science

no doomsday from Gulf methane

Somehow, a hysterical fringe-science blog post by Terrence Aym -- a grade-A teabagger nutball who has previously argued that states should seceed from the U.S. and claimed that North Korea was behind the Deepwater Horizon explosion -- has managed to capture the imaginations of many scientifically illiterate journalists and bloggers.

Aym takes the fact there are elevated levels of methane in the vicinity of the Deepwater Horizon leak, combines it with a gross misunderstanding of a speculative theory by Gregory Ryskin about methane and the Permo-Triassic Extinction, and concludes that "OMG we're all gonna die!".

It is, of course, a load of hooey. Sorry, but we won't get out of this so easily as the world ending; we're going to have to do the hard work of cleaning up the mess. io9.com does a fine job of debunking the nonsense, with several good links.

Feynman and the "map of the cat"

Richard Feynman was a Nobel Prize winning physicist and one of the most brilliant minds of the twentieth century. He was also a drummer, an artist, a ladies' man, and a raconteur. His book Surely You're Joking, Mr. Feynman! is a collection of stories about his adventures. This excerpt, where Feynman takes a graduate-level class in biology while he's at Princeton, just to see what's going on in other fields, is one of my favorites.

The next paper selected for me was by Adrian and Bronk. They demonstrated that nerve impulses were sharp, single-pulse phenomena. They had done experiments with cats in which they had measured voltages on nerves.

I began to read the paper. It kept talking about extensors and flexors, the gastrocnemius muscle, and so on. This and that muscle were named, but I hadn't the foggiest idea of where they were located in relation to the nerves or to the cat. So I went to the librarian in the biology section and asked her if she could find me a map of the cat.

"A map of the cat, sir?" she asked, horrified. "You mean a zoological chart!" From then on there were rumors about some dumb biology graduate student who was looking for a "map of the cat."

When it came time for me to give my talk on the subject, I started off by drawing an outline of the cat and began to name the various muscles.

The other students in the class interrupt me: "We know all that!"

"Oh," I say, "you do? Then no wonder I can catch up with you so fast after you've had four years of biology." They had wasted all their time memorizing stuff like that, when it could be looked up in fifteen minutes.

BPA can cross the placenta from mother to fetus

I've previously reported on Bisphenol-A (BPA), the ubiquitous endocrine-disrupting chemical found in water bottles and many other forms of packaging and linked to breast cancer, insulin resistance, miscarriage, obesity, prostate enlargement, early onset of sexual maturation, and other problems.

The latest: new research shows that BPA can cross the placenta from mother to fetus, where it can affect development during a particularly vulnerable period. And other new research suggests that fetal exposure to BPA and other endocrine disruptors can increase the risk of breast cancer later in life.

More and more I suspect that future generations will look back at our cavalier use of endocrine disruptors the way we look at the Romans' use of lead, and wonder: WTF were they thinking?

GM corn contains pesticides that -- surprise! -- might be harmful

Research published in the International Journal of Biological Sciences looks at the effects of feeding three strains of genetically-modified corn -- two of which produce Bacillus thuringiensis derived pesticides ("Bt"), and one of which is "Roundup ready", meaning that it contains derivatives of this herbicide -- to rats.

Looking at data that was actually provided by Monsanto (though in some cases, only after disclosure was mandated by courts), they found that

...in the three GM maize varieties that formed the basis of this investigation, new side effects linked to the consumption of these cereals were revealed, which were sex- and often dose-dependent. Effects were mostly concentrated in kidney and liver function, the two major diet detoxification organs, but in detail differed with each GM type. In addition, some effects on heart, adrenal, spleen and blood cells were also frequently noted. As there normally exists sex differences in liver and kidney metabolism, the highly statistically significant disturbances in the function of these organs, seen between male and female rats, cannot be dismissed as biologically insignificant as has been proposed by others. We therefore conclude that our data strongly suggests that these GM maize varieties induce a state of hepatorenal toxicity. This can be due to the new pesticides (herbicide or insecticide) present specifically in each type of GM maize, although unintended metabolic effects due to the mutagenic properties of the GM transformation process cannot be excluded. All three GM maize varieties contain a distinctly different pesticide residue associated with their particular GM event (glyphosate and AMPA in NK 603, modified Cry1Ab in MON 810, modified Cry3Bb1 in MON 863). These substances have never before been an integral part of the human or animal diet and therefore their health consequences for those who consume them, especially over long time periods are currently unknown.

Monsanto, of course, being one of the finest examples of pure concentrated evil on the planet, looked at this same data and applied weaker statistical methods to say that everything is hunky-dory.

corruption in H1N1 pandemic declaration

I've previously reported on the bad science around flu vaccine recommendations, and how the flu in general and H1N1 specifically have apparently been overblown as health threats.

(Please note that my considerations here are limited to the flu. This is not an "anti-vaccine" rant; I got a Tdap shot a few months ago -- and felt like crap for a day or two, but given the seriousness of diphtheria, pertussis, and tetanus and the effectiveness of those vaccines, it was worth it.)

Now, the BMJ reports on the conflicts of interest and lack of transparency around the World Health Organization's declaration of the H1N1 pandemic and its recommendations for responses.

Most shockingly, the WHO actually changed the definition of a pandemic in May 2009 so that H1N1 would qualify, removing the qualification that an outbreak must cause "enormous numbers of deaths and illness". And it estimated that 2 billion H1N1 cases were likely -- 1 out of 3 human beings on the whole planet -- even after the winter season in Australia and New Zealand showed that only about one to two out of 1000 people were infected.

It did this while taking advice from people with financial and research ties with Big Pharma companies that produced antivirals and vaccines; one researcher who wrote key guidelines had been paid by Roche and GlaxoSmithKline.

Neanderthals in the family tree

The science on the question of whether modern Homo sapiens interbred with Neanderthals, or came out of Africa and overran their cousins, has gone back and forth a few times over the years. In fact, I was just talking about this with someone at the Beltane festival over the weekend. (One gets into the most interesting discussions at Pagan gatherings -- ritual magic, evolutionary biology, BDSM, technogeekery, martial arts...)

When I look in the mirror and see my brow ridge, and feel that bit of an occipital bun on the back of my head, it seems sensible to me that my umpity-great grandpappy might have passed on a few genes from the Neanderthal part of the family tree, but -- I said a few days ago -- the evidence wasn't really there.

Well, now it is. Recent analysis of the Neanderthal genome, from bone fragements, reveals that those of us whose ancestral group developed outside Africa, may have from 1 to 4 percent of their genome from Neanderthal ancestors.

David Reich, a geneticist at Harvard Medical School, notes that this implies that "Neanderthals aren't quite extinct. [They] all live on a little bit in many of us."

bullet-proof t-shirts on the way?

At first hearing it sounds like something straight of Snow Crash: researchers at the University of South Carolina took a cotton t-shirt, treated it with boron, and ended up with a fabric reinforced with nanowires made of boron carbide -- a material used in tank armor.

Sadly, a bullet-proof t-shirt is probably some ways away yet. But the technique produces a strong, light material that could be used not only in body armor but in the manufacture of lightweight fuel-efficient vehicles.

a Turing machine

If you've never studied computer science -- move on, nothing to see here.

But if you have, you'll appreciate Mike Davey's realization of a Turing machine.

A Turing machine, for those non-geeks who still with me, is a theoretical entity that models the process of computation. In 1936, Alan Turing -- one of most brilliant mathematicians ever, who helped break the Nazi's "Enigma" code and save Western civilization, and for his reward was prosecuted and sentenced to "chemical castration" via hormone injections for his homosexuality, but I digress -- proposed a mathematical model of computation that every CS student still studies today.

Imagine an infinitely long tape, divided into cells, where each cell can hold one symbol. This tape moves back and forth under a read/write head (or the head moves over the tape, it's equivalent), which can read the symbol under it and/or write a new one. The machine has just enough memory to hold one number, its "state", and a finite set of rules that tell it what to do when it seems a given symbol while in a given state: for example, "in state 17, if you see a 0, move the tape 23 places to the right and write a 1".

Anything that can be computed, can be computed by a Turing machine. You might think, for example, that a machine that used a two-dimensional grid of cells could do more than a Turing machine, but it can be proven that a "TM" can simulate such a 2-d machine, and so compute anything that it can. I wrote a lot of proofs involving TMs when I was in grad school.

Of course this is not a practical thing to build. Turing meant it only as a sort of thought-experiment. That's part of the beauty of Davey's construction: it's absolutely useless, completely a work of math art.

"Electron Band Structure In Germanium, My Ass"

This lab report from a frustrated physics major reminds me all too much of my own lab work, before I gave up on my foolish notions of attempting a double physics/CS degree and decided to just major in hacking. (I especially remember optics lab. My data disproved every principle of the field...)

Abstract: The exponential dependence of resistivity on temperature in germanium is found to be a great big lie. My careful theoretical modeling and painstaking experimentation reveal 1) that my equipment is crap, as are all the available texts on the subject and 2) that this whole exercise was a complete waste of my time.

...

Results

Check this shit out (Fig. 1). That's bonafide, 100%-real data, my friends. I took it myself over the course of two weeks. And this was not a leisurely two weeks, either; I busted my ass day and night in order to provide you with nothing but the best data possible. Now, let's look a bit more closely at this data, remembering that it is absolutely first-rate. Do you see the exponential dependence? I sure don't. I see a bunch of crap.

However, his conclusion that "I should've declared CS. I still wouldn't have any women, but at least I'd be rolling in cash." might have been true in the dot-com boom, but sadly not so much any more, with more and more software jobs being sent overseas.

"if you believe what you read in the scientific literature, you shouldn’t believe what you read in the scientific literature."

Interesting article on the (mis)use of statistics in science over at Science News:

“There is increasing concern,” declared epidemiologist John Ioannidis in a highly cited 2005 paper in PLoS Medicine, “that in modern research, false findings may be the majority or even the vast majority of published research claims.”

...

Nobody contends that all of science is wrong, or that it hasn’t compiled an impressive array of truths about the natural world. Still, any single scientific study alone is quite likely to be incorrect, thanks largely to the fact that the standard statistical system for drawing conclusions is, in essence, illogical. “A lot of scientists don’t understand statistics,” says Goodman. “And they don’t understand statistics because the statistics don’t make sense.”

...

How could so many studies be wrong? Because their conclusions relied on “statistical significance,” a concept at the heart of the mathematical analysis of modern scientific experiments.

...

Statisticians perpetually caution against mistaking statistical significance for practical importance, but scientific papers commit that error often. Ziliak studied journals from various fields — psychology, medicine and economics among others — and reported frequent disregard for the distinction.

“I found that eight or nine of every 10 articles published in the leading journals make the fatal substitution” of equating statistical significance to importance, he said in an interview. Ziliak’s data are documented in the 2008 book The Cult of Statistical Significance, coauthored with Deirdre McCloskey of the University of Illinois at Chicago.

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