Author: Discover Main Feed

Ms. Kirshenbaum and Mr. Mooney have an article which they coauthored which will appear in The Best American Science Writing 2010.

For those folks in Los Angeles (and parts of Nevada, Idaho, western Montana, Calgary and Edmonton): if you are up at 03:34 Pacific time tonight, you can watch as an asteroid blocks the light of a naked-eye star!

Sky and Telescope has the details. Basically, the asteroid 824 Anastasia will pass directly in front of the star ζ (Zeta) Ophiuchi. At magnitude 2.5, the star is easily visible, about as bright as Polaris (though honestly, from LA you may need binoculars). The map shown here on the left is from Sky and Tel; click it for a higher-res version.

The asteroid itself will be invisible to the eye; it’s at magnitude 14.7, a thousandth as bright as the faintest object you can see even from a dark site. But when it passes in front of the star, the star will dim or blink out for up to 8 seconds. This occultation, as it’s called, is important because by mapping exact locations and timing from a large number of observers, the shape of the asteroid can be found! Well, more or less, since we only see it in profile, but it’s still a nice clue to the characteristics of an otherwise featureless point of light.

So if you plan on being out and about at that time, why not check out how to do some astronomy from literally your back yard? The more people who participate, the better our science is!

Image credit: Sky and Telescope.

If want to go out for a jog outside but don’t want to get your sneakers dirty, here’s a unique solution for you. Now you can work out to your heart’s content on the new treadmill bike, a treadmill that has been rigged up to a bike–to offer a workout that can only be described as unnecessarily complicated.

Describing the contraption, The Red Ferret Journal writes:

Built with rugged design and all-terrain tires, this 2-wheeled wonder will take you anywhere a standard bicycle will, and give you a great cardiovascular workout with the burn of that walking treadmill you’ve got a love-hate relationship with in the gym.

Gizmag reports that by taking the workout outside, the machine makes sure you are buff and not bored:

The Treadmill Bike is for people who love the feel of a treadmill beneath their feet but don’t want to be stuck inside pounding away when it’s a beautiful day outside. Bicycle Forest [which sells the machine] says the creation has the same fat-burning benefits of a conventional treadmill without the gym membership fees (although you do have to buy the bike).

Treehugger adds the bike is good for people who don’t actually like being outdoors.

“The Treadmill Bike’s hard wearing belt offers a sure grip while protecting your feet from dirt and other contaminants commonly found on the earth’s surface.”

And by “contaminants on the earth’s surface,” they mean dirt and dust and in some cases, depending on where you’re running, horrifying crushed bugs. Treehugger writes the machine sells for $2,500 Canadian, which seems like a lot of money just to fight boredom and to keep your sneakers clean.

Here’s a video of the treadmill bike in action.

Related Content:
Discoblog: Want More Oxygen for Your Workout? Pony Up $2700 for This Backpack
80beats: No Shoes, No Problem? Barefoot Runners Put Far Less Stress on Their Feet
80beats: Scientist Smackdown: Are A Sprinter’s Prosthetic Legs An Unfair Advantage?
DISCOVER: 20 Things You Didn’t Know About… Sports Technology
DISCOVER: Athletes On the Edge: Sword Swallowers, Arctic Swimmers, and Human Cannonballs

Image: The Red Ferret Journal

I’m going to posting links M-F which I don’t manage to blog (probably focus less on science in these links as well). I’m calling it the “Daily Data Dump.”

The Cloudy Revolution. 10 years after the initial hype the “cloud” is here. Somewhere Larry Ellison is crying.

You Don’t Need an iPad, but Farhad Manjoo really, really, loves it. It sounds like the reviews of the Kindle on steroids. I don’t have a TV because the device is all about consumption, and I think I’ll avoid the iPad for the same reason. But just as television and the net are merging through online streaming, I assume that the iPad is a foretaste of what’s to come in computing devices. At least outside of the office (I think a little artificial constraint and discomfort probably is necessary in a work environment).

You’re Born a Copy but Die an Original. The values of elderly individuals diverge in relation to their age cohort between 70 and 90.

Cassini Doubleheader: Flying By Titan and Dione. Spaceflight is so banal today that it isn’t necessarily newsworthy. Who remembers Dione?

Michael Steele calls his critics racist. That’s really weak dawg.

This August I will be teaching a week-long writing course on Appledore Island in the Gulf of Maine. Last year, the first time around, we had a blast, embarking on an Ahab-like quest for hagfish, observing the role played by mind-controlling parasites in the ecology of the island’s tidal zone, learning how to use broken 300-year-old pipe stems and cod ear bones to reconstruct American’s first economic boom, and much more. (Here are some articles the students wrote about their experiences.)

This year promises to be just as much fun (and intense).

The deadline for registering is April 16. You can reigster and get more information on the course page at the Shoals Marine Lab web site. (Shoals is jointly run by Cornell and the University of New Hampshire.) For those beyond college interested in the class, here are some details about taking the course non-credit.

I’ll be doing a weekly podcast with Kevin Zelnio & Dave Munger which we’ll post online early every week. The first one is up over at Research Blogging. Dave will probably set it up on iTunes at some point.

The day is approaching fast when grad-students-to-be need to be making decisions about where to choose. Probably undergrads, too, although I confess that I have no real idea what the calendar for that looks like.

So, good luck with all that decision-making! Here are links to our previous posts about the topic.

• Unsolicited Advice: Choosing a Grad School
• On Choosing a Grad School: A Dialogue
• Unsolicited Advice: Choosing an Undergraduate School

Not too much to add to the discussion there, but here’s an opportunity to chat about the process. My own strong feeling is that how successful you are in school (grad or undergrad) is much more up to you than up to the institution. Most places have more good opportunities than anyone can hope to take advantage of in a limited period of time. Take the initiative, don’t wait for good things to come to you, and have fun!

This may seriously be my favorite picture ever taken from space: the view from inside the International Space Station as it heads toward the aurora at 28,000 kilometers per hour:

This picture was taken by Soichi Noguchi looking out of the newly installed ISS cupola, which provides dramatic vistas of space from inside the station. You can see the Soyuz module that carried astronaut Tracy Caldwell Dyson on board– incidentally, with Discovery on its way to the ISS carrying three women, this will be the first time four women will have been in space simultaneously. [Update: According to commenter Ben Honey, that’s actually a Progress capsule, and not the Soyuz. The profile does match a Progress, so I assume he’s right. I stand corrected.]

This image is simply fantastic. The aurora, commonly called the northern lights, are caused by subatomic particles slamming into our atmosphere and ionizing the oxygen and nitrogen atoms there like shrapnel from bullets hitting a target. Guided by the Earth’s magnetic field, these particles tend to hit at high latitudes. The glow itself is similar to that of a neon sign: when the wayward electrons recombine with the atoms, they give off light. The colors are characteristic of the atom in question, and can be used to identify the atmospheric constituents.

The green glow is actually much lower than the ISS; that part of the aurora is usually at a height of 100 or so kilometers (60 miles), while ISS is at 400 km (240 miles). The red glow can reach higher, to more than 500 km (300 miles), so when Soichi says he is flying through the aurora he is literally correct. The fantastic speed of the ISS is apparent in the trailing of the stars in the image, and the streaking of the purple clouds below.

Astonishing, lovely, poetic, beautiful… and Holy Haleakala, real. When we humans want and choose to, we can fly through the northern lights. What else can we accomplish when we set our minds to it?

I am a big fan of The Late Late Show with Craig Ferguson, and I’m also a fan, bordering on a man crush, of the Mythbusters (Kari Byron, of course, is not a man, so my crush on her is purely — OK, mostly — platonic). Adam, of course, has been relegated to My Close Personal Friend™ status, but still.

As it happens, Craig is a big Mythbusters fan as well. When he came up with the idea of having a robot skeleton sidekick, he turned to the one man who could realize his dream: Miles Dyson. I mean, Mythbuster Grant Imahara.

Grant has been working feverishly on the auto-sidekick for weeks, and tonight it will be unveiled on the show! I’m really squeeing over this, and can’t wait to see it.

I love The Late Late Show for many reasons, but the biggest is Craig himself: he’s very funny, and extremely smart. He’s self-taught in many ways, and has had a rough life — he’ll be the first to say it was self-inflicted, but the bottom line is he’s pulled himself out of the muck and turned it all around. His humor is whip-crack fast, and he’s clearly a big fan of science, so of course I am powerless not to like him. Did you see his 5 minute rant about Copernicus (starting around the four minute mark)? I mean, seriously, Copernicus? Craig, I less-than-three you.

And as part of his Robot Skeleton Army — as he calls his Twitter followers — I am very pleased that he’s using this occasion to raise money for Lollipop Theater, a way to get movies and TV shows to sick kids. If you see the hashtag #lollipoptheater in my own tweets today, that’s why.

You can read more about Craig and Grant’s excellent adventure on NPR’s Monkey See blog (where I got the picture of Grant above) and in a great post by my friend Erin McCarthy at the Popular Mechanics site.

And check your local listings for Craig’s show tonight. It’s on CBS, and is usually at 12:35 a.m. (11:35 p.m. central) though it may be delayed by basketball. And remember: it’s a great day for America everybody.

Image credit: Grant Imahara.

Some of the weird wildlife on Madagascar—its mammals especially—probably arrived there by rafting from mainland Africa, we reported back in January. But not its blind snakes. According to a study out now in Biology Letters, these funny-looking creatures date back 150 million years to the Gondwana landmass, and have lived on Madagascar since before it broke off from India and drifted away. And, the researchers say, their story of spreading around the world carries many more twists.

Growing to about a foot long, blind snakes act a lot like worms, burrowing under the surface of every continent except Antarctica. Unlike worms, though, blind snakes have backbones and tiny scales [National Geographic]. They earned their moniker by having blurry vision and sensing chemicals through their skin to find their way around. But despite having backbones, there are few blind snakes in the fossil record, making it hard for researchers to study their evolutionary history. So lead researchers Blair Hedges and Nicolas Vidal had to rely on living species. They extracted five nuclear genes, which code for proteins, from 96 different species of worm-like snakes to reconstruct the branching pattern of their evolution, allowing the team to estimate the times of divergence of different lineages using molecular clocks [UPI].

Vidal and Hedges found that the snakes date back all the way to Gondwana, and that the particular kind that live now on Madagascar date back to “Indigascar,” the name researchers use for the landmass of Madagascar and India before they separated nearly 100 million years ago. Says Hedges, “Then some of resident blind snakes left and dispersed over land to other areas in southern Asia” [LiveScience], while the ones left on Madagascar eventually became a separate family.

But they also found something rather unlikely: These small snakes must have done at least some of their worldwide travels by rafting across the water. They say that blind snakes showed up in Australia 28 million years ago, but at that time no land connections to the continent remained. And African and South American blind snake lineages apparently separated only 63 million years ago. That’s some 40 million years after Africa and South America split up, so moving landmasses can’t have caused the later evolutionary divide [National Geographic].

Burrowing animals don’t tend to travel by rafting, Hedges acknowledges. But because the timetable doesn’t work out for the snakes to have spread to those places by continental drift, and because blind snakes aren’t exactly the flying type, she says this unlikely answer is the most likely one.

Related Content:
80beats: Study: Madagascar’s Weird Mammals Got There by Rafts
80beats: Madagascar Chameleon Makes the Most of a 4-Month Life
Discoblog: Scientists Find Oddball Right-Side-Up Bat in Madagascar
DISCOVER: A Bridge To Madagascar

Image: Blair Hedges

A couple of my articles are included in a new book, The New York Times Reader: Science and Technology. Edited by S. Holly Stocking, it’s an anthology that can stand on its own, or serve as reading for a journalism class. Here’s a description of the book from the publisher’s web site:

Science writing poses specific challenges: Science writers must engage their audiences while also explaining unfamiliar scientific concepts and processes. Further, they must illuminate arcane research methods and statistics and at the same time cope with scientific ignorance and uncertainty. Stocking’s volume not only tackles these challenges, but also includes extraordinary breadth in story selection, from prize-winning narratives, profiles and explanatory pieces to accounts of scientific meetings and new discoveries, Q&A’s, traditional trend and issue stories, reviews, essays and blog posts. These Times exemplars, together with Stocking’s guide to reading stories about science and technology, are perfect for science writers who aspire to diversify and hone their reporting and writing skills in a changing media climate. Holly Stocking is an experienced science writer, award-winning teacher, and a fellow of the American Association for the Advancement of Science.

You can order it from CQ Press. Here’s the Amazon page, too.

(Hat tip: Leigh Boerner)

I’ll be giving a talk at the Museum of Science in Boston on Saturday, April 17. It’s the keynote address at the annual meeting of the Massachusetts Academy of Science. I’m going to talk about spangled dinosaurs, how scientists are splashing colors all over the history of life, and what all that color can tell us about evolution.

My talk is just one part of an all-day celebration of science for all ages. (The entire Zimmer clan will be in attendance.) For information on registration and tickets, visit the meeting web site.

We are pleased to announce that a recent co-authored article we wrote has been chosen to appear in The Best American Science Writing 2010, edited by the New Yorker’s Jerome Groopman and Jesse Cohen. Our piece, entitled Unpopular Science, originally ran in The Nation last July. It was our documentation of the death of science journalism, and the failure of science on the web to fill the gap, and we are honored to have it featured among the year’s collected essays. Here’s an excerpt:
In light of the media upheaval, scientists can no longer assume that a responsible, high-minded press will treat their ideas with the seriousness they deserve, delivering them to policy-makers and the public for sober consideration. Instead, partisan media will convey diametrically opposed versions of where science actually stands on any contentious subject–consider, for example, the difference between how Fox News and NPR cover climate change–even as most of the public (and many policy-makers) will tune out science more or less completely, besieged by other information options. That’s the media reality we live with, and facing it head-on is necessary not only for scientists but for everyone who cares about the impact of science and good information on public …

Over the weekend a huge Chinese freighter loaded down with coal and fuel oil crashed into part of the Great Barrier Reef off the Australian coast. Today, salvage teams are still struggling with how to extricate the Shen Neng 1 without dumping any more of its dirty cargo into the delicate marine ecosystem.

The ship had left the port of Gladstone just a few hours before striking the reef in Douglas Shoal. It ran aground in a restricted zone of the marine park, almost 30km [18.6 miles] from the authorised shipping channels it should have been using [Sydney Morning Herald]. Both the main engine and the rudders sustained serious damage. While rescuers debate how to orchestrate a salvage operation, the Shen Neng 1 has slid another 20 or 30 yards along the reef, destroying more coral in its path.

Rushing into a salvage operation, however, could be a disaster. The ship is holding more than 1,000 U.S. tons of fuel oil, and more than 70,000 U.S. tons of coal. Patrick Quirk, the maritime safety manager for Queensland (the province of Australia where this happened) says that two tons of overflow fuel has already leaked out, but the rest, so far, has been saved. “The oil is being held from the breach tank by a hydrostatic plug of water,” Mr Quirk said. That `plug’ was caused by the pressure of the ocean water outside preventing the oil and water escaping from the ship’s engine room [Brisbane Times]. Quirk is worried that refloating the ship too soon could kill that pressure plug and cause a much more vigorous oil leak, or worse, cause the ship to break up.

Shipping experts like Basil M. Karatzas say it was not unusual that the 755-foot Shen Neng 1 would be carrying so much bunker fuel. A ship of that size and design would burn about 35 tons of fuel a day, he said, and would require at least two weeks to travel from eastern Australia to China [The New York Times]. Also, because China imports so much material, ships must be prepared for long waits to unload when they reach port.

While the salvage teams commence their work, the Australian maritime investigators have begun trying to ascertain just how the Shen Neng 1 got so far off course in the first place. The shipping company could be fined $1 million and the ship’s captain $250,000 if proven to have broken Australia’s shipping laws [Sydney Morning Herald].

Related Content:
80beats: Sudden Slowdown in Coral Growth Could Signal Collapse of the Great Barrier Reef
80beats: “Ghost Fleet” of WWII-Era Ships Will Finally Fade Away—Along with Its Pollution
80beats: 21 Years After Spill, Exxon Valdez Oil Is *Still* Stuck in Alaska’s Beaches
Not Exactly Rocket Science: Fish Make Rapid Comeback in the World’s Largest No-Fishing Zone, on fish recovery in the Great Barrier Reef

Image: Maritime Safety Queensland

Once upon a time, celebrities could just pop on a pair of large sunglasses and melt away, unnoticed, into the crowds. But things are harder these days with sophisticated cameras and software that can literally identify strangers on the street. Even everyday smartphones may soon be able to ID people.

But Adam Harvey, a designer and technologist with NYU’s Interactive Telecommunications Program has figured out a way to fly under the radar by reverse engineering the algorithms in software that is used for face recognition.

For any face to be detected, PopSci reports, the algorithm must match a cascade or series of features in the expected locations. By strategically camouflaging a particular feature, like the eyes, Harvey found a way to fool the software.

In order not to be picked up the cameras, stealth-obsessed operatives would need to apply camo-style makeup right underneath or over the eyes. They could choose between vintage Batman or Catgirl looks, or could go a step further with Blade Runner-style makeup. While the cameras then wouldn’t recognize them, Harvey can’t guarantee that the striking camouflage won’t turn heads on the streets.

Related Content:
Discoblog: Augmented Reality Phone App Can Identify Strangers on the Street
Discoblog: Augmented Reality Tattoos Are Visible Only to a Special Camera
Science, Not Fiction: Seeing The Future, Literally
Discoblog: One Small Step Closer to Superhuman Cyborg Vision
Discoblog: Will the Laptops of the Future Be a Pair of Eye Glasses?

Image: Adam Harvey Projects

Take a look at this poster. British people will probably be familiar with it already. For everyone else, it was released last year by our National Health Service when fears of a flu pandemic were at their height. When we see images of diseases and their symptoms, we typically feel disgust and repulsion. But unbeknownst to us, our immune systems have started reacting too.

In a small but compelling study, Mark Schaller from the University of British Columbia found that people who see images of sneezes and other signs of disease mount a stronger immune response to later infections than people who see unrelated images. This is the first evidence that the mere sight of a possible infection, even through a photograph, can set our bodies’ defences on high alert.

Previously, Schaller has suggested that the visual signs of disease trigger a variety of psychological tics that reduce our chances of infection. A disgusted reaction fulfils this role by making us less likely to approach potential sources of contagion. Last year, another group showed that a sneezing passer-by can make people more worried about completely unrelated threats, like heart attacks, crime and accidents. To Schaller, these reactions are all part of our “behavioural immune system” – our means of preventing infections by changing our behaviour.

But his latest study suggests that images of sickness can prime our actual immune systems too. He recruited 28 volunteers, split them into two groups, and showed them two slide shows. The first slides were just shots of furniture. The second set showed either signs of infectious diseases, such as pox, skin lesions or sneezing, or images of people brandishing guns, mostly aimed directly at the viewers.

Schaller collected blood samples from the volunteers before and after each slide show, and mixed them with molecules that give away the presence of marauding bacteria. He wanted to see how strongly the white cells in the blood would respond to these danger signs. To do that, he measured the concentrations of a protein called interleukin-6 (IL-6), which while blood cells secrete in response to infections, burns or wounds. The more IL-6 there is, the stronger the body’s immune reaction.

He found that the white blood cells responded much more aggressively to the bacterial molecules after the volunteers saw the symptom slides. The furniture images didn’t change the amount of IL-6 in the recruits’ blood samples, the gun images raised these levels by 7%, but the disease images increased them by 24%.

This suggests that the immune system reacts with extra vigour after its owner sees an image specifically related to disease, rather than one that invokes a general sense of threat or danger. Indeed, when questioned later, both groups reported the same levels of stress and fear even though only one of them manifested an actual physical reaction.

There is one caveat – the people who saw the gun images had higher levels of IL-6 in their blood samples before the experiment than those who saw the disease images. The difference wasn’t statistically significant, but it could suggest that Schaller didn’t split his groups randomly enough. He acknowledges this possibility but he says that the two groups weren’t any different in terms of their personality traits or how worried they were about disease. Nonetheless, this is an issue that could easily be addressed by doing a larger follow-up study using more volunteers.

For the moment, the effect is certainly plausible. From an evolutionary point of view, putting our immune systems on alert if we see signs of infection might reduce the odds of contracting a disease without having to distance ourselves from our social groups. However, Schaller suggests that in modern times, such responses might be counterproductive. An image of a sneeze is clearly not a sign that disease is imminent, and priming our immune systems to a non-existent threat isn’t the best use of our valuable energy.

Reference: Psychological Science http://dx.doi.org/10.1177/0956797610368064

More on immune systems:

• Smell a lady, shrug off flu – how female odours give male mice an immune boost
• Pocket Science – when enslaved bacteria go bad, gut microbes and fat mice, and stretchy beards of iron
• Genes from Chagas parasite can transfer to humans and be passed on to children
• New plant species arise from conflicts between immune system genes

The folks at Spitzer Space Telescope recently released a new image, and it’s a stunner:

Wow, what beauty! This picture shows the famous Orion nebula, one of the galaxy’s largest and most active star forming gas clouds. Spitzer is an infrared telescope, so blue here depicts light at 3.6 microns, roughly 5 times the wavelength your eye can see, and red/orange is 4.5 microns.

I could go on and on about the ethereal beauty of this image, about how we can actually see stars forming here, about why there are streamers and shock waves that sculpt this vast light-years long structure. But you can find me expositing at length on all those topics in other posts about other nebulae. That’s not the point I want to make here.

When I first saw the image, the email from JPL had the subject line “Colony of Young Stars Shines in New Spitzer Image”, so I didn’t know what nebula it was showing. I simply clicked the link, and the image above popped up. I smiled when I saw it because of its beauty, at least at first. But after a moment I was puzzled. The nebula looked familiar, but for a brief moment I couldn’t place it. Then I focused my attention on the big cloud on the left, and my mind snapped into clarity.

Any amateur astronomer on this planet can identify the picture at the left in a heartbeat. That’s an optical picture of the Orion nebula, one taken using visible light (the picture is by Hubble; click it to get more info and access to much, much larger versions). I’ve rotated the picture to match the one from Spitzer; you can see the same curved shock front going across the lower left corner, and the round comma-shaped cloud with a star near its center to the right. While the Hubble image is far more detailed (and colorful!) than what you see through an eyepiece, it still strongly resembles the view through a good telescope. But the Spitzer image…?

Have you ever met up unexpectedly with a friend you haven’t seen in five years? Maybe they grew a beard, or lost weight, or dyed their hair, or changed their clothing style. It’s the same person, clearly, but somehow different. It takes a second to recognize them, and when you do, it’s a bit of a jolt.

That’s exactly how I felt when I saw the Spitzer image (and like many an astronomer, I consider Orion an old friend). Spitzer’s image is just a little bit into the infrared, enough that details are different while the overall shape and features are the same. I knew it was my old friend, but it took me a moment to recognize its face.

And in many ways, like seeing that acquaintance after a few years, there were new things to learn, new ways to experience our friendship. The stars in the Spitzer image that are in the narrow bridge between the two halves of the nebula seem a bit more vibrant, a bit more obvious… as they should, since they are young stars in the throes of birth, and veiled substantially by dust. More stars overall are apparent in the image, since fainter ones can shine through the dust in the infrared, while their light is blocked by that dust in the visible. The streamers in the infrared image are more vivid, but the dust features less so, again as expected, but still somehow new and interesting.

In my travels I do happen to run across friends I haven’t seen in many years, and when I have time to actually sit and chat, I’m delighted when they have grown and done things they have previously not experienced. It brings a new side of them to light for me, lets me see them in a new way and appreciate them all the more.

And this is true on Earth as it is in the heavens. There are so many things to see in and above this world, and so many ways to see them! New eyes, new perspectives, new ways of seeing… it makes me always eager to find out what’s next, and to cherish what we already know.

It’s possible we may get there today, or soon as the recovery continues. The stock market hasn’t been that high since before it fell off a cliff in October of 2008. So, cast your votes, kids: Did Obama save the economy?

About five years ago Kari Stefansson published an interesting paper, A common inversion under selection in Europeans. The basic thrust of the results was that a particular genomic region in Europeans exhibited a pattern of variation whereby there was one variant which was inverted in relation to the modal type. They labelled them “H2″ and “H1″ respectively. The region in question is spans ~900 kilobases on chromosome 17 and has within it the MAPT gene which is implicated in several neurological diseases. Stefansson et al. argued that H2 and H1 were long coexistent lineages, prevented from recombining due to the molecular genetic constraints of the chromosomal inversion, and each preserved within several human populations by balancing selection dynamics. That is, natural selection exhibited dynamics whereby neither variant could replace the other because their fitness was optimized at intermediate frequencies. In the human population as a whole H2 is far less common and seems to have less genetic variation. In the Icelandic population they also found that H2 seemed to be correlated with greater fertility, suggesting that natural selection was currently operating upon it (any trait correlated with fertility is naturally a more “fit” one).

A new paper puts the focus once more on this region, but takes a broader view by moving away from looking at Icelanders as a test population and surveying a wider range of peoples, as well as comparing the genetic variation in this region across primate species. The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans:

The polymorphic inversion on 17q21, sometimes called the microtubular associated protein tau (MAPT) inversion, is an ∼900 kb inversion found primarily in Europeans and Southwest Asians. We have identified 21 SNPs that act as markers of the inverted, i.e., H2, haplotype. The inversion is found at the highest frequencies in Southwest Asia and Southern Europe (frequencies of ∼30%); elsewhere in Europe, frequencies vary from < 5%, in Finns, to 28%, in Orcadians. The H2 inversion haplotype also occurs at low frequencies in Africa, Central Asia, East Asia, and the Americas, though the East Asian and Amerindian alleles may be due to recent gene flow from Europe. Molecular evolution analyses indicate that the H2 haplotype originally arose in Africa or Southwest Asia. Though the H2 inversion has many fixed differences across the ∼900 kb, short tandem repeat polymorphism data indicate a very recent date for the most recent common ancestor, with dates ranging from 13,600 to 108,400 years, depending on assumptions and estimation methods. This estimate range is much more recent than the 3 million year age estimated by Stefansson et al. in 2005.

Note that the differences between H1 and H2 are not simply ones of particular marker SNPs, particular variants of H1 carry versions of MAPT which exhibit far greater transcriptional activity than those on H2. And there are significant differences between the two genomic variants when it comes to correlations with disease susceptibility, even if the underlying mechanistic relations have not been elucidated.

In any case one of the more intriguing aspects of this paper is that they looked at 66 human populations (a mix of Alfred and HGDP) and our nearest evolutionary relatives among the apes. The sample size for apes was only 15, and the results seemed a bit muddled (or perhaps the prose in this region was a bit unclear). They identified H1 and H2 by runs of particular alleles, a sequence of genetic variants diagnostic to H1 or H2. In some regions the various apes seemed to resemble H1 and in others H2. Interestingly on sites where H1 is polymorphic the ape samples seem to resemble H2, implying that the genetic background against which H2 arose was rather ancient (since the divergence from apes is an ancient event). And, of alleles where H1 was polymorphic and H2 had an allele which was in H1, in four out of five cases H2 was ancestral.

The results from human populations are easier to visual because there’s a map associated:

Really this isn’t a “European” variant. Here’s the relevant text:

The inversion haplotype is found at highest frequency in Mediterranean regions of Southwest Asia and Europe (31.6% in Druze, 31% in Samaritans, 23.5% in Palestinians, 26% in Bedouins, 23.9% in French Basques, 32.2% in Spanish Basques, 20.9% in Catalans, 27.7% in Greeks, 37.5% in Sardinians, 31.9% in Toscani, and 36.8% in Roman Jews) and at moderately high levels in Northern Africa (13.3% in the Mozabite). It is also found at a high frequency in Ashkenazi Jews (25.6%), which we have shown to group with the Southwest Asians….Elsewhere in Europe, we see that the frequency is high in Western, Central, and Southeast Europe (18.9% in French, 15% in Danes, 17.7% in the Irish, 28% in Orcadians, 21.4% in European Americans, 23.9% in Hungarians, and 15.7% in the Adygei) and much lower in Eastern and Northern Europe (9.8% in the Chuvash, 6% in the Archangel Russians, 9.4% in the Vologda Russians, and 4.3% in the Finns) and on the Arabian Peninsula (11.9% in the Yemenite Jews and 9.4% in Kuwaitis).

Since they mention it, I thought I would quickly post a map of the spread of farming in Europe. Darker represents earlier dates for the dominance of agriculture within a particular region. H2 is found in other Eurasian populations as well, though at lower frequencies, from from ~10% in the Arabian peninsula and in Pakistan to ~3% in South India. It is absent in East Asia, and there are strong suspicions that its presence in the Amerindian samples is due to recent admixture (this is something that regularly crops up with these HGDP samples). But, importantly it is also notable that H2 is present as low frequencies in many African populations, including the Pygmies (though seemingly almost absent from West Africa). If H2 is very ancient (as Stefansson et al. argue) then its origins lay in Africa, and it was introduced to Eurasia by the Out of Africa expansion which saw the replacement of archaic H. sapiens by anatomically modern H. sapiens from Africa. Its later higher frequency in parts of western Eurasia could be due to demographic parameters such as random genetic drift through a bottleneck, or localized natural selection, or a combination. If H2 arose in the Middle East its presence in Africa could be explained by back-migration. I immediately was skeptical of this model because H2 is extant at frequencies of 5% among the Mbuti Pygmies. The Mbuti are relatively isolated genetically from the Bantu farmers who have come to dominate their region. If there was any group which represented the ancient genetic variation of Central Africa, it is likely the Mbuti. There are suggestive patterns in the data of this paper which points to an African origin for H2 originally:

We identified an H1 haplotype (blue stripes) that differs from the H2 haplotype (red stripes) only at the inversion marker sites and is therefore the likely haplotype on which the inversion initially arose. This haplotype is found throughout the world at an average frequency of 7.8%. It is most frequent in Africa ranging from 6.9% in the Mbuti Pygmies to 25% in the Biaka Pygmies with an average frequency of 14.8%. It is much less frequent in Southwest Asia, ranging from 4.8%–9.2% with an average frequency of 6.5%. These data support an African origin of the inversion, but are not sufficient to rule out a Southwest Asian origin.

Haplotypes, sequences of genetic variants, can be related to each other on a phylogenetic tree. There are haplotypes which have more derived variants, and those which have more ancestral variants. It seems that the African H2 variants are more likely to be that which arose from the genetic background of H1. So in this model the high frequency of H2 in the Middle East is not due to time of residence, but a function of random processes or natural selection.

But perhaps the most interesting find in this paper is their result that H2 is relatively recently derived in relation to H1, as opposed having diverged 3 million years ago as implied by Stefansson et al. They looked at the variation on short tandem repeats and using a molecular clock method inferred the point of coalescence back to an ancestral lineage. Here’s what they found:

Assuming an average generation time of 25 years, this puts the MCRA at 16,400–32,800 years ago. However, if we assume that the African haplotype is the ancestral haplotype, we get an estimate of 2167.4–4334.7 generations. With 25 years per generation, this puts the MCRA at 54,200–108,400 years ago.

This recent date for the MRCA is also supported by our SNP data. Of the 90 SNPs typed, only four were variable on the H2 chromosomes, whereas 68 of the 90 are variable on the H1 chromosomes. This lack of polymorphism on the H2 chromosomes in comparison to H1 chromosomes would suggest that the H2 inversion is younger than the H1 orientation.

The first number assumes that the Middle Eastern variant is the ancestral one, while the second the African. Unlike the authors I suspect that the African variant is probably ancestral to a relatively high degree of confidence because of the Mbuti data point. This would place the emergence of H2 from the H1 background around the time of the Out of Africa migration. Humans would have exhibited polymorphism on this locus before they emigrated. Since H2 is not found in West Africa it may even reflect population substructure within Africa from before the Out of Africa migration (Eurasians are derived from northeast Africans).

And yet remember the earlier data using non-human primates which implied that perhaps H2 was the more ancient variant? From the discussion you can see how the authors resolve the conflict here:

Given the global distribution described here combined with the data of Zody et al., we propose a model in which the H2 orientation is the NHP [non-human primate] ancestral orientation; however, the H1 orientation is ancestral in humans. Under this theory, sometime after the divergence of Pan and Homo the region inverted to the H1 orientation in the Homo line. The H1 then rose to fixation. Then, in modern humans the inversion occurred once again, leading to the H2 chromosomes found in humans. Zody et al. showed that the region is susceptible to inversion, so it is not impossible to imagine an inversion occurring twice on the Homo line

The authors point out that some have suggested that the H2 inversion might have jumped from archaic H. sapiens into west Eurasian populations, in particular Neandertals. This would explain the lack of recombination, as two distinct breeding populations would naturally not recombine their genetic material. The authors seem skeptical of this finding, and I am again more skeptical than they because I assume an African origin for H2 to a higher degree of confidence than they do. That being said they note that further reconstruction of the Neandertal genome would likely solve this dispute.

Finally they touch upon the question of neutral vs. adaptive dynamics. That is, can the frequencies of H2 vs. H1 be explained by a combination of various demographic parameters such as random genetic drift and subsequent admixture between isolated populations, or natural selection whereby traits on H2 entailed a higher fitness for H2, ergo it rose in frequency across disparate populations. Naturally the two do not necessarily exclude each other. A simple neutral model would explain the lack of H2 in East Asia through genetic drift, as populations go through serial bottlenecks most genetic variation is lost, and a few lineages predominate. So H2 went extinct in East Asia via this model. In the Middle East H2 rose in frequency through random forces and then was spread to Europe through the migration of Neolithic farmers.

As the authors have already complexified the history of this genomic region, proposing two inversions to render explicable the particular patterns on H1 and H2 and their relation to non-human primates, I think there is no need to hew too closely to the principle of parsimony. It is suggestive to me that H2 is found at high frequencies in the Middle East, the region where agriculture arose first, and can be seen to correlate with regions where agriculturalists later settled. It may be that genes on H2 are useful for agriculturalists, at least as a form of balancing selection whereby the fitness of H2 decreases as its frequency rises, converging upon an equilibrium proportion with H1. These may be behavioral, recall that MAPT is implicated in neurological function, and it differs along the two lineages. Additionally, H2 may have spread to Europe with agriculture and the agriculturalists. The very low frequency of H2 among Finns is in line with my suggestion that northeastern Europe is the refugium for the pre-Neolithic genetic substrate of the continent. The low frequency among the Finns may be a function of their low rates of admixture with farmers whose original genetic signal was from the Middle East as well as the fact that the Finns adapted a fully agricultural lifestyle relatively late, so selective pressures for H2 was weak until relatively recently.

I’ll let the authors finish:

We have shown here that the 17q21 inversion is found at its highest frequencies in the Mediterranean region in Southern Europe, Southwest Asia, and North Africa. We have also shown that the MRCA of the inversion is much younger than the estimated date of divergence for the H1 and H2 haplotypes. Though we cannot rule out selection acting at the region, we think that both the restricted global distribution and the recent MRCA fit with a neutral model coinciding with an origin in Africa or Southwest Asia followed by demographic events occurring during the migration out of Africa into Southwest Asia and/or the Neolithic expansion out of Southwest Asia into Europe.

Citation: Donnelly, M., Paschou, P., Grigorenko, E., Gurwitz, D., Mehdi, S., Kajuna, S., Barta, C., Kungulilo, S., Karoma, N., & Lu, R. (2010). The Distribution and Most Recent Common Ancestor of the 17q21 Inversion in Humans The American Journal of Human Genetics, 86 (2), 161-171 DOI: 10.1016/j.ajhg.2010.01.007

A week ago I pointed to a controversy about the rate of growth of human cranial capacities over the past few million years. I asserted that the rate of growth was gradual, with no major discontinuity. Over at Genetic Inference Luke Jostins’ has done a more formal analysis.
He finds:

The model shows a definite speed-up of brain size increase recently, and fits the data significantly better than a simple trend line (F(1,90) = 15.8, p < 10^-5). I estimate that the speed-up occured 252kya, and can say with 95% confidence that it lies between 203 and 377 kya. This result is pretty robust to exactly what model we use; I also tried using a model where brain size grew exponentially with time, and this gave a similar break-point: 250kya, with a 95% interval of 167-402 kya (see this graph).

Read the whole thing. I personally don’t find an increased rate of encephalization 200-300 years ago that implausible; the emergence of behavioral modernity about 50 thousand years ago resulted much more rapid cultural evolution than before. But perhaps John Hawks could add some context here. It may be that Neandertals are oversampled in this dataset within the last few hundred thousand years vis-a-vis other archaic H. sapiens, distorting the trend line somehow. To me it still seems that the secular trend of increase over such a long period is somewhat puzzling, especially in light of relative stasis in toolkits. It makes me almost wonder if modern humans in their present highly cultural form were almost inevitable barring extinction due to some deep evolutionary positive feedback loop which was set in motion ~2 million years ago.