The Atlantic hurricane season begins June 1, and forecasts suggest an above average year. And as we all know, Atlantic hurricanes are deadliest when they get into the warm Gulf of Mexico. It is almost like a hurricane jumping on a trampoline. They can go from Category 1 to Category 5 in 24 hours in such a favorable environment. But this year, as we also know, there is something different about the Gulf. It is full of oil. What are the implications of this fact for hurricanes? And conversely, what might a powerful hurricane do to the oil spill if it were to run across it? This is a topic I've been thinking about, and I don't have definitive answers yet. I'd like to do more research and interview some experts--but for now, let's take a rough and dirty approach to the issue, based on what is already out there. And let's tackle the first question first: What would an oil slick do to a hurricane? According to storm ace Jeff Masters, the answer is not very much. Here's what Masters is thinking. It's certainly true that oil on the surface of the ocean could inhibit a hurricane's access to its fuel source--the warm seawater ...

In that their demographic history is complicated. The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius:

… domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.

I wonder if domesticates in particular exhibit these more complex reticulated patterns in their phylogenies because they spread along human trade routes.

Supernovae (plural for supernova) are such intense, powerful events, we can never seem to get enough of them.  Some things in the universe are so overwhelming that we return to them again and again, trying to encompass them.  Supernovae grab us on all levels; the science is there, the beauty, the drama… they even appeal to the child in us; you know, the one that likes to set off fireworks and watch them go “boom”.

I couldn't resist

Folks, you don’t get much bigger “booms” than supernovae.

There are several types of supernovae, and in this post I talked about the mechanics of supernovae (if you’re interested).  As talked about in the linked post, getting as close as 6,000 light years to a supernova may be a really bad idea, but let’s pretend we’re in a special spacecraft that lets us get right up next to a supernova.

Hush.  I can pretend whatever I want.

NASA/JPL Hubble ST - SN1994D

Okay, we’re skimming along the surface of a star at least 10X the size of our sun.  Let’s say we’re studying it as we know it’s a candidate for supernova.  We’ve known for thousands of years.  Now, all of a sudden, the trigger is pulled.  The core begins runaway nuclear fusion, and at this point nothing known in the universe will stop the inevitable.  The core collapses.

As we have been skimming along the surface, the star’s gravity has us and we’re suddenly pulled inward toward the core, along with the rest of the star’s mass.   Almost instantly the core rebounds, and we’re blasted out at about 30,000 km/s, along with most of the star’s mass.  During the initial shock wave, you’ll be surrounded by a light greater than that of an entire galaxy, with its millions and billions of stars.  You are surrounded by as much energy as our sun will radiate in its entire life span, all being blasted out into space.  You are riding a wave like none other.

NASA/JJ Hester/ Hubble ST -- Cygnus Loop SN Remnant -- What a beauty!

There’s a probability of one supernova every 50 years in a galaxy the size of  the Milky Way.  So… until we get intergalactic space travel, you’re stuck with just one supernova…

… but what a ride!

Whither the lizards?

That’s what biologist Barry Sinervo has been asking lately. In a study published on Friday in Science, Sinvero’s team raised the alarm about lizards around the world, saying that at the very least 6 percent of lizard species will go extinct by 2050, and as many as 20 percent could disappear forever by 2080.

Sinervo and his colleagues make this claim based in part on surveys they did in Mexico.

Sinervo and his team surveyed 48 species of spiny lizards at 200 sites on the Yucatan peninsula in Mexico that had been studied in detail from 1975 to 1995 and found that 12 percent of that population had already become extinct by 2009.

The lizards lived in well-protected areas like national parks, so it wasn’t habitat destruction that caused the population decline, Sinervo said. Instead, it was a tale of rising temperatures disrupting lizard lives [San Francisco Chronicle].

A lot of studies point the finger at global warming in one way or another, but Sinervo’s team says that there’s a good reason why lizard populations would fade in a warmer world.

Global warming appears to be lengthening the period of the day when lizards must seek shelter or risk fatal overheating. In the breeding season, that sheltering period is now so long that females of many species are unable to eat enough food to produce eggs and offspring [Washington Post].

To bolster their claim, the team created their own fake lizards equipped with thermometers and set them out in the Mexican sun. In two areas where the lizards seem to have disappeared, Sinervo says, there were more than 9 hours a day on average that would’ve been too hot for the lizards to come out of hiding. In two areas where lizards still remained, the midday heat was far less brutal.

In an accompanying essay in Science, Raymond Huey writes that the case is a strong one, and worrisome. However, he wonders, can you really make extinction predictions based on these findings?

Huey warns that not seeing lizards doesn’t mean that they’re not there. They may just have been overlooked. “Populations go up and down,” he says. Still, he notes, Sceloporus [a Mexican lizard] is very conspicuous. “It would be hard to miss” [Nature].

Only follow-up surveys can truly confirm that the lizards’ slow disappearance is real and not “psuedo-extinction,” Huey says. Sinervo and his team are presently in Spain, preparing to do a survey in the Pyrenees Mountains.

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Image: Fausto Mendez de la Cruz

Hitchhiking women's hair color. "To test the effect of women's hair color on the frequency of offering help, male (n = 1,508) and female (n = 892) French motorists were tested in a hitchhiking situation. Five 20- to 22- yr.-old female confederates wore a wig with blonde, brown, or black hair. Each confederate was instructed to stand by the side of a road frequented by hitchhikers and hold out her thumb to catch a ride. Blonde hair, compared with brown hair or black hair, was associated with a small but significantly larger number of male drivers who stopped to offer a ride (18 vs 14%). No difference was found for those with brown and black hair (14 and 13%, respectively). No effect of hair color was found for female drivers who stopped. The greater attractiveness associated with blonde hair for women appears to explain these data." Photo: Wikimedia commons/Roger McLassus Related content:
Discoblog: NCBI ROFL: Bust size and hitchhiking: a field study.
Discoblog: NCBI ROFL: Women's bust size and men's courtship solicitation.
Discoblog: NCBI ROFL: Eye Tracking of Men’s Preferences for Female Breast Size and Areola Pigmentation. WTF is NCBI ROFL? Read our FAQ!

Didn’t spend enough time on the internet today for a Daily Data Dump. But,

1) ResearchBlogCast #6, sans Kevin Zelnio.

2) Noah Millman is on Bloggingheads.tv.

In the post below I pointed to various differences in regards to acceptance of evolution by demographic. One of the issues is that just because X correlates with Y, does not entail that X causes Y (and of course, if X correlates with Y, and Y correlates with Z, that does not entail that X correlates with Z). You can use the GSS to run some regressions and see what the strongest predictive variables. Because of this I know that the variable BIBLE is very predictive of skepticism of evolution. Additionally, even smart people with college educations who have a literal inerrant view of the Bible are skeptical of evolution. To show the power of Biblical fundamentalism I thought it would be useful to plot differences in regards to the Index of Creationism by various demographics for both Fundamentalists and non-Fundamentalists. So below I have a set of charts which have two series, one for Fundamentalists, and one for non-Fundamentalists, of a given demographic. So for example one chart has Fundamentalists and non-Fundamentalists separated by attainment or non-attainment of college educations.

The primary variables are BIBLE & SCITEST4.

BIBLE is:

Which of these statements comes closest to describing your feelings about teh Bible? 1. The Bible is the actual word of God and is to be taken literally, word for word. 2. The Bible is the inspired word of God but not everything in it should be taken literally, word for word. 3. The Bible is an ancient book of fables, legends, history, and moral precepts recorded by men.

I recoded so that responses 2 and 3 are classed as non-Fundamentalist.

SCITEST4:

For each statement below, just check the box that comes closest to your opinion of how true it is. In your opinion, how true is this? d. Human beings developed from earlier species of animals.

I created the Index of Creationism = (% “definitely not true”) X 3 + (% “probably not true”) X 2 + (% “probably true”) X 1, from three of the four responses to SCITEST4.

In the charts below the blue squares = Fundamentalists. The red diamonds = non-Fundamentalists. I rescaled so that 1 is the minimum for the Index of Creationism on all charts.

Reminder: blue squares = Fundamentalists, red diamonds = non-Fundamentalists. A few notes. For stupid, average and smart, I simply recoded the WORDSUM vocabulary test. Stupid = 0-4, Average = 5-7 and Smart = 8-10. For region, it’s pretty self-explanatory, though do note that I placed Texas and such in the South, not the West. The West are the Pacific & Mountain regions only. Those with no college degree includes all those without bachelor’s degrees (non-four year degrees).

Do you notice the counterintuitive pattern when it comes to intelligence and Creationism, and income and Creationism? The sample size for SCITEST4 isn’t that hot, so you could chalk it up to noise, but I’ve done enough poking around the GSS to trust this. There is a pattern where very intelligent and/or high socioeconomic status Fundamentalists adhere to the viewpoint which in the general population is correlated with lower intelligence and socioeconomic status. I think the dynamic here is partly the same one when it comes to political polarization: stupid and lower status people tend to be less ideologically coherent because they don’t spend much time thinking about abstract questions. From what little field investigation I’ve performed dull human tends to fixate on sensory or interpersonal questions, not intellectual ones. In other words, very stupid Fundamentalists may not even understand what they’re being asked. Very stupid people also tend to agree that they’re political moderates more often than the intelligent; moderate seems like a good thing to say for someone who never thinks about politics. I think this issue to some extent explains the lack of effect among Roman Catholics. Unlike Protestants views about the Bible are less emphasized in Roman Catholicism traditionally, so many Catholics may not have well thought out opinions on the topic. Those who answer that they believe the Bible is the literal and inerrant Word of God may not really even know what this really should mean. The question is geared toward those with Protestant presuppositions.

There may also be the secondary effect of self-selection when it comes to intelligence and income for Fundamentalists. Fundamentalism tends to correlate with lower intelligence and income, and those who choose to remain Fundamentalists despite higher intelligence and income may self-select for the most extreme and rigorous subset of this class. More theologically liberal and lax Protestant denominations tend to be biased toward wealthy and well-educated individuals, some of whom have switched denominations as they go up the class hierarchy. Those who refuse to switch as they ascend the class ladder may be a peculiar subset. By contrast, lower class status denominations may include more lax individuals in relation to belief or practice who would not feel comfortable in a liberal denomination because of their class status.

This pattern of social sorting probably explains the fact that region still has a significant predictive power even controlling for Fundamentalism. Northeastern Fundamentalists are equivalent in skepticism toward evolution as Southern non-Fundamentalists. I have seen similar tendencies among black Americans in relation to social issues and religion; secular individuals who are black are invariably more socially conservative that secular individuals who are white. I think this is a function of the fact that secular blacks are embedded in a more socially conservative cultural milieu. Similarly, non-Fundamentalist Southerners are embedded in a more Creationist culture, as Fundamentalists are numerically more preponderant in the South than non-Fundamentalists. New Englanders exhibit the inverted tendency. Someone who is a conservative, Fundamentalist or Republican in New England may actually be liberal, theologically moderate and a Democrat in the South.

Variables: Region, Wordsum, Relig, Income, Degree, Scitest4

After a quarter-million scientific papers, you’d better hope your methodology was solid.

Most of the studies you’ve probably heard of that try to tie a specific region of the brain to an action or feeling probably relied on a functional MRI technique that tracks the flow of oxygenated blood–so when you see a region “light up” on an fMRI image, that’s not the fMRI picking up the actual neurons firing. Rather, it watches for small changes in blood oxygen levels in the region. This method, called blood oxygenation level-dependence (BOLD), presumes that active neurons use more energy and thus require more oxygen. Now, in a study in Nature, researchers at Stanford Medical Center have provided direct evidence that the inference is correct.

Lead researcher Karl Deisseroth employed a technique called optogenetics to prove the point. He and his colleagues engineered brain cells that respond to a flash of blue light; when they did this trick on cells in the motor cortex of rats, the flash of light acted as a trigger to active the neurons there. The idea was that they would examine these rats with fMRI at the same time they stimulated those motor neurons with the blue light. If the fMRI lit up in the same places where the researchers knew they were stimulating neurons, they could be confident that fMRI was really picking up brain activation.

Sure enough, when the neurons were turned on with a pulse of blue light, the researchers detected a strong BOLD signal emanating from the motor cortex neurons’ neighborhood. The BOLD signals were exactly what was expected. “It was very compelling and reassuring,” Deisseroth says. “Everyone can breathe a sigh of relief” [Science News].

Still, the brain’s complexity never ceases to amaze: While the optogenetic stimulation produced neuron activity that the fMRI scans registered as a BOLD signal, there was other activity besides that showing up as BOLD activity. But, Deisseroth says, those seem to be secondary signals caused by the initial neuron activity.

“We’re certainly not saying that other processes don’t contribute to these signals,” he says. “We’re saying that driving these excitatory neurons kicks it off” [Science News].

Besides reassuring neuroscientists, the Stanford work could also open doors for them, like allowing them to see when brain activity is one region is connected to activity on the other side of the brain.

Optogenetics works at micro scale and fMRI covers wide regions of the brain—together this means that scientists have a way to intervene and experiment with entire brain circuits, to finally see how a certain type of brain cell affects the wider global activity of the entire brain [Scientific American].

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Image: NASA

Right from the moment of birth, women face a ticking clock, counting down to the end of their life’s fertile phase. In their fourth month in the womb, their immature ovaries begin to develop primordial follicles, the structures that will eventually give rise to egg cells. At birth, each ovary has around 400,000 follicles and won’t make any more. During each menstrual cycle, around a thousand of these cells become activated per ovary. By the time a woman goes through menopause, she has less than a thousand left and her chances of being a biological mother are slim to none.

Follicles stay in a dormant phase that can last for months or even years, until they are gradually activated. Now, a team of Chinese, Japanese and American scientists, led by Jing Li from Stanford University, have found a way to activate these dormant cells at will. It’s a step that could help infertile women, or those who freeze their ovaries before cancer treatments, to eventually have their own children.

Li’s work shows that despite their ability to slumber for decades, follicles only need a gentle nudge to awaken. She managed to activate dormant follicles in the ovaries of newborn mice using chemicals that shut off a single gene called PTEN. When she transplanted these clusters into mice whose ovaries had been removed, they developed into mature follicles. From these came eggs that could ultimately be fertilised and develop into healthy pups.

As with most such discoveries, Li’s work hinges on a lot of previous research. In particular, two years ago, Pradeep Reddy from Umea Universit showed that PTEN controls the steady activation of follicles. If mice lack the gene entirely, all of their dormant follicles become activated at once and their entire supply is exhausted in early adulthood. This dramatic switch means that their ovaries fail prematurely. Li wanted to see if she could achieve the same ends in a more controlled way.

Rather than knocking out the PTEN gene altogether, she temporarily blocked it by soaking ovaries from newborn mice in a chemical called bpV(pic). PTEN works by holding back another gene called PI3K, so Li also tried a chemical called 740Y-P, which activates PI3K. In normal ovaries, the unleashed PI3K targets a protein called Foxo3, which is then removed from the nucleus of follicle cells. This is the trigger that activates them, and that’s exactly what Li saw in her chemically treated ovaries. Foxo3 left the building and the follicles matured, particularly if they were transplanted into a living host.

None of the cells ever developed into a tumour, which is a real concern since one of PTEN’s role is to keep cancer at bay. Instead, the activated follicles eventually produced oocytes, the precursors of egg cells, which seemed normal in every important respect. They showed the standard patterns of methylation – chemical ‘Post-it’ notes that add onto genes and affect how, when and where they are activated. When fertilised, the oocytes grew into healthy embryos and eventually into 20 healthy pups. And best of all, these pups were themselves able to bear live young of their own.

Li showed that the same trick might work in humans too, but with more technical challenges. During operations on women with ovarian cancer, she managed to get pieces of ovary containing primodial follicles. She treated the tissues with the same chemicals as before and transplanted them into mice. The result: mature follicles and oocytes. These weren’t fertilised for obvious ethical concerns, but they seemed to show some problems with their nuclei – that will need to be checked in studies using other primates before this technique could ever be used safely in people.

Reference: PNAS http://dx.doi.org/10.1073/pnas.1001198107

More on fertility:

• One gene stops ovaries from turning into testes
• Fertility rates climb back up in the most developed countries
• The heavy cost of having children
• Did conflict between old and young women drive origin of menopause?

According to Dale Evans, a professor at University College Cork in Ireland, he just wanted to bring up an interesting tidbit of animal behavior while chatting with a colleague. But the journal article he referenced, "Fellatio in fruit bats prolongs copulation time," didn't just cause raised eyebrows, it also prompted a sexual harassment complaint. New Scientist reports:
As part of what he says was an ongoing discussion on human uniqueness, Evans showed a copy of the fellatio paper to a female colleague in the school of medicine. "There was not a shred of a sign of offence taken at the time," Evans says. "She asked for a copy of the article." A week later he got a letter informing him that he was being accused of sexual harassment. The female colleague later said that she asked for a copy of the article only to cut short the conversation, which she found disgusting and offensive. Let's just hope that she didn't take a look at the video the original researchers put together of the bats in action. Related Content:
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Add one more to the list of environmental factors that could contribute to the rise in attention deficit hyperactivity disorder (ADHD): pesticides. A new study out in Pediatrics argues that there’s a connection between high exposure to common pesticides and increased risk for children developing ADHD.

Maryse Bouchard and colleagues looked at more than 1,100 children aged between 8 and 15. All of them had been sampled by the National Health and Nutrition Examination Survey (NHANES) between 2000 and 2004, and 119 had been diagnosed with ADHD. Bouchard’s team studied their urine samples for chemicals called dialkyl phosphates, which result from the breakdown of organophosphate pesticides used to protect fruits and vegetables.

For a 10-fold increase in one class of those compounds, the odds of ADHD increased by more than half. And for the most common breakdown product, called dimethyl triophosphate, the odds of ADHD almost doubled in kids with above-average levels compared to those without detectable levels [Reuters].

According to the researchers, there are about 40 organophosphate pesticides in use in the United States, the most famous of which is malathion. It was heavily sprayed in California in the early 1980s to try to kill the Mediterranean fruit fly, and also about a decade ago to try to stop the spread of West Nile virus.

In 2008, detectable concentrations of malathion were found in 28 percent of frozen blueberry samples, 25 percent of fresh strawberry samples and 19 percent of celery samples, a government report found [MSNBC].

Using the large sample of children from NHANES allowed the researchers to adjust for location, race, and other factors that have confounded studies like this trying to link an environmental factor to a particular condition. However, the scientists admit, the weakness of their study is that using NHANES data allowed them to see just one urine sample taken at one point. Thus, they couldn’t determine the source of contamination, nor could they see how levels of the chemicals in question built up over time. And since that buildup over time is what would spur the potential neurochemical changes that would increase ADHD risk, Bouchard and colleagues write, their study shows correlation but not causation.

Bouchard’s analysis is the first to home in on organophosphate pesticides as a potential contributor to ADHD in young children. But the author stresses that her study uncovers only an association, not a direct causal link between pesticide exposure and the developmental condition. There is evidence, however, that the mechanism of the link may be worth studying further: organophosphates are known to cause damage to the nerve connections in the brain — that’s how they kill agricultural pests, after all [TIME].

So there’s a lot left to be proven. But Bouchard’s study is another reminder in favor of the old stand-by: wash your fruits and vegetables thoroughly.

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Image: iStockphoto

I know that there are rules to the way laws are made by our government here in the U.S., and that sometimes these rules seem weird and arcane. In general, these rules have evolved to make sure that the majority doesn’t stomp on the minority, and the minority still has a voice.

But it’s also clear that those rules can be abused. In the case of U.S. Congressman Ralph Hall (R-TX), “abuse” isn’t nearly a big enough word. “Cynically manipulated” might be a bit better. He killed a bill that would fund science innovation and education by tying it to punishing people who look at porn at work.

Seriously. This is truly disgusting, and has to be seen to be believed. Please read that link above.

Basically, the America COMPETES act, instituted under the Bush Administration in 2007, funds a lot of technology and other endeavors to keep the US competitive in the world market. Of course, in the current economic market, we don’t have a lot of money to go around. But this bill would have re-authorized that earlier act, funding what is essentially seed corn, making sure that in the years to come we have a robust investment in our own economy. I wasn’t that familiar with it, but after reading about it I’ll say it’s one of the few things done by the previous President I think is a good idea. So did a lot of others: this reauthorization bill had over 100 co-sponsors in the House.

I say “had”, because after the shameful and politically transparent move by Rep. Hall, the bill is basically dead.

This bill would have extended funding for several more years in key places, including science education. Hall is the ranking Republican on the House Science and Technology Committee that prepped the bill. There had been objections by Republicans on the committee to the amount of spending of the bill. The Democrat-controlled committee made some concessions in that area (shaving 10% of the spending off), but still passed the bill out of committee. The next step would be a vote on the floor of the House.

However, right before it was to go to the floor, Rep. Hall called a Motion to Recommit. Because of those weird rules I mentioned above, this meant that Congress would either have to agree to the Motion and have the bill sent back to committee — where it would die — or overrule the Motion. Now follow this carefully: part of the Motion Rep. Hall submitted was language added to the bill that said that it would prevent the government from paying salaries to employees who looked at porn on government computers.

By doing this, Hall basically bet all his chips. Hall’s move left Congress, notably Democrats, with two options: kill this much-needed bill that invests in America’s future in science and technology, or overrule a motion punishing people for downloading pornography. If they did the latter, the far right noise machine, always eager for red meat in the political arena, could then say Democrats voted to continue paying employees who looked at porn.

Facing this sort of choice, a large number of Democrats backed off. Hall’s Motion passed, and the bill went back to committee where it’s now essentially dead.

Of course, watching porn on the government’s dime has nothing to do with this bill. The only reason I can think of that this language was added is that it was a gambit where Hall wins either way: the bill dies, or Democrats put their head in the right-wing media guillotine. Representative Bart Gordon (D-TN), who is the Chairman of the committee, agrees:

We’re all opposed to federal employees watching pornography. That is not a question; but that’s not what this was about… The Motion to Recommit was about gutting funding for our science agencies.

And while Representative Hall pulls this deplorable stunt, our nation is suffering mightily in scientific education. In this heart-rending post by my friend, astronomer and educator Pamela Gay, she laments how we’re letting our teachers and our children down by not funding science, technology, engineering, and mathematics. Read her post, then read again what Hall did.

Our future is more important than being a chip in a political game of poker. Unfortunately, in this case, Congress folded.

This photograph of a young man born without eyes is from Stefano De Luigi’s new book “Blanco”. Photographer Stefano De Luigi said that this moment was one of the most difficult in his five-year project. “When you are confronted with blind people there is always the question-shall he/she become sighted some day? In this case the answer was straight and standing in front of me, and this lack of hope was very hard.”

Aiming to raise awareness of the daily battle blind people face, De Luigi started began his project in 2003. With the support of “Vision 2020: The Right to Sight”, an initiative spearheaded by the World Health Organization and a broad coalition of international, non-governmental and private organizations seeking to eliminate avoidable blindness by the year 2020, he photographed blind people in 14 countries – Bolivia, Brazil, Bulgaria, China, Congo, Laos, Liberia, Lithuania, Nigeria, Peru, Rwanda, Thailand, Uganda and Vietnam.

A boy without eyes—birth defect from exposure to Agent Orange—seen at the Nguyen Dinh Chieu school in Hanoi, Vietnam.

It was Friday evening, Gawker writer Ryan Tate's wife was out of town, and he was whiling away the lonely hours by watching 30 Rock when an iPad commercial popped up that touted the new Apple gadget as nothing less than a revolution. Tate got annoyed, fired off an email, and soon found himself in an email fight with Steve Jobs himself. Apple's CEO is known to personally answer some of the emails that flood into the sjobs@apple.com address, and it seems that Tate's pointed message goaded the exec into action. Tate, who has long taken issue with Apple's tight rules on how apps can be written and what content is permissible, argued that the iPad couldn't be considered revolutionary because "revolutions are about freedom." Several hours later, Jobs fired back with his version of what the iPad offers: "Yep, freedom from programs that steal your private data. Freedom from programs that trash your battery. Freedom from porn. Yep, freedom." And it was on. Tate got pretty heated in some of his messages to Jobs, but in the aftermath he stresses his respect for Jobs and his methods. As Tate writes in his blog post digesting the whole affair:
Rare is the CEO who ...

Here’s a fun logic puzzle (see also here; originally found here). There’s a family resemblance to the Monty Hall problem, but the basic ideas are pretty distinct.

An eccentric benefactor holds two envelopes, and explains to you that they each contain money; one has two times as much cash as the other one. You are encouraged to open one, and you find $4,000 inside. Now your benefactor — who is a bit eccentric, remember — offers you a deal: you can either keep the $4,000, or you can trade for the other envelope. Which do you choose?

If you’re a tiny bit mathematically inclined, but don’t think too hard about it, it’s easy to jump to the conclusion that you should definitely switch. After all, there seems to be a 50% chance that the other envelope contains $2,000, and a 50% chance that it contains $8,000. So your expected value from switching is the average of what you will gain — ($2,000 + $8,000)/2 = $5,000 — minus the $4,000 you lose, for a net gain of $1,000. Pretty easy choice, right?

A moment’s reflection reveals a puzzle. The logic that convinces you to switch would have worked perfectly well no matter what had been in the first envelope you opened. But that original choice was complete arbitrary — you had an equal chance to choose either of the envelopes. So how could it always be right to switch after the choice was made, even though there is no Monty Hall figure who has given you new inside information?

Here’s where the non-normalizable measure comes in, as explained here and here. Think of it this way: imagine that we tweaked the setup by positing that one envelope had 100,000 times as much money as the other one. Then, upon opening the first one, you found $100,000 inside. Would you be tempted to switch?

I’m guessing you wouldn’t, for a simple reason: the two alternatives are that the other envelope contains $1 or $10,000,000,000, and they don’t seem equally likely. Eccentric or not, your benefactor is more likely to be risking one dollar as part of a crazy logic game than to be risking ten billion dollars. This seems like something of a extra-logical cop-out, but in fact it’s exactly the opposite; it takes the parameters of the problem very seriously.

The issue in this problem is that there couldn’t be a uniform distribution of probabilities for the amounts of money in the envelopes that stretches from zero to infinity. The total probability has to be normalized to one, which means that there can’t be an equal probability (no matter how small) for all possible initial values. Like it or not, you have to pick some initial probability distribution for how much money was in the envelopes — and if that distribution is finite (”normalizable”), you can extract yourself from the original puzzle.

We can make it more concrete. In the initial formulation of the problem, where one envelope has twice as much money as the other one, imagine that your assumed probability distribution is the following: it’s equally probable that the envelope with less money has any possible amount between $1 and $10,000. You see immediately that this changes the problem: namely, if you open the first envelope and find some amount between $10,001 and $20,000, you should absolutely not switch! Whereas, if you find $10,000 or less, there is a good argument for switching. But now it’s clear that you have indeed obtained new information by opening the first envelope; you can compare what was in that envelope to the assumed probability distribution. That particular probability distribution makes the point especially clear, but any well-defined choice will lead to a clear answer to the problem.

.

My post last week about Creationism by region set off a fair number of follow up questions. I’ve actually probed the GSS evolution related variables a lot in the past, but I thought I would put it together in one post in a simple fashion for new readers. I used the SCITEST4 variable since its sample size is the largest. The question asked was: ” Human beings developed from earlier species of animals.” It was asked between 1993 and 2000.

There are four answers, definitely true, probably true, probably not true, definitely not true. I put the frequencies in a table below, but I thought it would be useful to have one number to summarize the propensity toward creationism in a demographic. Therefore, I created a simple “index of creationism.” The formula to create it is pretty obvious:

Index of Creationism = (% “definitely not true”) X 3 + (% “probably not true”) X 2 + (% “probably true”) X 1

If the Index of Creationism for a demographic was zero, that means that everyone in the demographic accepted that evolution was definitely true. In contrast, if it was three, that means that everyone in the demographic believed that evolution was definitely not true. The bar chart below has the Indices of Creationism sorted. Below it is a table with the frequencies as well (unsorted, clustered by demographic kind).

HUMANS DEVELOPED FROM ANIMALS….

Update: I forgot to add the variables for the GSS query:

Row: sex race degree(r:0-2″Non-College”;3-4″College”) wordsum(r:0-4″stupid”;5-7″average”;8-10″smart”) sei(r:17-37″low”;38-67″middle”;68-97″high”) god(r:1-2″atheist & agnostic”;3″higher power”;4-5″Believe in god with doubts”;6″Know god exists”) relig bible age(r:18-40″18-40″;40-*”40+”) polviews(r:1-3″Liberal”;4″Moderate”;5-7″Conservative”)

Column: scitest4

Sex Lives of Supreme Court Justices:

Now that the sex lives of Supreme Court justices have become grist for commentators, we are finally free to discuss a question formerly only whispered about in the shadows: Why does Justice Antonin Scalia, by common consent the leading intellectual force on the Court, have nine children? Is this normal? Or should I say “normal,” as some people choose to define it? Can he represent the views of ordinary Americans when he practices such a minority lifestyle? After all, having nine children is far more unusual in this country than, say, being a lesbian.

The GSS can answer this question. Sort of. It turns out that the highest number of children it asks about are “8 or more.” Limiting the sample to 1998-2008 so it has some contemporary relevance, ~1% of respondents in the GSS has 8 or more children. But that’s not quite fair, since many respondents are young adults, or just starting their families. Limiting the sample to those who are 60 years or older you have ~3.5%. Limiting to 70 and above it goes up to ~4.5%. Scalia is 74 years old, so I think it might be appropriate to judge him by his generation, though the relative gerontocracy of the Supreme Court, and American politics in general, might warrant examination. In 2008 in the GSS asked about sexual orientation, and ~2% of women stated they were lesbian, gay or homosexual. So whether Scalia is more abnormal than a lesbian measured against the general population depends on the reference population you use. For his generation, probably not, but for this generation, perhaps.

From fantasy to fact? Personal Genomics, tipping points and a personal perspective:

But now I think we’ve turned a corner. It feels, to mix metaphors, that we’ve hit a tipping point. The Human genome project, the mapping and sequencing of the/a human genome from 1990 to 2003, cost approximately 2,700,000,000 dollars (that’s 2.7 billion, I wanted to get all the zeros in). Celera did the genome for 300,000,000. The cost of sequencing an entire human genome has been plummeting ever since. In 2007, the cost of sequencing the genome of James Watson (co-discoverer of DNA) was about 2,000,000. The today cost is about 10,000. Complete Genomics and other companies are on the march to quickly reducing the cost of sequencing a genome under 1,000.
…
So, within a year, the cost of sequencing your, my, genome will reach 1,000. If not less. We’ve seen this coming for years now, and it’s upon us. But what does it mean? A lot of data. But data means nothing without context and analysis. Sequencing my genome would be a waste of 1,000 dollars if I gleaned nothing from it.

I can believe that we’ll be able to get a tarball with our own full sequence for a reasonable price in a few years. Cheaper than orthodontia and cosmetic surgery even. Though the utility in prevention and treatment is a different matter. Most people already have a treasure trove of data through family history, and that doesn’t seem to change behavior for many in the short-term. Once the magical power of genomics wears off I suspect that knowing you have variant X with risk Y will be less transformative than not.

The Wringer washing machine: an unusual cause of breast trauma. "A 66-year-old woman... ...sustained a left-breast injury with a wringer washing machine. While manually feeding clothes through the rollers of her wringer washing machine, her left breast was drawn into the rollers when her blouse became entangled with the clothing she was wringing. The patient was not wearing a brassiere. Her husband immediately responded to her cries for help by disconnecting the electricity to the washing machine and pressing the emergency release for the rollers. This washing machine was immediately discarded." Related content:
Discoblog: NCBI ROFL: Vacuum cleaner injury to penis: a common urologic problem?
Discoblog: NCBI ROFL: Bonus double feature: Acute management of the zipper-entrapped penis.
Discoblog: NCBI ROFL: Rectal oven mitt. WTF is NCBI ROFL? Read our FAQ!

The argonauts are a group of octopuses unlike any other. The females secrete a thin, white, brittle shell called the paper nautilus. Nestled with their arms tucked inside this beautiful, translucent home, they drift through the open ocean while other octopus species crawl along the sea floor. The shell is often described as an egg-case, but octopus specialists Julian Finn and Mark Norman have discovered that it has another function – it’s an organic ballast tank.

An argonaut uses its shell to trap air from the surface and dives to a depth where the encased gas perfectly counteracts its own weight, allowing it to bob effortlessly without rising or sinking. Finn and Norman filmed and photographed live animals in the act of trapping their air bubbles, solving a mystery that has been debated for millennia.

Scientists have long wondered about the purpose of the argonaut’s paper nautilus. No less a thinker than Aristotle put forward a hypothesis. In 300 BC, he suggested that the female octopus uses its shell as a boat, floating on the ocean surface and using her tentacles as oars and sails. Despite a total lack of evidence for this ‘sailing hypothesis’, it was later championed thousands of years later by Jules Verne, who wrote about sailing argonauts in Twenty Thousand Leagues Under the Sea.

Since 1923 and the work of Adolf Naef, the shell has been viewed as a container for the argonaut’s eggs. After mating with a male (who is around 8 times smaller and 600 times lighter), the female secretes the papery shell using the tips of two large tentacles. She lays her eggs within the structure before snuggling inside herself. Besides her eggs, her only housemate is one of the male’s arms – the hectocotylus. The arm doubled as a penis, snapped off during sex and stays inside the female’s body.

Besides the female, her eggs and her disembodied sperm package, the paper nautiluses often contain pockets of air. Naef viewed these as a problem. According to him, the unintended pockets eventually trap argonauts at the sea surface and cost them their lives. That would certainly explain the mass argonaut strandings that are sometimes found, but Naef didn’t have any evidence to back up his claims. Others have speculated that the air bubbles were caused by aeration devices in aquariums and are only seen in captive argonauts. Yet others have suggested that the animals deliberately use the air pockets to maintain their buoyancy but until now, that’s been mere speculation.

Into this debate came Finn and Norman. Their names may be familiar to regular readers – they have discovered the smash-hit octopus that carries coconut shells as a suit of armour, dolphin chefs that can prepare a cuttlefish meal, and the awesome mimic octopus. As with these earlier discoveries, their work on argonauts was based on observations of wild animals. They rescued three greater argonauts (Argonauta argo) from nets in the Sea of Japan, released them into Okidomari Harbour and filmed them as they adjusted to their freedom. It’s their beautiful video that graces the top of this post.

All of the females were checked before their release to make sure that they had no air already trapped in their shells. Without this air, they were in danger of sinking and had trouble keeping their shells upright. All three animals fixed this problem in the same way.

Each one used its their funnel to jet to the ocean surface and bob the top of its shell in the overlying air. The shell has a couple of apertures at the top, which allows the argonaut to gulp in air, sealing it inside with a quick flick of two of its arms. Having sealed away this pocket, it points its funnel upwards, rolling the shell away from the water surface and forcing itself downwards. At the depth where this compressed bubble cancels out its weight, the argonaut levels off and starts swimming.

Naef was clearly wrong. The air isn’t life-threatening or even unintended – the argonaut deliberately introduces it and has total control over it. Once the animals dived again, Finn and Norman grabbed them and rotated them through 360 degrees – not a single bubble emerged. “To my delight the argonauts immediately put to rest decades of conflicting opinions, demonstrating their expert ability at obtaining and managing surface-acquired air,” says Finn.

This neutral buoyancy is a big boon for animals that live in the open ocean, because they don’t have to expend energy on keeping their place in the water column. Other cephalopods use a combination of fins, jets of water and, in the case of the actual nautilus, chambered shells. The argonauts are the only species known to use bubbles, but it’s clearly an efficient tactic. Finn and Norman observed that once they had trapped their air pockets and reached the right depth, they could swim fast enough to outpace a human diver.

By rocking at the surface, the argonaut can also trap a sizeable volume of air, which, in turn, allows it to reach a greater depth before becoming neutrally buoyant. Finn and Norman think that this may allow these unusual octopuses to avoid the surface layers of the ocean, where they would be vulnerable to birds and other top-level hunters.

This penchant for deeper waters may also explain why this behaviour has never been seen before, even though argonauts have featured in aquariums. They simply weren’t kept in tanks that were deep enough. The animals created air pockets as they would in the wild but without the ability to dive to the right depth, the air just brought them back to the surface again.

As a buoyancy aid, the argonaut’s paper nautilus is superficially similar to the much harder shell of its namesake, the chambered nautiluses (right). These animals also use shells with trapped air, but theirs are permanently stuck to their bodies and divided internally into many gas-filled chambers. The two groups – nautiluses and argonauts – are only distant relatives, but they have both arrived at similar ways of controlling their buoyancy.

The argonaut’s solution is undoubtedly simpler and more flexible, but the nautilus’s sturdier shell prevents increasing water pressure from compressing the trapped air too much. As a result, the nautilus can dive far deeper than the argonaut, to a depth of 750 metres.

Finn and Norman’s study may have solved a longstanding argonaut mystery but there’s still much to learn about these enigmatic and beautiful animals. Even though people have known about them since Ancient Greece, their behaviour, distribution and biology are still shrouded in secrecy. To find out more, Finn and Norman are conducting a survey reviewing Australia’s argonauts, and they’ve set up a website with details about how you could help them in their Argosearch.

Reference: Proc Roy Soc B http://dx.doi.org/10.1098/rspb.2010.0155

Photos: Video and bottom photo by Yasushi Okumura, Japan Underwater Films; all other photos by Julian Finn

More on octopuses:

• Octopus carries around coconut shells as suits of armour
• The mimic octopus (my first ever post)
• How to tell Wonderpus Joe from Wonderpus Bob