we have difficulty in understanding how witch doctors could ever have existed, when nothing that they proposed ever really worked--or very little of it did.

But even today I meet lots of people who sooner or later get me into a conversation about UFOS, or astrology, or some form of mysticism, expanded consciousness, new types of awareness, ESP, and so forth. And I've concluded that it's not a scientific world.

Most people believe so many wonderful things that I decided to investigate why they did. And what has been referred to as my curiosity for investigation has landed me in a difficulty where I found so much junk that I'm overwhelmed. First I started out by investigating various ideas of mysticism, and mystic experiences. I went into isolation tanks and got many hours of hallucinations, so I know something about that. Then I went to Esalen, which is a hotbed of this kind of thought (it's a wonderful place; you should go visit there). Then I became overwhelmed. I didn't realize how much there was.

At Esalen there are some large baths fed by hot springs situated on a ledge about thirty feet above the ocean. One of my most pleasurable experiences has been to sit in one of those baths and watch the waves crashing onto the rocky shore below, to gaze into the clear blue sky above, and to study a beautiful nude as she quietly appears and settles into the bath with me.

One time I sat down in a bath where there was a beautiful girl sitting with a guy who didn't seem to know her. Right away I began thinking, "Gee! How am I gonna get started talking to this beautiful nude babe?"

I'm trying to figure out what to say, when the guy says to her, I'm, uh, studying massage. Could I practice on you?"

"Sure," she says. They get out of the bath and she lies down on a massage table nearby.

I think to myself, "What a nifty line! I can never think of anything like that!" He starts to rub her big toe. "I think I feel it, "he says. "I feel a kind of dent--is that the pituitary?"

I blurt out, "You're a helluva long way from the pituitary, man!"

They looked at me, horrified--I had blown my cover--and said, "It's reflexology!"

I quickly closed my eyes and appeared to be meditating.

That's just an example of the kind of things that overwhelm me. I also looked into extrasensory perception and PSI phenomena, and the latest craze there was Uri Geller, a man who is supposed to be able to bend keys by rubbing them with his finger. So I went to his hotel room, on his invitation, to see a demonstration of both mindreading and bending keys. He didn't do any mindreading that succeeded; nobody can read my mind, I guess. And my boy held a key and Geller rubbed it, and nothing happened. Then he told us it works better under water, and so you can picture all of us standing in the bathroom with the water turned on and the key under it, and him rubbing the key with his finger. Nothing happened. So I was unable to investigate that phenomenon.

But then I began to think, what else is there that we believe? (And I thought then about the witch doctors, and how easy it would have been to cheek on them by noticing that nothing really worked.) So I found things that even more people believe, such as that we have some knowledge of how to educate. There are big schools of reading methods and mathematics methods, and so forth, but if you notice, you'll see the reading scores keep going down--or hardly going up in spite of the fact that we continually use these same people to improve the methods. There's a witch doctor remedy that doesn't work. It ought to be looked into; how do they know that their method should work? Another example is how to treat criminals. We obviously have made no progress--lots of theory, but no progress--in decreasing the amount of crime by the method that we use to handle criminals.

Yet these things are said to be scientific. We study them. And I think ordinary people with commonsense ideas are intimidated by this pseudoscience. A teacher who has some good idea of how to teach her children to read is forced by the school system to do it some other way--or is even fooled by the school system into thinking that her method is not necessarily a good one. Or a parent of bad boys, after disciplining them in one way or another, feels guilty for the rest of her life because she didn't do "the right thing," according to the experts.

So we really ought to look into theories that don't work, and science that isn't science.

I think the educational and psychological studies I mentioned are examples of what I would like to call cargo cult science. In the South Seas there is a cargo cult of people. During the war they saw airplanes land with lots of good materials, and they want the same thing to happen now. So they've arranged to imitate things like runways, to put fires along the sides of the runways, to make a wooden hut for a man to sit in, with two wooden pieces on his head like headphones and bars of bamboo sticking out like antennas--he's the controller--and they wait for the airplanes to land. They're doing everything right. The form is perfect. It looks exactly the way it looked before. But it doesn't work. No airplanes land. So I call these things cargo cult science, because they follow all the apparent precepts and forms of scientific investigation, but they're missing something essential, because the planes don't land.

Now it behooves me, of course, to tell you what they're missing. But it would be just about as difficult to explain to the South Sea Islanders how they have to arrange things so that they get some wealth in their system. It is not something simple like telling them how to improve the shapes of the earphones. But there is one feature I notice that is generally missing in cargo cult science. That is the idea that we all hope you have learned in studying science in school--we never explicitly say what this is, but just hope that you catch on by all the examples of scientific investigation. It is interesting, therefore, to bring it out now and speak of it explicitly. It's a kind of scientific integrity, a principle of scientific thought that corresponds to a kind of utter honesty--a kind of leaning over backwards. For example, if you're doing an experiment, you should report everything that you think might make it invalid--not only what you think is right about it: other causes that could possibly explain your results; and things you thought of that you've eliminated by some other experiment, and how they worked--to make sure the other fellow can tell they have been eliminated.

Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can--if you know anything at all wrong, or possibly wrong--to explain it. If you make a theory, for example, and advertise it, or put it out, then you must also put down all the facts that disagree with it, as well as those that agree with it. There is also a more subtle problem. When you have put a lot of ideas together to make an elaborate theory, you want to make sure, when explaining what it fits, that those things it fits are not just the things that gave you the idea for the theory; but that the finished theory makes something else come out right, in addition.

In summary, the idea is to try to give all of the information to help others to judge the value of your contribution; not just the information that leads to judgment in one particular direction or another.

The easiest way to explain this idea is to contrast it, for example, with advertising. Last night I heard that Wesson oil doesn't soak through food. Well, that's true. It's not dishonest; but the thing I'm talking about is not just a matter of not being dishonest, it's a matter of scientific integrity, which is another level. The fact that should be added to that advertising statement is that no oils soak through food, if operated at a certain temperature. If operated at another temperature, they all will--including Wesson oil. So it's the implication which has been conveyed, not the fact, which is true, and the difference is what we have to deal with.

We've learned from experience that the truth will come out. Other experimenters will repeat your experiment and find out whether you were wrong or right. Nature's phenomena will agree or they'll disagree with your theory. And, although you may gain some temporary fame and excitement, you will not gain a good reputation as a scientist if you haven't tried to be very careful in this kind of work. And it's this type of integrity, this kind of care not to fool yourself, that is missing to a large extent in much of the research in cargo cult science.

A great deal of their difficulty is, of course, the difficulty of the subject and the inapplicability of the scientific method to the subject. Nevertheless it should be remarked that this is not the only difficulty. That's why the planes didn't land--but they don't land.

We have learned a lot from experience about how to handle some of the ways we fool ourselves. One example: Millikan measured the charge on an electron by an experiment with falling oil drops, and got an answer which we now know not to be quite right. It's a little bit off, because he had the incorrect value for the viscosity of air. It's interesting to look at the history of measurements of the charge of the electron, after Millikan. If you plot them as a function of time, you find that one is a little bigger than Millikan's, and the next one's a little bit bigger than that, and the next one's a little bit bigger than that, until finally they settle down to a number which is higher.

Why didn't they discover that the new number was higher right away? It's a thing that scientists are ashamed of--this history--because it's apparent that people did things like this: When they got a number that was too high above Millikan's, they thought something must be wrong--and they would look for and find a reason why something might be wrong. When they got a number closer to Millikan's value they didn't look so hard. And so they eliminated the numbers that were too far off, and did other things like that. We've learned those tricks nowadays, and now we don't have that kind of a disease.

But this long history of learning how not to fool ourselves--of having utter scientific integrity--is, I'm sorry to say, something that we haven't specifically included in any particular course that I know of. We just hope you've caught on by osmosis.

The first principle is that you must not fool yourself--and you are the easiest person to fool. So you have to be very careful about that. After you've not fooled yourself, it's easy not to fool other scientists. You just have to be honest in a conventional way after that.

I would like to add something that's not essential to the science, but something I kind of believe, which is that you should not fool the layman when you're talking as a scientist. I am not trying to tell you what to do about cheating on your wife, or fooling your girlfriend, or something like that, when you're not trying to be a scientist, but just trying to be an ordinary human being. We'll leave those problems up to you and your rabbi. I'm talking about a specific, extra type of integrity that is not lying, but bending over backwards to show how you are maybe wrong, that you ought to have when acting as a scientist. And this is our responsibility as scientists, certainly to other scientists, and I think to laymen.

For example, I was a little surprised when I was talking to a friend who was going to go on the radio. He does work on cosmology and astronomy, and he wondered how he would explain what the applications of this work were. "Well," I said, "there aren't any." He said, "Yes, but then we won't get support for more research of this kind." I think that's kind of dishonest. If you're representing yourself as a scientist, then you should explain to the layman what you're doing--and if they don't want to support you under those circumstances, then that's their decision.

One example of the principle is this: If you've made up your mind to test a theory, or you want to explain some idea, you should always decide to publish it whichever way it comes out. If we only publish results of a certain kind, we can make the argument look good. We must publish both kinds of results.

I say that's also important in giving certain types of government advice. Supposing a senator asked you for advice about whether drilling a hole should be done in his state; and you decide it would be better in some other state. If you don't publish such a result, it seems to me you're not giving scientific advice. You're being used. If your answer happens to come out in the direction the government or the politicians like, they can use it as an argument in their favor; if it comes out the other way, they don't publish it at all. That's not giving scientific advice.

Other kinds of errors are more characteristic of poor science. When I was at Cornell, I often talked to the people in the psychology department. One of the students told me she wanted to do an experiment that went something like this--it had been found by others that under certain circumstances, X, rats did something, A. She was curious as to whether, if she changed the circumstances to Y, they would still do A. So her proposal was to do the experiment under circumstances Y and see if they still did A.

I explained to her that it was necessary first to repeat in her laboratory the experiment of the other person--to do it under condition X to see if she could also get result A, and then change to Y and see if A changed. Then she would know that the real difference was the thing she thought she had under control.

She was very delighted with this new idea, and went to her professor. And his reply was, no, you cannot do that, because the experiment has already been done and you would be wasting time. This was in about 1947 or so, and it seems to have been the general policy then to not try to repeat psychological experiments, but only to change the conditions and see what happens.

Nowadays there's a certain danger of the same thing happening, even in the famous (?) field of physics. I was shocked to hear of an experiment done at the big accelerator at the National Accelerator Laboratory, where a person used deuterium. In order to compare his heavy hydrogen results to what might happen with light hydrogen" he had to use data from someone else's experiment on light hydrogen, which was done on different apparatus. When asked why, he said it was because he couldn't get time on the program (because there's so little time and it's such expensive apparatus) to do the experiment with light hydrogen on this apparatus because there wouldn't be any new result. And so the men in charge of programs at NAL are so anxious for new results, in order to get more money to keep the thing going for public relations purposes, they are destroying--possibly--the value of the experiments themselves, which is the whole purpose of the thing. It is often hard for the experimenters there to complete their work as their scientific integrity demands.

All experiments in psychology are not of this type, however. For example, there have been many experiments running rats through all kinds of mazes, and so on--with little clear result. But in 1937 a man named Young did a very interesting one. He had a long corridor with doors all along one side where the rats came in, and doors along the other side where the food was. He wanted to see if he could train the rats to go in at the third door down from wherever he started them off. No. The rats went immediately to the door where the food had been the time before.

The question was, how did the rats know, because the corridor was so beautifully built and so uniform, that this was the same door as before? Obviously there was something about the door that was different from the other doors. So he painted the doors very carefully, arranging the textures on the faces of the doors exactly the same. Still the rats could tell. Then he thought maybe the rats were smelling the food, so he used chemicals to change the smell after each run. Still the rats could tell. Then he realized the rats might be able to tell by seeing the lights and the arrangement in the laboratory like any commonsense person. So he covered the corridor, and still the rats could tell.

He finally found that they could tell by the way the floor sounded when they ran over it. And he could only fix that by putting his corridor in sand. So he covered one after another of all possible clues and finally was able to fool the rats so that they had to learn to go in the third door. If he relaxed any of his conditions, the rats could tell.

Now, from a scientific standpoint, that is an A-number-one experiment. That is the experiment that makes rat-running experiments sensible, because it uncovers the clues that the rat is really using--not what you think it's using. And that is the experiment that tells exactly what conditions you have to use in order to be careful and control everything in an experiment with rat-running.

I looked into the subsequent history of this research. The next experiment, and the one after that, never referred to Mr. Young. They never used any of his criteria of putting the corridor on sand, or being very careful. They just went right on running rats in the same old way, and paid no attention to the great discoveries of Mr. Young, and his papers are not referred to, because he didn't discover anything about the rats. In fact, he discovered all the things you have to do to discover something about rats. But not paying attention to experiments like that is a characteristic of cargo cult science.

Another example is the ESP experiments of Mr. Rhine, and other people. As various people have made criticisms--and they themselves have made criticisms of their own experiments--they improve the techniques so that the effects are smaller, and smaller, and smaller until they gradually disappear. All the parapsychologists are looking for some experiment that can be repeated--that you can do again and get the same effect--statistically, even. They run a million rats no, it's people this time they do a lot of things and get a certain statistical effect. Next time they try it they don't get it any more. And now you find a man saying that it is anirrelevant demand to expect a repeatable experiment. This is science?

This man also speaks about a new institution, in a talk in which he was resigning as Director of the Institute of Parapsychology. And, in telling people what to do next, he says that one of the things they have to do is be sure they only train students who have shown their ability to get PSI results to an acceptable extent--not to waste their time on those ambitious and interested students who get only chance results. It is very dangerous to have such a policy in teaching--to teach students only how to get certain results, rather than how to do an experiment with scientific integrity.

So I have just one wish for you--the good luck to be somewhere where you are free to maintain the kind of integrity I have described, and where you do not feel forced by a need to maintain your position in the organization, or financial support, or so on, to lose your integrity. May you have that freedom.

Sunday, June 07, 2009

Population and p-value

A week ago, I reported on what seemed to be a case of apparent statistical illiteracy. I have a question for my more statistically sophisticated readers.

The study in question appears to take into account the entire population of all Chrysler dealers. Is the p-value even meaningful in this case? Doesn't the p-value talk about sampling error? Under what circumstances is the p-value meaningful when applied to a population statistic, instead of a sample statistic? Should the population of Chrysler dealers be considered a sample of some larger population?

Monday, June 01, 2009

Lies, damned lies and statistics

Matt Taibbi picks up the story about the study noting:
a highly positive correlation between dealer survival and Clinton donors[.] Granted, that P-Value (0.125) isn’t enough to reject the null hypothesis at 95% confidence intervals (our null hypothesis being that the effect is due to random chance), but a 12.5% chance of a Type I error in rejecting a null hypothesis (false rejection of a true hypothesis) is at least eyebrow raising.

(Taibbi's article is noteworthy for the quip, "Hell, if you want to punish a Chrysler dealer, it seems to me that the best thing to do is force him to keep trying to sell Chryslers.")

Finding such a p-value "eyebrow raising" reveals an inexcusible ignorance of statistics. First of all, the 95% confidence interval is not a high bar or a "gold standard". It is, rather, a relatively low standard, a rule of thumb to indicate whether some correlation is worth investigating further. One in twenty studies where the null hypothesis is actually true will find results good to 95% by chance. That we found a one in eight chance to accept the null hypothesis indicates the correlation is not worth investigating further.

Second, the original authors admit they "matched dealer data against several variables including" (but presumably not limited to) seven specific criteria (party affiliation, donations to three candidates and "other", donation amount and zip code). When you compare several variables, you are doing several studies. Even assuming they calculated only seven different possible correlations, the probability that one of them would have achieved a p-value of 12.5% by chance is extremely high. There are statistical tests, such as Tukey's test, that correctly account for doing multiple comparisons. The authors do not report the results of any multiple comparison analyses.

I realize that even my two-week tutelage under a statistician gives me a better understanding of statistics than most scientists (and perhaps many professional statistiticans), but really, it's completely indefensible and evidence of nothing but statistical illiteracy to see this study as having anything but a completely negative result.

Update: The hypothesis that the Obama administration would favor Clinton donors (p 0.125) more strongly than Obama donors (p 0.509), and treat Republican (p 0.636) and Democratic (p 0.676) donors equally is wildly implausible. It's hard to interpret drawing a causal conclusion as anything but incompetence or dishonesty.

Sunday, May 10, 2009

The Dunning-Kruger effect

Kristjan Wager explains the Dunning-Kruger effect [pdf]:
The "above-average syndrome" is, simply put, that the average person in a given field will believe themselves to be above average. In other words, more people believe themselves above average than really are. Obviously, only 50% can be above average, but there are perhaps 80% who believe they are. ...

Dunning and Kruger looked at the above-average effect, and formed the hypothesis that it takes skills to evaluate yourself. With that hypothesis in mind, they set out to make a number of experiments to either disprove it, or to support it. Since I'm writing about the effect now, you've probably already figured out that their experiments supported their hypothesis.
Read the rest.

Tuesday, May 05, 2009

Accommodation and compatibility

Jerry Coyne's article* has raised the question sharply to our attention: are science and religion compatible?

*I'm a lazy scholar: many of the quotations I use here were first cited in Coyne's article, others were first cited by Larry Moran.

They are definitely compatible in one sense: there are in fact people, such as Francis Collins and Ken Miller, who are both competent scientists and religious believers. But this sense of compatibility is trivial. One could in the same sense say that vigorously prosecuting prostitution is compatible with employing the services of a prostitute, or that denouncing homosexuality as evil and perversion is compatible with fucking a guy in the ass.

Indeed, we could not justly object if Collins, Miller, et al. were to simply say that their religious beliefs were part of their private lives, no one's business but their own.

But they don't so restrict their remarks. They make a stronger claim: that religion and science are compatible at a philosophical level, that one can be both a competent scientist and a religious believer without hypocrisy or cognitive dissonance.

They explicitly disclaim achieving this compatibility by removing god from the domain of the physical world. As Francis Collins writes:
Christianity, for example, professes a God actively involved in creation. Many faiths share the concept of an interactive God, or theism. The opposing belief — the belief in an uninvolved, disinterested God — is deism.
An uninvolved, disinterested god is indeed no god at all.

Just as religious scientists must differentiate religion from no religion at all, they must differentiate science and religion. If religion is the exact same thing as science, if "god" is just an pantheistic metaphor for the laws of physics and/or the universe as a whole, compatibility is trivially reduced to identity. Liking vanilla ice cream might be compatible with liking chocolate ice cream, but it's trivial or vacuous to say that liking vanilla ice cream is compatible with liking vanilla ice cream.

There are only two ways for religion to be both different from and compatible with science: Either religion and science must comprise different kinds of statements, or religion and science must evaluate statements in different ways. Furthermore, if there is any overlap between either the domain of statements or their evaluation, both religion and science must yield the same answer.

One way of achieving this separation is to define religion to comprise normative statements, and science to comprise descriptive statements. This strategy is inept on several points: on what basis should we ascribe ethical authority to mostly white mostly men whose sole claim to expertise is the study of the mythology of an ancient society most modern, civilized people would disapprove of?

But religious scientists take another approach. They ascribe to religion statements about reality that are scientifically unfalsifiable, notably the ascription of teleology to the present state of the universe and human beings. For example, Ken Miller asserts:
In reality, the potential for human existence is woven into every fiber of that universe, from the starry furnaces that forged the carbon upon which life is based, to the chemical bonds that fashioned our DNA from the muck and dust of this rocky planet. Seems like a plan to me.
Miller explicitly claims to describe reality, and describe it as teleological. Miller also states:
We are talking about a being whose intelligence is transcendent; we’re talking about a being who brought the universe into existence, who set up the rules of existence, and uses those rules and that universe and the natural world in which we live to bring about his will.
It is hard to read this statement as not making ontological claims: God is a being, a being with attributes (transcendental intelligence), a being who acts, and a being who acts to deliberate ends. Either Miller is using language entirely metaphorically, writing poetry, not philosophy, or he is speaking in almost exactly the same sense that we would speak of Mt. Rushmore as being the product of a being (Gutzon Borglum) with intelligence who acts to deliberate ends; the only difference is ascribing to god a specifically transcendent intelligence.

Similarly, in God after Darwin (p. 83) John Haught approvingly cites Teilhard de Chardin:
[A] metaphysically adequate explanation of any universe in which evolution occurs requires — at some point beyond the limits that science has set for itself — a transcendent force of attraction to explain the overarching tendency of matter to evolve toward life, mind, and spirit.
Leaving aside the validity of the assertion that there's an "overarching tendency" of matter to evolve towards life, mind and spirit, de Chardin makes a strong claim here: any universe with evolution requires a transcendent force to explain some observable phenomena, and this explanation must be beyond the limits of science.

It is unclear, however, how to read de Chardin as saying anything other than that science and religion are actually incompatible: science is limited precisely and exclusively to those explanations that are required to explain observable phenomena. It is important to note here that materialism and the fundamentally ateleological nature of the universe are scientific conclusions, not a priori limitations: only an ateleological, material universe is required to explain observable phenomena.

Similarly, Ken Miller mentions miracles:
Any God worthy of the name has to be capable of miracles, and each of the great Western religions attributes a number of very special miracles to their conception of God. What can science say about a miracle? Nothing. By definition, the miraculous is beyond explanation, beyond our understanding, beyond science. [Finding Darwin's God p. 239]
Why, we must ask, are miracles by definition beyond science? Hume's view was that because a miracle contradicts so many ordinary observations, it can never overcome our natural skepticism; it is more plausible to explain reports of miracles by appeal to inattention, hallucination, delusion, or outright mendacity.

But there's a deeper philosophical reason why a "miracle" is by definition "beyond science", if we take a miracle to be a violation of the laws of physics. But for any observable phenomenon to "violate" the laws of physics, we must be able to determine the laws of physics independently of our observations of phenomena. Such a view directly contradicts not the "limits" of science, but its very basis: the laws of physics are precisely those explanations required to explain all observable phenomena. If one accepts that some phenomenon in any sense "violates" any law of physics, one must abandon the law itself: it is definitely false. To fail to do so is to declare one's incompatibility with science.

To save the theory from the phenomena, religious scientists try to put God's interaction with the world beyond the bounds not of materialism but of detectability. Collins continues:
In order to understand how God could take an active role, or how the world could have any inherent freedom, the laws of nature must be somehow open or flexible. The world’s future cannot be entirely determined or predictable from any given moment. ... It is thus perfectly possible that God might influence the creation in subtle ways that are unrecognizable to scientific observation. In this way, modern science opens the door to divine action without the need for law breaking miracles.
For a scientist, Collins exhibits a woeful (but, I'm reliably informed, all-too-common) ignorance of statistics. To call some behavior random is to say only that it is unpredictable in specific ways; we can, perhaps counter-intuitively, actually determine whether some phenomena is indeed unpredictable, and we can actually derive statistical theorems from the premise of unpredictability.

Therefore, to say that god's interaction is in principle undetectable or unrecognizable is to say only and exactly that god's interaction is random. God, in Collins' view, can only substitute one random distribution for another random distribution. Such an "interaction" is no interaction at all; Collins implicitly endorses an covert form of nothing more than deism.

Most importantly, if god is beyond scientific understanding, then in what sense is god beyond any kind of understanding? If we cannot understand anything about god, then in what sense can we say anything at all about god? Contrawise, if we can make any definite statement about god, then we must understand god, at least partially: on what basis do we make such definite statements?

And thus we come to the fundamental incompatibility between science and religion. As Hume noted centuries ago, if one cannot say anything at all about god, one is indistinguishable from an atheist. There is nothing to distinguish a purely mysterious god from no god at all. It seems absurd to believe that religious scientists such as Miller and Collins refuse to say anything at all about god, and descend into de facto atheists. If they want to say anything definite about god, and they want to place such statements beyond the bounds of scientific understanding, then it seems incumbent on them to to provide some alternative basis for understanding, a basis more consistent than the exercise of imagination.

Merely to say they are entitled to exercise their imagination is to say nothing more than that they are entitled to create poetry and fictional literature, an entitlement trivially granted by even the most die-hard materialist scientist.

Thursday, April 23, 2009

Truckling to the Faithful

Jerry Coyne blasts the accommodationists: Truckling to the Faithful: A Spoonful of Jesus Helps Darwin Go Down:
[T]he accommodationist position of the National Academy of Sciences, and especially that of the National Center for Science Education, is a self-defeating tactic, compromising the very science they aspire to defend. By seeking union with religious people, and emphasizing that there is no genuine conflict between faith and science, they are making accommodationism not just a tactical position, but a philosophical one. By ignoring the significant dissent in the scientific community about whether religion and science can be reconciled, they imply a unanimity that does not exist. Finally, by consorting with scientists and philosophers who incorporate supernaturalism into their view of evolution, they erode the naturalism that underpins modern evolutionary theory. ...

The NAS is saying that most religious people and scientists have no problem with evolution and faith. Given that 40% of Americans reject evolution outright (almost entirely on religious grounds), while 92% of NAS scientists reject the idea a personal god, the National Academy is clearly pushing its agenda in defiance of evidence. ...

In his accommodationist books God After Darwin and the more recent Deeper than Darwin, [NCSE website contributor John Haught] espouses a teleology in which evolution is ineluctably drawn by God to some future point of perfection. ... But any injection of teleology into evolutionary biology violates precisely the great advance of Darwin’s theory: to explain the appearance of design by a purely materialistic process — no deity required. ... If we’re to defend evolutionary biology, we must defend it as a science: a nonteleological theory in which the panoply of life results from the action of natural selection and genetic drift acting on random mutations. ...

If natural selection and evolution are as powerful as we all believe, then we should devote our time to making sure that they are more widely and accurately understood, and that their teaching is defended. Those should be the sole missions of the National Academy of Sciences and the National Center for Science Education. Leave theology to the theologians.


Also read PZ Myers, Larry Moran and Richard Dawkins on this important position.

The only way that religion can be compatible with science is to suck all the meaning out of "religion": To hold the position that God is a vague deity, with vague properties and no effect whatsoever on the world, neither physical nor moral; to hold an Einsteinian "God" as a metaphor for the nonteleological physical laws that govern our world. The vast majority of self-described religious people do not hold such a vacuous view of God: they see God has having some influence on the world, many see God as having a profound and continuing influence. I cannot imagine how those few self-described religious people who do talk about a "God Who Makes No Difference" (Greg Egan's phrase) and really mean it can muster up the energy to regularly meet.

Wednesday, April 15, 2009

Saturday, January 24, 2009

Liberal theology

Larry Moran on liberal theology:
The "sophisticated" version of Christianity that [liberal theologians] proclaim in public is just a sham designed to make them look as though they accept science and all its implications. ... [A]ccording to what we know about the natural world, humans are not special in any way and life does not have a purpose. There are very few believers who can stomach those ideas, hence their science and their religion are in conflict.
Larry Moran praises Seeing and Believing, Jerry A. Coyne's review of Saving Darwin and Only A Theory.