Notable paper: Macho GA, Lee-Thorp JA. (2014). Niche Partitioning in Sympatric Gorilla and Pan from Cameroon: Implications for Life History Strategies and for Reconstructing the Evolution of Hominin Life History. PLoS ONE 9(7): e102794. doi:10.1371/journal.pone.0102794
Synopsis: Even though chimpanzees and gorillas eat an overlapping range of foods, both almost entirely dependent on C3 plants, they have slightly different ratios of stable isotopes of carbon and nitrogen. Macho and Lee-Thorp show that the gorilla and chimpanzee populations that coexisted in the late 1920s in Cameroon can be clearly distinguished in their carbon-13 content. Additionally, from infants to adults the two species have different trajectories of nitrogen-15 content, likely reflecting different weaning strategies.
Important because: A very close study of the local resources may enable finer distinctions about diet preferences from stable isotope data than have been made so far for early hominins and prehistoric humans. In this case, the subtle differences in carbon-13 content between different C3 plant species, or between leaves and fruits within a plant, have left a mark on the chimpanzees and gorillas. The authors suspect that the gorillas were feeding in more closed-canopy context, not only eating different foods than chimpanzees but actively using different space.
Interesting... The data here come from hair samples taken from museum specimens collected by Major Percy Powell-Cotton, wild-shot between 1927 and 1935. It is a case where museum collections show the potential for interesting research -- in this case hair samples taken non-invasively from the field may prove useful for the same kind of analyses.
From Nautilus this month, a long profile article by Kat McGowan describing the work of Michael Tomasello: "Cooperation is what makes us human". The focus of Tomasello's experimental work has been uncovering the ways that chimpanzees act as individuals where humans seem naturally to intuit that others can help us.
“We naturally inform people of things that are interesting or useful to them,” Tomasello says. “That’s unusual. Other animals don’t do that.” Pointing is an attempt to change your mental state. It is also a request for a joint experience: She wants you to look at the dog with her.
Chimps, by contrast, do not point things out to each other. Captive chimps will point for humans, but it’s to make a demand rather than to share information: I want that! Open the door! They do not understand informational human pointing, because they do not expect anyone to share information with them. In one of Tomasello’s experiments, food is hidden in one of two buckets. Even if the experimenter points to where it is, the chimp still chooses randomly. “It’s absolutely surprising,” Tomasello says. “They just don’t seem to get it.”.
The end of the article briefly describes work on dogs and the Belyaev fox experiment; in both cases these species have taken on the ability to see humans as helpers, including an ability to understand pointing.
The noted television popular science educator Bill Nye has a new book in which he looks at the evidence for evolution: Undeniable: Evolution and the Science of Creation.
Popular Science is running an excerpt of his book, in which he looks at the future of human evolution: "Is the human species still evolving?".
I give a great many talks or lectures at universities and for general audiences. I enjoy performing, the part where I’m doing the talking and all, but my favorite part of any evening is when audience members come up to microphones and ask me questions. One of the most common themes is what people call “The Singularity.” This is a supposed imminent time (2029, in some versions of the story) when computers will become as sophisticated as human brains. From there, it is proposed, machines will be able to outcompete humans at just about everything. There will be superior car-parking algorithms, disaster-relief coordination, legal briefs, rocket science, great thinking in general. Taking it to the next logical step, this artificial intelligence will have to be managed carefully, because after all, any of these future brain machines will outthink and outmaneuver us at every practical turn.
The chapter excerpt doesn't include any of the actual evidence of ongoing human evolution. Anthropologists and demographers have uncovered quite a lot of evidence about ongoing evolution in the last 50 years, and geneticists over the last 15 years have documented an immense store of information about evolution across the last few thousand years. Readers who want to find out more about this can check out my recent article in Scientific American, which has the online headline, "No, humans have not stopped evolving". And a free link on the theme of recent human evolution is my 2007 post, "Why human evolution accelerated", discussing our genetic work on the topic.
I pointed earlier this week to an article by Lydia Pyne about perceptions of Neandertals over the years, and hinted at a second recent article. That article is "To Russia, With Love", and details a correspondence between Raymond Dart, discoverer of the Taung skull, and a Professor Plissetzky, director of the State Museum and the Institute of Anthropology in Moscow.
Plissetzky wrote to Dart requesting a cast of the Taung child for a museum exhibit. Pyne followed the correspondence in the archives of the University of the Witwatersrand, which includes original copies of the letters, order requests and photographs of the anthropological exhibition at the Institute of Anthropology.
Ultimately Dart arranges to have a cast of Taung sent to Moscow, for exchange of some Russian casts. I don't know if the cast of the Kiik-Koba foot at the Evolution Studies Institute (originally from the Medical School collection) resulted from this exchange, but it might well have.
The episode is interesting on its own, and Pyne uses the historical event to explore the history of casting in paleoanthropology. She recounts the origin of hominin fossil casting under the direction of R. F. Damon at his company in London. Originally devoted to collecting and selling original fossils, production and sale of fossil replicas to museums and institutions became an increasing part of their business during the early twentieth century.
Dart held the “copyright” on the Taung Child fossil, according to R.F. Damon & Company’s paperwork and Dart was paid royalties based on how many fossil casts were sold. Dart worked with the company’s Mr. F.O. Barlow on both the nitty-gritty details of creating and describing the fossil casts as well as in sorting out the financial ledgers; dozens of letters between Barlow in London and Dart in Johannesburg hashed out the fossil’s financial deals. When Dart originally approached R.F. Damon & Company, he thought that each fossil cast ought to sell for more than what other, similar hominin casts had sold for (e.g. Pithecanthropus). Mr. Barlow begged Dart to reconsider his position about the cost of the cast, as Barlow noted, “The prices you suggested would result in killing the demand and would create in my customers a feeling of resentment which I am not willing to incur.” Once the question of price was properly sorted out, the company sold a lot of casts.
For more information on the history of casting fossil hominins, I recommend an article by Alan Mann and Janet Monge, published in the University of Pennsylvania Museum magazine Expedition in 1987: "Reproducing Our Ancestors". Mann and Monge have a detailed description of Barlow's cast-making technique.
In the 1920s and 1930s, F.O. Barlow, a leading mold and cast maker in Europe, fabricated more than 600 plaster-of-Paris molds of hominid fossils. In order to ease the removal of plaster from an often fragile fossil specimen, these molds were made of many pieces, waxed and keyed to each other. A complete mold of a skull, for example, could easily be composed of more than 100 plaster pieces, each replicating a small part of the whole fossil; fitted precisely together, they form what can only be described as a large three-dimensional jigsaw puzzle. Casts produced from Barlow’s molds have a surprising amount of detail. They appear to be dimensionally accurate replicas, but many cannot be adequately assessed because in the meantime, the original fossil has been modified, reconstructed, or even damaged. About 500 Barlow-produced molds of fossil hominid bones have survived, and are now in The University Museum Casting Program collection .
The article goes on to describe the development of the casting program of the Wenner-Gren Foundation for Anthropological Research, which was the source of the majority of fossil casts now used in university teaching and research. As they describe, Wenner-Gren instituted a research initiative to find better materials and better mold-making techniques for fossils. Molds are presently made from flexible silicone instead of hard plaster-of-Paris, and the resulting casts in epoxy reproduce the details of fossils with much higher fidelity than the old plaster versions. With this new mold-making technology in hand, Wenner-Gren instituted a much broader program of producing and distributing casts of fossil hominins than ever before:
From 1962 to 1976 the WennerGren Foundation sent mold makers all over the world. Using techniques developed by Gilbert, they were able to produce over 900 molds of the most famous human and primate fossils, including Zinjanthropus or “Nut Cracker Man,” Mrs. Ples and the Taung child from South Africa, and Kabwe Man. During this time the Wenner-Gren Foundation produced nearly 16,000 high-quality plastic casts of fossil remains, and distributed them to scientists and research and teaching institutions throughout the world.
In addition to the historical context of casting, Mann and Monge gave a detailed account of the process of making molds and casts, and the importance of the "patterns" that enable the long-term archiving of the shape of original fossils, sometimes even after the fossils themselves have been lost or damaged by later study.
Inclusion of fossils in a museum collection does not guarantee their safety. Ancient bones are very frequently fragile: some are only partially mineralized or fossilized, others are not mineralized at all. Often, they are held together by toothpicks and bits of wire. With the interest in human origins expanding each year, and the number of professional scholars involved in active research steadily increasing, these fossils are being handled, examined, photographed, measured, and broken with greater frequency. Many researchers have had the experience of examining a fossil they had first looked at several years before, only to find that, due to handling or an accident, the fossil specimen is now different in appearance.
The PDF version of the article (at the link) includes illustrations of the process of molding and casting; these are not included in the HTML version of the article.
In addition to its importance as a way to archive fossils, the casting process retains its original role of communicating the three-dimensional properties of casts and artifacts to international colleagues. The world created by Barlow, Damon and others was an enormous advance over the previous generation, in which only a fortunate few internationally-traveled scientists might have examined the primary evidence of fossil forms.
International travel has become much easier, which has enabled many more researchers to see fossil collections first-hand in their countries of origin. But in the past the fossil record was very sparse, while today the fossil record is an order of magnitude greater. No expert has seen every important original fossil. Most major fossil collections and research universities keep collections of casts to facilitate the study and comparison of these fossils. We now train a much broader number of students in the details of the human fossil record, not only those who will enter the speciality of paleoanthropology, but also those who will bring insights about human evolution into fields as disparate as archaeology, human ecology, evolutionary medicine. Paleoanthropology relies upon the widespread distribution of high-resolution casts of fossils; without these casts, what we do would not be science.
A recent issue of Current Biology has a short interview with paleoanthropologist Bernard Wood: "Bernard Wood". The interview covers his transition from a training in medicine to human evolution, and his subsequent work on the hominin fossil remains from East Turkana:
Why did you choose to work on skulls and teeth? I didn’t. I was one of three anatomists (the others were Michael Day and Alan Walker) Richard Leakey had invited to describe and interpret the hominin fossils recovered from Lake Rudolf. The majority of the fossils were from the skull and dentition, but each of us wanted to work on the limb bones. In 1972, we met in New York to discuss the impasse, but none of us would give in. So, not a little frustrated, Richard broke three matches into different lengths and made us draw. Mine was the shortest match, so I had no choice but to work on the cranial remains. This task, which involved determining how many taxa were represented among the hominin cranial fossils, led to the topic of my PhD, sexual dimorphism, and my interest in patterns of intra- versus interspecific variation.
I always find it so illuminating to think about how today's well-known paleoanthropologists started doing the work that would bring them scientific prominence. Having just come from working with so many early career scientists on the Rising Star Workshop, it is valuable to remember that most of today's experts in paleoanthropology got their start as PhD students describing new fossil remains, before substantial datasets of fossil variation even existed.
Vox writer Joseph Stromberg visited the Forensic Anthropology Center at Texas State University, and has written an in-depth description of his visit: "The science of human decay: Inside the world's largest body farm". The article features the work of Daniel Wescott at Texas State, and provides a great account of how the science of human decomposition developed.
The article gives some historical perspective, describing how Bill Bass got started studying decomposition at Tennessee, and goes into some detail about how today's research differs from that history. Among other things, forensic anthropologists have developed a much stronger understanding of the microbes that are involved in decomposition:
For Wescott and the other researchers, caged decomposition presents the most interesting scientific experiment at the body farm. It was once thought that the bacteria that drive decay are simply the same species inside you while you're alive, but it's since been discovered that a succession of different species carries it out over time. Some of them are indeed present during life, but others are brought to the body by flies and beetles. Meanwhile, some bacteria species release chemicals that actually attract particular kinds of insects — and proteins in those insects' saliva kill off competing bacteria. Further, these insects are prey for mice, which in turn attract rattlesnakes and other larger predators. A decomposing human body, it turns out, creates a remarkably complex, tightly evolved, and underappreciated ecosystem. Scientists are now calling it the necrobiome.
This seems to be decomp week in the media, which is probably due to Halloween coming up this Friday. But this article is really superb. I will be distributing it to my introductory anthropology students when we approach our forensic anthropology inquiry at the end of the semester.
One important thing to note is that all the research is done upon bodies that are donated for this purpose. Body donation has become incredibly important to anthropological work of all kinds. The article has a sidebar that discusses the reasons why people donate their bodies for science, and why the study of decomposition can be a really important avenue for body donation.
One thing that the article doesn't discuss is the scientific value of the bones, after the body's use in decomposition research has ended. Some decomposition research does involve damage to the bones (the article discusses the effects of vultures; some decomposition research also investigates the effects of cremation). But the overwhelming majority of bones become available for accession into study collections at these forensic anthropology research centers.
The skeletal material from the University of Tennessee forensic research unit constitutes the single most important collection for understanding variation within the skeletons of living Americans. Most collections of human skeletal material in museums and universities were acquired early in the twentieth century, or represent archaeological remains. Those are important collections, but do not represent today's biology -- people today are much heavier, live longer, suffer fewer ill health episodes early in their lives, and often survive surgeries and skeletal implants when they reach advanced ages. To understand how human biology affects bone today, and to understand the variation in bones of living people, new collections are incredibly important. They are literally priceless, because collections of this kind cannot be bought. They result only from the generosity and interest of donors who leave their remains for this purpose.
John Ioannidis is well known as a critic of the way science has usually been practiced. I've linked to his work before ("Link: John Ioannidis and the scientific workforce core", "Conference criticisms"), although I haven't written directly about his most famous work on the reasons why most scientific findings go unreplicated.
Ioannidis has a recent article in PLoS Medicine that discusses ways to change the scientific research enterprise. He focuses on two criticisms of the present scientific research practice: Most published articles are based on samples that lack sufficient power to justify the claimed associations or effects, and a large majority of resources (he cites 85% as an estimate) are "wasted". Based on these considerations, he writes about several ways that scientific research could be changed to increase the pace of genuine discovery and reduce the rate of spurious results.
The current system values publications, grants, academic titles, and previously accumulated power. Researchers at higher ranks have more papers and more grants. However, scholars at the very top of the ladder (e.g., university presidents) have modest, mediocre, or weak publication and citation records . This might be because their lobbying dexterity compensates for their lack of such credentials, and their success comes at the expense of other worthier candidates who would bring more intellectual rigor and value to senior decision making; equally, it could be because they excel at the bureaucratic work necessary to keep the mind-boggling academic machine going, and their skills enable more scientifically gifted colleagues to concentrate on research. The current system does not reward replication—it often even penalizes people who want to rigorously replicate previous work, and it pushes investigators to claim that their work is highly novel and significant . Sharing (data, protocols, analysis codes, etc.) is not incentivized or requested, with some notable exceptions –. With lack of supportive resources and with competition (“competitors will steal my data, my ideas, and eventually my funding”), sharing becomes even disincentivized. Other aspects of scientific citizenship, such as high-quality peer review, are not valued. Peer review can be a beneficial process, acting as a safety net and a mechanism for augmenting quality. It can also be superficial, lead to only modest improvements of the reviewed work, and allow for the acceptance of blatantly wrong papers ,. That it is so little valued and rewarded is not calculated to encourage its benefits and minimize its harms.
I don't endorse all of his arguments, which are heavily skewed toward the biomedical research fields. These areas are after all his specialty, and more "pure science" areas of research such as paleontology and astronomy are not his aim. On the other hand, physics and genetics share a great deal in the way they approach new scientific research projects today: Both fields have come to rely more strongly upon large-scale collaborations, both have begun to institute more quality assurance in their software and tool development, and both have adopted more open access protocols toward data collection. Both also have recognized that very stringent standards on statistical significance are necessary to reduce the reporting of results that will almost certainly fail to be replicated in larger-scale studies.
Paleoanthropology has begun to embrace a scientific approach with wider-scale collaboration and data sharing. I think we are fortunate in being a relatively small field in which the contributions of peer reviewers and editors are much more recognized than in many fields. I think this recognition would be even greater if the reviews were less anonymous, and I have encountered an increasing number of reviewers who have refused anonymity (often including myself). But even more important than peer review is a greater discussion and conversation about research directions and priorities. If we can get students and professionals collaborating with each other on larger-scale research datasets instead of working alone in isolation, we'll increase the replicability of results and improve the significance of everyone's work.
Ioannidis JPA (2014) How to Make More Published Research True. PLoS Med 11(10): e1001747. doi:10.1371/journal.pmed.1001747
Notable paper: Kopp GH, Roos C, Butynski TM, Wildman DE, Alagaili AN, Groeneveld LF, Zinner D. (2014). Out of Africa, but how and when? The case of hamadryas baboons (Papio hamadryas). Journal of Human Evolution (in press) doi:10.1016/j.jhevol.2014.08.003
Synopsis: Humans are not the only primate to have dispersed from Africa during the Pleistocene. Savanna baboons, widespread across eastern Africa, established a population on the Arabian peninsula during the last 150,000 years. Gisela Kopp and colleagues show that the diversity of baboons increases from north to south along the Red Sea coast in Arabia, and suggest that the baboons may have crossed the Strait of Bab-el-Mandab during the low water period of the Late Pleistocene, more than 70,000 years ago.
Important because: Archaeologists and geneticists have recurrently suggested that humans may have made a Bab-el-Mandab crossing via a "southern route", instead of coming across land via the Sinai peninsula. The interest in a southern route for humans has most recently been spurred by archaeological similarties between Arabian and African Middle Paleolithic-era assemblages. Those similarities date to the same general time period that baboons were establishing this Arabian population.
But... The genetic data here don't exclude an overland or mixed source for the Arabian baboon population. And of course, the dispersal abilities of baboons are probably not the same as humans, so the baboon analogy may not be relevant to us. Still, along with other African fauna like cheetahs and striped hyenas, the baboons help to show that Arabia was repeatedly colonized by African forms.
The historian of science Lydia Pyne has published a couple of recent articles that detail interesting aspects of the history human evolution. The first is about science's changing perspective on Neandertals, "Our Neanderthal complex", which appears in the most recent issue of Nautilus.
I must say my favorite part is how she traces Boule's concept of stupid and inferior Neandertals up through the years: Instead of describing these ideas as simply outmoded, she recognizes how they contributed to the work of recent anthropologists, with Richard Klein as a visible manifestation.
Even the language of extinction imbued Neanderthals with an aura of evolutionary fatalism: “demise,” “fate,” and “loss” helped us cast our interspecies interaction as a relationship between winners and losers. “It is not difficult to understand why the Neanderthals failed to survive,” noted Richard Klein in the third edition of his seminal textbook, The Human Career, in 2009. “The archaeological record shows that in virtually every detectable aspect—artifacts, site modification, ability to adapt to extreme environments, subsistence, and so forth—the Neanderthals lagged their modern successors, and their more primitive behavior limited their ability to compete for game and other shared resources.”
Pyne comes at the end to an essential point about Neandertals: We long defined ourselves as whatever the Neandertals are not. Now we have begun to explore the implications of defining them as part of our family.
The Chicago Tribune sent reporter Christopher Borrelli to the Field Museum to see how bodies are reduced to skeletons: "Inside the Field Museum's hidden flesh-eating beetle room".
There are nine beetle cages, each roughly the size of a home aquarium, each topped with mesh lids, each layered with a sedimentary bedrock of exoskeleton, excrement and freshly dead flesh-eating beetles. As Goldman lifted the lid of a cage and sifted around the white ribs and skull of a raven, she considered how many beetles were in this room.
She decided she didn't know — millions? Occupancy rates are unknown.
Now, to shiver your spines: The flesh-eating beetles of the Field Museum are a bit of a mystery. A stray dead chipmunk or two aside, "everything in this museum is documented, even the most mundane objects," Goldman said. "Yet these beetles: It's completely unknown how we got them. When I came here I was curious (about where they came from). This colony is a black hole.
It's a great story for Halloween week, complete with creepy slideshow.
Qiaomei Fu and colleagues from Svante Pääbo's lab have reported on a genome from northern Siberia that dates to 45,000 years ago. The genome comes from a human femur that was eroding out of a bank of the river Irtysh, which is in the Siberian plain near Omsk. The specimen is the shaft of a femur lacking its ends, and has no special similarities to archaic humans such as the Neandertals. It would certainly be unsurprising for a modern human to have this anatomy, and would likely be categorized as a modern human femur even without the genome. But the genome is the earliest ever recovered from a modern human individual, and therefore gives us some very useful information that we could not get in any other way.
Another mystery population?
To me, the most interesting part of the paper is the D-statistic comparison with other ancient and modern genomes. The D-statistic is basically a measure of genome-wide similarity, considering only those alleles derived relative to some outgroup. The results are useful for assessing mixture between ancient populations. For example, people who have ancestry within sub-Saharan Africa have fewer derived alleles in common with Neandertals than people who lack recent sub-Saharan ancestry. The D-statistic in a comparison of a non-African and a sub-Saharan African genome with Neandertals will show a skew toward Neandertal similarity in the non-African genome. That is one way of assessing Neandertal ancestry of living people.
The Ust'-Ishim genome seems to be ancestral to nobody. Consider the result of D-statistic comparisons with living Asians, Native Americans and Europeans, and two ancient genomes from Eurasia -- the Mal'ta and La Braña specimens. Here is the figure showing the D-statistics as compared with other specimens:
In that figure, the value of zero (with a vertical line across comparisons) indicates that the genomes listed on left and right sides of the figure have the same proportion of derived similarities with the index genome (in all cases, the Ust'-Ishim genome). A positive value skews toward the right genome; a negative value toward the left. The top panel shows that Ust'-Ishim is more similar to genomes of non-Africans than it is to sub-Saharan African genomes.
The case of Mal'ta is most interesting as a comparison. This individual from eastern Siberia near Lake Baikal dates to around 24,000 years ago. Its genome was described earlier this year by Raghavan and colleagues (2014), and one of their major conclusions was that the similarity of this genome with Europeans on the one hand, and Native Americans on the other, probably shows a common source population in Siberia that had contributed to the rise of both these living populations. That is not to say that both these populations derive fully from ancient Siberians, but that some ancient Siberians related to Mal'ta later became part of the population that entered the Americans, and that some other ancient Siberians related to Mal'ta would ultimately migrate into Europe.
Ust'-Ishim shows no such pattern. It is not more like the Mal'ta genome than it is like any other genomes of Asians or Native Americans. It is not like any living population of Asians or Native Americans more than any other.
At the same time, Ust'-Ishim is less like living Europeans than it is like any of these Asian populations, and less like living Europeans than it is like the Mesolithic-era La Braña individual, even though that individual lived in Iberia. Fu and colleagues suggest that the recent population of Europe must have gotten some of its ancestry from other populations that were not part of the initial out-of-Africa spread represented by the Ust'-Ishim individual. That could mean later Africans, or it could mean one or more West Asian populations that contributed neither to the later dispersal of humans into the rest of Eurasia and the New World nor to the Mesolithic occupation of Europe by modern humans. I wrote "Mesolithic" there very consciously, because it seems plausible until demonstrated otherwise that earlier Upper Paleolithic Europeans might represent yet some other population.
Considering the fact that Ust'-Ishim is equally similar to all Asian and Native American populations and equally similar to the two ancient genomes, Fu and colleagues write this:
This suggests that the population to which the Ust’- Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other.
I would give a strong interpretation to this. It seems unlikely that Chinese (Han) and Andaman Island (Onge) populations could be uniquely descended from this ancient Siberian individual, so Ust'-Ishim is not at the stem of the later diversification of Eurasian people. That means that these later people derive from a different group than that represented by Ust'-Ishim. The initial dispersal of humans into Eurasia contained at least one dead-end population that contributed at most some very small amount of ancestry to living people.
This is not an isolated case, it is another example of what we see throughout the world: Ancient people represented by DNA that seem to have very little to do with the people who live in the same areas today. We're not finding the ancestors of living populations so much as we are finding branches of populations we did not know existed.
I've written about the human mutation rate many times here, and in print (Hawks 2012). The new paper is interesting because it is the first modern human we have at high coverage, where the age is sufficient to estimate the number of missing mutations that would be expected in a descendant living today. Even though Ust'-Ishim may have no living descendants, this is a measure of how short his DNA branches are compared to the branches connecting living humans to their common ancestors.
Given that, the authors find that the mutation rate would need to be fairly low, on the order of 1 times 10-8 mutations per site per generation, to account for the Ust'-Ishim data. That low rate is more or less the same as estimated from looking at parents and offspring living today, which is a good piece of evidence that the per-generation rate we measure in living people is not different from the per-generation rate averaged over longer periods of time. As the authors point out, this means that a lot of ancient events estimated from DNA only must have happened longer ago than was claimed prior to a couple of years ago.
Several notable aspects of this genome can tell us more about Neandertal ancestry than we knew before.
The genome has no greater Neandertal ancestry than in living non-Africans. At least in this part of Asia, there was no greater opportunity to interbreed with Neandertals than elsewhere for ancient people.
Shared alleles with Neandertals are co-inherited across longer distances in the Ust'-Ishim genome than in living people. That is, there is greater linkage disequilibrium between Neandertal-derived alleles in the Ust'-Ishim genome. That indicates that Ust'-Ishim lived much sooner after its Neandertal ancestors than we do.
The pattern of linkage disequilibrium indicated by the Neandertal segments of his genome allows us to estimate the time that the Ust'-Ishim individual had Neandertal ancestors. This time seems to have been between 50,000 and 60,000 years ago.
Here's an excerpt from the section of the paper where they describe the identification of Neandertal-derived segments:
To test if this is indeed the case, we identified putative Neanderthal DNA segments in the Ust’-Ishim and present- day genomes based on derived alleles shared with the Neanderthal ge- nome at positions where Africans are fixed for ancestral alleles. Figure 5 shows that fragments of putative Neanderthal origin in the Ust’-Ishim individual are substantially longer than those in present-day humans. We use the covariance in such derived alleles of putative Neanderthal origin across the Ust’-Ishim genome to infer that mean fragment sizes in the Ust’-Ishim genome are in the order of 1.8–4.2 times longer than in present-day genomes and that the Neanderthal gene flow occurred 232–430 generations before the Ust’-Ishim individual lived (Supplementary Information section 18; Fig. 6). Under the simplifying assumption that the gene flow occurred as a single event, and assuming a generation time of 29 years, we estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East. How- ever, we also note that the presence of some longer fragments (Fig. 5) may indicate that additional admixture occurred even later. Nevertheless, these results suggest that the bulk of the Neanderthal contribution to present-day people outside Africa does not go back to mixture between Neanderthals and the anatomically modern humans who lived in the Middle East at earlier times; for example, the modern humans whose remains have been found at Skhul and Qafzeh
As usual, we should be cautious about assumptions. In particular, the assumption that admixture happened at a single time is almost certainly wrong. This amounts to the idea that the last Neandertal ancestors of Ust'-Ishim were his only Neandertal ancestors. As the paper suggests, there may have been more recent ancestors. I would point out that a small amount of Neandertal ancestry going further back in time would be indistinguishable from this pattern. If we imagine that Neandertal mixture into Eurasian modern human populations may have happened over some range of times, these data show that the modal time was probably in the time range from 50,000 to 60,000 years ago but do not exclude tails going further back in time or closer to the present.
That being said, it is pretty important that this genome adds resolution to the timing of Neandertal ancestry. We are not looking at a situation in which the bulk of mixture happened earlier than 100,000 years ago. We're looking at mixture that happened not too long before humans reached China, Australia, and obviously Arctic Siberia.
In contrast to its Neandertal DNA heritage, the Ust'-Ishim genome has no evidence of ancestry from the Denisovan population. That may or may not be surprising -- the genome may be from the same time zone but that doesn't make it especially close to Denisova; we don't know when the Denisovans lived there or where other modern humans may have mixed with them. But it is at least unfortunate, as it deprives us of the opportunity to examine the date of Denisovan ancestry with the same method as Fu and colleagues used for Neandertal ancestry.
Fu, Q. and many others. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514, 445-450. doi:10.1038/nature13810
Hawks, J. (2012). Longer time scale for human evolution. Proceedings of the National Academy of Sciences, 109(39), 15531-15532. doi:10.1073/pnas.1212718109
Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., ... & Willerslev, E. (2014). Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature, 505, 87–91. doi:10.1038/nature12736
Notable paper: Aubert M, Brumm A, Ramli M, Sutikna T, Saptomo EW, Hakim B, Morwood MJ, van den Burgh GD, Kinsley L, Dosseto A. (2014). Pleistocene cave art from Sulawesi, Indonesia. Nature 514:223-227. doi:10.1038/nature13422
Synopsis: The paper is mostly devoted to providing date estimates for the formation of speleothems, in this case "cave popcorn" deposits of calcite that have formed on surfaces that bear rock art. The authors show that many examples of rock art are Paleolithic in age, and paintings from at least three sites are more than 35,000 years old -- making these older than Chauvet Cave in France, the oldest example of figurative art in Europe. The oldest date for the Sulawesi rock art is 46,000 years ago, from Leang Barugayya 2.
Important because: The paper provides a second dot on the map of representational art before 30,000 years ago.The rock art from this area of Sulawesi was first noted by prehistorians more than 50 years ago. In southwestern Europe, rock art specialists have worked hard to develop a chronology of cave art based on chronology, but really that effort depends on assumptions about cultural groups that we cannot generally justify -- and rock art far from Europe could never fit into a European chronology. The appearance of new methods of dating the overlying speleothems has helped to open the science.
A clever article by Rose Eveleth for The Atlantic looks into a peculiar regularity in the history of art: "Nobody Knows What Running Looks Like". Eveleth reviews the findings of a recent paper by Julian Meltzer, which investigates representations of human gait throughout the history of art.
Normal human gait has the arms swinging opposite the legs. A step forward with the right leg is accompanied by a swing forward with the left arm. This arm swing facilitates a counter-rotation of the trunk and overall conservation of energy, and is natural for most people as soon as they learn to walk.
Strangely, most artists who depicted humans running or walking have gotten it backward: showing people swinging the same arm and leg forward, not opposites. Eveleth shows some great examples from ancient Egypt up to the present day.
When it comes to art, it’s possible that rather than being an error, the awkward, one sided lurch forward is an artistic choice. In Egyptian art, for example, artists followed strict rules about the position of the head and body. But as art evolved, and as accuracy of form become more and more important, it’s hard to imagine why someone like Da Vinci or Donatello would intentionally draw a person running in such an inaccurate pose. And modern “how to draw” guides are certainly not intentionally teaching someone the wrong posture.
A survey of people shows that they report this aspect of gait significantly worse than chance...
And when participants were asked to pose in mid-run, only 14 percent of them picked the pose that actually reflected running. The other 86 percent froze with the same sided arm and leg moving forward.
The investigation into this common error leads to some interesting conclusions about how we learn to move.
Meltzoff J. (2014). Errors in the making and perception of art images of human gait: Psychological explanations. Psychology of Aesthetics, Creativity, and the Arts 8(3):321-329. doi:10.1037/a0036669
The Mail and Guardian has a nice article about the work of John Gurche, written by Sarah Wild: "The next best thing to a time machine". Gurche is doing a guest lecture at the University of the Witwatersrand this week, and the article reviews his work and the importance of paleoartistic reconstruction to the science of paleontology:
“The world – worlds? – that science reveals is breathtaking, full of wonder. But the language of science is not accessible to many people. To convey that wonder, or even just to create an image that communicates what the scientific literature is saying, you need art,” he says, arguing that this is an example of science serving art. “Science can feel like a muse to the artist.”
But in this case, the muse is a collection of bones, painstakingly excavated from the ground over the course of years. In the coffee room in the Bernard Price Institute at Wits, the researchers have a puzzle on the table to help them to sharpen their visual abilities for piecing together ancient fossils.
When it comes to palaeoscience, these researchers have to put together a puzzle without knowing much of the picture in advance, and Gurche in effect has to colour it in.
I've seen skilled anatomists spend an awful lot of time with those jigsaw puzzles in the tea room.
The collaboration between artists and anatomists is so important to both fields of study. The best artists share with anatomists a skill of vision, developed over thousands of hours of close study, that is impossible to describe with words.
Gurche's recent book, Shaping Humanity: How Science, Art, and Imagination Help Us Understand Our Origins, provides a deep perspective on the creation of his distinct visions of ancient human ancestors.
ScienceOnline has now ended forever. Many people in the next several weeks will doubtless offer their perspective on why the organization failed. They will point to a series of poor decisions, a tone-deaf response to a sexual harassment scandal, and an organization's alienation of thoughtful community members.
I'd like to consider for a moment why it succeeded so brilliantly for more than five years. ScienceOnline represented a new wave of fusion between scientists and culture. That spirit has been taken outward into many directions by many of the participants, including me. The conferences provided a nexus for people from all walks of science to experience a changing landscape of sharing and doing science.
Here's a list of six things that I think helped to make ScienceOnline work.
Youth. The fascination of science is not obvious to everyone, and science has always relied on talented interlocutors to translate important results into popular culture. From the 1990s to the mid-2000s, many of the most widely influential science communicators -- journalists and high-ranking scientists -- were old, crusty, and hidebound. Online culture was new, young and full of revolutionary and romantic ideas. In science, where the most senior ranks are very white and very male, youth also brings diversity. The participants in ScienceOnline were well placed to write and speak about science in new ways, which was exciting to people.
Community. ScienceOnline created a forum in which online friends could meet. More important, the conference enabled people to meet who didn't know each other's online work. Many participants didn't even have online work, in the sense of a blog or other regular writing presence. The conference was built around their mutual interests in new forms of doing, publishing and communicating science. They already formed an informal network of people across institutions, disciplines, and professional callings -- from students to writers to full-time scientists. ScienceOnline helped to solidify this network and enable its members to call upon each other's skills outside of the usual professional silos.
Maker culture. People who engage with science and the internet are creators. They make things, grapple with new technology, hack the source. ScienceOnline gave these people a place to share what they were making. Artwork, ebooks, video, websites, software -- even new startups like Mendeley -- were all shared at ScienceOnline. The conference was full of "how-to" sessions, focusing on the practical side of making things. Some were beginner sessions that helped people learn how to blog, how to manage intellectual property, how to be a better writer. One year, I even organized a nuts-and-bolts workshop on how to migrate to a new server. Where else could one go from a session on documentary film techniques to a session on e-book platforms, and have both of them hit the right level? It is just fun to be around so many different people who are making different kinds of things.
Populism. Science is hierarchical. Senior scientists get the most resources and are allocated the most attention at conferences. At ScienceOnline, students, upcoming writers and journalists, and more established scientists and other academics all collaborated to present the program, all attended the same events and sessions, and most importantly all interacted on an equal footing. The conference encouraged sessions in which the attendees were active participants, not a passive audience. Much has been written about the deficiencies of the "unconference" format, in particular how relying on the crowd of attendees can miss valuable expert knowledge. But giving a broader sample of attendees a voice enabled them to help create knowledge instead of passively receiving it.
The Waiting List. Let's face it, nothing is cooler than the nightclub with a line out the door. At its peak, the tickets for the ScienceOnline conferences were snapped up within minutes of registration opening. In those years, more than a hundred potential attendees might get on a list to wait for cancellations. The organization did something very smart with this popularity: It gave away spaces to people who were willing to propose and organize great sessions. That idea fueled a diverse program with highly motivated presenters and facilitators. These people helped to minimize the inherent disadvantages of the "unconference" format, preparing and focusing material that would be engaging to the participants. As the organization started to falter, it neglected the value of session organizers increasingly discarded this strength, devaluing the contributions of session organizers.
The Backchannel. ScienceOnline was not the first conference with an active Twitter backchannel, nor was it the first to have livestreaming of sessions. But it was the conference that made offchannel more important than onchannel. What other conference had bandwidth demands on the scale of the Superbowl? The video streams enabled people offsite to participate virtually in the meeting through Twitter, reacting to sessions with their blogs, and thinking about how to organize similar sessions at other meetings.
Many of the great things about ScienceOnline have spread across the culture of scientific meetings. Those of us who tweet from scientific meetings have developed a backchannel bond, almost a shadow conference going on behind the scenes. Other meetings may not be egalitarian unconferences, but at least the senior scientists don't seem to grandstand during the question period quite so much as they used to. Some of today's best-known and most talented science journalists are people who met and learned from each other at ScienceOnline. Those relationships continue to shape the landscape of science communication.
Many of these changes may have been more or less inevitable, as a wave of technology enabled new forms of interaction among younger scientists and journalists. ScienceOnline rode this technology wave, capitalizing on the interests of people adopting new modes of writing and interacting. But it rode the wave in style, actively encouraging or driving some changes, with so many of its attendees involved across disciplines in other areas of science and culture.
The next ScienceOnline, whatever it may be called, will have to catch a different wave. The original never really evolved beyond the time when blogs were new. Blogs were quick and nimble mainly because they were small, with few layers of editorial decision-making. This gave them an unmatched power to respond to events, but has limited their reach. The leaders of online science have gone beyond the blog, exploring many other avenues of creativity. Already, online technologies are making an impact on documentary filmmaking, education, granting agencies, scientific publishing and field research. Interactive video, MOOCs, massive Facebook communities, and live-online hybrid events have pushed the boundaries of science communication in new ways. We are still making stuff -- even knocking on the door of that most hidebound mode of communication, the television news. With these successes, the makers have become leaders in their fields, spreading new approaches and techniques into more specialized communities. Tomorrow's online science conversations must look forward to this diverse future.