...apparently. A viewer sends this picture. The Australian Broadcasting Corporation is airing a talk I gave in March at the National Press Club in Canberra, as the keynote address for the Science Meets Parliament annual event hosted by the Federation of Australian Scientific and Technological Societies. The talk, composed in a burst of inspiration on the flight across the Pacific, is one I've never given before or since--but I'm kinda proud of it. I am going to see if it will be available in any watchable format stateside, and then I may say some more about the subject matter.

There’s new paper in Genome Biology (tip: Dienekes) which doesn’t present too much in terms of new results, Characterizing the admixed African ancestry of African Americans, but has really, really, good visualization of the data:

Results
From cluster analysis, we found that all the African Americans are admixed in their African components of ancestry, with the majority contributions being from West and West-Central Africa, and only modest variation in these African-ancestry proportions among individuals. Furthermore, by principal components analysis, we found little evidence of genetic structure within the African component of ancestry in African Americans.

Conclusions
These results are consistent with historic mating patterns among African Americans that are largely uncorrelated to African ancestral origins, and they cast doubt on the general utility of mtDNA or Y-chromosome markers alone to delineate the full African ancestry of African Americans. Our results also indicate that the genetic architecture of African Americans is distinct from that of Africans, and that the greatest source of potential genetic stratification bias in case-control studies of African Americans derives from the proportion of European ancestry.

I want to emphasize the part about lack of utility of uniparental markers. These were the first markers which became widely used in scientific genealogy, and African Americans made a great deal of recourse to these so as to identify the tribe from which their ancestors came. There are obvious historical reasons why this would have more valence for this group than for others, as their ancestral identity was consciously erased during the period of slavery.

But even though generating trees of mtDNA or Y markers is more tractable using a coalescent model, and it gives you a clean answer, it’s only a tiny slice of your ancestry. And not necessarily a representative one. Perhaps better than nothing 10 years ago, but in the days of 450 K SNP chips probably outdated. As I said above I think the paper is interesting mostly because the graphical representation is really good. Most of the time I add labels, but this figure needs no additional explanatory editing!

The blue represents European ancestry in individual African Americans, and in the text they note that the frappe bar plot nearly perfectly aligns with the distribution on the PCA plot. Remember that the two axes on the PCA plot represent the two largest axes of variation, with the first component (largest) on the x, and the second component (second largest) on the y. The largest component naturally separates Europeans from the African groups, while the second largest component separates the various African groups. The difference between the two Pygmy groups is not surprising, the Biaka have been found to be much more admixed with their Bantu neighbors than the Mbuti. I wouldn’t put too much weight in the closeness of the San and Mbuti on the plot, because you’re seeing only a two-dimensional view of the total genomic variation, the two largest dimensions as evaluated by looking at the total range of variation of genes among the set of individuals (European, African American and African) within the data set. The relationships may differ if you constrain the sample space of genetic variation to African genotypes only, and other dimensions may also indicate different relationships.

Here are the estimates of ancestral quanta for African Americans by region against different potential ancestral groups. They had 136 African Americans, so I wouldn’t put too much weight on the interregional differences.

22% of the ancestry of African Americans in the sample is European, with a standard deviation of 12%. It seems that around 10% of the African American population is more than half European in ancestry. Interestingly, in Henry Louis Gates Jr.’s Faces of America, all three of the people with black ancestry, two of whom clearly identified as African American, were more than 50% European in ancestry.* When it comes to African ancestry the affinity with the region of the west of the Bight of Benin seems clear if you view the data through a more granular lens.

The Mandenka are from the western fringe of West Africa, while the Bantu are a linguistic group which seems to have emerged just to the east of Nigeria, and swept east and south with the spread of a particular agricultural lifestyle until pushed up against the Nilotic and Khoisan groups of East and South Africa respectively. But this is on the population level. Could it be that individuals exhibit variance by African region, as they do on European ancestry? Not too much (at least beyond a level of noise, and perhaps a few outliers).

The two figures below are based on African genotypes within the African American population.

Note the contrast with the linear topology evident when European ancestry is added into the mix. Verbally what is clear is that while some African Americans have more European ancestry than others, on an individual level very few are reasonably identified as Yoruba people, or Mandenka people. Rather, individual African Americans exhibit a mix of African lineages in proportion to the various weights of sources in the slave trade.

Why might this be? I have observed before that the vast majority of the ancestry of African Americans is likely colonial. Though a few African American communities, such as the Gullah of coastal South Carolina, preserve distinctive regional African folkways, by and large black Americans as a culture are American, and derive many of their distinctive aspects from elaborations on Anglo norms or a novel synthesis of African ones (in particular, it seems clear that black Americans have been strongly influenced by the two Southern British settler folkways in their speech and religion). The deep history of African Americans within this country means that a great deal of time has elapsed whereby people of Yoruba, Mandenka or Kongo ancestry could have intermarried. Without positive assortative mating by tribe the various ancestral quanta would have become intermixed in subsequent generations. The Gullah exception supports this model, because they lived in relative isolation from whites. The rice agriculture which they practiced required less direct supervision than cotton or tobacco to extract economic productivity, and the South Carolina coastal country was notoriously unhealthful for whites. The relatively humane nature of rice agriculture as opposed to cotton (and especially sugar) also manifested in the more stable family life of the ancestors of the Gullah. So the relationship between white planters and Africans in this region was closer to that between lord and serf than owner and property, and the ancestors of the Gullah could develop their culture in America more organically than African Americans elsewhere.

In contrast, white ancestry does exhibit a great deal of individual variation. Why? There are two obvious ones that jump out. First, much of the ancestry may be much more recent. Recent ancestry has less time to be “dispersed” across the population through intermarriage. Though certainly whites and blacks mixed genetically in the colonial era, the process continued uninterrupted down to emancipation, while the addition of new African ancestry ceased in near totality by 1810 (there was some trade in slavery which reached the United States of America after this period, but not much), and had greatly diminished in the decades before 1810. The endogenous population growth of the black American community was sufficient to provide slaves for the new cotton lands of the early 19th century. After 1865 white-black relations were more surreptitious but continued nonetheless (e.g., Malcolm X’s mother’s father was white). Second, there is naturally the reality that there was, assortative mating for European features (e.g., “good hair”, skin lighter than “a brown paper bag”) among the African American elite. Though ancestry and phenotype can become decoupled, this takes time, and as I suggest above much of the European ancestry is recent. The image above is of a black American Congressman, Adam Clayton Powell Jr. I assume most readers are aware that W. E. B. Du Bois’ “Talented Tenth” were disproportionately what in other societies would be recognized as people of mixed-race, but who in the United States were classed within the general black population because of the white Southern paradigm of hypodescent.

Overall, nothing too new in the paper, but really great charts!

Citation: Zakharia F, Basu A, Absher D, Assimes TL, Go AS, Hlatky MA, Iribarren C, Knowles JW, Li J, Narasimhan B, Sidney S, Southwick A, Myers RM, Quertermous T, Risch N, & Tang H (2009). Characterizing the admixed African ancestry of African Americans. Genome biology, 10 (12) PMID: 20025784

* Gates is more than 50% European, while Elizabeth Wright is 65% European in ancestry. This aligns with intuition based on physical appearance. Malcolm Gladwell, who may not identify as African American (his father was a white Englishman, his mother a mixed-race Jamaican, and he is a Canadian immigrant), is likely to be ~75% European, though the number was not noted in the special.

Image Credit: Library of Congress

As neuroscientists refine their techniques for imaging the brain, scans like the fMRI keep creeping toward the courtroom and getting closer to joining to polygraph tests as means to sort liars from truth-tellers through physiology. In Brooklyn, lawyer David Levin is now offering the fMRI brain scan of a witness as proof of her honesty. If the court accepts it, it could be the first time such a brain scan was ever admitted as evidence. For what would be a legal breakthrough, the case is a rather minor one: Levin's client, Cynette Wilson, claims she was treated poorly at her job at a staffing center after filing a sexual harassment complaint. The lawyer found a coworker of Wilson's to corroborate her story, but wanted to bolster his credibility. Wired.com reports:
So, Levin had the coworker undergo an fMRI brain scan by the company Cephos, which claims to provide “independent, scientific validation that someone is telling the truth.”
Laboratory studies using fMRI, which measures blood-oxygen levels in the brain, have suggested that when someone lies, the brain sends more blood to the ventrolateral area of the prefrontal cortex. In a very small number of studies, researchers have identified lying in study subjects (.pdf) with ...

The necessary parts: one salad spinner, some hair combs, a yogurt container, plastic lids, and a glue gun. The finished product: a manual, push-pump centrifuge that could be a lifesaver in developing world medical clinics. Its name: the Sally Centrifuge.
A team of college students invented this low-cost centrifuge, which can be built for about $30, as a project for a global health class at Rice University. The teacher challenged them to build an inexpensive, portable tool that could diagnose anemia without access to electricity, and the tinkerers got to work.
The students, Lila Kerr and Lauren Theis, found that spinning tiny tubes of blood in the device for 10 minutes was enough to separate the blood into heavier red blood cells and lighter plasma. Then they used a gauge to measure the hematocrit, the ratio of red blood cells to the total volume. That information tells a doctor whether a patient is anemic, which can in turn help to diagnose conditions like malnutrition, tuberculosis, HIV/AIDS, and malaria.
In a press release, Rice University listed some of the advantages of the Sally Centrifuge:
It requires no electricity - just a bit of muscle. "We've pumped it for 20 minutes with no problem," Theis said. ...

Here’s the UCSF Genome Browser page for the Neandertal genome. Ensembl is supposed to have something up soon, but I don’t see it. Here’s the Anfo Short Read Aligner/Mapper; you can download it on that page. Page 21 of the online supplement has some configuration file code on it which might be useful.

It’s that time of year again. Young graduate students, having toiled for several years at the feet of Science, are kicked out of the nest to take their places among the ancient and honorable community of scholars. If you will forgive the mixed metaphors.

This week we had a double-decker celebration: both Heywood Tam and Moira Gresham successfully defended their Ph.D. theses. Congratulations to both!

Heywood was stuck with me as an advisor, but he seems to have turned out okay. We worked together on a number of papers that looked into models of Lorentz violation, including issues of extra dimensions and stability. More recently we’ve been finishing a couple of papers on fine-tuning in the early universe — coming soon to a preprint server near you! In the Fall Heywood will leave the dry heat of SoCal for the damp heat of Florida.

Moira’s advisor was Mark Wise, but we also interacted quite a bit. She and I collaborated with Heywood and Tim Dulaney on a couple of aether papers, and she and Tim recently wrote a really interesting paper on anisotropic inflation. But she promises that her next project will be completely Lorentz-invariant. And she’ll be doing it from Ann Arbor, where she’ll be joining the Michigan physics department as a member of the Society of Fellows.

Always bittersweet when students graduate; it will be a loss to Caltech when the leave, but it’s great to see people launch their independent research careers. Best of luck to both Moira and Heywood!

Good clean fun? A content analysis of profanity in video games and its prevalence across game systems and ratings. "Although violent video game content and its effects have been examined extensively by empirical research, verbal aggression in the form of profanity has received less attention. Building on preliminary findings from previous studies, an extensive content analysis of profanity in video games was conducted using a sample of the 150 top-selling video games across all popular game platforms (including home consoles, portable consoles, and personal computers). The frequency of profanity, both in general and across three profanity categories, was measured and compared to games' ratings, sales, and platforms. Generally, profanity was found in about one in five games and appeared primarily in games rated for teenagers or above. Games containing profanity, however, tended to contain it frequently. Profanity was not found to be related to games' sales or platforms." Photo: flickr/marioanima Related content:
Discoblog: NCBI ROFL: Beware of Wii tennis.
Discoblog: NCBI ROFL: Is Mr Pac Man eating our children? A review of the effect of video games on children.
Discoblog: NCBI ROFL: Sex differences in Nintendo Wii performance as expected from hunter-gatherer selection.

The last scheduled flight of the Space Shuttle Atlantis, STS-132, is scheduled for May 14 at 14:20 EDT (18:20 UT). It will, as usual, bring supplies and spare parts to the space station, as well as Rassvet, a Russian Mini Research Module and docking component.

You can always get more info on the Shuttles at the NASA Shuttle Mission Pages.

I’ll note in passing that the mission commander for this flight is named Ken Ham. Happily, he’s no relation.

My thoughts on the topic are pretty disjointed, and I can’t come up with a post that adds anything to what others have already said. And there’s still the primary documents to digest in full. So I’m going to open this post up to stray thoughts/comments (though try to keep it at least at the level of a Neandertal cognitively). Question: what other human evolution story is of the same order of magnitude in terms of significance? I think the last one of this magnitude was the Cann, et. al. “mitochondrial Eve” narrative of the mid-80s. Before that Lucy?

NEXT>

Allison Davies has a spacesuit, and she’s not waiting for a call from NASA for a chance to wear it. In fact, she designed it herself to better haunt her sci-fi vistas. Davies’s photography is an amalgam of self-portrait, landscape, and science spoofing satire. These images suggest Davies has traveled to the far reaches of the solar system, or perhaps to the future, in order to conduct urgent but entirely mysterious experiments. All your reasonable questions—where, what and why?—will remain purposefully unanswered. Davies’s book, “Outerland”, edited by Richard Renaldi, was launched on Earth Day by Charles Lane Press.

All images courtesy Charles Lane Press.

Ever since anthropologists figured out that early humans and Neanderthals coexisted for a span of prehistory, they’ve wondered–did the two species, you know, make friends? Now a fascinating new genetics study reveals that Homo sapiens and Neanderthals did indeed interbreed, and the evidence is still to be found in the human genome.

Researchers from Germany’s Max Planck Institute for Evolutionary Anthropology first sequenced the entire Neanderthal genome from powdered bone fragments found in Europe and dating from 40,000 years ago–a marvelous accomplishment in itself. Then, they compared the Neanderthal genome to that of five modern humans, including Africans, Europeans, and Asians. The researchers found that between 1 percent and 4 percent of the DNA in modern Europeans and Asians was inherited from Neanderthals, which suggests that the interbreeding took place after the first groups of humans left Africa.

Anthropologists have long speculated that early humans may have mated with Neanderthals, but the latest study provides the strongest evidence so far, suggesting that such encounters took place around 60,000 years ago in the Fertile Crescent region of the Middle East [The Guardian].

The study, published in Science and made available to the public for free, opens up new areas for research. Geneticists will now probe the function of the Neanderthal genes that humans have hung on to, and can also look for human genes that may have given us a competitive edge over Neanderthals.

Erik Trinkaus, an anthropologist at Washington University in St. Louis, who has long argued that Neanderthals contributed to the human genome, welcomed the study, commenting that now researchers “can get on to other things than who was having sex with who in the Pleistocene” [AP].

For a much deeper dive into these issues, head to Carl Zimmer’s post at The Loom and Razib Khan’s post at Gene Expression.

Related Content:
The Loom: Skull Caps and Genomes
Gene Expression: Breaking: There’s a Little Bit of Neandertal in All of Us
80beats: We May Soon Be Able to Clone Neanderthals. But Should We?
80beats: Crafty & Clever Neanderthals Made Jewelry 50,000 Years Ago
80beats: Did Spear-Throwing Humans Kill Neanderthals?
80beats: Rough Draft of the Neanderthal Genome is Complete!
DISCOVER: Works in Progress asks whether we rubbed out Neanderthals, or rubbed off on them

Image: Max Planck Institute EVA. The researchers hang out with their Neanderthal relation.

John Hawks has a very long post up. This part caught my attention:

We don’t really know the answers, but now we have a chance to test hypotheses about ancient population size and expansion in Neandertals. My point at the moment is only this: If today Neandertal genes make up only one percent of the gene pool of the 5 billion people outside Africa, that’s the genetic equivalent of 50 million Neandertals.

As Hawks notes later, this paper comes pretty close to resolving whether Neandertals were of the same species as we moderns, at least using the biological species concept. There were fertile hybrids. That should not be too surprising, a few years ago when the Neandertal introgression story was big I looked into mammalian embryology, and our lineage had to be very special as mammals went for their to be inter-population sterility.

This is not just a science story. Dave Chamberlain observes:

Anyone else notice that the artists depictions of neanderthals have slowly changed from stupid brute monkey men to ruggedly handsome moderns with a protruding brow? Hmmm, I bet they get even more good looking now. Hawks promises all neanderthals all the time, I for one can’t get enough of it.

I think that this will change our perceptions, and “artists’ renderings” quite a bit. A few years ago when it seemed that Neandertals may have been highly depigmented I observed that it was a bit strange that in most depictions they tended to be rather dark and swarthy as Europeans go (most famously in Jean Auel’s work the H. sapiens sapiens were Aryan Übermensch while the Neandertals were small and dark). I think some of the same subconscious dynamic was at play as when Tom Coburn was outraged at the TV nudity of Schindler’s List. Coloured people naked on a National Geographic special is one thing, but white people should be decent! (and please, don’t accuse me of seeing racism where it isn’t. If you know me you know that I’m not super-obsessed with that sort of thing, but I think it’s pretty obvious that there’s a lot of implicit assumptions which go into being a white European, and how one views someone and how they should behave)

The leaking oil pipeline in the Gulf of Mexico is gearing up to be the worst environmental disaster in American history. It’s still second to the Exxon Valdez incident, but at this rate it will pass the Alaska spill soon. Reading about this is breaking my heart, and angering me a lot. It’s difficult to express in words how truly awful this is… so maybe a picture will help.

This image, taken by NASA’s Aqua satellite, shows the slick as it was on May 4 — well over 50 km (30 miles) long and growing. An earlier image shows the slick when it was half that size, just three days earlier. "Alarming" is a terribly understated word to say the least. Against the natural browns and greens of the land, and the steely blue of the Gulf waters, the gray of the oil is threatening, menacing, sick. It reminds me of The Black Thing from A Wrinkle In Time.

Efforts are underway to mitigate the leak — more on that in a later post — but I want to point out that these satellite images are useful to those on the ground, so to speak, to track the growth and spread of the oil. The efficacy of space exploration may not spring to mind when contemplating environmental disasters, but it’s there nonetheless.

I have one more thing to add, which is somewhat contrary to my point above. There is an irony here: Some images of the leak from space almost make this disaster look less impacting. Here is a shot taken by astronaut Soichi Noguchi, as the space station flew past the Gulf on May 5:

This picture is actually lovely, which is such a disturbing dichotomy from reality! It’s difficult to see how truly apocalyptic 200,000 gallons a day of crude oil gushing up from the sea floor is when looking at this — and it may get far worse.

I am not implying any deeper meanings to this second image, though you may feel free to take away whatever metaphor you wish. But pictures themselves are only telling us a story. It’s up to us to interpret them, and to extract what useful information we can.

I’m still digesting the papers on the Neandertals which just came out. You can find them here. If you have questions, please read the papers first. They’re open access, so free to all. There’s a lot to mull over, and I don’t know what I can add right now, but I will note:

1) There’s a lot of stuff that doesn’t have to do with admixture, but focuses on genes where Neandertals and modern humans differ. There is for example an enrichment of differences in genes which relate to skin morphology. But my friends who think that modern human uniqueness can’t be pinned down to changes in SNPs will probably feel even more validated by this paper.

2) The fact that non-Africans as a whole, including Papuans, have Neandertal admixture, presumably from interactions in the Middle East, seem close to falsifying the “two-wave” model of expansion “Out of Africa” which came to prominence in the early aughts. That is, one group of Africans went north through the Middle East, and another swept along the Indian ocean fringe and onto southeast Asia. If there were two waves then they interacted a lot because they both received the same proportion of Neandertal alleles, which makes the idea of two genetically distinct waves a bit useless.

For lovers of stellar beauty, the Herschel space telescope may have already earned its keep. Just one year after its launch, researchers from the European Space Agency have released this stunning image of a massive star being born in a vast bubble of cold dust.

Herschel’s far-infrared detectors are finely attuned to stellar nurseries. When a star begins to form, the dust and gas surrounding it heats up to a few tens of degrees above absolute zero, and it begins to emit far-infrared wavelengths. In the galactic bubble shown, known as RCW 120, the newborn star is the white blob at the bottom of the bubble.

The “baby” star is perhaps a few tens of thousands of years old. It is some eight to 10 times the mass of our Sun but is surrounded by about 200 times as much material. If more of that gas and dust continues to fall in on the star, the object has the potential to become one of the Milky Way Galaxy’s true giants [BBC].

Giant stars pose a particular challenge to our understanding of star formation, researchers say. Present theories suggest that stars that are larger than about 10 solar masses shouldn’t exist, because their fierce radiation should blast away the clouds that feed them materials to grow on. Yet astronomers have spotted stars that have 120 times the mass of our Sun.

Click through the gallery for a couple more amazing shots from Herschel.

Read Carl Zimmer’s post, Skull Caps and Genomes. The papers aren’t on the Science website yet. And of course, Google News. I think I’m just going to wait on the papers before I say much more….

Good time to be alive, no?

Update: John Hawks.

Update II: Science got the page up.

The skull cap is thick and flat. It looks distinctively human, and yet its massive brow ridge, hanging over the eyes like a boney pair of goggles, is impossible to ignore. In 1857, an anatomist named Hermann Schaafhausen stared at the skull cap in his laboratory at the University of Bonn and tried to make sense of it. Quarry workers had found it the year before in a cave in a valley called Neander. A schoolteacher had saved the skull cap, along with a few other bones, from destruction and brought it to Schaafhausen to examine. And now Schaafhausen had to make the call. Was it human? Or was it some human-like ape?

Schaafhausen did not have much help to fall back on. At the time, archaeologists had only found faint hints that humans had coexisted with fossil animals, such as spears buried in caves near the bones of hyenas. Charles Darwin was still two years away from publishing the Origin of Species and providing a theory to make sense of human evolution. Naturalists tended to look at humanity as a collection of races arranged in a rank from savagery to civilization. The most savage races barely ranked above apes, while the naturalists themselves, of course, belonged to the race at the top of the ladder. When anatomists looked at human bodies, they found what they thought was a validation of this hierarchy: differences in the size of skulls, the slopes of brows, the width of noses. Yet all their attempts to neatly sort humanity were bedeviled by the tremendous variation in our species. Within a single so-called race, people varied in color, height, facial features–even in their brow ridges. Schaafhausen knew, for example, about a skull dug up from an ancient grave in Germany that “resembled that of a Negro,” as he later wrote.

To make sense of the “Neanderthal cranium,” as he called it, Schaafhausen tried to fit it into this confusing landscape of human variation. As peculiar as the bone was, he decided it must belong to a human. It was very much unlike the cranium of living Europeans, but Schaafhausen speculated that it belonged to an ancient forerunner. Yet for naturalists of Schaafhausen’s age, such a heavy brow ridge implied not the advanced refinement of European civilization, but wild savagery.

Well, Schaafhausen thought, Europeans were pretty savage back in the day. “Even of the Germans,” Schaafhausen wrote in his report on the Neanderthal cranium, “Caesar remarks that the Roman soldiers were unable to withstand their aspect and the flashing of their eyes, and that a sudden panic seized his army.” Schaafhausen found many other passages in classical history that suggested to him a pracitically monstrous past for Europe. “The Irish were voracious cannibals, and considered it praiseworthy to eat the bodies of their parents,” he wrote. Even in the 1200s, ancient tribes in Scandinavia still lived in the mountains and forests, wearing animal skins, “uttering sounds more like the cries of wild beasts than human speech.”

Surely this heavy-browed Neanderthal would have fit right in.

Some 150 years later, pieces of that original Neanderthal cranium now sit in another laboratory in Leipzig, just 230 miles away from Schaafhausen’s lab. Instead of calipers, it is filled with a different set of measuring tools: ones that can read out sequences of DNA that have been hiding in Neanderthal fossils for 50,000 years or more. And today a team of scientists based at the Max Planck Institute of Evolutionary Anthropology published a rough draft of the entire Neanderthal genome.

It is an historic day, but it reminds us, once again, that the publication of a genome does not automatically answer all the questions scientists have about the organism to whom the genome belongs. In fact, a careful look at the new report is a humbling experience. We gaze at the Neanderthal genome today as Schaafhausen gazed at the Neanderthal skull cap that first introduced us to these ambiguous humans.

Since Schaafhausen’s day, paleoanthropologists have discovered Neanderthals across a huge range stretching from Spain to Israel to Siberia. Their fossils range from about 400,000 years ago to about 28,000 years ago. Instead of a lone skull cap, scientists now have just about every bone from its skeleton. Neanderthals were stocky and strong, with a brain about the size of our own. The isotopes in their bones suggest a diet rich in meat, and their fractured bones suggest a rough time getting that food. There’s no evidence that Neanderthals could paint spectacular images of rhinos and deer on cave walls like humans did. But they still left behind many traces of very sophisticated behavior, from intricate tools to painted jewelry.

Ideas about our own kinship to Neanderthals have swung dramatically over the years. For many decades after their initial discovery, paleoanthropologists only found Neanderthal bones in Europe. Many researchers decided, like Schaafhausen, that Neanderthals were the ancestors of living Europeans. But they were also part of a much larger lineage of humans that spanned the Old World. Their peculiar features, like the heavy brow, were just a local variation. Over the past million years, the linked populations of humans in Africa, Europe, and Asia all evolved together into modern humans.

In the 1980s, a different view emerged. All living humans could trace their ancestry to a small population in Africa perhaps 150,000 years ago. They spread out across all of Africa, and then moved into Europe and Asia about 50,000 years ago. If they encountered other hominins in their way, such as the Neanderthals, they did not interbreed. Eventually, only our own species, the African-originating Homo sapiens, was left.

The evidence scientists marshalled for this “Out of Africa” view of human evolution took the form of both fossils and genes. The stocky, heavy browed Neanderthals did not evolve smoothly into slender, flat-faced Europeans, scientists argued. Instead, modern-looking Europeans just popped up about 40,000 years ago. What’s more, they argued, those modern-looking Europeans resembled older humans from Africa.

At the time, geneticists were learning how to sequence genes and compare different versions of the same genes among individuals. Some of the first genes that scientists sequenced were in the mitochondria, little blobs in our cells that generate energy. Mitochondria also carry DNA, and they have the added attraction of being passed down only from mothers to their children. The mitochondrial DNA of Europeans was much closer to that of Asians than either was to Africans. What’s more, the diversity of mitochondrial DNA among Africans was huge compared to the rest of the world. These sorts of results suggested that living humans shared a common ancestor in Africa. And the amount of mutations in each branch of the human tree suggested that that common ancestor lived about 150,000 years ago, not a million years ago.

Over the past 30 years, scientists have battled over which of these views–multi-regionalism versus Out of Africa–is right. And along the way, they’ve also developed more complex variations that fall in between the two extremes. Some have suggested, for example, that modern humans emerged out of Africa in a series of waves. Some have suggested that modern humans and other hominins interbred, leaving us with a mix of genetic material.

Reconstructing this history is important for many reasons, not the least of which is that scientists can use it to plot out the rise of the human mind. If Neanderthals could make their own jewelry 50,000 years ago, for example, they might well have had brains capable of recognizing themselves as both individuals and as members of a group. Humans are the only living animals with that package of cognitive skills. Perhaps that package had already evolved in the common ancestor of humans and Neanderthals. Or perhaps it evolved independently in both lineages.

In the 1990s, the geneticist Svante Pääbo led a team of scientists in search of a new kind of evidence to test these ideas: ancient DNA. They were able to extract bits of DNA from bones that were found along with Schaafhausen’s skull cap in the Neander valley cave. Despite being 42,000 years old, the fossils still retained some genetic material. But reading that DNA proved to be a collossal challenge. Over thousands of years, DNA breaks into tiny pieces, and some of the individual “letters” (or nucleotides) in the Neanderthal genes become damaged, effectively turning parts of its genome into gibberish. It’s also hard to isolate Neanderthal DNA from the far more abundant DNA of microbes that live in the fossils today. And the scientists themselves can contaminate the samples with their own DNA as well.

Over the years,Pääbo and his colleagues have found ways to overcome a lot of these problems. They’ve also taken advantage of the awesome leaps that genome-sequencing technology has taken since they started the project. They have been able to reconstruct bigger and bigger stretches of DNA. They’ve been able to fish them out of a number of Neanderthal fossils from many parts of the Old World. And today they can offer us a rough picture of all the DNA it takes to be a Neanderthal.

To create a rough draft of the Neanderthal genome, the scientists gathered DNA from the fossils of individual Neanderthals that lived in Croatia about 40,000 years ago. The scientists sequenced fragments of DNA totalling more than 4 billion nucleotides. To figure out what spot on which chromosome each fragment belonged, they lined up the Neanderthal DNA against the genomes of humans and chimpanzees. They are far from having a precise read on all 3 billion nucleotides in the Neanderthal genome. But they were able to zero in on many regions of the rough draft and get a much finer picture of interesting genes.

One of the big questions the scientists wanted to tackle was how those interesting genes evolved over the past six million years, since our ancestors split off from the ancestors of chimpanzees. So they compared the Neanderthal genome to the genome of chimpanzees, as well as to humans from different regions of the world, including Africa, Europe, Asia, and New Guinea.

This comparison is tricky because human DNA, like human skulls, is loaded with variations. The DNA of any two people can differ at millions of spots. Those differences may consist of as little a single nucleotide, or a long stretch of duplicated DNA. Each of us picks up a few dozen new mutations when we’re born, but most of the variations in our genome have been circulating in our species for centuries, millennia, and, in some cases, hundreds of thousands of years. Over the course of history these variants have gotten mixed and matched in different human populations. Some of them vary from continent to continent. It’s possible to tell someone from Nigeria from someone from China based on just a couple hundred genetic markers. But a lot of the same variations that Chinese people have also exist in Nigeria. That’s because Chinese people and Nigerians descend from an ancestral population. The gene variants first arose in that ancestral variation and then were all passed down from generation to generation, even as humans migrated and diverged across the planet. And when Paabo and his colleagues looked at the Neanderthal genome, they discovered that Neanderthals carried some of the same variants in their genome too.

The scientists compared the variants in the Neanderthal genome to those in humans to figure out when the two kinds of humans diverged. They estimate that the two populations became distinct between 270,000 and 440,000 years ago. After the split, our own ancestors continued to evolve. It’s possible that genes that evolved after that split helped to make us uniquely human. To identify some of those genes,Pääbo and his colleagues looked for genes that were identical in Neaderthals and chimpanzees, but had undergone a significant change in humans.

They didn’t find many. In one search, they looked for protein-coding genes. Genes give cells instructions for how to assemble amino acids into proteins. Some mutations don’t change the final recipe for a protein, while some do. Pääbo and his colleagues found that just 78 human genes have evolved to make a new kind of protein, differing from the ancestral form by one or more amino acids. (We have, bear in mind, 20,000 protein-coding genes.) Only five genes have more than one altered amino acid.

The scientists also found some potentially important changes in stretched of human DNA that doesn’t encode genes. Some of these non-coding stretches act as switches for neighboring genes. Others encode tiny pieces of single-stranded versions of DNA, called microRNAs. MicroRNAs can act as volume knobs for other genes, boosting or squelching the proteins they make.

Another way to look for uniquely human DNA is to search for stretches of genetic material that still retain the fingerprint of natural selection. In the case of many genes, several variants of the same gene have coexisted for hundreds of thousands of years. Some variants found in living humans also turn up in the Neanderthal genome. But there are some cases in which natural selection has strongly favored humans with one variant of a gene over others. The selection has been so strong sometimes that all the other variants have vanished. Today, living humans all share one successful variant, while the Neanderthal genome contains one that no longer exists in our species. The scientists discovered 212 regions of the human genome that have experienced this so-called “selective sweep.”

You can see the full list of all these promising pieces of DNA in the paper Pääbo and his colleagues published today. If you’re looking for a revelation of what it means to be human, be prepared to be disappointed by a dreary catalog of sterile names like RPTN and GREB1 and OR1K1. You may find yourself with a case of Yet Another Genome Syndrome. In all fairness, the scientists do take a crack at finding meaning in their catalog. They note that a number of evolved genes are active in skin cells. But does that mean that we evolved a new kind of skin color? A new way of sweating? A better ability to heal wounds? At this point, nobody really knows.

If you believe the difference between humans and Neanderthals is primarily in the way we think, then you may be intrigued by the strongly selected genes that have been linked to the brain. These genes got their links to the brain thanks to the mental disorders that they can help produce when they mutate. For exampe, one gene, called AUTS2, gets its name from its link to autism. Another strongly-selected human gene, NRG3, has been linked to schizophrenia. Unfortunately, these disease associations just tell scientists what happens when these genes go awry, not what they do in normal brains.

The most satisfying hypothesis the scientists offer is also the one with the deepest historical resonance. It has to do with the brow ridge that so puzzled Schaafhausen back in 1857. One of the strongly selected genes in humans, known as RUNX2, has been linked to a condition known as cleiodocranial dysplasia. People who suffer from this condition have a bell-shaped rib cage, deformed shoulder bones, and a thick brow ridge. All three traits distinguish Neanderthals from humans.

Pääbo and his colleagues then turned to the debate over what happened when humans emerged from Africa. Scientists have debated for years what happened when our ancestors encountered Neanderthals and other extinct hominin populations. Some have argued that they kept their distance and never interbred. Others have scoffed that any human could show such self-restraint. After all, humans have been known to have sex with all sorts of mammals when given the opportunity, so why should they have been so scrupulous about a very human-like mammal?

The evidence that scientists have gathered up till now has been very confusing. If you just look at mitochondria, for example, all the Neanderthal form tiny twigs on a branch that’s distant from the human branch. If Neanderthals and humans had interbred often enough, then some people today might be carrying mitochondrial DNA that was more like that of Neanderthals than like other humans.

On the other hand, some scientists looking at other genes have found what they claim to be evidence of interbreeding. They would find gene variants in living humans that had evolved from an ancestral gene about a million years ago. One way to explain this pattern was to propose that modern humans interbred with Neanderthals or other hominins. Some of their DNA then entered our gene pool and has survived till today. In one case, a team of scientists proposed that a gene variant called Microcephalin D hopped into our species from Neanderthals and then spread very quickly, driven perhaps by natural selection. Making this hypothesis even more intriguing was the fact that the gene is involved in building the brain.

Pääbo and his colleagues looked for pieces of the Neanderthal genome scattered in the genomes of living humans. The scientists found that on average, the Neanderthal genome is a little more similar to the genomes of people in Europe, China, and New Guinea, than it is to the genomes of people from Africa. After carefully comparing the most similar segments of the genomes, the scientists propose that Neanderthals interbred with the first immigrants out of Africa–perhaps in the Middle East, where the bones of both early humans and Neanderthals have been found.

Today, the people of Europe and Asia have genomes that are 1 to 4 percent Neanderthal.That interbreeding doesn’t seem to have meant much to us, in any biological sense. None of the segments our species picked up from Neanderthals was favored by natural selection. (Microcephalin D turns out to have been nothing special.)

While working on this post, I contacted two experts who have been critical of some earlier studies on hominin interbreeding, Laurence Excoffier of the University of Bern and Nick Barton of the University of Edinburgh. Both scientist gave the Neanderthal genome paper high marks and agree in particular that the interbreeding hypothesis is a good one. But they do think some alternative hypotheses have to be tested. For example, interbreeding is not the only way that some living humans might have ended up with Neanderthal-like pieces of DNA. Cast your mind back 500,000 years, before the populations of humans and Neanderthals had diverged. Imagine that those ancestral Africans were not trading genes freely. Instead imagine that some kind of barrier emerged to keep some gene variants in one part of Africa and other variants in another part.

Now imagine that the ancestors of Neanderthals leave Africa, and then much later the ancestors of Europeans and Asians leave Africa. It’s possible that both sets of immigrants came from the same part of Africa. They might have both taken some gene variants with them did not exist in other parts of Africa. Today, some living Africans still lack those variants. This scenario could lead to Europeans and Asians with Neanderthal-like pieces of DNA without a single hybrid baby ever being born.

If humans and Neanderthals did indeed interbreed, Excoffier thinks there’s huge puzzle to be solved. The new paper suggests that genes flowed from Neanderthals to humans only at some point between 50,000 and 80,000 years ago–before Europeans and Asians diverged. Yet we know that humans and Neanderthals coexisted for another 20,000 years in Europe, and probably about as long in Asia. If humans and Neanderthals interbred during that later period, Excoffier argues, the evidence should be sitting in the genomes of Europeans or Asians. The fact that the evidence is not there means that somehow humans really did find the self-restraint not to mate with Neanderthals.

Because interbreeding involves sex, it dominates the headlines about Pääbo’s research. But I’m left wondering about the Neanderthals themselves. We now have a rough draft of the operating instructions for a kind of human that has been gone from the planet for 28,000 years, which had its own kind of culture, its own way of making its way through the world. Yet I found very little in the paper about what the Neanderthal genome tells us about their owners. It’s wonderful to use the Neanderthal genome as a tool for subtracting away our ancestral DNA and figure out what makes us uniquely human. But it would also be great to know what made Neanderthals uniquely Neanderthal.

[Image from Project Gutenberg]

We’re all a bit of a Neanderthal:

As a result, between 1pc [percent] and 4pc of the DNA of non-African people alive today is Neanderthal, according to the research. The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree. Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.

…

Prof Svante Paabo, of the Institute for Evolutionary Anthropology in Leipzig, Germany, said: “Those of us who live outside Africa carry a little Neanderthal DNA in us.”

I will have a thorough write-up when I get a hold of the paper, which should be soon. As I said, this is a story of genomics, not just genetics. 1-4% is not trivial. The Daily Telegraph has more:

They were surprised to find that Neanderthals were more closely related to modern humans from outside Africa than to Africans.

Even more mysteriously, the relationship extended to people from eastern Asia and the western Pacific – even though no Neanderthal remains have been found outside Europe and western Asia.

The most likely explanation is that Neanderthals and Homo sapiens interbred before early modern humans struck out east, taking traces of Neanderthal with them in their genes.

Professor Svante Paabo, director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the international project, said: “Since we see this pattern in all people outside Africa, not just the region where Neanderthals existed, we speculate that this happened in some population of modern humans that then became the ancestors of all present-day non-Africans.

“The most plausible region is in the Middle East, where the first modern humans appeared before 100,000 years ago and where there were Neanderthals until at least 60,000 years ago.

“Modern humans that came out of Africa to colonise the rest of the world had to pass through that region.”

…

Several genes were discovered that differed between Neanderthals and Homo sapiens and may have played important roles in the evolution of modern humans.

They included genes involved in mental functions, metabolism, and development of the skull, collar bone and rib cage.

Image Credit: United Press International

I don’t subscribe to Science or Nature’s RSS feeds because I assume if there’s something of interest to me, I’ll hear about it when it comes out. But I do subscribe to the RSS feeds of more obscure journals of interest (e.g., THe American Journal of Human Genetics). What journals do you subscribe to which don’t have such a higher profile?

Cassini continues making loop-de-loops around Saturn, returning tens of thousands of way cool pictures. Like this one:

From 1.3 million kilometers (800,000 miles) away — 3 times as far as the Moon is from the Earth — Cassini spied this pretty scene. It shows, obviously, Saturn’s rings to the right. The very thin ring extending to the left is the F-ring; it’s very faint and wasn’t even discovered until 1979, when Pioneer 11 passed the planet.

The two moons are Pandora (the flying saucer-shaped one) on the left, and Epimetheus on the right. Usually, in pictures like this, perspective is a problem; one moon is much farther away than the other, so your sense of scale gets a bit bollixed. But in this case, both moons are about the same distance from Cassini! Pandora is about 114 x 84 x 63 km (68 x 50 x 38 miles) in size, and Epimetheus is a bit heftier at about 144 x 108 x 98 km (86 x 64 x 58 miles). In this shot, the rings are in the background relative to the moons, and Pandora is just a hair closer to Cassini than Epimetheus.

I was surprised that they appeared so close together, so I did some checking. Pandora orbits Saturn at a distance of about 141,700 km (85,000 miles), and Epimetheus orbits at 151,400 km (91,000 miles). So really, they never get any closer than 10,000 km (6000 miles) to each other. Since they do look pretty cozy in this image, there really is a little perspective going on, since Epimetheus must be a few thousand kilometers farther away. That’s only a trifle compared to the more than 1 million km distance Cassini was from the pair when it took this shot, though. What this means is that if you compare the sizes of the two moons you get a good idea of their relative diameters, but their positions relative to Saturn are a little messed up due to perspective. Got it?

Once I got the orbital distance of the moons, I was curious how long it takes them to orbit Saturn. Turns out, it only takes about 15 hours for Pandora and about 17 hours for Epimetheus! So both moons are screaming around the planet at speeds of roughly 60,000 kph (36,000 mph), far faster than even low Earth satellites move. That’s because Saturn is a lot more massive than the Earth, and has far more gravity. It yanks much harder on those moons, whipping them around at greater speeds.

There’s more, too. Pandora is one of the shepherd moons of the F-ring, helping it maintain its shape. It shares an orbit (more or less) with the moon Prometheus. As it happens, Epimetheus shares an orbit (more or less) with the moon Janus.

Now follow along here: in mythology, Epimetheus and Prometheus were very close brothers. Their names means hindsight and foresight, respectively. Prometheus gave us fire and civilization, and had his liver pecked out by birds every night for his sins against the gods. Epimetheus was supposed to give mankind positive traits, but was a bit of an absent-minded goofball, and he ran out of raw materials before he got to us. For this, the gods gave him the "gift" of Pandora, whom he married.

Well, that’s not fair! Being smart and clever and helpful gets your organs ripped out of you, and being an idiot with no eye for the future gets you rewarded^*.

Of course, in reality, Epimetheus’s wife shares an orbit with his brother. That’s gotta hurt.

Sigh. I think I prefer the confusion of the actual Prometheus and Epimetheus to the confusion of their mythical namesakes. Reality may not always be fair, but at least (to borrow a phrase from George Hrab) it’s fair in its unfairness.

Related posts:

Watch Saturn’s shadow dancing

Cassini eavesdrops on orbit-swapping moons

Saturnian eclipse