The study uses a fairly simple concept—take a lot of unidentifiable bone fragments and test them with a protein mass spectrometry toolkit (ZooMS) to identify them to genus if possible. They were pretty successful. The real innovation is that they were able to identify a protein polymorphism for which 99% of living humans have a derived amino acid, and all known Neandertals have the ancestral amino acid. In the context of a Châtelperronian archaeological layer, finding the ancestral allele gives a strong indication (but not an infallible one) that a bone fragment probably has a Neandertal heritage.
I think the result is pretty cool because Welker and colleagues were able to identify a large number of bone fragments that probably belong to an infant skeleton, which they already knew was in the site based on a handful of identifiable remains.
Despite their spatial proximity within Layer X and squares C7 and C8, none of the newly described specimens could be fitted together to form larger fragments. The morphologically informative specimens, however, seem to represent small fragments of an immature cranium and an unfused vertebral hemiarch of neonatal age (SI Appendix, Fig. S10 and Table S13). This is supported by isotopic evidence suggesting that these fragments belonged to a nonweaned infant and by proteomic evidence in the form of proteins present in bone before bone remodeling has started. All the newly identified specimens were found in close spatial association with a previously described hominin temporal bone from square C7, Layer Xb, assigned to an infant around 1 y old, as well as 10 dental specimens from squares C7 and C8 (6, 7). These dental specimens overlap in developmental age, suggesting they represent one or possibly two individuals between 6 and 18 mo old (7). The 28 newly identified specimens, together with already described specimens, may therefore represent the skeletal remains of a single infant.
The reporting on this paper has emphasized the conclusion that the bones are Neandertal, which in addition to the protein evidence is also indicated by some mtDNA sequence fragments from some of the remains. To me this is basically a failure to reject a long-substantiated association: Neandertals made the Châtelperronian industry.
The Châtelperronian has been found across much of France and into the Pyrenées of Spain, and dates to around 40,000 years ago. It is termed a “transitional” industry because although it is based upon flaking strategies typical of earlier Mousterian assemblages, the Châtelperronian includes elements usually attributed to Upper Paleolithic toolkits including many bone artifacts and elongated flake tools that share many details with the blades of later Aurignacian assemblages.
The identity of the makers of the Châtelperronian has been a white whale for some archaeologists. The only diagnostic skeletal remains ever found with Châtelperronian tools have been Neandertals, notably the Saint-Césaire skeleton but also more fragmentary skeletal remains from Arcy-sur-Cure. Yet despite this association, some archaeologists have doubted that Neandertals made such apparently “sophisticated” tools. They have examined whether Châtelperronian assemblages are a palimpsest or mixture of elements from earlier Mousterian and later Upper Paleolithic contexts, whether Neandertal remains might have moved out of stratigraphic position, whether Châtelperronian layers may have slumped in a way not recognized in old excavations.
Today it would be truly surprising if an unambiguous modern human skeleton turned up in a Châtelperronian archaeological layer. If a specimen with modern human traits emerged, or a tooth that shared traits with modern humans, I would not be surprised, but that’s because I expect there was likely population mixture in Europe at the time of the Châtelperronian some 40,000 years ago.
Ten years ago, a debate erupted about the type locality of the Châtelperronian industry, Grotte des Fées du Châtelperron. I wrote about that episode here (Interstratified palimpsests), and it was never really satisfactorily resolved.
Why was it such a big deal? The last refuge of scoundrels has been the notion that Neandertals were incapable of making Châtelperronian artifacts on their own and needed the enculturating influence of modern humans to do so. This idea was popularized by Jared Diamond in his book, The Third Chimpanzee and has hung around within European archaeology for more than thirty years. The importance of possible interstratification of Châtelperronian and Aurignacian industries is a test that Neandertals who made Châtelperronian artifacts and modern humans who made Aurignacian artifacts might really have encountered each other on the same landscape. Without the possibility of such contact, it is hard to conceive of the idea that Neandertals were “acculturated” by their encounters with modern humans.
What is my opinion? I have to say, two or three thousand years is a lot of time, and it is hard for me to imagine that populations did not exchange a good amount of information across Europe during that time, whether they lived in overlapping areas or not. I doubt that the early Aurignacian people were very much different from late Neandertals in their cultural and technical abilities. Even if they were different on average for some cognitive abilities, which I can well imagine, I expect their abilities would have overlapped to a substantial degree.
The conclusion of the paper sums up my feelings fairly well.
Our biomolecular data provide evidence that hominins contemporaneous with the Châtelperronian layers have archaic nuclear and Neandertal mitochondrial ancestry, supporting previous morphological studies (6, 7). They are therefore among some of the latest Neandertals in western Eurasia, and possible candidates to be involved in gene flow from Neandertals into AMHs (or vice versa) (48). Future analysis of the nuclear genome of these or other Châtelperronian specimens might be able to provide further insights into the direction, extent, and age of gene flow between Late Pleistocene Western European Neandertals and “incoming” AMHs (49, 50).
More results coming
Doing more to uncover the hominin remains at a site is valuable even if the anatomical information to be gained is minimal, and even if genetic information cannot be reliably obtained from the fragments with today’s techniques.
Still, in the short term at many sites, what the method reveals about the fauna will be even more interesting. Identifying rare species in faunal assemblages from non-diagnostic fragments should greatly increase the representativeness of the archaeological record. As reported by Welker and colleagues in an earlier paper (2015), they can reliably identify bone fragments to genus in a large fraction of cases, even for bone fragments that have passed through a carnivore’s digestive tract.
This result is published this week just after a number of studies were presented in talks at an international conference on ancient biomolecules. That other work is reported by Ann Gibbons (“Oldest-ever proteins extracted from 3.8-million-year-old ostrich shells”), which includes a statement that protein has now been recovered from tooth enamel of extinct fauna from Dmanisi. Protein analysis of ancient fossils suddenly looks like a very big deal.
Brown, S., Higham, T., Slon, V., Pääbo, S., Meyer, M., Douka, K., ... & Derevianko, A. (2016). Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Scientific reports, 6. doi:10.1038/srep23559
Welker, F and others. 2016. Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne. Proceedings of the National Academy of Sciences, U.S.A. (early edition). doi:10.1073/pnas.1605834113
Welker, F., Soressi, M., Rendu, W., Hublin, J. J., & Collins, M. (2015). Using ZooMS to identify fragmentary bone from the late Middle/Early Upper Palaeolithic sequence of Les Cottes, France. Journal of Archaeological Science, 54, 279-286. doi:10.1016/j.jas.2014.12.010
Retraction Watch: You say that the numbers of systematic reviews and meta-analyses have reached “epidemic proportions,” and that there is currently a “massive production of unnecessary, misleading, and conflicted systematic reviews and meta-analyses.” Indeed, you note the number of each has risen more than 2500% since 1991, often with more than 20 meta-analyses on the same topic. Why the massive increase, and why is it a problem?
John Ioannidis: The increase is a consequence of the higher prestige that systematic reviews and meta-analyses have acquired over the years, since they are (justifiably) considered to represent the highest level of evidence. Many scientists now want to do them, leading journals want to publish them, and sponsors and other conflicted stakeholders want to exploit them to promote their products, beliefs, and agendas. Systematic reviews and meta-analyses that are carefully done and that are done by players who do not have conflicts and pre-determined agendas are not a problem, quite the opposite. The problem is that most of them are not carefully done and/or are done with pre-determined agendas on what to find and report.
This comment resonated with me. This year has seen an explosion of review papers on hominin diversity.
The review papers that have appeared so far this year mostly seem to reflect symposium contributions that were presented in 2014 or 2015. Few of them have significant updates since they entered review sometime in 2015, and so they do not discuss findings of the last couple of years except very superficially. Most do not integrate findings from across different time intervals in human origins.
So, for example there have been three or four review papers this year summarizing hominin diversity in the Middle Pliocene. This is the time period that has produced evidence of Australopithecus afarensis, as well as a bunch of other species represented by a few fossils each, including A. bahrelghazali, Kenyanthropus platyops, and most recently A. deyiremeda.
Each of the review articles this year reads basically like a position paper by its authors about Australopithecus deyiremeda, either for or against.
This is a difficult area to review right now. The fossil evidence is sparse. Many of the authors consider the “best” evidence of species diversity to be the partial foot skeleton from Burtele, Ethiopia, which has not been assigned to a species. Few scientists have studied all the relevant material.
A real answer to the question of Middle Pliocene hominin diversity should start from a full and free examination of the variation found within the largest fossil samples, not excluding any specimens, and without any prior assumptions about their taxonomic status. We would need to revisit and test ideas from the 1980s about the taxonomy of Hadar fossils, relying upon the larger dataset that has since accumulated from Hadar and other sites. This would require us to seriously examine the idea that the cranial and dental fossils may represent more than a single species, and the postcranial fossils may represent more than a single adaptive pattern.
This kind of open examination would have many beneficial outcomes. Not least, it would provide some clear idea of what kind of evidence should be supplied to support the diagnosis of new species.
I recognize the root of my dissatisfaction in Ioannidis’ comments. The current crop of review articles, which serve the purposes of journals and players with pre-determined agendas, does little to advance the science. It is one thing when such a review is in a journal dedicated to review for non-specialists, like Annual Reviews in Anthropology or the Yearbook of Physical Anthropology. But it’s depressing to realize how little actual synthesis we are seeing in other contexts.
President Obama echoed this sentiment in February. “I would like to think that if somebody does a test on me or my genes, that that’s mine,” he said.
STILL, IT’S OFTEN HARD to know if you have signed away your ownership rights because of lengthy and obtuse privacy policies. “If you look at enough terms of service and privacy policies you will see the word ‘may’ or ‘might’ being used a lot — as in we ‘may share’ — which leaves the door open,” says Jan Charbonneau, a PhD candidate at the Centre for Law and Genetics at the University of Tasmania in Australia.
Tumours and cancers are collectively known as neoplastic diseases. Until now, the oldest evidence of neoplasia in the hominin fossil record dated back 120,000 years. This was found in a rib fragment of a Neanderthal from Krapina in Croatia.
But our discovery, in two South African cave sites, offers definitive evidence of cancer in hominins – human ancestors – as far back as 1.7 million years ago.
We forget the privilege it is to have lifelong security of employment at a spectacular university. And I don’t think we use it for its intended purpose. I think that faculty on average through the generations are becoming a bit careerist and staying inside our comfort zones. [But] If we’re perceived as being an ivory tower and talking to one another and being proud of our discoveries and our awards and our accomplishments and the letters after our name, I think in the long run the enterprise is going to suffer in society’s eyes, and our potential for impact will diminish. The willingness of society to support us will decrease.
In these comments, Schlissel encapsulated one perspective on the “ivory tower” problem. It’s hard to run a state university in today’s budget and political climate when many faculty appear to have little interest in serving the public. Within the U.S., state funding of universities is declining. They depend increasingly on federal research funding, which has remained steadier, but with an increasing proportion sucked up by overhead. Universities’ share of federal research funding has increased even as individual research grants become more difficult to obtain, but this cannot be sustainable in the long run. Particularly if the public interest in academic work is not sustained.
Many academics would respond that it is wrong to expect research to be useful or to have an impact on society. Or they might say that the topics of research are irrelevant to the purpose of the university, which is to advance learning and provide students with the tools to push the boundaries of knowledge.
But as it turns out, today’s students enter academic training hoping to make a difference in the world, not within a cloister:
Many graduate students report that they have chosen a research career precisely because they want to contribute to the real world: to offer their knowledge and expertise in order to make a difference. And many report that if academia doesn’t value engagement or worse discourages it, they will follow a different route, either toward schools that reward such behavior or leave academia for think tanks, NGOs, the government or other organizations that value practical relevance and impact.
The frustration is such that some no longer tell their advisors that they are involved in any form of public engagement, whether it be writing blogs or editorials, working with local communities or organizing training for their peers on public engagement. Will academia eventually spit these emergent scholars out, or will they remain and change academia? Many senior academics hope for the latter, fearing a worrying trend toward a reduction in the level of diversity and quality in the next generation of faculty.
These trends make me worry about the future. Students are clever and come into academic work with energy and goals to expand the importance of their fields. But so many established academic advisors actually diminish students’ abilities to reach out to the public.
Worse, the students who are successful at public engagement are often selected out of academia. What matters in tenure-track job competition is research funding, not engagement or broader impacts. Federal grants have included a “broader impacts” criterion for a long time. But in my experience reviewing grant applications, a negative assessment of a broader impacts plan has never resulted in a failure to fund the grant. I just do not see this criterion making any difference at all to the level of engagement expected for funding. As long as public engagement remains unimportant in the process of hiring, tenure, and grant funding, the students and early career academics who are most out of touch will continue to win positions and prestige, and students who succeed at engagement and public impact will continue to seek other opportunities.
The most difficult section of my final exam was multiple choice. I told the students that they could pick the one question about which they were most unsure, and write down the name of a classmate who might know the answer — the equivalent of a lifeline on the game show “Who Wants to Be a Millionaire?” If the classmate got it right, they would both earn the points.
Essentially, I was trying to build a collaborative culture with a reward system where one person’s success benefited someone else. It was a small offering — two points on a 120-point exam — but it made a big difference. More students started studying together in small groups, then the groups started pooling their knowledge.
The latest research indicates that the nature of the bonobos’ sororal bonds shifts depending on circumstances, and that the most effective deterrent to male harassment may be a cross-generational pact.
“I sometimes think that bonobos sit up late at night reading papers about primates, and then decide to do the opposite,” said Joan Silk, a primatologist at Arizona State University. “They’re unusual in so many ways.”
The problem of drug-resistant infections is terrifying but also abstract; by their nature, microbes are invisible to the naked eye, and the process by which they defy our drugs is even harder to visualise.
But now you can: just watch that video again. You’re seeing evolution in action. You’re watching living things facing down new challenges, dying, competing, thriving, invading, and adapting—all in a two-minute movie.
An experimental setup in which bacteria colonize progressively more antibiotic-laced environments when they have favorable mutations, all put on video.
Various people suggested to me on twitter that the public has become a little blase about exoplanets, possibly because they have been a bit oversold. (One person suggested that astronomers may have cried wolf too often, which I mention mainly in order to link to this bit of brilliance from Mitchell and Webb). With regular announcements of planets more “earthlike” than the last — but with no evidence that any of them is actually remotely like the Earth — the fact that this one was nearer than any of the others hardly seemed like that big of a step forward.
It is a real challenge in the public communication of science to explain the interesting parts of incremental progress.
Sequencing new animal genomes is no longer newsworthy absent some additional and surprising scientific finding from them. Technology has progressed and new data are coming in, but each incremental data point is not advancing theory.
When the buildup of data starts leading to new scientific predictions and insights, that will make much more of an impact.
For the last decade, Taylor and her renters have been visited by all kinds of mysterious trouble. They’ve been accused of being identity thieves, spammers, scammers and fraudsters. They’ve gotten visited by FBI agents, federal marshals, IRS collectors, ambulances searching for suicidal veterans, and police officers searching for runaway children. They’ve found people scrounging around in their barn. The renters have been doxxed, their names and addresses posted on the internet by vigilantes. Once, someone left a broken toilet in the driveway as a strange, indefinite threat.
All in all, the residents of the Taylor property have been treated like criminals for a decade. And until I called them this week, they had no idea why.
In the wild, both monkeys host different and distinctive communities of gut microbes. But in captivity, these communities converge, so they become harder to tell apart. Even though doucs and howlers come from different continents and naturally eat different kinds of plants, and even though those specific captive individuals lived in three zoos across three different countries, their gut microbiomes ended up looking very similar. They were closer to each other than to their wild counterparts, and oddly similar to the microbiomes of humans.
Why the changes? Zoo animals often get antibiotics, but Clayton found that even untreated animals had different microbiomes from wild ones. Instead, these changes were most likely due to diet.
This is not too surprising but raises many interesting questions about microbiome evolution. Clearly there is a rapid shift in the microbiome based on dietary environment in primates. How much of this is caused by the colonization of the guts of these primates by microbes from humans (or other captive animals)? How much change can be attributed to selection within the microbiomes of these primates? And what does the pace of colonization by microbes of primate guts imply about the evolutionary dynamics of these microbiomes in wild populations?
I have no trouble believing that Lucy might have fallen to her death. Why not? The Lucy skeleton has several features compatible with a lifetime of climbing, and other fossils attributed to her species, A. afarensis, have even more. So I am not primed to be skeptical of the conclusion of the new paper by John Kappelman and colleagues in Nature.
But I’m struggling to figure out why the authors decided to publish without addressing basic questions that any paleontologist would ask.
The Lucy skeleton was recently on tour in the United States, beginning at the Houston Museum of Natural Science, and on this tour the bones were scanned in a high-resolution CT machine at the University of Texas. Studying the scans, Kappelman and his team decided that some of the fracture patterns are consistent with injury near the time of death, called perimortem trauma.
Their strongest evidence is the fracture pattern of the right humerus. The surface of the humeral head was crushed downward, with large chunks of the neighboring bone shattered outward and fossilized in place. Previous scientists have interpreted this damage as the product of fossilization and crushing under layers of sediment. Kappelman and colleagues examined the fragments and found two aspects that are indicative of a “green” fracture, made while the tissue was still fresh. Putting the fragments back together like a jigsaw puzzle, they saw that the entire proximal end of the bone first sheared off diagonally in a pattern called a spiral fracture. The fracture left some small shards of bone, only millimeters in size, still adhering to the fractured fossil. Kappelman and colleagues argue that if this breakage had happened with fossilization, after the soft tissue of the shoulder joint was completely gone, then these tiny shards of bone should be missing. Their presence suggests that the bone was broken near the time of death, buried with soft tissue still present, and fossilized in place.
It is not hard to find comparable proximal humerus fractures in modern clinical cases. For example, this one is from a paper on treating humeral fractures by Shane Nho and colleagues:
Here is a diagram of the fragments of the Lucy proximal humerus from Kappelman and colleagues:
Comparing those images, you can see how the proximal humerus of Lucy resembles a fracture injury. Kappelman and colleagues build a broader case involving many other bones. Of the rest of the skeleton, the other obvious instance of damage from compression is the left distal femur, which has condyles that were jammed upward and laterally. Kappelman and colleagues show that the contour of the damaged bone is a mirror-image to the proximal end of the right tibia, the left being missing from the skeleton.
In all, they argue that some 20 bones of Lucy’s skeleton present evidence of perimortem fractures. Nearly every break present on the bones, including the broken edges of preserved fragments like the clavicle, they interpret as perimortem.
On the surface, it might seem like a watertight case. But as my Facebook feed began to pulse with messages from other anthropologists this morning, the authors defined perimortem fractures so loosely, every break in any fossil might be described as perimortem. If Lucy really had fractures on more than 75% of her preserved bones, she didn’t fall out of a tree, she fell out of an airplane.
As an example, consider the first rib. The authors do not illustrate this rib, but they argue that the rib has a “hinge fracture” at the neck, and several fractures at midshaft that were made at the time of death. They note that the first rib is almost never fractured, even in accidents where the other ribs suffer many fractures, because of the extensive soft tissue around it–dramatically, they call it a “a hallmark of severe trauma”. Their scenario for Lucy is that the extreme stresses on the shoulder at impact caused the clavicle to break, deflecting downward into the first rib and breaking it in multiple places.
But there is another process that breaks first ribs very commonly in the fossil record: Becoming a fossil.
I am not aware of any first rib from a Plio-Pleistocene hominin that is intact. The Nariokotome Homo erectus first rib appears to have a very similar pattern of breakage to the Lucy first rib. The first ribs from Dmanisi are broken, as are first ribs from Malapa and Sterkfontein. The first hypothesis to turn to for all these broken ribs is damage in the process of natural deposition and fossilization. Fossil bones are usually broken, and Lucy is no exception.
Does it matter that the authors describe some of these breaks as “hinge fractures”? Dry bones lacking the strength of their organic matrix often fracture in a straight line, like broken Greek columns, while a hinge fracture is one that changes in direction at one edge. When people see such a fracture that deflects in direction, they often attribute the fracture to fresh bone instead of dry bone.
But in reality, a fracture that passes through a cortical bone layer may deflect in a direction more perpendicular to the bone surface even if the bone is dry, beneath sediment, or mineralized. The paper uses the term “hinge fracture” many times, but neither defines it nor gives examples of how this evidences perimortem fracturing. If they examined a large collection of faunal fossils from the same context, they would find similar patterns, not from falling out of a tree but from simple post-depositional breakage.
The lack of comparison is a fatal deficit of the paper. The authors make no attempt to show that the pattern of fractures in the Lucy skeleton is different from that found in non-hominin bones from similar contexts. How many of the faunal remains from Hadar have similar fracture patterns? What about hominin bones from other sites?
In comments to Science News, Tim White provides a clear illustration of why comparisons are necessary to support the authors’ conclusion. Here in a photo is Lucy’s right proximal humerus compared to a fossil horse humerus:
The horse did not fall from a tree.
Now, to be fair the horse doesn’t show the same degree of compression of the humeral head as Lucy. But like most paleontologists I’ve seen plenty of fossils that are much more deformed than the Lucy humerus and femur. Understanding whether that deformation is perimortem requires a close comparison with many other fossil specimens from similar contexts. None of that comparison is in this paper. No data concerning the preservation of non-hominin remains from Hadar or any other site are in this paper. If the authors want anyone to believe their analysis of the Lucy skeleton, they need to demonstrate that the fractures on the Lucy skeleton are different from those present on other fossils.
As it stands today, those paleontologists who are most knowledgeable about the Hadar fauna have been vocal: Similar fractures are common on other animal fossils including rhinos and elephants.
The paper provides no answer to this obvious criticism. It lacks minimal basic comparisons and therefore gives little reason to believe the authors’ conclusions.
The lack of data does not mean the authors’ hypothesis is necessarily wrong. I still think it is credible that Lucy may have had perimortem fractures, and I consider it possible that the humerus and femur may have compressive fracture damage consistent with a fall. But the authors frame their hypothesis as a just-so story, and only examine evidence consistent with it instead of looking for contrary evidence.
Skilled forensic anthropologists have only a limited degree of accuracy assessing perimortem versus postmortem fractures, when they are looking at buried skeletal remains that are only a few years old. With Lucy, we are talking about fractures that have been evident since the skeleton was found, and every previous scientist who examined them has concluded that they are likely postmortem damage consistent with the pattern on other fossils from Hadar. Showing that these fractures came from a particular traumatic event is going to take much better data than this paper provides.
Kappelman, John, Richard A. Ketcham, Stephen Pearce, Lawrence Todd, Wiley Akins, Matthew W. Colbert, Mulugeta Feseha, Jessica A. Maisano and Adrienne Witzel. 2016. Perimortem fractures in Lucy suggest mortality from fall out of tall tree. Nature doi:10.1038/nature19332
Nho, S.J., Brophy, R.H., Barker, J.U., Cornell, C.N. and MacGillivray, J.D., 2007. Management of proximal humeral fractures based on current literature. The Journal of Bone & Joint Surgery, 89(suppl 3), pp.44-58. doi:10.2106/JBJS.G.00648
One of the earliest artist renderings of a Neanderthal (1887), published in a magazine called The Open Court, which was dedicated to the dialogue between religion and science. The artist was Guernsey Mitchell.
National Geographic is running a fascinating story about “desert kites”, ancient structures dating to the Iron Age or earlier in Central Asia and the Levant: “Giant ‘Arrows’ Seen From Space Point to a Vanished World”. They are hunting traps that work on the psychology of herding antelopes, who will avoid a low wall or ditch and can thereby be herded into traps.
Equally striking, Amirov’s team found dozens of desert kites arrayed like a giant net across a hundred miles of tablelands east of the Aral Sea. Such a huge construction project hints at a collective hunting effort by large numbers of ancient nomads. They could have harvested entire antelope herds, Amirov writes. The haul of meat must have far exceeded the needs of immediate consumption. The excess was probably traded away. Today these kites still stand with their V-shaped mouths gaping northward, awaiting a ghostly migration that never comes.
Science magazine: “Americans may know more than you think about science”. Looking at a more expansive view of knowledge that tries to get at how people actually process knowledge into action. But there’s “bad news” – people may know plenty about science, but this doesn’t make them support spending a lot of public money on new scientific research:
But the bad news is that researchers may have misled policymakers and educators about the connection between literacy and support for science. “Available research does not support the claim that increasing science literacy will lead to appreciably greater support for science in general,” the report concludes. Scientists are partly to blame for that misconception, it adds, because the metrics they typically use to assess literacy “are only weakly correlated” with how people behave.
This is related to the “deficit model” for science communication; the idea that people will support the same policies supported by scientists if the people only know enough about science.