Relics of a lost race?

One of the issues which I have been exploring and mulling over the past year and a half on this weblog has been the idea that population movements were much more extensive in the past than we have thought until late. I can say a year and a half because my thinking was clarified and made more urgent by the publication in January of 2010 a paper which totally overturned what we’d thought we’d known about what Y chromosomal phylogeography told us about European prehistory. A very common marker in Western Europe which had been assumed to be diagnostic of roots in Europe in the Pleistocene past was now argued to be a signature of the pulse of farmers out of the Middle East! The extremely high frequency of this marker among the Basques, and the presumption that the Basques were the Paleolithic ur-Europeans, allowed researchers in the early 2000s to peg the proportion of Paleolithic hunter-gatherer ancestry across Europe on the order of ~75%. At this point we don’t have total clarity, though I would argue that we need to lean ever ...

“The present study examined the relationship between aggression and players’ names on uniforms in collegiate women’s ice hockey. Aggression was defined as mean penalty minutes per game. Information, i.e., win/loss record, penalties, and names on uniforms, about the 2002-2003 season women’s ice hockey team was obtained via e-mail from 53 of 72 (74% return rate) sports information directors (Division I = 23, Division II = 2, Division III = 28). Analysis indicated that teams with personalized jerseys had significantly more penalty minutes per game than teams without personalized jerseys. However, as the majority of the teams with personalized jerseys were Division I teams and the majority of the teams without personalized jerseys were Division III teams, it is unclear whether results were due to personalized jersey or competition level of play.”

Photo: flickr/ericts8

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Blindfolded and fitted with noise-canceling headphones, this seal might better fit a marine-creature hostage crisis than a scientific study. In reality, it’s making history by showing for the first time that the whiskers of harbor seals are so sensitive that they can discern the shapes of objects by the ripples they make. Marine biologists have known for a while that seals use their whiskers to find fish in dark, murky waters, but as lead researcher Wolf Hanke told LiveScience, whiskers had “never been shown to analyze things” beyond that. Being able to discern shape and size means that seals may use their whiskers to pick out the fattest fish.

Henry, a 12-year-old harbor seal, was plopped into an open-air pool in a Cologne zoo to put his whiskers to the test. Researchers blindfolded and placed headphones on him so that he could only use his whiskers to sense underwater objects. In the pool, the researchers placed a plastic box containing an assortment of variably-shaped paddles. Because they trained Henry to touch his nose to a small plastic sphere whenever he thought a paddle’s ripples were different from a control paddle’s ripples, the ...

Staphylococcus aureus

What’s the News: Adding sugar to certain antibiotics can boost their bacteria-battling ability, according to a study published today in Nature. In particular, sugar helps the drugs wipe out persisters, bacteria that evade antibiotics by essentially going dormant only to flare up again once the danger has passed. This technique could lead to the development of inexpensive, more effective treatments for bacterial infections.

How the Heck:

The study looked at two common bacteria: E. coli, which can lead to urinary tract and gastrointestinal infections, and Staphylococcus aureus, the bugs that cause staph infections. Both can be treated with gentamicin, one of a larger group of antibiotics called aminoglycosides.
The researchers combined gentamicin with different kinds of sugars, including mannitol, fructose and glucose. (Sucrose, the stuff you put in your coffee, is just one of many types of sugars as far as biochemistry’s concerned.
When the scientists added these sweetened antibiotics to bacteria grown in Petri dishes, it killed over 99% of the bacterial persisters. The type of sugar seemed to make a difference, as well; only fructose helped the drug kill S. aureus, for instance.
The goal, said senior author James Collins, was essentially to ...

No expecting mother would ever wish harm to befall her children. Unfortunately, she may have no choice in the matter. Due to the rules of genetics, mums always run the risk of passing a “mother’s curse” onto their sons, but not their daughters.

The curse is an ancient one, the result of events that happened billions of years ago. At a time when all life consisted of single microscopic cells, one of these swallowed another. Normally, the engulfed cell would be digested, but not this time – this time, the two cells formed an alliance. The swallowed cell transferred many of its genes to its host, keeping only those involved in providing energy. It evolved into a mitochondrion – a tiny, efficient battery that would power its host, giving it the energy to become more complex. This alliance is the foundation of all complex life on the planet. All animals, plants, fungi and algae run on mitochondria power.

This means that all animals really have two genomes – their main nuclear one, and a far smaller secondary one in their mitochondria. The two sets of genes work together, each controlling ...

Fabio Gironi recently interviewed me at length for an issue of Speculations, a “Journal of Speculative Realism.” The subject was science and philosophy, which I’ve been known to opine about at some length. But here we’re talking great length indeed. The interview isn’t available separately, but you can download the pdf of the whole issue here (or buy it as a bound copy). My bit starts on page 313. (The rest of the issue is also worth checking out.)

I’m a big believer that academic disciplines should engage in messy interactions, not keep demurely separate from each other. But it’s a tricky business. Just because I’m (purportedly) an expert in one thing doesn’t make me an expert in everything else; on the other hand, it is possible that one area has something to offer another one. So I am in favor of dabbling, but with humility. It’s good for people to have thoughts and opinions about issues outside their immediate expertise, and to offer them in good faith, but it’s bad if they become convinced that experts in other areas are all idiots. So when you find yourself disagreeing with the consensus of expertise in some well-established field, it might very well be because of your superior insight and training, or maybe you’re just missing something. Hopefully in an exchange like this I have something to offer without making too many blunders that would make real experts cringe.

Here’s a sample of the interview.

SC: I would be extremely suspicious of any attempts to judge that the world must ‘necessarily’ be some way rather than any other. I can imagine different worlds—or at least I think I can—so I don’t believe that this is the only possible world. That would also go for any particular feature of the laws this world follows, including their stability. Maybe the laws are constant through time, maybe they are not. (Maybe time is a fundamental concept, maybe it isn’t). We don’t yet know, but it seems clear to me that these are empirical questions, not a priori ones. Because we want to understand the world in terms that are as simple as possible, the idea that the underlying laws are stable is an obvious first guess, but one that must then be tested against the data. Said in a slightly different language: any metaphysical considerations concerning what qualities the world should properly have can be taken seriously and incorporated into Bayesian priors for evaluating theories, but ultimately those theories are judged against experiment. We should listen to the world, not decide ahead of time what it must be.

In a lab in MIT, a flatworm is dying. It’s a planarian – a simple animal that is normally very difficult to kill. Planarians are masters of regeneration; whole animals can be reborn from small clumps of tissue. If you cut one in half, it will simply grow into two planarians. But this animal has been bombarded with high doses of radiation that have wiped out its ability to regenerate. Slowly, its cells are bursting apart. With no new ones to replace them, the planarian has a few weeks to live.

But Daniel Wagner and Irving Wang are about to save it, in a fashion. They transplant one special cell from a donor planarian into the terminal individual’s tail. The cell starts to divide. It produces skin, guts, nerves, muscle, eyes and a mouth.

As the planarian dies from the head backwards, the transplanted cells spread from the tail upwards. At its worst, the animal is a stunted mass with no discernible head. But two weeks after the transplant, it has completely regenerated. A new planarian has risen, phoenix-like, from the ashes. Its entire body is now genetically identical to the ...

With VizWiz, the blind can take a picture, ask a question, and get an answer back from a real person in seconds.

What’s the News: With the web as their eyes, the blind will able to read menus, identify canned foods, and tell whether that park has any free benches without having to walk over. That’s the vision of a team of computer scientists behind an iPhone app called VizWiz, which lets people take a photo of whatever’s perplexing them, record a question like “What denomination is this bill?” and send it off to real people online who’ll respond in a matter of seconds with “That’s a 20.”

How the Heck:

Blind people have workarounds for the kinds of tasks the sighted use their eyes for—folding dollar bills in certain shapes, keeping the cans of tomatoes separate from the cans of beans, and so on—but these measures often require the input of a sighted person at some point, and they’re not very efficient. An app like this would give the blind more independence.
Many simple tasks, like reading an address off a letter, are phenomenally difficult for computer intelligences. So the scientists are working with Amazon’s Mechanical ...

This is a guest post by Jamie L. Vernon, Ph.D., an HIV research scientist and aspiring policy wonk, who recently moved to D.C. to get a taste of the action

In Chris’ recent Mother Jones article, he wrote of a case study in “motivated reasoning.” The study involved a group of individuals called “The Seekers” whose members believed they were receiving an alien message that predicted the date that the end of the world would come: December 21, 1954. Leon Festinger, a social psychologist, identified the organization as a good candidate for a study of disconfirmation, the moment at which a strongly held belief is unequivocally refuted. Festinger wished to study the responses among the members of the group at the very moment when they were forced to acknowledge their mistake. To get the whole story, you can read Festinger’s book When Prophecy Fails.

Out of this research came the principles of cognitive dissonance. Today, we attempt to apply Festinger’s theory to various denialist movements and conspiracy theories, as I have discussed in previous posts. Occasionally, we are given the opportunity to reflect on behaviors that carry the hallmarks of cognitive dissonance but, as in the case of the “deathers,” not all the criteria are met for classical cognitive dissonance. For example, in order to truly exhibit traits of cognitive dissonance, the believer must be confronted with irrefutable evidence of disconfirmation. In the case of the deathers, birthers, climate denialists, vaxxers and a group I’m now calling the “frackers,” no evidence will be sufficient to meet the sceptics definition of iron clad proof of their wrongness. In each of these cases, the subscribers to these beliefs will seek and find ways to dismiss the evidence, by claiming forgeries and/or contesting the methods by which the evidence was collected, by questioning the motives of those who produce the data, etc. We’ve seen it all. Instead, the canonical disconfirmation event is represented by apocalyptic prophecies that fail to manifest, as with “the Seekers.”

Yesterday, it was brought to my attention by Sam Harris that a group of Christian activists have predicted that the world will end on May 21, 2011. Bonanza!

This is a ripe opportunity for those of us who are interested in the psychology of denial to collect data. Although I won’t be infiltrating the group, I will be watching from afar. I hope the media will provide ample follow-up. In my opinion, it is of equal importance in these cases to have a post-game as well as a pre-game show.

The group is a non-denominational Christian organization. They have erected billboards, handed out pamphlets and paid for ads on subway trains that claim “Judgment Day is coming.” Their leader is a not-so-youthful 89 year old radio host Harold Camping, who has a long history of doomsaying. In fact, Camping has once before been forced to face disconfirmation when his prediction that the end of days would come in 1994 (accompanied by a book of the same name) was proven false. In true cognitive dissonance form, Camping conveniently realized that he had overlooked the Book of Jeremiah. After recalculating, he concluded that May 21, 2011 was the actual date for the rapture. And, oh boy, what a day it will be. For a detailed account of what to expect, read the Slate.com article about the group.

Festinger’s theory predicts that, despite the warnings ahead of time, once the world is shown to still exist on May 22, we should expect Camping and his group to express increased fervor for their beliefs, likely accompanied by a new prediction.

My question is, “how do we intercede to relieve these individuals from being forced into a cognitive dissonant state of mind?”

Festinger says that the circling of wagons that occurs during the initial refutation of a strongly held belief provides support for those within the group to maintain their paradoxical beliefs. Together they develop a response to the disconfirmation and together they defend their position. He also argues that heckling and antagonism from the external community only serves to solidify their beliefs. In the case of Camping and his followers, perhaps family and friends could intervene by offering them support and protection (without judgment) if they choose to step away from the group.

Looking more broadly, with the climate debate in mind, it would be reasonable to consider that individuals in close proximity to those with denialist beliefs, particularly those who share similar values, should be more vocal about their position on the issue. This should not be done in an antagonistic way. Rather, by simply expressing the opinion that is counter to the denialists’ opinions, the group think mentality can be broken up. Try it when you go home for Thanksgiving or the 4th of July.

I believe this is what has happened with the “birthers” and “deathers” of late. Initially, they were looking to their community for support. As long as they received that support, they were very vocal about their opinions. Once those who supported their beliefs, albeit with less vehemence, were silenced (by the evidence), the denialist buzz was eventually silenced or at least quieted. Those who have a costly investment in their beliefs, however, will continue to hold them. They will likely seek out others who agree with them. However, once the masses have been disseminated, the volume is significantly lowered.

***One interesting aside is how the internet has changed the interpretation of Festinger’s principles. Whereas Festinger worked during a time without social media, the current environment does not reflect the community in which Festinger made his observations. Festinger concluded based on the lifestyles during the 50′s and 60′s that an individual’s beliefs were shaped by those who lived and worked in close proximity to the individual. Today, we know that is unlikely to be the case. We now have the internet to flatten and shorten the planet. We can create our own “proximal” communities that include individuals who agree with us. We can also block out those opinions that contradict our own.

I have ideas here, but I’ll pose this question to you.

How shall we proceed?

It’s said that all roads lead to Rome, but on May 11, the opposite was true as thousands of Romans fled the Eternal City for fear of a massive earthquake. The mass exodus was spurred by internet rumors that said an Italian pseudoscientist predicted a devastating quake on this date over thirty years ago. It goes without saying, but here’s why you probably shouldn’t trust the seismic predictions of someone who thought earthquakes were caused by planetary alignments:

Meet Raffaele Bendandi, a “scientist” who believed that aligned planets could change Earth’s gravitational force and trigger earthquakes. He’s thought to have correctly predicted a 1915 earthquake in Avezzano, Italy, but he didn’t become famous until he “correctly” predicted a January 4, 1923 earthquake in Le Marche. (He was actually two days off.) It was close enough for Benito Mussolini, though, who later granted Bendandi a knighthood.

While Bendandi might’ve gotten lucky a couple of times, it’s well established that planetary alignments don’t cause earthquakes. “The force from aligned planets is irrelevant compared to the tectonic forces of the Earth’s plates whose movements create ...

On May 7th, Robert Krulwich gave the commencement speech to Berkeley Journalism School’s Class of 2011. That’s Robert Krulwich, who hosts the singular radio show Radiolab, one of the most accomplished pieces of science broadcasting in any nation. Robert Krulwich, who won a Peabody Award for broadcast excellence a few months ago. Robert Krulwich, whose blog Krulwich Wonders should be on everyone’s reading list.

Robert emailed me a few days after the speech with the following:

“I wanted to let you know that after the meeting in North Carolina [Science Online 2011 - Ed], and after watching the little brigade of you and Carl and Brian and your sisteren and bretheren doing your up-from-the-streets form of journalism, I decided to turn you guys into a Important New Thing in The World. Over the weekend, I gave the commencement speech at Berkeley’s Journalism School and if you wade through the first two thirds, you become A Paradigm at the end. I don’t know if this is a gross over-Romanticization, but this is how it seems to me.”

I’ve always wanted to be a paradigm. I might get a T-shirt made.

Robert ...

In this lab image, the toadfish’s twin bladders
are visible in the middle of its body.

There’s nothing like a bizarre fish call to shake you out of your complacency about the universe. With that in mind, we bring you the bottom-feeding three-spined toadfish, which produces its foghorn hoots and guttural grunts by vibrating the muscles around its two swim bladders, the sacs of air that keep it afloat. And these aren’t just any hoots and grunts, a new study reveals—some of these cries have qualities that have been seen the animal kingdom over, from babies’ cries to frog calls to bird song, but never before seen in fish, though fish have been known to make an incredible array of sounds (really!).

These qualities, called nonlinearities, are harmonics and dissonances that are overlaid on the linear qualities—rising and falling pitch, for instance—of a call, like elaborate icing on an otherwise plain cake. Birds are the virtuosos of nonlinear calls, using their double-piped throats to create complex songs that no wimpy human larynx can replicate, but the cries of distressed human babies have nonlinearities, as do the calls of many

One of my favorite types of object in the sky are planetary nebulae. These are typically compact, fantastically-shaped baubles caused the winds blown from stars as they die. One of the most complex and interesting is the famous Cat’s Eye nebula (NGC 6543, seen here). It’s easy to spot in a small telescope, and with large telescope an incredible amount of detail can be seen.

What most people don’t know is that there’s more to PNe (as we in the know call them) than the bright inner region. Many have giant outer halos, too! And the one surrounding the Cat’s Eye is fantastically complex and a treat for the eye and brain:

[Click to felinopticenate.]

That stunning image is from the 2.5 meter Isaac Newton Telescope on the island of La Palma in the Canaries. The halo around the bright inner region is actually huge expanding shell of material centered on the nebula’s central star. And I do mean huge; that halo is nearly 6 light years across — 60 trillion km, or almost 40 trillion miles!

When the star first started ...

Evolutionary Adaptations Can Be Reversed, but Rarely:

Physicists’ study of evolution in bacteria shows that adaptations can be undone, but rarely. Ever since Charles Darwin proposed his theory of evolution in 1859, scientists have wondered whether evolutionary adaptations can be reversed. Answering that question has proved difficult, partly due to conflicting evidence. In 2003, scientists showed that some species of insects have gained, lost and regained wings over millions of years. But a few years later, a different team found that a protein that helps control cells’ stress responses could not evolve back to its original form.

Here are the primary results:

They found that a very small percentage of evolutionary adaptations in a drug-resistance gene can be reversed, but only if the adaptations involve fewer than four discrete genetic mutations. The findings will appear in the May 13 issue of the journal Physical Review Letters. Lead authors of the paper are two MIT juniors, Longzhi Tan and Stephen Serene.

The paper is not online yet. I’ll definitely check it out when it comes out, at least if the math isn’t too difficult. The reason is that these sorts of models always rely on simplifying assumptions, and they may not have ...

It is the annual Edge “question.” This year, “What Scientific Concept Would Improve Everybody’s Cognitive Toolkit”? It looks like Edge finally updated their design a touch! (happy Chad?) Nothing too fancy, which is probably a good thing. I haven’t read all the answers, but I would submit that everyone needs to digest John Ioannidis’ insight, Why Most Published Research Findings Are False:

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs ...

Mock jurors’ perceptions of facial hair on criminal offenders.

“Two studies were conducted to measure whether mock jurors would stereotype criminal offenders as having facial hair. In Study 1, participants were asked which photograph belonged to a defendant in a rape case and which photograph belonged to a plaintiff in a head-injury case after they were “accidentally” dropped. The photographs were similar in appearance except one had facial hair. 78% of 63 participants (or 49) identified the photograph with facial hair as being involved in the rape case. In Study 2, 371 participants were asked to sketch the face of a criminal offender. 82% of the sketches (or 249) contained some form of facial hair. Results are consistent with the hypothesis that criminal defendants are perceived as having facial hair.”

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Photo: memebase.com

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Recently a friend got their 23andMe genotype results, and was wondering if there was something they could do for the “greater good.” I told him that he should throw his genotype out to the public domain and attach his name to it. For various reasons he declined to go that far, but he did consent to me to putting his genotype online without personal identifying information. I can tell you that he is a relatively young male of 100% (to his knowledge) Ashkenazi Jewish heritage.

You can get a zipped folder with the raw text file and a binary pedigree formatted file here. If you click the free download option after 30 seconds you’ll get the file within about 5 minutes on a broadband connection (that was my experience at least).

If anyone else wants to throw their genotype to the public domain with as much or as little information as you want just email me at contactgxnp -at- gmail -dot- com. Here’s a spreadsheet with other people who have put their gentoypes online. I want to put up a “roundup” post with a bunch of people who do just that in the near future.