If you’re Portuguese. . .

October 12, 2012 • 6:39 am

. . . and want a copy of WEIT in your own language, you can order it here from the estimable firm Tinta da China, a Lisbon firm run by three young women. They’re starting a science series (my book is the first) and are also looking for good popular-science books in English to translate into Portuguese. I suggested Pinker’s The Language Instinct and Pollan’s The Botany of Desire (Dennett, Dawkins, Sagan, etc. have already been translated and published by other firms.  If you have any suggestions, put them in the comments below and I’ll call them to the firm’s attention.

They’re hoping to sell it in Brazil, too. If you’re a university professor in Brazil and want to use the book in a course, do contact me.

 

Lance Armstrong masterminds blood-doping scheme

October 11, 2012 • 9:42 pm

At one time Lance Armstrong was my hero. Having beaten testicular cancer that metastasized to his brain, he came back to win the Tour de France seven times. What an inspiring story!

And now it’s fallen apart.  As most of us know from extensive reports in The New York Times and other places (see here and here, for instance), Armstrong was the mastermind of a scheme of illegal blood-doping and drug use (including testosterone), forcing his teammates to participate as well. The U.S. Anti-Doping agency has released 1000 pages of evidence and testimony against Armstrong, and the CEO of that Agency released a statement that includes the following:

The evidence of the US Postal Service Pro Cycling Team-run scheme is overwhelming and is in excess of 1000 pages, and includes sworn testimony from 26 people, including 15 riders with knowledge of the US Postal Service Team (USPS Team) and its participants’ doping activities. The evidence also includes direct documentary evidence including financial payments, emails, scientific data and laboratory test results that further prove the use, possession and distribution of performance enhancing drugs by Lance Armstrong and confirm the disappointing truth about the deceptive activities of the USPS Team, a team that received tens of millions of American taxpayer dollars in funding.

Together these different categories of eyewitness, documentary, first-hand, scientific, direct and circumstantial evidence reveal conclusive and undeniable proof that brings to the light of day for the first time this systemic, sustained and highly professionalized team-run doping conspiracy. All of the material will be made available later this afternoon on the USADA website at http://www.usada.org.

The New York Times quotes the USADA report:

[Armstrong’s] goal led him to depend on EPO, testosterone and blood transfusions but also, more ruthlessly, to expect and to require that his teammates would likewise use drugs to support his goals if not their own,” the agency said in its 202-page report. . .

At the same time the drug use was nonchalant, it was also carefully orchestrated by Armstrong, team management and team staff, the antidoping agency said.

“Mr. Armstrong did not act alone,” the agency said in its report. “He acted with the help of a small army of enablers, including doping doctors, drug smugglers, and others within and outside the sport and on his team.”

The NYT gives a lot of gory details, which include the following:

Kristin Armstrong, Armstrong’s former wife, handed out cortisone tablets wrapped tightly in foil to the team at the 1998 world championships.

Riders were given water bottles containing EPO [the blood booster erythropoietin] as if they were boxed lunches. Jonathan Vaughters said the bottles were carefully labeled for them: “Jonathan — 5×2” meant five vials of 2,000 international units each of EPO were tucked inside. Once when Vaughters was in Armstrong’s room borrowing his laptop, Armstrong injected himself with EPO and said, now “that you are doing EPO too, you can’t go write a book about it.”

And last night the NYT published a piece about how Armstrong managed to avoid getting caught, including getting tipped off about impending drug testing and using saline infusions to dilute the drugs he took.

There’s no Schadenfreude here, as there would be with people who, after a time in the public eye, have fallen low without having achieved anything (Paris Hilton and the Kardashians come to mind). Armstrong did work hard, and was immensely dedicated. It’s a pity that his dedication led him to the conclusion that any means justified his winning the Tour de France.

What’s immensely sadder is that Armstrong, despite all the evidence, still refuses to admit guilt. He’s forever disgraced, and has been stripped of his Tour de France titles and Olympic gold medal. Unaccountably, criminal charges against him have not proceeded, despite his actions having violated several U.S. laws.

Illegal performance-enhancing use of drugs is pervasive in professional sports, especially in America. Football players take them, baseball players take them, and even racehorses are injected with them.  It hasn’t been a level playing field for a long time, and drug use spurs on “arms races” in sports in which one must go along to remain competitive.

The 1000-page report on Armstrong’s illegal activities has now been put up, along with supporting materials. Go here to see it if you have the stomach.

Pharoah’s snake in a vivarium

October 11, 2012 • 1:38 pm

by Matthew Cobb

This kind of thing could have got you burnt at the stake a few centuries ago – or gained you the favour of easily-impressed influential people. The video’s a slow burner (ha!) – the action starts at around 1:10. They presumably did the experiment in a vivarium for safety reasons (and they very sensibly wear gloves).

Mercury(II) thiocyanate  – Hg(SCN)2 – used to be used to make Pharoah’s Serpent fireworks (I remember this from ‘indoor fireworks’). It’s expensive, but impressive. It obviously wowed Pharoah…

h/t Lisa Adamson’s FB page

50th anniversary of the LED + 2 days

October 11, 2012 • 6:37 am

Yep, it was first demonstrated on October 9, 1962 by Nick Holonyak, Jr., an employee of General Electric.  As Wired notes,

In the early 1960s, the only light emitted from LEDs was infrared. The race to produce a visible LED had GE researchers scrambling to be first.

Holonyak suggested using a mixture of gallium arsenide and gallium phosphide (GaAs phosphide). His fellow scientists said the mixture would not work. In fact, they were pretty vocal in their disagreement with Holonyak’s hypothesis.

“You so and so, if you would have been a chemist, you would have known that wouldn’t work and all that,” Holonyak told the producers of A Brilliant Idea: Nick Holonyak, Jr. and the LED, a video about his colleagues’ lack of faith in his idea.

Undeterred, Holonyak forged head and created a GaAs phosphide crystal. Fifty years ago today, he presented the first visible LED to GE executives. His mixture created a red glow that’s still seen today. But Holonyak believed that the dim glow of his invention was just the beginning.

Holonyak thought LEDs would replace incandescent bulbs, and they may still, for they’re already in flashlights.  We’re in a fluorescent-light phase now, but I suspect Holonyak will be proved right.

Here’s a short video featuring the still-extant inventor, and the longer film, with the link given above (I can’t embed it), is worth watching if you have 23 minutes to spare.  You should, because you use LEDs every day.

Planet of the viruses

October 11, 2012 • 6:36 am

by Matthew Cobb

In the early 1670s, pioneer microscopist Antoni Leeuwenhoek peered into the tiny glass ball of his single-lens microscope and looked at a capillary tube that contained water and crushed pepper-corns. Leeuwenhoek was trying to discover why pepper was hot, and although he never found the answer to that question, he made a momentous discovery: microbes. To his amazement, the water was full of bazillions of tiny organisms, and there seemed to be no end to them –  life appeared to extend into the infinitely small.

That isn’t quite true, but it is true that our planet is covered with microbial life and above all with viruses. For most biologists, viruses aren’t actually alive – they are bits of DNA (or sometimes RNA) and protein that pirate cell machinery to reproduce. However, whatever their formal status, their consequences on health and well-being can be devastating.

In a recent study published in the Journal of Virology, Tae Woong Whon and his co-workers from Kyung Hee University in South Korea decided to try and estimate how many viruses there are in a cubic metre of air, and to see how that density varies in space and time.

They collected air samples from just above the ground in three different environments – a residential area, a forest and a factory, and also collected rainwater from the residential area. They then filtered their collections and then – like Leeuwenhoek – looked at what they had found, and then used those sampling counts to estimate how many viruses and bacteria there would have been in each of the land sites. Here are some examples of the viruses they saw, imaged through transmission electron microscopy:

Fig 2

Intriguingly, they found no differences between the three kinds of sites, and overall the number of particles was lowest in the winter (temperature and vapour pressure seem to be the key factors, but not humidity).

The overall numbers are mind-boggling:

The number of viruses in a m3 of air ranged from 1,700,000 to 40,000,000, while the number of bacteria ranged from 860,000 to 11,000,000. Even though these things are very small, that’s still an awful lot!

In a healthy young adult, the “tidal volume” – the amount of air you breathe in on an average breath – is about 500 ml, or 1/2000th of a cubic metre. So if you were to lie close to the ground and just breathe, you could be inhaling up to 20,000 viruses and 5,500 bacteria with each breath.

Things might not be quite so alarming, however, as most of the viruses the team identified were not human viruses. They sequenced the bits of DNA they were able to capture, and many of them were known to infect bacteria, plants, fungi and various birds. However, over 50% of the sequences could not be identified.

So how many viruses and bacteria might there be around us? The volume of the troposphere (the lower part of the atmosphere) is around 8 x 1018 m3. If we assume that the average density of viruses in a m3 of troposphere is, say, 1 millionth of that found by Whon and his colleagues, then that would mean that, swirling about above our heads, there would be about 320,000,000,000,000,000,000 viral particles.

The amazing density of bacterial and viral DNA covering the planet – including in the sea, which isn’t included in these guestimates – suggests that if aliens were to look down at our world, they wouldn’t identify it as the planet of the humans, or of the cats, or even of the insects. It would be the planet of the viruses.

Reference: Tae Woong Whon, Min-Soo Kim, Seong Woon Roh, Na-Ri Shin, Hae-Won Lee and Jin-Woo Bae (2012) Metagenomic Characterization of Airborne Viral DNA Diversity in the Near-Surface Atmosphere. J. Virol. 86:8221-8231

h/t Pierre Barthélémy (@PasseurSciences)

PS I may well have tripped up with the guestimate calculations. Feel free to chip in either to correct (nicely!) or to add – measures of the number of viruses in the sea would be good, as would some kind of guess of the weight of all that DNA.

EDIT (13 October): Carl Zimmer, author of the excellent A Planet of Viruses (see comment thread) has just had this comment tweeted: “If you stacked all viruses on Earth end-to-end the stack would be 200 million lightyears tall.” Wow.

Curious gorillas gaze at a caterpillar

October 11, 2012 • 1:13 am

by Matthew Cobb

We’ve discussed animal cognition and play a number of times at WEIT, but I don’t think we’ve ever looked at curiosity (perhaps not surprisingly given what it allegedly did to our feline friends). This video from Calgary Zoo shows a couple of gorillas gazing intensely at a caterpillar. A dominant male even shoves the other out of the way to get a better look.

Your questions (write on one side of the paper only):

Does this tell us anything about animal cognition?

Are the gorillas so bored in their enclosure that even a caterpillar distracts them from the tedium of their life?

Are they contemplating the fact that the wriggling larva is apparently able to move through the fence with ease, whereas they remain forever trapped?

Are they curious or are they just looking?

What would happen if the zoo introduced more caterpillars into the enclosure? Would the gorillas simply lose interest?

h/t @TheAtavism

HuffPo blogger makes case for ESP

October 11, 2012 • 12:03 am

James Carpenter, Ph.D., is a psychologist and a parapsychologist; the second characterization should give you pause, since about 90% of parapsychologists believe in ESP, precognition, and other forms of woo.  Sure enough, Carpenter pushes these ideas in a new post at HuffPo: “Not second sight, but first sight.”

Here is his theory, which is his:

Parts of this theory are familiar. Research has told us that brain events stand behind every thought we think and lead to them. And we have learned that many implicit psychological processes precede our experiences too, processes like subliminal sensations, stored memories and long-term values. These things aren’t conscious in themselves, but the unconscious mind uses them to help lead to whatever we do become conscious of.

That’s not a part of Carpenter’s theory; it’s simply the working assumption, supported by a lot of data, of all reputable neuroscientists.

Here’s the woo-ey part, which Carpenter is flogging in a new book (I won’t mention it here):

A difference about this theory, called “First Sight,” is that it assumes that a much bigger domain of unconscious information stands behind experience. This includes things that are beyond the reach of our senses — it includes the extrasensory. And it assumes that this reference to extrasensory information is not rare, but that it is continual.

First Sight brings in what is popularly called the “paranormal.” It is different from previous ways of thinking about the paranormal in that it shows that our use of extrasensory information is actually normal and helpful, although unconscious. No “para” is needed anymore. This theory leads us to an expanded idea of our normal psychology.

. . . It also shows that our unconscious use of non-local information is essentially continuous with how we use other kinds of implicit information. ESP, memory, subliminal perception, implicit physiological responses to emotional events and many other things all follow the same tacit rules. No need for “para.”

The “new” part of his theory is a distinction without a difference.  Simply saying that ESP is “normal” doesn’t make it something with either a known mechanistic basis or solid evidence behind it (there isn’t any). One might as well say that because God’s intervention in the world is an everyday occurrence (many Sophisticated Theologians™ believe this), there’s no need for the “super” in “supernatural.”

Here’s more of Carpenter’s “theory”:

My major thesis is that psychic abilities such as ESP — long considered to occur only in “gifted” individuals or on rare traumatic occasions — are, in fact, ongoing subconscious processes that continuously influence all of us in making everyday decisions. As the model’s name implies, these common abilities should not be regarded as an incidental “second sight” but as a critical “first sight,” an immediate initial contact with information not otherwise presented to our known senses. And just as we are not typically aware of other subliminal or incidental stimuli that impinge upon us and influence us in myriad ways, so too we typically remain unaware of this extrasensory information and its influence. Subliminal primes lead us to experience related things more quickly and more emotionally than we otherwise would. Psi information does the same.

This is not new, either: parapsychology researchers have long differed in how they view ESP and precognition: some think that only special individuals have it; others that it’s present in all individuals (though sometimes to varying degrees). Carpenter’s theory is simply the same old discredited woo recycled by changing a few words.

As support for Carpenter’s “theory” of ESP, he cites the “precognition” study of Daryl Bem (reference below) apparently unaware that Bem’s study has repeatedly failed to be replicated (see also here), and is now in disrepute.

And of course HuffPo is also in disrepute; were I the editor of the “science” section of that site, I’d be furious, for in one place HuffPo purports to push good science and debunk antiscientific nonsense (see, for instance, Cara Santa Maria’s nice anti-woo video series “Talk Nerdy to Me“), while on the other it claims that debunked parapsychology is “solid science”. (I’ll drop a line to Santa Maria and let her know of this journalistic dissonance).

I’m currently reading Nick Humphrey’s 1996 book on why people believe supernatural phenomena (reference below). In it, Humphrey makes no real distinction between religious belief on the one hand and belief in paranormal phenomena on the other. Indeed, they show many similarities. In both cases belief stems from a combination of personal experience, second-hand information and a priori reasoning, and in both cases people continue to believe in the supernatural (or paranormal) after hearing solid evidence to the contrary. Further, in both cases the advocacy of supernatural woo is combined with a denigration of science itself, and the claim that scientists are both blind to real supernatural phenomena and committed to ignoring non-materialistic claims. (I have very often encountered attacks on the “limitations of science” in my last year of reading theology.)

Two other parallels: most Americans believe in paranomal phenomena like ESP, though they haven’t had a paranomal experience themselves (same with religion and personal revelation), and both paranormal and religious claims are accorded an unwarranted “deference,” as if the acceptance of supernatural claims deserves some kind of respect. (I’m not sure why that is; it could have to do either with the fact that it’s a majority view or with the notion that we shouldn’t criticize the possibility of “higher powers”).

At any rate, I hope that Santa Maria or someone like her will go after ESP on the HuffPo’s pages. How delicious to see claims in one part of that blog refuted in another! Their whole mission of promoting good science (or so the editor told me) is completely undermined by the religious nonsense and woo pushed in other parts of the site.

____________

Bem, D. 2011. Feeling the future: experimental evidence for anomalous retroactive influences on cognition and affect . Journal of Personality and Social Psychology 100: 407-425.

Humphrey, Nicholas.  1996.  Leaps of faith: Science, Miracles, and the Search for Supernatural Consolation. Basic Books, New York.