Reading phylogenetic trees.

As cladistics, facilitated by genetic comparisons and molecular-clock modeling, has become the dominant taxonomic method, the phylogenetic tree diagram has become nearly ubiquitous, but little explanation is given for its meaning. Where the branch points occur along one axis has meaning; placement on the other axis is a matter of taste.

In a 11 November 2005 short article in Science, entitled The Tree Thinking Challenge, David A. Baum and Susan DeWitt Smith of the University of Wisconsin, and Samuel S. S. Donovan at the University of Pittsburg present a simple phylogeny and ask the reader to, based on that information, determine which of two critters is more closely related to humans. Take their quiz and see how you fare. If you get it wrong, the article--a very quick read--will set you straight and establish a good habit.

A recommended climate lecturer.

Paul Kushner of the University of Toronto gives a truly outstanding hour-long introduction to climate modeling for the scientifically literate audience, managing also to slip in some of his current work, for illustrative purposes, near the end.

I got a chance to sit in on it earlier today, while visiting Stanford University. I recommend him highly as a speaker, if you get the chance to invite him.

Journalist error of least import.

On page 48 of the February 2009 issue of Saveur:

A nonstick pan is our choice for frying eggs and delicate fish filets [sic]. The 10-inch T-Fal Ultimate Fry Pan, from the French company that pioneered nonstick cooking in the 1950s, is the sturdiest around. Unlike Teflon-coated pans, it has a hard surface, made of a plastic-based resin called PTFE, that is virtually scratchproof and stands up to metal utensils.

The last time I checked, Teflon was an old trademark synonym for PTFE. I doubt T-Fal printed this claim on its box and figure Saveur's staff writer made up some pitchman's nonsense to pretend to be insightful.

Compared to when journalists botch diet advice or environmental news, this is of little import. But I'm still going to write a letter, because I'm that kind of guy.

Did a meta-analysis published in the Lancet really vindicate homeopathy?

The audacity of con artists knows few limits. In response to my recent Epinions beat-up of Oscillococcinum, a "homeopathic" sugar pill made and marketed by French quack cure behemoth Boiron, Inc., a representative of the company, one Alissa Gould, posted fifteen studies which supposedly prove the efficiacy of homeopathy or Oscillococcinum. Some of these studies were merely low quality garbage published in faux journals set up to promote quackery (Journal of Alternative and Complementary Medicine", British Homeopathy Journal), others were inconclusive and more than one actually supported the opposite of what Ms Gould claims.

The one that caught my attention was a 2005 study by Shang et al, "Are the clinical effects of homoeopathy placebo effects? Comparative study of placebo-controlled trials of homoeopathy and allopathy", Lancet 366, and not only because I was shocked that the editors at such a prestigious journal let the use of "allopathy" as a synonym for mainstream medicine make it to press. (Whether "allopathy" was ever practiced is questionable, but it is clear that modern medicine is not based on some tawdry "cure disease with its opposite" maxim.)

Shang and co-authors compared 110 placebo-controlled trials of homeopathy and 110 matched trials of evidence-based medicine, finding a trend toward bias in small trials of both, but significant evidence from the large trials that conventional medicine has specific effects, whereas homeopathy is similar to placebo. The paper is a bit difficult to read--I can't think of another field in which those "funnel plots" are used--but worthwhile not only for its frank assessment of homeopathy but also as an exemplar of method.

Take-home lesson?: Beware Boiron employees pushing studies: they don't limit their hucksterism to the sugar-pill trade.

The Double-Bind of the Incompetent

As Bertrand Russell once put it, the trouble is that "the stupid are cocksure."

We've all encountered them: people who think a talk argument they just made up, be it regarding quantum mechanics, the origin of life, climatology, or (to pull an example from my e-mail box), numerological connections in cosmology, trumps the intellectual "heavy lifting" and rigor of scientists building on the work of previous scientists.

It strikes us as hubris, or even dishonesty. As scientists we see this behavior not merely as being incorrect but as a manifestation of a moral failing. Perhaps that is so and perhaps it is not; regardless, a study by Justin Kruger and David Dunning, published in the Journal of Personality and Social Psychology, shows this lack of insight to be universal among the incompetent.

Kruger and Dunning had student volunteers (given extra credit) take the logic portion of the LSAT, a grammar exam, and a "test" in which their rating of the quality of jokes was compared to that given by professionals, and also rate their performance on each. On all three, the low performers assessed their own performance as being above average. Top quartile performers underestimated their own ability, but they revised their assessment after grading five others' grammar exams. The bottom performers gained no insight from grading their peers' exams; they were unable to recognize better work when they saw it!

It may be "old news"--the paper dates to 1999--but it is particularly rich, with more insights than I've summarized here. Among other things, it provides some insight into the obstinacy of the armchair global warming denialist, HIV/AIDS denialist, or quantum-mechanics contrarian. Not only are they ill informed, but they are unable to recognize expertise. Read the full article (which may be behind a pay wall) for more.

"We have foregrounded the redistributional dreams of "social justice" over heroic aspirations to discover, invent, and thereby create new wealth..."

Peter Wood, of the National Association of Scholars, has a brilliant essay in this week's Chronicle of Higher Education connecting American high culture's obsession with identity and diversity to the drought of native-born scientists and engineers.

The science "problems" we now ask students to think about aren't really science problems at all...a society that worries itself about which chromosomes scientists have isn't a society that takes science education seriously.

This is bound to anger precisely those who deserve it. A defense of merit, achievement, and a call for culture to respect merit and achievement is long overdue.

What's happening to Bangladesh?

Hearing climate contrarians called "skeptics" is, to my ears, like nails on a chalkboard. Not only is there a tendency to fumble about looking for evidence or any argument, good or bad, in support of a predetermined conclusion--the opposite of a skeptic's behavior--but when it comes to evidence supposedly in favor of their position, they more often than not act more like simpletons.

Consider the latest fad in the denialosphere, a pop report on land accretion in Bangladesh. (Of course, the buzz is not about a scientific paper. Denialists don't usually read those, and tend to kick and scream when one insists they must!) It has been widely predicted that sea-level rise will inundate low-lying areas of Bangladesh, but, currently, sedimentation is adding 20 km^2 to the country, annually.

To hear it from Paul Biggs on Jennifer Marohasy's 'blog or CLS at Classically Liberal, this is proof that sea-level rise will not inundate Bangladesh at all, that the IPCC and unnamed predictors of "catastrophists" are wrong, wrong, wrong.

This is nonsense, and it's so patently nonsense that one wonders if Biggs and CLS have any shame at all. Sedimentation and sea-level rise are competing effects: that one and not the other currently determines the sign of land-mass growth doesn't mean that it will always determine that sign. Let's take Paul Biggs' number as gospel for a second, that the IPCC predicts that 17% of Bangladesh will be under water by 2050. (What the IPCC predicts--and what it means for the IPCC as opposed to an individual group's paper to predict anything--is, of course, more complicated than this.) Bangladesh has an area equal to 134,000 km^2 according to the CIA World Factbook 17% of this is 22,780 km^2, far more than 20 km^2/year times 42 years, or even the Yahoo report's sanguine 5000 km^2 of "reclaimed" land.

Comparing percentages is not, of course, the way to go about this problem; one needs a model of land accretion during a time of sea level rise. Neither Mahfuzur Rahman nor Maminul Haque Sarker, the scientists/engineers cited in the Yahoo article, are working is not working with one, and neither are the denialists. At worst, I'm being no more flimsy than the wannabe "skeptics"; the comparison is good for a rough estimate and I have better things to do with my time than change field of study.

What's incontrovertible is that Bangladesh is already feeling the effects of rising sea levels, mainly through saltwater pollution of soils an aquafiers. See the IPCC AR4 WGII report for discussion and references. (I'd put 5-1 odds on the denialists not looking at the IPCC report at all!)

But maybe I'm wasting my time even without changing field of study. CLS talks of a "Church of Saint Al" as though the tail is wagging the dog and climate scientists are taking marching orders from a mere popularizer. And he gives hints that, like Ronald Bailey prior to his Road to Damascus moment, he's choosing a position on a scientific question based on what he wishes public policy to be, a dishonest practice. To quote:

Well that technology costs money and that means an improved economy and that means more carbon emissions so that can’t be allowed.

Yep, it's the usual Bircher-esque paranoia, the party line from glibertarians who talk a lot about free markets but lack the imagination to put such markets to use: Improved economies mean more carbon emissions, economic growth can't be carbon-neutral or carbon-negative or happen in a cap-and-trade framework. You can either have economic growth or you can stop fouling the nest. Want prosperity? Then take unlimited global warming and ocean acidification.

Now there's a teenage pinko's dream argument! "Capitalism and economic growth can only survive by fouling the nest."