Discover Human Origins

Hispanos and Sephardic ancestry | Gene Expression

Thu, 24 May 2012 19:06:07 +0000

A correspondent emailed me to tell me that Linda Chavez, whose father was a New Mexican Hispano, was found to have Sephardic Jewish ancestry in Henry Louise Gates Jr’s Finding your Roots series. This brings me to point to a recent paper, The impact of Converso Jews on the genomes of modern Latin Americans:

Modern day Latin America resulted from the encounter of Europeans with the indigenous peoples of the Americas in 1492, followed by waves of migration from Europe and Africa. As a result, the genomic structure of present day Latin Americans was determined both by the genetic structure of the founding populations and the numbers of migrants from these different populations. Here, we analyzed DNA collected from two well-established communities in Colorado (33 unrelated individuals) and Ecuador (20 unrelated individuals) with a measurable prevalence of the BRCA1 c.185delAG and the GHR c.E180 mutations, respectively, using Affymetrix Genome-wide Human SNP 6.0 arrays to identify their ancestry. These mutations are thought to have been brought to these communities by Sephardic Jewish progenitors. Principal component analysis and clustering methods were employed to determine the genome-wide patterns of continental ancestry within both populations using single nucleotide polymorphisms, complemented by determination of ...

Ancient Golden Earring Discovered Hidden in a Jar in Israel | 80beats

Wed, 23 May 2012 19:01:02 +0000

This beautiful golden earring, decorated with figures of goats, was one of a trove of jewelry pieces that were wrapped in cloth and stuffed into a jar discovered by archaeologists at the Tel Meggido dig in Israel. When the team flushed the jar’s interior with water, earrings, a ring, and carnelian beads came tumbling out.

They aren’t sure why the jewelry was in the jar, but they posit that it could have been hidden there by the inhabitants of the home where the jar was found for safekeeping. The layer of soil where the find occurred dates from the 11th century BCE, a period when Meggido was under Egyptian rule, and the team believes the jewelry is either of Egyptian origin or inspired by Egyptian designs.

Image courtesy of American Friends of Tel Aviv University

In The Beginning Was the Mudskipper? | The Loom

Wed, 23 May 2012 17:00:05 +0000

In 1893, the Norwegian zoologist Fridtjof Nansen set off to find the North Pole. He would not use pack dogs to cross the Arctic Ice. Instead, he locked his fate into the ice itself. He sailed his ship The Fram directly into the congealing autumn Arctic, until it became locked in the frozen sea. Nansen was convinced that the ice itself would drift up to the pole, taking him and his crew along for the ride.

For two and a half years they drifted with the pack. It gradually became clear to Nansen that The Fram had stopped moving north and was now traveling east instead, back towards Europe. He leaped out of the ship and tried to sled up to the pole, only to discover that the ice he was now traveling on was moving south. Only four degrees away from true north, he decided to retreat. He bolted back for Franz Josef Land.

The Fram meanwhile continued to drift east. After several months, it broke free of the ice, and the crew sailed the ship south to the island of Spitzbergen. There on the bare flats they saw a giant ...

A Flu Shot For Life | The Loom

Sat, 19 May 2012 14:58:05 +0000

Why do flu shots only protect us for a single season? Why can’t influenza vaccines be like polio vaccines: get them in childhood and be done with them? Wouldn’t that be the best way to prepare ourselves for the next pandemic?

These are among the questions that will be addressed at next month’s World Science Festival. To lay the groundwork, I’ve written a blog post at the festival web site on where we stand on the road to a universal flu vaccine. At this point, we have good reason to believe that such a vaccine could be invented. Which makes it all the more urgent that we do so. Check it out.

The Vital Chain: Why Manta Rays Need Forests | The Loom

Thu, 17 May 2012 16:33:19 +0000

Manta rays spend their lives in the ocean, sweeping up microscopic animals. And yet scientists have found that their well-being depends on forests. Meadows in the northwestern United States are ecologically linked to salmon thousands of miles out at sea. Today, I’ve got a piece in Yale Environment 360 in which I explore the bonds that join land and sea together. Check it out.

Abraham’s genetic threads | Gene Expression

Wed, 16 May 2012 06:46:08 +0000

Every few days my Google Alerts have been dropping in my inbox reviews of Harry Osters’ Legacy: A Genetic History of the Jewish People. The latest is in the The Tablet, A Case for Genetic Jewishness:

For a Jewish genetics researcher, being told in print that ‘Hitler would certainly have been very pleased’ by your work can’t be pleasant. But that’s what happened in 2010 to Harry Ostrer, a geneticist at the Albert Einstein College of Medicine, when he and his colleagues published a study showing that Jews in three different geographical areas had certain collections of genes that made them more biologically similar to one another than they were to non-Jews in the same regions. The work also showed that Jews around the world could trace their ancestry to a group of people who lived in the Middle East 2,000 years ago; that meant, however, that certain genetic signatures could be used to identify Jews, indicating that Jews share a common biological identity beyond their religious affiliation—which is what inspired the Hitler crack.

I don’t plan on reading Legacy because I already read the paper which it is based on, Abraham’s Children in the Genome Era: Major Jewish Diaspora ...

It doesn’t always get “better” | Gene Expression

Wed, 16 May 2012 05:28:15 +0000

The History News Network has a post up, Now It’s Obama Who’s Our First Gay President!, which hammers home points which I’ve been making implicitly and explicitly about historical processes, especially in the United States:

Today, I know no historian who has studied the matter and thinks Buchanan was heterosexual. Fifteen years ago, historian John Howard, author of Men Like That, a pioneering study of queer culture in Mississippi, shared with me the key documents, including Buchanan’s May 13, 1844, letter to a Mrs. Roosevelt. Describing his deteriorating social life after his great love, William Rufus King, senator from Alabama, had moved to Paris to become our ambassador to France, Buchanan wrote

…

This ideology of progress amounts to a chronological form of ethnocentrism. Thus chronological ethnocentrism is the belief that we now live in a better society, compared to past societies. Of course, ethnocentrism is the anthropological term for the attitude that our society is better than any other society now existing, and theirs are OK to the degree that they are like ours.

The specific aspect of James Buchanan’s sexuality is not particularly interesting to me. Rather, the bigger picture is that the social milieu of the 1850s is ...

Tapeworms in the brain: Fearfully common | The Loom

Tue, 15 May 2012 21:29:03 +0000

We’ve all heard about tapeworms getting into the intestines. That’s bad enough. But sometimes they can also end up in the brain. In my column in the latest issue of Discover, I write about neurocysticercosis, which is shockingly common in some parts of the world, causing an estimated five million cases of epilepsy. Yet neurocysticercosis experts consider the disease as a fairly easy one to wipe out. We have the tools to do it, but not the will. Check it out.

Murals in an Ancient Mayan Chamber Include Calendar Calculations | 80beats

Mon, 14 May 2012 18:18:39 +0000

The Xultun scribe’s chamber, with A, B, and C showing the locations of the calculations.

In a small closet-like chamber off a central plaza of the ancient Mayan city of Xultun, a scribe once sat with a paintbrush in hand.

On the north walls of the room, he painted an apparent self-portrait, facing a figure with an elaborate headdress, perhaps a ruler. But on adjacent walls, he and his successors, starting in about 800 C.E., painted and inscribed various astrological calculations. They are very similar to those found in the Dresden Codex, one of the most famous extant Mayan books, which contains numerous astrological and ritualistic cycles and is thought to have been copied from older books sometime between the 11th and 15th centuries. The markings on the scribe’s walls in Xultun, unveiled last week in a paper in Science, represent the earliest known depictions of some of these calculations.

The glyphs in location C, which consist of columns of dates

National Geographic, which helped fund the work, has a news feature on the discovery that gives perspective on the calculations’ purpose:

For ninth-century Maya, tabulating astronomical calendars ...

Lost voyages to the North Pole and more: Catching up with Download the Universe | The Loom

Mon, 14 May 2012 15:37:26 +0000

Over at Download the Universe, we’ve added another crop of entertaining reviews about ebooks that you definitely should–or, in some cases, definitely should not–check out:

“When an Autism Diagnosis Comes as a Blessing”: Steve Silberman writes a powerful review about the reality of autism and a Kindle memoir about living with the condition.

“Meandering Mississippi: An early journalism iBook is all wet”: Seth Mnookin reads an account of last year’s Mississippi floods and wonders why newspapers are squandering the opportunities that ebooks are offering them.

“A Lost Explorer Returns: Todd Balf’s Farthest North: David Dobbs revels in a well-told story of an ill-fated scientific voyage across the Arctic.

“Leonardo: The First Great Science Ebook”: I take a look at a lavishly-produced ebook about Leonardo da Vinci’s forgotten work as a pioneer of anatomy. Staggeringly impressive.

“A Time Machine for the Face of Earth”: My review of a coffee-table-like ebook about how humans (and other forces) are changing the surface of the planet.

“Artificial Epidemics: You’re Not Sick, You’re Just Overdiagnosed”: Neuroscience blogger “Scicurious” is unimpressed with an ebook that claims that depression and prostate cancer are all in your head. (Confused? You should ...

Scanning man’s best friend | The Loom

Fri, 11 May 2012 22:26:26 +0000

We’ve learned a lot about how the brain works from functional magnetic resonance images. I should clarify: we’ve learned a lot about the human brain. Thousands of people have volunteered to lie down inside fMRI scanners and have the activity in their brains monitored as they perform different kinds of mental tasks, or even just do nothing at all. We must resist the temptation to look at the pretty fMRI images and think they’re just photographs of the mind. They’re actually more like very complex, statistically worked-over graphs. But even with those caveats, there’s a lot to learn from them. But fMRI only works if you hold very, very still. Having been scanned myself for a story a few years back, I can vouch that this experience takes a lot of patience, and a high tolerance for loud buzzing noises and for narrow, confined spaces. Scientists have managed to take fMRI scans of monkeys and rats, but they’ve either been knocked out cold, or restrained so the images of their brains don’t blur. If you can persuade a gorilla to lie peacefully in the bore of a scanner for half ...

Cancer evolution at TEDMED | The Loom

Fri, 11 May 2012 13:00:44 +0000

Earlier this year, TEDMED took place in Washington DC, showcasing people doing innovative research in medicine. This year’s talks are now being loaded online, and today I was happy to see that cancer and evolution got their due. Franziska Michor of Harvard explained how the threat of cancer is a legacy of our evolution into multicellular animals, and how every case of cancer is a miniature unfolding of evolution within our own bodies. What makes Michor’s work particular exciting is that she is bringing the mathematical precision of population genetics and other aspects of evolution to the treatment of cancer.

I wrote about some of Michor’s work in my 2007 Scientific American article, “Evolved for Cancer?” (carlzimmer.com, sciam.com) I’ve also explored cancer evolution here on the Loom: “Inside Darwin’s Tumor” and “The Mere Existence of Whales.” And you can find lots of Michor’s papers as free pdf’s on her publication page.

The Malagasy Ancestry Project | Gene Expression

Fri, 11 May 2012 04:45:51 +0000

Just a heads up, Dr. Joseph K. Pickrell has begun moving on the Malagasy Ancestry Project. More information:

The genetics of the Malagasy people have been essentially unstudied. Analysis of Y chromosome and mitochondrial DNA markers have corroborated the lingustic evidence that the Malagasy result from admixture between southeast Asian and east African populations [1,2]. However, no genome-wide data from Malagasy individuals has been analyzed to date (with the exception of the individuals in this project).

Our goal is to address a number of questions about the genetics of the Malagasy. These include, but are not limited to:

1. What fraction of ancestry in the Malagasy is from Africa rather than southeast Asia?
2. Does this fraction vary geographically and/or ethnically?
3. Who were the populations that first settled Madagascar?
4. Was Madagascar settled once from southeast Asia, or multiple times?
5. Can we use genetics to more precisely date the arrival of African populations in Madagascar?

Our approach to this project is to use data contributed from Malagasy individuals who have been genotyped by a personal genomics companies. If you would like to contribute your data, please contact us.

Current results are available from the tabs at the top of this ...

You ask for signed bookplates, you get signed bookplates | The Loom

Thu, 10 May 2012 23:27:45 +0000

At some of my recent talks, I’ve been running into people who’ve been annoyed that they forgot to bring a book of mine to get signed. You really couldn’t think of a better way to cheer up a writer, and so I feel the need to reciprocate.

So if you’ve gotten a book of mine and want to get it signed, I’ve printed up some bookplates that I can autograph and send to you.

Just to ensure I’m not signing bookplates for alien robots who will take these bookplates to their home planet to…do whatever evil thing alien robots do with bookplates from science writers…please follow these steps:

1. Take your picture with the book.

2. Email it to me, with your mailing address and any special signing request. As in, “To Ken Ham, so that someday he may appreciate transitional fossils….”

Optional step 3. For those on Twitter: instead of emailing me your photo, you can upload it to Twitter (mentioning my Twitter name @carlzimmer). Be sure to email me your address, too, so that I know where to send the bookplate.

So far, I’ve got three bookplates–one for Parasite Rex, one for Science Ink (in matching Goth type), and one for ...

Next Thursday: author Florence Williams and me at McNally Jackson in New York | The Loom

Wed, 09 May 2012 15:05:17 +0000

Gothamites: please join Florence Williams and myself at the bookstore McNally Jackson in New York on Thursday May 17. Williams is the author of the new book, Breasts: A Natural and Unnatural History, a smart, wry synthesis of evolution, physiology, microbiology, environmental science, and even biomechanics.

Where: McNally Jackson, 52 Prince St., New York, NY (Phone: 212.274.1160)

When: May 17, 7 pm.

More details are here.

The great pruning, and the great synthesis | Gene Expression

Wed, 09 May 2012 07:11:13 +0000

Sahul 10,000 years ago

John Hawks has a very long rumination on the story of blonde Melanesians which came out last week. If I can read between the lines I think some of the implications dovetail with John’s thesis in his 2007 paper on adaptive acceleration. But I’ll leave the deep reading of tea leaves to those better versed in such affairs. Rather, I will comment on two issues. The first is specific. I believe that the TYRP1 R93C allele responsible for blonde hair among the Solomon Islanders is going to be found to be the same one responsible for blonde hair around New Guinea and among some Australian Aboriginals.

There are several reasons why I suspect this. First, these Oceanian populations do seem to be a distinctive clade. There are some disagreements among geneticists as to whether they are the descendants of the first settlers of Oceania in totality, or whether they’re a compound lineage. The natural historical details need to be teased apart, but there’s no doubt that they’re a distinct and separate phylogenetic lineage in relation to other human populations (with some admixture ...

Thick, 1,000-Year-Old Dental Plaque Is Gross, Useful to Archaeologists | Discoblog

Tue, 08 May 2012 18:46:23 +0000

What big plaque deposits you have!

A dentist will tell you to floss everyday, but an archeologist might, well, have different priorities. Turns out the nitrogen and carbon isotopes in dental plaque can give archeologists a look at 1,000-year-old diets.

The buildup of plaque on this set of teeth is, um, impressive. (Cut the skull some slack though, this was before we had dentists to chide us about daily flossing.) Without the benefit of modern dental hygiene, the plaque built up over a lifetime, layer upon layer like a stalagmite. In a paper recently published in the Journal of Archeological Science researchers exhumed 58 medieval Spanish skeletons and scraped off their dental plaque to test carbon and nitrogen isotopes. When they compared the isotope profiles of the Spaniards to that of plaque from an Alaskan Inuit, the scientists found the ratio of nitrogen-15 to be quite different. That makes sense, as the Intuit ate a predominantly marine diet, and there is more nitrogen-15 in the protein molecules of organisms living in sea than on land.

Another benefit of plaque is that it’s easier to test than bone, which has to be dissolved in acid to extract from ...

The Guardian reviews A Planet of Viruses: “Fascinating and enlightening” | The Loom

Tue, 08 May 2012 13:17:53 +0000

Today the Guardian reviews A Planet of Viruses:

Viruses are everywhere: scientists have found them under Antarctic ice; they lurk inside your lungs which until recently were believed to be sterile; and seawater, which was once thought to contain very few, has now been found to be teeming with viruses. In fact, they outnumber all other residents of the ocean by 15 to 1. Even the human genome contains genes that came from viruses which infected our ancestors some 30m years ago, an idea that Zimmer describes as “almost philosophical in its weirdness.” In this succinct yet elegantly written survey, he explores the vital role viruses play in the evolution of life on Earth and how scientists have begun to reveal their often deadly secrets. Smallpox – the only human virus to have been eradicated – killed an astonishing 500m people every century in Europe between 1400 and 1800. From the common cold, first described 3,500 years ago by the Egyptians, to a new type of giant virus discovered in a Bradford water-cooler that mimics bacteria, this book is a fascinating and enlightening introduction.

Reification is alright by me! | Gene Expression

Tue, 08 May 2012 08:01:43 +0000

Long time readers know that I’m generally OK with reification as long as we don’t take it too seriously. And we do that all the time. An “object” is really only an “object” in a human-sense. Reduced down to particle physics it is an altogether different entity. But on the human-scale asserting that a chair is indeed a chair, rather than cellulose, etc., (or now, polymers), and further down basic macromolecules, is a useful “fudge.” Similarly, I’m generally skeptical of the idea that we have a clear & distinct model for what a “species” is. The framework is very different when you’re talking about prokaryotes, as opposed to plants, as opposed to mammals. The question is not species, but what utility or instrumental value does the category or class species have?

For most of the stuff I’m concerned with, the messy shapes of reality which are the purview of biological science, we are all fundamentally nominalists in our metaphysic. We may accept that we’re idealists in the sense of cognitive or evolutionary psychology, but human intuition does not make it so. The categories and classes we construct are simply the semantic sugar which makes the reality go down ...

How frogs climbed up into the Lost World: My story in tomorrow’s New York Times | The Loom

Tue, 08 May 2012 00:36:52 +0000

The tepuis of northern South America–tabletop mountains ringed by sheer cliffs rising up thousands of feet–inspired Sir Arthur Conan Doyle’s novel The Lost World. Doyle envisioned dinosaurs and other primordial creatures surviving on these remote islands in the sky.

It turns out that the tepuis are indeed ancient vestiges. The surrounding land eroded away 70 million years ago. Biologists have long been fascinated by the plants and animals that live on top of them today. In many cases, the species on a tepui are found nowhere else on Earth. Many have argued for the wonderfully-named “Lost World Hypothesis”–the unique species of the tepuis been stranded up there for 70 million years.

In tomorrow’s New York Times, I report on a team of scientists who tested that hypothesis by looking at the DNA of frogs that live on tepuis. And for them, at least, the hypothesis fails. Somehow, those tiny frogs managed to scale walls that strike fear in even the toughest rock climbers. For the full details, check out the story.

Image by Xyrenita on Flickr/via Creative Commons

The stories doctors tell, Noah’s flood, and more: two interviews on writing about science | The Loom

Mon, 07 May 2012 15:01:38 +0000

I recently sat down for two stimulating conversations which are now in print. One was with Ben Lillie for Story Collider, the new magazine that Lillie has launched to complement his wonderful storytelling series. The other was with Ben Goldfarb of Sage, a student-run environmental arts and journalism publication of the Yale University School of Forestry & Environmental Studies. Ben L. and Ben G. asked lots of thoughtful questions about the art of science writing, and the place of the science writer in society. It’s a little painful to read my ramblings taken down verbatim–I want to reach out and edit away the extra verbiage–but you may still find them interesting.

Finding fake roots | Gene Expression

Mon, 07 May 2012 08:56:50 +0000

I haven’t watched much of Henry Louis Gates Jr.’s Finding Your Roots series. It seems like Gates has kind of created a mini-empire in genealogical series on PBS. More power to him, but it hit diminishing returns for me a long time ago. But I see clips online here and there. And something which I saw really kind of disturbed me. From what I can gather Gates regales his subjects with their DNA results, and tells them their ancestral quanta fractions. Nothing too amazing. But it seemed clear to me that when Gates referred to “European”, “Asian” and “African” ancestors, he was communicating to the audience that these quanta really represented those exact populations!

I assume that the geneticists Gates works with explained to him the falsity of this typology. I also understand that the television format results in natural license. But Henry Louis Gates Jr. has produced lots of these shows now. He has the leisure to unpack the concepts for the lay audience. As it is, it seems he is repeating misconceptions of model-based clustering algorithms. Misconceptions mind you which persist even within the biological community. But that doesn’t ...

In Memory of Lucy #scienceink | The Loom

Sun, 06 May 2012 15:13:11 +0000

Victoria McGowan writes,

Please find attached a photo of my Australopithecus tattoo. I’m a medical anthropologist researching the historical relationship between school meals and obesity in children as part of my PhD at Durham University. Obviously this has very little to do with Australopithecus but my interest in “Lucy” began when I started my UG degree in Anthropology here at Durham. One of my first lectures was on our Biological and Social Origins and we learnt about our evolutionary heritage. Lucy caught my eye because she was one of the most complete finds of this species at that time. Also as it was thought that she was more closely related to Homo genus than any other Australopithecus at that time.

I found it fascinating that from her remains we could postulate that she was bipedal and from her pelvis we could deduce that she would have gave birth to a larger brained infant than previous species. We can further postulate that her infant care practices would be more similar to our own, larger brained infant would have to complete their growth outside the womb and would require ...

Bell Beakers and R1b | Gene Expression

Sun, 06 May 2012 07:20:45 +0000

Over at Dienekes blog he has a post up about the extraction of R1b from a male who lived in Germany 4-5,000 in the past. This is important because R1b is one of the two most common male lineages (on the Y chromosome, passed from father to son) in Europe, and, it has inexplicably been underrepresented or absent in the ancient DNA samples. The other modal lineage is R1a (it too is underrepresented).

I have a pretty good grasp of variation on the autosomal dimension. A modest familiarity with uniparental lineages, Y and mtDNA. And finally, a rather weak understanding of archaeological patterns. Since mtDNA tends to be found at very high concentrations in subfossil remains you’ll get a good yield of that in the near future (as in the paper Dienekes covers). Y chromosomal information is more difficult. The problem with autosomal information is that you need more of it to make robust genealogical inferences (due to confounding with selection, as well as recombination breaking apart haplotypes), though if you manage to hit a functional region that can be very informative.

I assume in the year 2020, and perhaps well ...

Join Ed Yong and me for a transatlantic talk about killer flu, feathery dinosaurs, and every living thing in between | The Loom

Fri, 04 May 2012 20:45:21 +0000

Ed Yong and I may live on either side of the Atlantic, but our minds are in the same place: that strange realm where fungi take over the minds of ants, where dinosaurs sprout feathers, and where ducks shatter glass with their genitals. In other words, Earth.

We don’t get to see each other in person more than once a year, if that, but we always have a good time when we do. Which is why I’m looking forward to having an online conversation with Ed on May 14. And you’re invited.

This event is brought to you by Shindig, a new company that’s set up a web site for video chat events. The design of the site is quite elegant: the speakers appear on the top of the event page, where everyone can watch them talk. Audience members appear in their own screens on the page as well, and when speakers ask for questions, they can hit a “raise hand” button. The audience member asking a question then zooms up to the top of the screen, where he or she can have a conversation with the speaker. (You’ll obviously ...

Case closed: blonde Melanesians understood | Gene Expression

Fri, 04 May 2012 06:21:26 +0000

As a small child perusing old physical anthropology books I would occasionally stumble upon images of people of Oceanian stock with light hair color. I would wonder: is this a biological or cultural feature? In other words, were people bleaching their hair? If it was biological, was it heritable, or was it simply malnutrition? Another aspect of the phenotype was also straightforward: it did not seem that light hair color resulted in any concomitant lightening of the skin. Granting that this was a heritable biological trait, the questions then were simple: was this trait an independent occurrence of de-pigmentation in Oceania, or was it due to introgression of European alleles?

First, one must note that this is not an isolated feature in Oceania. Rather, blondism crops up in the Solomon Islands, in New Guinea, as well as among some Australian desert groups. This in itself should make us skeptical of the model of European admixture. Additionally, blue eyes, which exhibits a higher frequency in Europeans than blonde hair, is not similarly common in these populations. But all this speculation is now a historical curiosity. The results are widely known from conference ...

Unz Historical Research Competition | Gene Expression

Thu, 03 May 2012 03:52:34 +0000

For your consideration:

As a means of publicizing the vast quantity of high-quality content material uniquely available on its recently released website, UNZ.org is announcing a historical research competition.

A First Prize of $10,000 and several other cash prizes will be awarded for the most significant and interesting historical discovery based on UNZ.org source material. All entries must be received by August 31, 2012, and awards will be made by September 30, 2012.

Interested participants should examine the rules, read the description of the available content source material, and then register for the competition.

Good luck!

Not that it matters, but I am on the judging panel. I’m hoping that there are some cliometric oriented submissions using the text data, though I’m a fan of good history, period.

Behold The Forbidden Flu: A Loom Explainer | The Loom

Wed, 02 May 2012 17:00:01 +0000

Here, for your viewing pleasure, is a very important part of a very special flu virus. It may look like an ordinary protein, but in fact it’s been at the center of a blazing debate about whether our increasing power to experiment on life could lead to a disaster. Not that long ago, in fact, a national security advisory board didn’t even want you to see this. So feast your eyes.

For those who are new to this story let me start back at the beginning, in 1997.

In that year, a child in Hong Kong died of the flu. Doctors shipped a sample of his blood to virus experts in Europe, but they didn’t bother taking a look at it for months. When they did, they were startled to discover that it was unlike any flu they’d seen in a human being before.

Each year, several different flu strains circulate from person to person around the world. They’re known by the initials of the proteins that cover their surface–H3N2, for example, is one common strain. The H stands for haemagglutinin, a protein that latches to a host cell so that the ...

Pygmies: “old” populations, and a new “look” (?) | Gene Expression

Mon, 30 Apr 2012 07:32:00 +0000

Over the years one issue that crops up repeatedly in human evolutionary genetics and paleoanthropology (or more precisely, the popular exposition of the topics in the media) is the idea that is that “population X are the most ancient Y.” X will always refer to a population within a larger set, Y, which is defined by relative marginalization or retention of older cultural folkways. So, for example, I have seen it said that the Andaman Islanders are the “most ancient Asian population.” Why? The standard model for a while now has been that non-Africans derive from a line of Africans which left the ancestral continent 50 to 100 thousand years ago, and began to diversify. Presumably Andaman Islanders have ancestry which goes back to this original dispersion, just as Europeans and Chinese do (revisions which suggest that Aboriginals may have been part of an earlier wave, still put the Andamanese in the second wave). The reason that the Andaman populations are termed ancient is pretty straightforward: they’re Asia’s last hunter-gatherers, literally chucking spears at outsiders. An ancient lifestyle gets conflated with ancient genetics.

This is a much bigger problem with the ...

Facing the ocean | Gene Expression

Sun, 29 Apr 2012 06:35:47 +0000

Halford Mackinder’s conceptualization of the world

With the recent publication of the paper on the archaeogenetics of Neolithic Sweden I feel like we’re nearing a precipice. That precipice overlooks lands of great richness, filled with hope. It’s nothing to fear. It is in short a total re-ordering of our conception of the recent human past, at minimum. The “pots not people” paradigm arose in archaeology over the past few generations due to both scholarly and ideological factors. The scholarly ones being that intellectuals of the 19th and early 20th century made assumptions of extremely tight correspondence between material and cultural characteristics, and demographic dynamics, which seem to have been false. Therefore, the rise of an Anglo-Saxon England and the marginalization of Celtic Britain to the western fringes was not just a cultural reality, but also a fundamentally racial one, as Germans replaced Celts in totality. The ideological problem is that this particular framework was take as a given by the Nazis during World War II, lending a bad odor to the

hypotheses of migration which were once so ascendant.

No ...

A Multitude of Hands: My new essay for National Geographic | The Loom

Fri, 27 Apr 2012 15:26:38 +0000

In the May issue of National Geographic, I contemplate the hand. Human hands are unique and versatile–and yet we are far from the only animals with them. By looking at the variety of hands in nature, we can see some of the most striking evidence of how evolution tinkers in all sorts of unexpected way. Check it out.

The print version is accompanied by lovely sketches of a wide range of hands. If you read the story online, you can see an animation of the human hand. And if you have the National Geographic iPad app, you can see videos of other hands, from frogs to aye-ayes.

[Image: White -handed gibbon by Ingo Arndt, on Arkive.]

The last days of Grendel | Gene Expression

Fri, 27 Apr 2012 05:27:47 +0000

A new paper in Science has just been published which in its broad outlines has been described in conference presentations. When examining the autosomal genetic variation of three individuals of the hunter-gatherer Pitted Ware Culture (PWC), and one of the agriculturalist Funnel Beaker Culture (TRB), the authors found that the two groups were sharply differentiated. The number of SNPs was on the order of 10,000 or so if I read the methods correctly. This is rather thin for studying contemporary within European population differences (~100,000 or more seems to be safe), in particular using hypothesis based clustering algorithms (it seems more manageable for PCA). But the findings are strong enough that I think we shouldn’t discount them. The most fascinating aspect of the results is that while the PWC seem to exhibit affinities with Northern and Northeastern Europeans, the TRB individual seems more similar to extant Southern Europeans!

Others have already commented extensively on the results. Keeping in mind the small sample sizes, limitation of comparisons, and the relatively thin marker set, I think the primary result we can take away from these findings is that old models ...

Early Skeleton Stolen From Underwater Cave in Mexico | 80beats

Thu, 26 Apr 2012 15:47:03 +0000

The interior of a cenote

The cenotes of the Mexican state of Quintana Roo are peppered with mysterious skeletons. Over the millennia, these water-filled caves have served as burying grounds and sacrificial sites for native peoples, and in fact, several ancient sets of remains have been found so deep in the caves that they are inaccessible without diving equipment, suggesting that they must have been placed there when the caves were dry, before the ice caps melted around 8,ooo BCE, and putting them in the range of 10-14,000 years old.

Now, though, one of those ancient skeletons, called the Young Man of Chan Hol II since its discovery in 2010, has gone missing from its cenote. New Scientist reports that the National Institute of Anthropology and History has put up posters in bakeries, supermarkets, and divers’ shops throughout the town of Tulum in hopes of receiving tips as to the skeleton’s whereabouts and is considering legal action, though we’re not sure what actions are possible against thieves. Apparently there have been other archaeological thefts from cenotes as well; the cenotes are frequented by divers, and the authorities cannot guard them all.

Image courtesy of ...

DC and Philly: A Bundle of Talks | The Loom

Wed, 25 Apr 2012 14:14:25 +0000

I’m heading south to give a series of talks about everything from evolution to science tattoos, the future of journalism, and the mutant bird flu saga. Most of these talks are open to the public. Here’s the rundown, with the public talks noted:

Thursday 11 am: Bethesda, MD: “Telling the Stories of Science in Words and Images.”
National Institute of Diabetes and Digestive and Kidney Diseases Fellows Scientific Retreat.

Thursday 3 pm: Arlington VA: “The Darwin Beat.”
National Science Foundation

Friday 9:30 am: US Science Engineering Festival, Washington DC Convention Center:
I’m part of the festival’s “Nifty Fifty”–speakers who talk to high school students about science. In room 146A, I’ll be giving a sneak peek of my Science Ink talk to a group of students, in advance of the festival, which officially starts on Saturday.

Saturday: US Science and Engineering Festival, Washington DC Convention Center: open to the public

I’ll be speaking twice about Science Ink –both talks are open to the public

10:55 AM-11:40 AM Stage Meeting Room Number: 147AB

Noon to 1: Book signing Expo Hall B

2-2:30 PM National Academy of Sciences Booth 603

Sunday 2pm: Philadelphia : open to the public
Philadelphia Science Festival. I’ll be talking about Science ...

One baby, alone on a PCA island | Gene Expression

Wed, 25 Apr 2012 03:40:15 +0000

A week ago I reported that according to 23andMe I’m 40% Asian, and she is 8% Asian (in the future if I say “she” without explanation, you know of whom I speak). Obviously something is off here. The situation resolved itself when I tuned my parameters and increased my sampled populations in Interpretome. By now I’ve already done the estimates of recombination on the chromosomes which came together to produce her, and the realized value of 8 percent instead of 20 percent “Asian” simply can not be due to a particular set of unlikely crossing over events. From what I can gather it seems like ancestry painting should be viewed as a qualitative rather than a quantitative assessment. This sounds really strange when you are given percentages, but the results are strange, and obviously wrong too often in terms of the specific values.

Here’s an admixture plot which shows more realistically informative values:

I’ve run several admixture plots already with my daughter, and ...

How Our Brains Set the World Spinning | The Loom

Tue, 24 Apr 2012 21:00:10 +0000

If there’s ever excuse to publish an optical illusion as cool as the “Rotating Snakes,” I’ll take it. This illusion was invented in 2003 by Akiyoshi Kitaoka of Ritsumeikan University in Japan, and ever since, Kitaoka and other scientists have been trying to figure out why it works. A new paper by Stephen Macknik at the Barrow Neurological Institute in Phoenix may have the answer.

As you’ll notice, the circles seem to rotate in response to where you look at the illusion. So Macknik and his colleagues tracked the movement of people’s eyes as they gazed at two of these wheels on a computer screen. Their subjects kept a finger pressed on a button, lifting it whenever they seemed to see the wheels move.

Macnick and his colleagues found a tight correlation between the onset of the illusion and a kind of involuntary movement our eyes make, known as microsaccades. Even when we’re staring at a still object, our eyes keep darting around. These movements, called microsaccades, help us compensate for a peculiar property of the eye: if we stare at an object for too long, the signals each photoreceptor sends ...

An algorithm is just an algorithm | Gene Expression

Tue, 24 Apr 2012 04:48:08 +0000

In the comments below:

You should include a Moroccan or otherwise native North African sample. Without a North African sample West Africans act as proxy for some of that North African ancestry that does exist in Iberia, specially the Western third (Portugal, Galicia, Extremadura, León, etc.) Doing that your analysis would become more precise and you could make better informed claims.

I was reading through all the entry and there was no mention to the rather surprising notable West African component in Iberians other than Basques. For my somewhat trained eye it is clear that this is a proxy for North African ancestry and not directly West African ancestry. This is demonstratedly also the case in Canary Islands, at least to a large extent, and, by extension in Cuba (which is nearly identical to your average Canarian), at least Cuba-1. Cuba-2 seems actually admixed at low levels and both seem to have some Amerindian ancestry not existent in Spain.

This is a fair point. I switched computers recently, and the Behar et al. data set I had seems to have become corrupted. So I snatched the Mozabites from the HGDP, and removed the Gujaratis from the previous run. I also added Russians, ...

Paternity most assured | Gene Expression

Mon, 23 Apr 2012 07:32:54 +0000

The myth that 10 percent of children the product of ‘non-paternity events’ is rather persistent. I have no idea why, but I do know that even biologists accept it. But how we can we continue to accept this when surnames can provide population genetic information 400 years after the fact? The population of Belgium is famously divided between Latinate Walloons and Germanic Flemings. But is notable that a substantial number of Flemings carry surnames of clear Romance origin. This is in large part due to acculturation. Nevertheless, even 400 years after the largest of the migration and assimilation events males with Romance-origin surnames reflect their genetic background:

If non-paternity events occurred at a rate of 1 out of 10 the correlation between surnames and genetic lineage would have been decoupled long ago. These results have been confirmed in other societies. I predict that low non-paternity rates will also be confirmed in China; as that nation has a long history of surnames. Of course, one might posit a scenario where males who are the products of non-paternity events tend to be less fit than those who are not, so over ...

A deeper dive analysis of two Cubans | Gene Expression

Mon, 23 Apr 2012 06:42:08 +0000

About a week ago I put up a post put on an analysis of a paper which reported on the ancestral make up of 50 Cubans (as well as assorted other Hispanic/Latino groups). One aspect of the paper which was somewhat notable is that 1 out of 3 Cubans were 90 percent or more European in ancestry. The notability of this is that is that 5 out of 6 Cuban Americans identify as white. That is, of European ancestry. The main caveat here is that these Cubans were sampled from New York City, and to a lesser extent the Midwest. The fact of non-European admixture in putatively white European individuals from Latin America is not surprising. Our prior expectation should be that the admixture is non-trivial, though not preponderant. For example, the majority of the white population of Argentina has Amerindian ancestry (or, more precisely ~15 percent of the aggregate ancestry of Argentineans is Amerindian). At least notionally Cuba is a much more racially mixed culture than Argentina, so non-white admixture in even white Cubans is not surprising.

Based on the above paper (and the data which you can find on other Latin American whites), as well as ...

Bricolage and the Tangled Bank: Happy Mistranslations of Evolution | The Loom

Sun, 22 Apr 2012 15:43:55 +0000

I got back home last night to a pleasant surprise: a copy of the new French translation of The Tangled Bank: An Introduction to Evolution. One of the most interesting parts of writing a book is seeing what emerges from the mind of your translator. I’ve usually had good luck with translators. We’ll exchange emails to find a way to capture the spirit of sentences in my books that would make no sense in another language, thanks to the odd figures of speech we use in English. When the book actually arrives, I usually can do little more than hope that it makes sense in Korean or Japanese or Dutch.

Once in a while, however, things don’t go well, though. I once got a disturbing email from a German reader, who had read the original edition of Parasite Rex and then picked up the German translation. “Believe me, I have never seen something like this before. It is a sin. If you could read it, you would get tears in your eyes.” (Fortunately, my American publisher was able to use his email as a cudgel, and got that edition ...

Brains, Genes, and You: My Discover column on the Duke Neurogenetics Study | The Loom

Thu, 19 Apr 2012 00:49:38 +0000

I’ve got a new column in Discover on a scientist tracing the links from our genes to our personality. Here’s how it starts:

Ahmad Hariri stands in a dim room at the Duke University Medical Center, watching his experiment unfold. There are five computer monitors spread out before him. On one screen, a giant eye jerks its gaze from one corner to another. On a second, three female faces project terror, only to vanish as three more female faces, this time devoid of emotion, pop up instead. A giant window above the monitors looks into a darkened room illuminated only by the curve of light from the interior of a powerful functional magnetic resonance imaging (fMRI) scanner. A Duke undergraduate—we’ll call him Ross—is lying in the tube of the scanner. He’s looking into his own monitor, where he can observe pictures as the apparatus tracks his eye movements and the blood oxygen levels in his brain.

Ross has just come to the end of an hour-long brain scanning session. One of Hariri’s graduate students, Yuliya Nikolova, speaks into a microphone. “Okay, we’re done,” she says. Ross emerges from the machine, pulls his sweater over his head, and signs ...

Fresh Air interview: links to information on viruses, antivirals, the microbiome, and more | The Loom

Wed, 18 Apr 2012 14:16:24 +0000

Yesterday my Fresh Air interview was broadcast. You can listen to it here. I’ve been lots of emails with follow-up questions, and it occurred to me that I really ought to gather up some links to more information about the topics I discussed.

If I haven’t addressed a question you had listening to the show, leave a comment to this post and I’ll add a link.

Antivirals:
My feature in Wired on the search for antiviral drugs

The “virome”–the viruses that live in our body:
A Loom post about the swarms of viruses in the mouth, where they kill off bacteria
An article in Nature about a study of the viruses in identical twins

The microbiome
My article in the New York Times
My essay on the Loom about medical ecology
My Wired atlas of the human ecosystem
An example of microbiome research: extreme navel gazing
Maryn McKenna’s story in Scientific American on the struggle to mainstream fecal transplants to treat deadly infections
Ed Yong’s oeuvre on the microbiome at Not Exactly Rocket Science
Mayrn McKenna on her blog at Wired writing on the link between beneficial ...

Retraction Watch in the Boston Globe: Make Science More Transparent | The Loom

Tue, 17 Apr 2012 14:08:40 +0000

As I blogged yesterday, I have a story in the New York Times today about some scientists who are calling for a reformation of science, pointing to troubling indicators such as the rise in retractions of scientific papers.

As any sane journalist would do, I consulted the fantastic Retraction Watch, written by Adam Marcus (left) and Ivan Oransky, while working on my own piece. I also called Oransky for his thoughts on the argument I was describing, championed by, among others, Ferric Fang of the University of Washington and Arturo Casadevall of Albert Einstein College of Medicine.

Oransky was a huge help. But by the time my editor and I had shaped the story to fit in the paper, only a brief mention and a link to Retraction remained. Oransky’s own opinions were left behind on the cutting room floor. Fortunately, he knows that floor very well, having swung the journalism scimitar plenty of times himself as the executive editor at Reuters Health.

Even more fortunately, the Boston Globe has published some extended reflections from Oransky and Marcus on what retractions mean for the state of science.

Reprising genes & geography | Gene Expression

Tue, 17 Apr 2012 06:25:59 +0000

Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis:

Recent applications of principal components analysis (PCA) and multidimensional scaling (MDS) in human population genetics have found that “statistical maps” based on the genotypes in population-genetic samples often resemble geographic maps of the underlying sampling locations. To provide formal tests of these qualitative observations, we describe a Procrustes analysis approach for quantitatively assessing the similarity of population-genetic and geographic maps. We confirm in two scenarios, one using single-nucleotide polymorphism (SNP) data from Europe and one using SNP data worldwide, that a measurably high level of concordance exists between statistical maps of population-genetic variation and geographic maps of sampling locations….

There is concordance. But look at the figure below. On the left are populations where they were sampled, and the right shows the populations displayed in a manner to reflect genetic distances.

I don’t want to make too much of this. The HGDP populations tend to be sampled from particularly distinctive groups consciously. But it does look like there is a stronger genetic clustering effect than one can predict from geography alone. That warrants investigation. I will leave the rest for ...

Dysfunctional science: My story in tomorrow’s New York Times | The Loom

Mon, 16 Apr 2012 19:34:55 +0000

In tomorrow’s New York Times, I’ve got a long story about a growing sense among scientists that science itself is getting dysfunctional. For them, the clearest sign of this dysfunction is the growing rate of retractions of scientific papers, either due to errors or due to misconduct. But retractions represent just the most obvious symptom of deep institutional problems with how science is done these days–how projects get funded, how scientists find jobs, and how they keep labs up and running.

Along with the main story, I also wrote a sidebar about how hard it is to hear from the scientists who write retracted papers. I also spoke on the latest Timescast video, which I’ve embedded below. I show up with Arturo Casadevall at about 4:30. There are also lots of links in my story to the original papers. And if you don’t already read it, be sure to check out the blog Retraction Watch, which has been digging deep into the retraction story for years now.

Heads up: Appearing on Fresh Air tomorrow on NPR | The Loom

Mon, 16 Apr 2012 17:55:56 +0000

Recently I talked with Dave Davies, guest host on Fresh Air, about viruses and other things invisible. Our conversation airs tomorrow (Tuesday 4/17) on National Public Radio. More details can be found on the program’s web site.

Monet’s Ultraviolet Eye and other Ebook Epiphanies: Catching Up With Download the Universe | The Loom

Mon, 16 Apr 2012 14:52:42 +0000

Over at Download the Universe, we’ve posted a bunch of new reviews of science ebooks. We fell in love with some titles, we hated others, and we had a love-hate relationship with ebooks that were great in some ways and awful in others. When we started Download the Universe, we thought we were coming together to start something pretty straightforward: a book review dedicated to a neglected category of creations–namely, science ebooks. But ebooks are in such an early stage that our reviews often end up being contemplations of the form itself. In 10 years, I wonder if these questions will be sorted out, or if a new raft of questions will float in to take their place.

Here are the reviews we’ve published since I last posted an update on the Loom, in reverse order:

Monet’s Ultraviolet Eye My review of an app about color, and some thoughts on what ebook designers can learn from museum exhibits

A Disorganized Celebration of Skulls Brian Switek reviews an ebook about the box of bones on top of our spines

Blowing Windmills and Seeing the Future: Al Gore’s Our Choice Dan Fagin reviews Gore’s ebook about energy and climate

World’s Oldest  Deep-Sea Fishermen | DISCOVER

Fri, 13 Apr 2012 03:25:00 +0000

One of the earliest signs of advanced maritime skill, deep-sea fishing has been tenuously traced back roughly 12,000 years. Now an archaeologist has lengthened that timeline another 30,000 years.

The researcher, Sue O’Connor of Australian National University, began her search on an island off the northern coast of Australia where colonizers from Asia are thought to have landed. O’Connor had already found early fishing technology in the area, so when local hunters led her to a nearby limestone cave, she wondered whether it had once sheltered ancient mariners...

Another look at mtDNA | Gene Expression

Mon, 09 Apr 2012 01:55:04 +0000

The new article in The American Journal of Human Genetics, A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root, is open access, so you should check it out. The discussion gets to the heart of the matter:

Supported by a consensus of many colleagues and after a few years of hesitation, we have reached the conclusion that on the verge of the deep-sequencing revolution…when perhaps tens of thousands of additional complete mtDNA sequences are expected to be generated over the next few years, the principal change we suggest cannot be postponed any longer: an ancestral rather than a “phylogenetically peripheral” and modern mitogenome from Europe should serve as the epicenter of the human mtDNA reference system. Inevitably, the proposed change could raise some temporary inconveniences. For this reason, we provide tables and software to aid data transition.

What we propose is much more than a mere clerical change. We use the Ptolemaian geocentric versus Copernican heliocentric systems as a metaphor. And the metaphor extends further: as the acceptance of the heliocentric system circumvented epicycles in the orbits of planets, switching the mtDNA reference to an ancestral RSRS will end an academically inadmissible conjuncture where virtually all mitochondrial genome ...

In run-up to Easter, fasting Ethiopians force hyenas to kill donkeys | Not Exactly Rocket Science

Fri, 06 Apr 2012 01:15:45 +0000

It’s Easter. For some of people, this means they can take up all the vices they gave up for Lent, and binge on chocolate till they feel sick. For the hyenas of northern Ethiopia, it means it’s time to stop hunting donkeys.

Spotted hyenas are unfussy eaters and incredible opportunists. They can feast on rotting meat, anthrax-infected corpses, garbage and dung. They digest their food so completely that their droppings tend to consist of hair, hooves, and white powder made from broken-down bones. Unsurprisingly, they do rather well near urban environments, where humans provide them with a bonanza of scraps, leftovers, and livestock. The hyenas of northern Ethiopia get almost all of their food by scavenging on such sources.

Local humans tolerate the hyenas, which are affectionately known as “municipal workers”. The animals clean the waste from butchers, households, and even the local veterinary college. They’re seen and heard almost every night, and they almost never attack humans. Instead, they have come to depend on the Ethiopians for their food.

But that changes in the run-up to Easter. For 55 days, the local Orthodox Christians go through a period of fasting. Meat goes off the ...