If I had some ham, I could make a ham sandwich, if I had some bread

What is it with these loons? They’ve got nothing, but they’re continually telling us what they could accomplish, if only they…what? I don’t know.

The latest trend in kook blogs is to tell us all the things that would happen if we only accepted their weird premises. Here, for example, is Terry Hurlbut, explaining what America would be like if creationists controlled science.

This hypothetical creation-oriented society would take scientific education, research, and investigation in a new direction. Astronomers would stop looking for “dark matter” and “dark energy,” and instead develop a uniform cosmology with insights from the Annals of Creation. It would find this model much simpler than the Big Bang model has now become.

That’s right, astronomers, forget about math and radio telescopes and Hubble and all your new-fangled physics. Throw out the textbooks and roll the curriculum back to 1625 — the only source you need is the theology of James Ussher, Archbishop of Armagh, Primate of All Ireland!

Geology would return to its pre-Lyell understanding. The result might, perhaps, lead to improved fossil-fuel exploration, and would be more likely to lead to improvements in prospecting for uranium, thorium, and other radioactive minerals. The realization that radioactive elements on earth had their origins in a spate of ultra-high-magnitude earthquakes might lead to an investigation of whether more radioactive materials might suddenly become “discoverable” near the epicenters of any future magnitude-eight or stronger earthquakes. Indeed, the careful study of veins of uranium, thorium, and similar ores, and of the magnetic ores, might lead to better mapping of earthquake zones.

Your turn, geologists. Uniformitarianism is out. You only have to roll your discipline back to about 1830, though, throwing out everything in Lyell’s Principles of Geology and anything since. Wait…you might also have to get rid of Hutton, which pushes the date back a bit further. Don’t worry, though, you’ll have an easier job finding fossil fuels if you forget the “fossil” part and pretend they were all generated within the last 4000 years.

Medicine would abandon its hubristic seeking after “designer drugs,” its careless disregard of the possible functions of various organs (like the vermiform appendix), and its almost willful ignorance of the role of diet in human health (and animal husbandry). Creationism would reinforce the notion that mankind, and for that matter every animal, is specifically designed to use certain foodstuffs that are, in turn, specifically designed to serve as good, healthful food. Such a society would necessarily abandon the modern Western diet and rediscover the health-maintaining practices that the Bible mentions (and that are still current, in only slightly modified form, in the Middle East, and especially in Israel).

Oh, right. Let’s get back to the standards of health care of Palestine in the 1st century AD.

Zoology would become a much more exciting discipline than it is today. Zoologists would look on the woolly mammoth with new understanding. Expeditions to find live dinosaurs would be more than the stuff of science fiction (cf. The Lost World, by Sir Arthur Conan Doyle) and would receive serious attention and funding. And this Examiner does not doubt that at least some would be successful.

Of course, creationists can seek dinosaurs in the vasty tropics. Why, so can I, or so can any man; but will they find them when they do search for them?

Hurlbut clearly lives in a fantasy world that has no connection to reality. But I have found someone even crazier: John Benneth. Benneth has written one long-ass post in which he lists every deplorable statistic he can find, and then announces that “homeopathy would have helped”. Oh, really?

In one year 85,000 Americans were wounded by firearms, of which 38,000 die, 2,600 children. Homeopathy could have helped with ledum pelustre , aconitum napellum, arnica Montana and individualized constitutional treatments.

I think homeopathic firearms certainly would have helped, but otherwise, no, throwing water at wounds isn’t going to cure them.

150,000 American children are reported missing every year. 50,000 of these simply vanish. Their ages range from one year to mid-teens. According to the New York Times, “Some of these are dead, perhaps half of the John and Jane Does annually buried in this country are unidentified kids.” Homeopathy could have helped with individualized treatments. Homeopathy could have helped with remedies like Absin. Cimic. OP. Phos. Plb. Rhus-t. Staph. Stram., Falco-p, and Magnesium muriaticum

Homeopathic body-burials? I don’t get it.

In one year 1,000,000 American children ran away from home, mostly because of abusive treatment, including sexual abuse from parents and other adults. Of the many sexually abused children among runaways, 83 percent came from white families. Homeopathy could have helped with remedies like Lyc., Falco-p. Herin.

If only those white families had been treated with John Benneth’s Patented Skin Darkener, those kids wouldn’t have run away!

2,000,000 to 4,000,00 American women were battered. Domestic violence was the single largest cause of injury and second largest cause of death to American women. Homeopathy could have helped the victim with recovery from the trauma with a remedies such as Arn. and Staph and helped the assailant with his anger with remedies such as Croc. Mez. and Sulph.

Ladies, next time the husband staggers home drunk and starts walloping you around, just ask him to drink a nice glass of water. Everything will be all better then.

With so much violence, should it be surprising that 135,000 American children took guns to school? Homeopathy could have helped.

More homeopathic firearms?

In one year African Americans constituted 13 percent of drug users but 35 percent of drug arrests, 55 percent of drug convictions and 74 percent of prison sentences. For non-drug offenses, African Americans got prison terms that averaged about 10 percent longer than Caucasians for similar crimes.
Homeopathy could have helped.

One moment it’s all those white kids running away from home, now it’s all the black people in prison, and homeopathy somehow fixes it all. Maybe it turns everyone gray?

Anyway, these guys are completely nuts, but anyone can play the “If X, then Y” game. If only magic really worked, then I could fix that drippy showerhead. If the sky were purple, I’d be able to knit. If squid wore hats, then monkeys would dance on Mars.

Doesn’t it matter that the centuries-old magic tricks both Hurlbut and Benneth think are panaceas were tried once, failed, and better solutions were discovered?

The Most Influential Female Atheist of 2010

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.

Why there are no missing links

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?)

New Year’s Eve party at my house…cancelled

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 10th day of 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!

Science is not dead

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.