Jen McCreight is running an online poll to determine the most influential female atheist of the year.
Uh-oh. You’d think she’d learn.
But given that the results will be utterly meaningless, it’s still useful — there’s quite a long list of good XX godless folk, and commenters keep mentioning more that were left out. Go there to see the depth and diversity of atheism, even if you don’t vote.
He has kept his blog Amygdala going for 9 years now. I have to keep Pharyngula up and running for two more years to catch up with him! (Oh, wait, then he’ll have been going for 11 years…dang.)
This topic came up earlier this week: creationists are always yammering about the “missing link” and how it’s missing and therefore evolution is unsupported by the evidence. It’s total nonsense, since evolution doesn’t predict a “missing link”, but it seemed worthwhile to explain why, since there was a recent publication of some exciting data that demonstrates the real complexity of the situation.
Jim Foley and John Hawks and Carl Zimmer have written up the story of the Denisovans. To summarize, another group of Pleistocene humans have been sequenced, called the Denisovans — their identity is murky, as they’ve only been recognized by a few bones, but the results show that they were genetically distinct from both modern humans and Neandertals, another Pleistocene group that has been sequenced. Like the Neandertal story, in which some Neandertal genes (less than 5%) were introduced into some modern human (European and Asian) populations, what we know about the Denisovans is that some of their genes, about 5%, also spread into a subset of modern human populations, in this case the Melanesians.
That’s awesome stuff. There are all these splintered bits of ancestry that come together in complex ways to produce the human species, and that’s why there is no missing link. Many people have this false notion that our evolution was a matter of a panmictic gemisch of people rolling fatefully down the smooth channel of history, everyone mingling, all of them tracing a common lineage back and back to a discrete ancestor. It wasn’t. Our river of time looked more like this, a braided stream:
This is what we mean when we talk about populations having structure. Branches emerge, whether we call them Neandertals or Denisovans or modern humans, and they are distinct but there can still be genes flowing between them to some degree. Even within modern humans we have structure, where groups maintain a kind of genetic integrity over space and time; I can look at my own recent lineage and see how my mother’s Scandinavian connections were maintained through several generations in America, or I can look at my father’s pedigree that goes back about 400 years in the New World and see that even though they were constantly scudding along at the very edge of the American frontier, mingling with Native Americans and black slaves and freedmen and Chinese railroad workers and Japanese farmers, somehow in their marriages, nothing but Scots/Irish/Anglo-Saxon names turn up.
That’s the nature of a species: many channels, many populations, not just one, separating and merging with circumstance. It’s always been this way; when humans and chimps first diverged from their common ancestors, it wasn’t like one tribe went left, one went right, and they never talked to each other again — it was many streams of ancient ape populations twisted about amongst each other, gradually disentangling to each form a spectrum of divergent channels for each separated species.
When a creationist demands to see the “missing link”, it’s like looking at the picture of a river above and asking for the one drop of water that started it all. There wasn’t one. The question doesn’t even make sense. It’s why BioLogos looks so ridiculous when they worry over whether we can trace our ancestry back to two people, Adam and Eve — of course we can’t, humanity has never been represented by just two unique individuals, and even considering the issue seriously reveals an absence of understanding of how populations evolve. It’s so confused, it’s not even wrong.
(I notice that Greg Laden comes to a similar conclusion, that using the term “missing link” should be avoided, but the nature of his argument looks about as tangled and discursive as the picture of the braided stream above…so maybe it’s more true to the reality?)
Sorry, gang, I know you were all counting on coming out to cheer me up in my lonely isolation — my wife is away, visiting relatives — but there was that nasty wet storm yesterday, and I just spent a couple of hours digging out the driveway and sidewalks from that (-20°C! A four foot high pile in front of the driveway!) and my face is numb and my fingers are burning and my feet are frozen. Now I learn that there is an even bigger blizzard on the way today.
So this is one of those days when you discover that Western Minnesota is not fit for human habitation. I’ll be celebrating the New Year by nestling in with a pot of hot tea, snowed in and inaccessible for a while. I’ll get wild tonight and have a beer.
The weather is abominable. We started out the day with thick, slushy, wet clumps of snow coming down with rain, and now we’ve got fierce winds and an icy fog of blowing blizzardy stuff everywhere. So I fixed myself a dinner of baked salmon and washed it down with Fire Rock Pale Ale.
If I close my eyes and turn up the music loud to drown out the howling winds, I can almost — almost — imagine it’s Hawaii.
The journal Nature has selected optogenetics as its “Method of the Year”, and it certainly is cool. But what really impressed me is this video, which explains the technique. It doesn’t talk down to the viewer, it doesn’t overhype, it doesn’t rely on telling you how it will cure cancer (it doesn’t), it just explains and shows how you can use light pulses to trigger changes in electrical activity in cells. Well done!
People keep sending me this link to an article by Jonah Lehrer in the New Yorker: The Decline Effect and the Scientific Method, which has the subheadings of “The Truth Wears Off” and “Is there something wrong with the scientific method?” Some of my correspondents sound rather distraught, like they’re concerned that science is breaking down and collapsing; a few, creationists mainly, are crowing over it and telling me they knew we couldn’t know anything all along (but then, how did they know…no, let’s not dive down that rabbit hole).
I read it. I was unimpressed with the overselling of the flaws in the science, but actually quite impressed with the article as an example of psychological manipulation.
The problem described is straightforward: many statistical results from scientific studies that showed great significance early in the analysis are less and less robust in later studies. For instance, a pharmaceutical company may release a new drug with great fanfare that showed extremely promising results in clinical trials, and then later, when numbers from its use in the general public trickle back, shows much smaller effects. Or a scientific observation of mate choice in swallows may first show a clear preference for symmetry, but as time passes and more species are examined or the same species is re-examined, the effect seems to fade.
This isn’t surprising at all. It’s what we expect, and there are many very good reasons for the shift.
Regression to the mean: As the number of data points increases, we expect the average values to regress to the true mean…and since often the initial work is done on the basis of promising early results, we expect more data to even out a fortuitously significant early outcome.
The file drawer effect: Results that are not significant are hard to publish, and end up stashed away in a cabinet. However, as a result becomes established, contrary results become more interesting and publishable.
Investigator bias: It’s difficult to maintain scientific dispassion. We’d all love to see our hypotheses validated, so we tend to consciously or unconsciously select reseults that favor our views.
Commercial bias: Drug companies want to make money. They can make money off a placebo if there is some statistical support for it; there is certainly a bias towards exploiting statistical outliers for profit.
Population variance: Success in a well-defined subset of the population may lead to a bit of creep: if the drug helps this group with well-defined symptoms, maybe we should try it on this other group with marginal symptoms. And it doesn’t…but those numbers will still be used in estimating its overall efficacy.
Simple chance: This is a hard one to get across to people, I’ve found. But if something is significant at the p=0.05 level, that still means that 1 in 20 experiments with a completely useless drug will still exhibit a significant effect.
Statistical fishing: I hate this one, and I see it all the time. The planned experiment revealed no significant results, so the data is pored over and any significant correlation is seized upon and published as if it was intended. See previous explanation. If the data set is complex enough, you’ll always find a correlation somewhere, purely by chance.
Here’s the thing about Lehrer’s article: he’s a smart guy, he knows this stuff. He touches on every single one of these explanations, and then some. In fact, the structure of the article is that it is a whole series of explanations of those sorts. Here’s phenomenon 1, and here’s explanation 1 for that result. But here’s phenomenon 2, and explanation 1 doesn’t work…but here’s explanation 2. But now look at phenomenon 3! Explanation 2 doesn’t fit! Oh, but here’s explanation 3. And on and on. It’s all right there, and Lehrer has explained it.
But that’s where the psychological dimension comes into play. Look at the loaded language in the article: scientists are “disturbed,” “depressed,” and “troubled.” The issues are presented as a crisis for all of science; the titles (which I hope were picked by an editor, not Lehrer) emphasize that science isn’t working, when nothing in the article backs that up. The conclusion goes from a reasonable suggestion to complete bullshit.
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.
I’ve highlighted the part that is true. Yes, science is hard. Especially when you are dealing with extremely complex phenomena with multiple variables, it can be extremely difficult to demonstrate the validity of a hypothesis (I detest the word “prove” in science, which we don’t do, and we know it; Lehrer should, too). What the decline effect demonstrates, when it occurs, is that just maybe the original hypothesis was wrong. This shouldn’t be disturbing, depressing, or troubling at all, except, as we see in his article, when we have scientists who have an emotional or profit-making attachment to an idea.
That’s all this fuss is really saying. Sometimes hypotheses are shown to be wrong, and sometimes if the support for the hypothesis is built on weak evidence or a highly derived interpretation of a complex data set, it may take a long time for the correct answer to emerge. So? This is not a failure of science, unless you’re somehow expecting instant gratification on everything, or confirmation of every cherished idea.
But those last few sentences, where Lehrer dribbles off into a delusion of subjectivity and essentially throws up his hands and surrenders himself to ignorance, is unjustifiable. Early in any scientific career, one should learn a couple of general rules: science is never about absolute certainty, and the absence of black & white binary results is not evidence against it; you don’t get to choose what you want to believe, but instead only accept provisionally a result; and when you’ve got a positive result, the proper response is not to claim that you’ve proved something, but instead to focus more tightly, scrutinize more strictly, and test, test, test ever more deeply. It’s unfortunate that Lehrer has tainted his story with all that unwarranted breast-beating, because as a summary of why science can be hard to do, and of the institutional flaws in doing science, it’s quite good.
But science works. That’s all that counts. One could whine that we still haven’t “proven” cell theory, but who cares? Cell and molecular biologists have found it a sufficiently robust platform to dive ever deeper into how life works, constantly pushing the boundaries of uncertainty.
The British government has been getting a bit mother-henish lately, arresting people for cruelty to religious texts, and clearly has it in mind to provide special legal protection for a certain class of books. My first thought would be that that is insane, books are mere objects that are easily replicable, and providing for a special privilege that we don’t also grant doorknobs or transistor radios or light bulbs is absurd. But a man named Eugenio has a better idea: we need to leap on the sacred book bandwagon.
I am therefore writing to you today to request that legal protection be accorded to all copies of the three editions of J.D. Jackson’s “Classical Electrodynamics” (ISBN 978-0471431329, ISBN 978-0471309321, ISBN 047130932X).
I believe it ticks all the boxes for a sacred text: by making me understand for the first time in all their clarity and power both Maxwell’s equations, the first step towards a Grand Unification theory that would give a single explanation for all physical phenomena in the universe, and Einstein’s Special Theory of Relativity, which let me glimpse for the first time the true nature of space, time and causality, it changed my view of the universe and my concept of our place and role in it; it opened my eyes to the beauty and harmony and marvelous complexity of everything that exists; it gave me a clear and understandable explanation of complex and baffling phenomena; it requires lengthy and intensive study under the guidance of learned masters to truly grasp its significance; I tend to swear on it when I need to prove my absolute sincerity and my cat is not around; finally, seeing it defaced, burnt, thrown in a skip, pulped or in any way damaged causes me emotional pain and occasional mild irritation.
I realise it appears to fail the test in important areas – for example, it seems to contain far less made-up stuff than, say, the Bible, the Koran, the Book of Mormon or Dianetics; but in fact, if you look at the exercises section, you’ll find plenty of perfect conductors, infinite planes, and continuous (in the mathematical sense) physical phenomena and bodies. All demonstrably imaginary, as any first-year physics student could easily prove. So in fact there is plenty of made-up stuff, it’s just well hidden, which should make it a better-than-average sacred text.
One thing though might be construed as a flaw – the fact that nowhere in the book, not even in the pre-New Age, 1962 first edition, there is a call to genocide, ethnic cleansing, war or mass rape. In spite of the fact that the title itself refers to classical electrodynamics, there isn’t even a call for the extermination of quantum physicists – something I tended to consider a major oversight in my last year at university, to be completely honest. I’m not sure this will be enough to disqualify it from the status of sacred text, if that should be the case perhaps we could add an appendix with Richard Feynman’s autobiography, which at least contains reference to a couple of punch-ups, as a sort of Saint Dick the Divine’s Apocalypse – although he wasn’t nearly high enough to be compared to the author of the original one, not even in the bit where he tells about Brazil and the bongos.
Although I blew up a considerable number of electrolytic capacitors during lab courses (I tended to get the polarities mixed up with annoying regularity) I haven’t caused any intentional explosive damage to anything/anyone since my mother threw away my chemistry set when I was 12 (and even then, the Kitchen Table Incident was at least partly an accident); therefore, alas, I cannot threaten you with an onslaught of terror, violence and murder in case you should not accede to my request, but I’ll be severely annoyed and possibly even a bit snappy if The Book does not receive the full protection of the law. After all, what matters is how I feel about it, not the actual fact that it is God-, Allah-, Xenu- or Flying Spaghetti Monster-inspired, and I feel very strongly about this.
I am not a physicist, but I’ve read enough of James Clerk Maxwell to be humbled before his obvious holiness, and agree that his works deserve the same or greater protection that we would give to frauds and poseurs like Jesus and Buddha and Mohammed. They never unified electromagnetism; they never even got off their butts long enough to ask the question, “Fuckin’ magnets, how do they work?”
Let’s not stop with Maxwell, either. Give me a minute, I’ll make a list.
