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paleoanthropology, genetics and evolution

Photo Credit: Okladnikov Cave. John Hawks CC-BY-NC-ND

Neandertal anti-defamation files, 22

This, from ScienceAlert:

We caught modern genital warts because our ancestors were banging Neanderthals

Nothing like this story as been such a race to the bottom for headlines for a long time.

I will note that Annalee Newitz has a much better version of the story with this winning quote:

[A]lways practice safer sex, even if you're getting down with a Denisovan.

There is, by the way, the interesting question of whether Neandertal immune variants might influence susceptibility to the strain in question, which has made little inroad into sub-Saharan Africa.

Race and the medical student

Ike Swetlitz in Stat has an article about the ways that some medical educators are trying to build a more anthropological knowledge of race and health in their students: “Teaching medical students to challenge ‘unscientific’ racial categories”. Unfortunately both the headline and article get a bit snarled in their use of language. Maybe that’s inevitable.

“You see ‘African American,’ automatically just circle ‘sickle cell,’” said Nermine Abdelwahab, a first-year student at the University of Minnesota Medical School, recounting tips she’s heard from older classmates describing the “sad reality” of the tests.
Medical school curricula traditionally leave little room for nuanced discussions about the impact of race and racism on health, physicians and sociologists say. Instead, students learn to see race as a diagnostic shortcut, as lectures, textbooks, and scientific journal articles divide patients by racial categories, reinforcing the idea that race is biological. That mind-set can lead to misdiagnoses, such as treating sickle cell anemia as a largely “black” disease.

In an episode of M*A*S*H from the early 1980s, Corporal Klinger starts suffering from a rare side effect of the anti-malarial drug primaquine. The doctors know that the drug has the potential of negative side effects in blacks, but issue it to everyone else. Hawkeye and the other doctors assume Klinger is just goldbricking. But another soldier, Private Goldman, starts to exhibit the same symptoms. The doctors determine that both Klinger and Goldman are suffering anemia, and take them off the primaquine. At the end of the program, it is revealed that people of Levantine origin (like Klinger) and Ashkenazi Jews (like Goldman) also may have the same susceptibility to primaquine side effects owing to their ancestry.

The side effect in question is a breakdown of blood cells and consequent anemia in people with G6PD deficiency, which is indeed very common in sub-Saharan and North Africans, and less common but still notable in people of broader Mediterranean descent.

I like the program quite a lot, and I remember it from the first time it was broadcast. It is a well-scripted way illustration of how a physician can make erroneous assumptions about ancestry and genetics that lead to bad treatment. But it also goes to show that there’s very little new in today’s attempts to improve medical school training with respect to race and medicine. These are all ideas that were well-known more than forty years ago and have been staples of anthropology.

Of course today we can know from anyone’s genotype data whether they have a susceptibility to some adverse drug reactions, and that includes many that do not have much higher frequencies in one population or another. Whatever there is to be said for genotyping, it beats census categories if you are looking to diagnose most common traits influenced by Mendelian genes. If we are training medical students for the world of five or ten years from now, allowing them to make effective use of this information should be the priority.

Will virtual reality compete with museums or help them?

Linking to a provocative piece that “VR Will Break Museums”.

The article discusses many issues with museums both large and small. The best museums add context to the objects that they display, putting them into a story that builds knowledge in the museum-goer. But some concepts are incredibly difficult to communicate in that fashion, and others rely so much on place that removing objects to a museum does not convey their context accurately.

And the crowds suck. Nothing is better than a huge museum on a very empty day, and those don’t happen very often.

The problem is, museums don’t scale well. The British Museum sees almost 7 million visitors a year. What would it take to accommodate double that number? Ten times that number? It simply cannot be done, not for any reasonable amount of money.
The Internet, on the other hand, is built for scale. The marginal cost of an extra YouTube viewer or app download is practically zero. That’s how a video about the history of Japan can be made for free, distributed for free, and enjoyed for free by more people in a single month than who walk through the doors of the Louvre in an entire year.

Museums are a very important part of human evolution research, both by serving as repositories for the objects we study and for helping the public to understand the importance of our science. I’ve consulted with many museums over the years and have visited a large fraction of the major museums of natural history in the world.

Human genetics is more and more important to how we understand human evolution. Yet this is one of the most difficult parts of science to illustrate in a museum setting. Museums excel at visual material and unique objects. While it is possible to do video or virtual content for genetics, whenever I encounter videos at a museum, I groan. They’re always a chore and rarely hit the mark as well as simple text accompanying an object.

Honestly, I think that museums face much the same problem as movies. Studios invest tremendous sums of money in movies that have bad scripts. There are many reasons for this – sometimes the director has too much power and keeps shifting the script, sometimes the original idea relied upon visuals that cannot be realized, sometimes studio executives ruin a cohesive script by committee. Whatever is the case, the ultimate reason why this situation happens so often is the same: Audience demand for certain kinds of movies is just not very responsive to script quality.

Likewise, public visitation to certain museums doesn’t respond much to the quality of stories they can effectively tell. A museum exhibition with bad videos is regrettable, but most people skip the videos anyway. Especially if the first few seconds of the first one doesn’t connect.

The great thing about the idea of virtual experiences is that they may be laboratories for real innovation in storytelling. The stories that work should be translated into the museums that audiences already value. As someone who has done a lot of museum consulting, I can really imagine having a lot of fun helping make virtual experiences that educate and convey exciting science.

Incidental capuchin flake manufacture

This is a nice article by Ed Yong about Michael Haslam’s research documenting how capuchin monkeys incidentally make stone flakes as a side effect of their nut smashing: “Rock-Smashing Monkeys Unintentionally Make Sharp Stone Tools”.

The interesting thing is that many of the flakes are indistinguishable on technical grounds from Oldowan flakes. That raises the possibility that intermittent, possibly local traditions of nut-cracking among some forms of primates might create the appearance of localized flake assemblages.

He also thinks that archaeologists should spend more time looking for the works of ancient monkeys and apes. “[We should] consider what other non-human primates in Africa and elsewhere may have been up to for the past tens of millions of years,” he says. “There is no reason why stone flakes may not be littered throughout primate history, at unknown places and times.”

Actually, I think there is nothing materially different about what these capuchins are doing and what early hominins were doing when they made flakes. One may say that the hominins made flakes “intentionally”, or with a goal in mind to use the flake. But the difference here is not cognitive, it that the capuchins have not learned socially to use flakes for anything.

Primatologists already observe capuchin monkeys learning socially to lift rocks nearly half their body weight, thrust them down onto a platform with a fruit, and repeat this until yummy bits of nutmeat scatter everywhere. It would not take any great cognitive advance for them to learn how to use flakes, if there were something useful for them to do. The ability to generalize is simply the ability to emulate others.

Notable paper: William Hutchison et al. (2016) A pulse of mid-Pleistocene rift volcanism in Ethiopia at the dawn of modern humans. Nature Communications 7, 13192. doi:10.1038/ncomms13192

Synopsis: Many of today’s lakes and volcanic calderas of the central Ethiopian rift were the outcome of a cluster of volcanic activity between 320,000 and 170,000 years ago.

Interesting because: Early examples of Middle Stone Age (MSA) archaeological industries were developing at this time, and possibly the immediate ancestors of most of today’s gene pool were making some of them. Volcanoes might have affected the local environment.

KILL THIS QUOTE WITH FIRE: “current evidence overwhelming [sic] suggests that all major events in hominin evolution occurred in East Africa”. No. Just no.

Bottom line: It is very hard to test how local environmental shifts may have affected hominin populations; either prompting adaptation or creating population sinks. My guess would be that a region full of active volcanoes probably acted either as a sink or a barrier to gene flow. As an extreme, these volcanoes may have impeded migration from the Afar region further south along the African rift during the later Middle Pleistocene, making this fossil-rich region a relative cul-de-sac. However, in my opinion a 30-km zone of unpleasantness surrounding a volcanic caldera is not much of a barrier to mobile and interconnected hominin populations. Ancient people probably looked in wonder at the great forces within the earth, and watched their children played in the snowing ash.

Theodosius Dobzhansky, in his essay, “On species and races of living and fossil man” (1944):

The opinion is often expressed that species and races are arbitrary categories. This opinion is false. If given the opportunity to secure the necessary data, a biologist is able in a majority of cases to decide beyond a reasonable doubt whether the forms under study are distinct species or only distinct races. Lion, tiger, leopard, and domestic cat are species ; Angora cat and alley cat are surely not species but races. However, “borderline cases”, in which it is impossible to decide whether one is dealing with species or with races, do exist. Indeed, their existence was used by Darwin to demonstrate organic evolution. If species are the primordial units of creation, or else if they arise by sudden leaps (as thought by G. St. Hilaire and recently by Goldschmidt), then we should be able to find methods to decide whether any two forms are still races or already species. If, on the other hand, species evolve gradually from races, then the decision will be possible only in some, perhaps in a majority, of cases, but at least some instances must be found in which forms are too distinct to be races but not distinct enough to be species. Evolutionists have concentrated their efforts on proving that such borderline cases do exist; by indirection they conveyed to biologists in general the impression that there are no other but borderline cases.

Misuse of statistics

This essay should be required reading for graduate students: “The problem with p-values”. David Colquhoun writes extensively about science and statistics, and in this essay he brings out many of the biggest misconceptions that drive poor conclusions in scientific practice.

Even quite respectable sources will tell you that the p-value is the probability that your observations occurred by chance. And that is plain wrong.

Paleoanthropology is one field in which papers that point out poor use of statistics are publishable. The primary fossil data are very sparse, and we work hard to establish what little we can say with confidence. There are generally scientists willing to criticize statistically misleading attempts to answer the unanswerable.

Personally, I’ve spent a good amount of time looking into the basic statistical underpinnings of human evolution datasets. For example, my paper “How much can cladistics tell us about early hominid relationships?” showed that the datasets of most hominin species are simply not big enough to yield confident conclusions about how they are related to each other. A later paper, “No brain expansion in Australopithecus boisei, worked through statistical issues with time-series data on which paleoanthropologists have often based conclusions about trends in morphological features over time.

My all-time favorite paper outlining statistical problems in human evolution research is by Richard Smith, “Biology and body size in human evolution: statistical inference misapplied.” Smith shows a systematic problem with the most common comparisons of ancient human relatives. Now, twenty years after that paper was first published, most papers that consider body masses of fossil hominins still get this wrong.

That’s a well-worn tale in science. Pointing out statistical errors is sisyphean. Many recent papers in human evolution reflect poor statistical practice. And a good number of “classic” results are based on datasets that today would be statistically doubtful. Science is self-correcting, but it is going to take some hard work to get this stuff straight.


Hawks, J. (2004). How much can cladistics tell us about early hominid relationships?. American journal of physical anthropology, 125(3), 207-219. doi:10.1002/ajpa.10280

Hawks, J. (2011). No brain expansion in Australopithecus boisei. American journal of physical anthropology, 146(2), 155-160. doi:10.1002/ajpa.21420

Smith, R. J. (1996). Biology and body size in human evolution: statistical inference misapplied. Current Anthropology, 37(3), 451-481. JSTOR

Everything Neandertal is not bad

This is not a bad story about Neandertals by Melissa Hogenboom: “What Neanderthals’ healthy teeth tell us about their minds”. It’s an overview of what scientists learn from various kinds of dental studies.

But I wanted to comment on one thing:

"We realised nobody had directly compared Neanderthal [teeth loss] to modern humans, so we didn't realise Neanderthals had [slightly less] tooth loss," says Weaver.
This flies in the face of previous studies, which suggested that several Neanderthals lived long after losing all, or nearly all, their teeth.
But bizarrely, the finding that Neanderthals apparently had healthy teeth actually suggests something rather negative about them.

I don’t disagree that there is a slight difference in tooth loss. That does not contradict the real observation that some Neandertal individuals had extensive premortem tooth loss.

La Chapelle-aux-Saints mandible, photo by Milford Wolpoff
Mandible of the Neandertal with the most premortem tooth loss, La Chapelle-aux-Saints. Photo by Milford Wolpoff.

I agree that some people have made more cultural conclusions from the observation of tooth loss than the data warrant. I wrote about this back in 2005, when the subject of discussion was total premortem tooth loss in the Dmanisi skull D3444: “Caring for the edentulous”. My conclusions today don’t differ from then:

In the case of life history variation, I think that the survival of a small number of individuals under extraordinary circumstances says little about the habitual capabilities of a species.

A handful of Neandertals lived with fairly extensive loss of dental function, but that probably doesn’t tell us much about Neandertals that we do not already know about many primates.

What I really object to in the linked article is the way this topic is framed: This good thing about Neandertals “bizarrely suggests something negative about them.”

Often in human evolution, research is presented with a simple storyline that goes like this: “This bad thing everybody knows about, well, guess what—it’s actually good when you think about it from the evolutionary perspective.”

That’s the storyline of the sickle cell mutation. It causes disease, but it is an adaptation to malaria. It’s also the storyline of the “thrifty genotype” idea: Diabetes is bad, but its occurrence today may be a side effect of ancient adaptations to food scarcity.

That framing doesn’t erase the bad aspects of such biological traits, but it does give people a different way of thinking about why bad things happen. “Everything bad is actually good” is a fairly useful frame for teaching human evolution.

The opposite storyline is also pretty common. “That good thing that everybody knows about? Well, guess what—it’s actually bad when you think about it from the evolutionary perspective.”

This is how the invention of agriculture gets portrayed nowadays. Jared Diamond famously called it, “The worst mistake in the history of the human race.” The idea is that once upon a time, humans were adapted to a hunter-gatherer existence, and agricultural subsistence caused scores of bad unforeseen effects.

This “everything good is actually bad” storyline is especially common when it comes to studying Neandertals. For example, Neandertals seem to have eaten lots of meat. Does that mean they were successful hunters optimizing resources in a harsh environment? No, it means they failed to build knowledge of plant foods, putting them at extreme risk of extinction when times got tough.

Another example: Some Neandertal sites seem to have different assemblages of tools that may be suited to different functional tasks, for example some toolkits include many scrapers for preparing hides, while others lack such a dominance of scrapers. Is this evidence of clever and flexible Neandertals? No, to some archaeologists it was evidence that Neandertals must have behaved like herd animals, with women and children in some camps, and small groups of bachelor males in others.

My favorite essay on such stereotypes is by the archaeologist John Speth: “News Flash: Negative Evidence Convicts Neanderthals of Gross Mental Incompetence”. He humorously reviews a series of extravagant claims about what Neandertals couldn’t do, mostly tests that would fail when applied to some groups of modern humans.

Every so often, new evidence convincingly debunks one of these Neandertal stereotypes. For example, over the past ten years, a series of papers describing starches and phytoliths in Neandertal dental calculus have documented their use of plant resources, including cooking of some grains and the possible use of medicinal plants. In this case and many others, the press has reported the “surprising” conclusion that Neandertals were very much like modern human subsistence foragers.

Just once, I would like to see a journalist report such results as unsurprising evidence that past archaeologists were incompetent.

Now I don’t want to go overboard in the opposite direction. There probably really were some strange things about some Neandertals. Culture did evolve, and the evolutionary history of Neandertals probably yielded cultural abilities that humans lack, just as modern humans may have abilities that they lacked. In other words, I do not assume that they were merely modern humans with browridges.

But these are among the hardest ideas to test with archaeological evidence. At the same time, ideas about Neandertal cognitive difference align with persistent stereotypes about Neandertals. For that reason, I maintain an attitude of skepticism.

We know a good amount. Some of the cultural behaviors of recent and living modern humans have never been noted in Neandertal sites. But their tools, the traces of animals and plants that they ate, and their use of space show that Neandertal subsistence behavior had a lot in common with modern human subsistence foragers.

Many modern human subsistence foraging groups have left little or no evidence of “symbolic” artifacts, “complex site structure”, musical instruments, projectile weapons or similar trappings. We now know that Neandertals used pigments, engraved objects and rock surfaces, wore ornaments, made and used many kinds of bone tools, used shellfish, birds and small mammals—basically all things that past stereotypes held they didn’t do.

The point is, the difference between Neandertal and modern human behavior is clearly not a yawning chasm. They overlapped.

Studying Neandertal biological traits in combination with archaeology has a lot to offer to understanding their behavior. Dental pathology is a great avenue to understand how their health relates to their subsistence behavior. For example, Neandertals were once believed to have a much higher incidence of developmental dental pathologies than modern humans, traits like linear enamel hypoplasias that result from stress on the developing teeth from nutritional shortfalls or disease. It turns out that many modern human groups have just as high an incidence of such dental traits as Neandertals, including children from many agricultural groups.

Both Neandertals and prehistoric modern human subsistence foragers have vastly lower incidence of dental pathologies like caries when compared to most agricultural peoples, so it’s interesting to see that tooth loss was actually less among Neandertals than in the prehistoric modern human groups.

Better teeth may reflect the basic fact that Neandertals died faster than the Upper Paleolithic modern humans that followed them. By our best estimates (provided by Rachel Caspari and Sang-Hee Lee), Neandertal mortality was greater across the adult life span. Most known Neandertal dental remains come from relatively young adults, less than thirty or so years old.

Such high mortality probably does indicate something about Neandertal social relationships. Today’s human cultures owe much to the knowledge and experience of older adults, common in human societies. If those older adults were rarer, with some groups lacking older adults altogether, Neandertal cultures must have been poorer for it.

But adults in their twenties and thirties are not poor caregivers today. In fact, they are the primary caregivers toward both children and the most aged adults in our societies.

For that reason, I resist the framing that Neandertals good teeth may have meant they took less care of the sick. It may well have been true that sick Neandertals did not live as long, or have as good a chance of recovery. But I attribute that to the basic challenges of subsistence, not social incompetence.


Caspari, R., & Lee, S. H. (2004). Older age becomes common late in human evolution. Proceedings of the National Academy of Sciences of the United States of America, 101(30), 10895-10900. doi:10.1073/pnas.0402857101

Speth, J. (2004). News flash: negative evidence convicts Neanderthals of gross mental incompetence. World archaeology, 36(4), 519-526. doi:10.1080/0043824042000303692

National Geographic has a neat story by Michael Greshko about ancient footprints near Lake Natron, in Tanzania: “Treasure Trove of Ancient Human Footprints Found Near Volcano.

Local villager Kongo Sakkae found some of the footprints prior to 2006, but the site didn’t reach scientists’ attention until 2008, when Pennsylvania-based conservationist Jim Brett happened to be staying at the Lake Natron Tented Camp, just a few hundred yards from the footprints. Stunned by what he saw, Brett snapped as many pictures as he could and resolved to pass them along to a scientist he knew he could trust: Liutkus-Pierce, whom he had met when she was a postdoctoral researcher.
The trouble was, Brett picked the worst possible day to call.
“It was April Fool’s Day, I kid you not,” says Liutkus-Price. “He called me and said, ‘I think I have found some really cool hominid footprints.’ And I said, ‘Jim, can you call me tomorrow, so I know that this is not a joke?’”

The article gives a very nice account of the realization that these are fossil footprints, notes that they had been known to some local people earlier, discusses how collaborators were brought into the project, does not avoid mentioning a big problem with one of the researchers, and generally does a great job of showing how science is done.

Talking to the public is essential to the future of science

Susanna Martinez-Conde, Stephen Macknik and Devin Powell have a short article with advice for would-be science popularizers: “How Scientists Can Engage the Public without Risking Their Careers”.

Daniel Kahneman, who published Thinking, Fast and Slow nearly a decade after he won the Nobel Memorial Prize in Economics, went to almost heroic lengths to ensure that traditional academics would approve of his book. “It took me four years to write my book—four exceedingly miserable years because I was explicitly trying to do two things,” he says. “I wanted to write a popular book, without losing the respect of my colleagues. I paid a lot of money to have my book reviewed anonymously by young associate professors, four of them, I paid them two thousand dollars each, to tell me whether this would damage my reputation. And interestingly enough, it did damage my reputation among a subset of my colleagues.” Even so, Kahneman feels that the academic reaction to his book was by and large, very positive

I admire scientists like Kahneman who make the decision to reallocate their time toward public activities. By doing so, they advance the work of their colleagues and their field in general. His solution seems a little extreme, but I am glad to see how he values the referee work and the opinions of other scientific colleagues.

Interacting with the public is hard work. Being effective at public communication is a skill that scientists develop only through extensive practice, talking and writing honestly about the value of scientific work and its implications. Being an effective teacher is equally challenging, and while the skillsets do overlap, they are not identical.

I do a lot of public writing, blogging, documentary consulting, and filming. This work has made me a better scientist. I see the effects throughout my research. I make discoveries, and as much as possible, I get to take lots of other people with me. I don’t want to work any other way.

Most academics in my field have been totally supportive of the way I work. I do everything I can to promote the great work of friends and colleagues around the world. It’s always great to hear about connections made, and I’ve found so many friends in unexpected places.

I can’t deny that I’ve heard some criticism over the years. That kind of criticism is what stops many young scientists from even trying to engage outside their narrow subdiscipline. It’s entirely rational to keep your head down and stick to academic journal articles.

But honestly, most critical comments come from a small number of professionals who spend a lot of effort trying to become “academic celebrities” themselves. Some people assume that a certain degree of success in science will automatically cause people to listen to everything they say. The world doesn’t work that way, nor would anyone sensible want it to.

I’ve learned a lot from those interactions. I’m still finding out new ways to persuade people that our origins matter, to show them how our scientific work makes a difference.

Brief thoughts on Upper Paleolithic 'hybrids'

Science News has a long feature article by Bruce Bower that recounts the new wave of examining hybridization in human origins: “Animal hybrids may hold clues to Neandertal-human interbreeding”. He features the symposium at the AAPA meetings this spring organized by Rebecca Ackermann, which involved many scientists researching hybridization in primates and other mammals.

The big idea is that the biological consequences of hybridization are often recognizable in the skeleton. Fossil human populations may include individuals with ancestry from diverse populations, like Neandertals and Denisovans, much more genetically different than any living populations are. Paleontologists might use insights from hybridization in other mammals to understand which fossils show evidence of such population mixture. The big success story is the Oase 1 mandible, which has a high proportion of Neandertal ancestry:

Since the fossil’s discovery in 2002, paleoanthropologist Erik Trinkaus of Washington University in St. Louis has argued that it displays signs of Neandertal influence, including a wide jaw and large teeth that get bigger toward the back of the mouth. In other ways, such as a distinct chin and narrow, high-set nose, a skull later found in Oase Cave looks more like that of a late Stone Age human than a Neandertal.
Roughly 6 to 9 percent of DNA extracted from the Romanian jaw comes from Neandertals, the team found.
“That study gave me great happiness,” Ackermann says. Genetic evidence of hybridization finally appeared in a fossil that had already been proposed as an example of what happened when humans dallied with Neandertals.

Not only does the Oase mandible have a high fraction of Neandertal ancestry, roughly 3 times higher than any living people today, but also that Neandertal-like DNA occurs in large chunks, indicating a recent Neandertal ancestry. This individual may have had a Neandertal great-great grandparent.

Such a recent potential Neandertal ancestor means that the population mixture in this real-life case is not too far from what occurs in some natural and laboratory experiments on hybridization. The models from the present day have great relevance to this past case.

I will add, the Oase individual is not a singular case. Many early Upper Paleolithic skeletal remains from Europe have comparable evidence of anatomical features that are common in Neandertals but very rare or absent in other populations. David Frayer has documented many of these in detail, joined by other scientists, especially Milford Wolpoff.

It just happens that Oase 1 is the first specimen with ancient DNA evidence showing substantially elevated Neandertal ancestry beyond that observed in later populations. The ‘Ust-Ishim femur does not have more Neandertal ancestry than recent humans, and although the value for Kostenki 14 is high, it is not an outlier. Both those specimens have Neandertal DNA in relatively longer linkage tracts than today’s people, allowing us to see that mixture had preceded the birth of these individuals by only 10,000–15,000 years or so. But Oase 1 was nearly on the scene; where this individual lived, population mixture was probably still underway.

We know from ancient DNA evidence of later specimens. The earlier Upper Paleolithic populations had more genetic influence from Neandertals than populations from the Mesolithic and later. In part, this reduction of Neandertal ancestry reflects natural selection against functional parts of the Neandertal genome; in part it probably reflects repeated immigration into Europe of people from West Asia or other parts of the world. A pattern that appears in morphological traits, with Neandertal resemblance declining over time in European Upper Paleolithic and later populations, is paralleled by genetics.

Joe Simmons on psychology: “What I Want Our Field To Prioritize”.

I am writing all of this because it’s hard to resolve a conflict when you don’t know what the other side wants. I honestly don’t know what those who are resistant to change want, but at least now they know what I want. I want to be in a field that prioritizes replicability over everything else. Maybe those who are resistant to change believe this too, and their resistance is about the means (e.g., public criticism) rather than the ends. Or maybe they don’t believe this, and think that concerns about replicability should take a back seat to something else. It would be helpful for those who are resistant to change to articulate their position. What do you want our field to prioritize, and why?

Simmons gives an example of his past work being shown false by non-replication in a vast sample, and makes some important points. Probably most salient, description of methods should allow other researchers to build on results.

Lichens did not grow on Homo naledi

Earlier this summer, Francis Thackeray published a short paper in the South African Journal of Science suggesting that lichens had deposited manganese upon the surfaces of hominin bone from the Dinaledi Chamber. Knowing that lichens depend upon light for their growth, Thackeray suggested that the Dinaledi bones had once been exposed to light for long enough to explain the lichen growth and manganese deposition.

Thackeray proposed that the geological evidence was somehow wrong, and that the Dinaledi Chamber had once been open to the surface. He elaborated on this view in an essay written for The Conversation:

I strongly believe that there was possibly a temporary entrance into the chamber, in addition to the one used by explorers today. This temporary entrance may been covered up by a rock fall that also trapped the individuals whose bones were found some time later.

Our team, including geologists and geochemists, has now published a response to Thackeray. We review some of the ways that manganese and other trace elements from dolomitic limestone can be deposited on fossil bone, and present additional evidence from the bone surfaces that rules out lichen involvement.

The Dinaledi bones bear traces of manganese and iron oxides. Some of the staining is dendritic, with very tiny features that suggest microbial involvement. The deposition process happens within sediment, in the dark

Several of the hominin fossils have linear tide marks of manganese or iron oxides. These mark an interface of air and sediment in which these bones were embedded.

Tide marks on DH2
Detail of DH2 skull, showing tide marks of manganese and iron deposition on surface

Looking through a microscope, the bones bear many different patterns of mineral staining and calcite deposition. Some of the fossils have calcium carbonate deposition on top of manganese staining; others have manganese deposition on top of calcium carbonate. Some have successive encrustations of iron oxide, manganese, and iron oxide, as visible in this photo:

Iron oxide and manganese encrustation on Dinaledi bone
Figure 4F from Randolph-Quinney et al. 2016, showing manganese stain formed on surface of iron oxide staining, with additional iron oxide encrustation overlying the manganese.

Additionally, some fossils have manganese deposits that have been removed by gastropod activity; others have manganese formed on top of old gastropod markings. All of this evidence is consistent with a long history of manganese and iron oxide deposition on the fossils within their current sedimentary environment.

None of this geochemical activity requires light.

One of the things that we have kept at the forefront of our papers describing the Rising Star cave system is that we must not set aside or ignore any of the geological evidence.

The geological evidence from the Dinaledi Chamber shows that it was an isolated depositional environment during and after the bones of Homo naledi entered the chamber. The sediments with the bones of H. naledi are very different in their chemical composition and particle characteristics from the neighboring Dragon’s Back Chamber. Dragon’s Back sediments have some input of surface material, the Dinaledi Chamber doesn’t. With articulated skeletal parts, complete representation of skeletons, and abundant fragile juvenile material, the bones of Homo naledi reject the hypothesis that the Dinaledi deposit could be a secondary accumulation from some other source. This is all compatible with the ceiling of the chamber, which is a chert layer with at most small thin fissures and no substantial openings, except for the vertical crack called the “Chute”.

Although the bone has been within the Dinaledi Chamber, that doesn’t mean it has been static. There has been erosion of the deposit since it began to form, with sediment and other material exiting the chamber through floor drains and some of the hominin bone being reworked along with the chamber’s surface. Bone within the Dinaledi Chamber was modified by gastropods and other cave-dwelling organisms, and minerals were deposited on its surfaces. The surfaces of many bones have been etched by the slightly acidic groundwater. Within parts of the deposit that are mere centimeters apart, the chemical circumstances differ.

It’s a very complicated picture, and whenever we make a new observation we must integrate it into the entire body of evidence. That work continues. This summer, members of our team published a review of the team’s 3D data collection strategies, including some mapping data from the cave. And our original research article on the context of the fossil assemblage remains open access in eLife, with detailed maps and analyses.

From earlier this year: “Deliberate deposition and Homo naledi


Dirks, P. H., Berger, L. R., Roberts, E. M., Kramers, J. D., Hawks, J., Randolph-Quinney, P. S., ... & Schmid, P. (2015). Geological and taphonomic context for the new hominin species Homo naledi from the Dinaledi Chamber, South Africa. eLife, 4, e09561.

Dirks, P. H. G. M., Berger, L. R., Hawks, J., Randolph-Quinney, P. S., Backwell, L. R., & Roberts, E. M. (2016). Deliberate body disposal by hominins in the Dinaledi Chamber, Cradle of Humankind, South Africa?. Journal of human evolution 96: 149-153. doi:10.1016/j.jhevol.2016.04.007

Kruger, A., Randolph-Quinney, P. S., & Elliott, M. (2016). Multimodal spatial mapping and visualisation of Dinaledi Chamber and Rising Star Cave. South African Journal of Science, 112(5/6) doi:10.17159/sajs.2016/20160032

Randolph-Quinney, P. S., L. R. Backwell, L. R. Berger, J. Hawks, P. H. G. M Dirks, E. M. Roberts, G. Nhauro, J. Kramers. 2016. Response to Thackeray (2016) – The possibility of lichen growth on bones of Homo naledi: Were they exposed to light? South African Journal of Science doi:10.17159/sajs.2016/a0177

Thackeray, J. F. (2016). The possibility of lichen growth on bones of Homo naledi: Were they exposed to light?: scientific correspondence. South African Journal of Science, 112(7-8), 1-5. doi:10.17159/sajs.2016/a0167

Val, A. (2016). Deliberate body disposal by hominins in the Dinaledi Chamber, Cradle of Humankind, South Africa? Journal of Human Evolution 96: 145-148. doi:10.1016/j.jhevol.2016.02.004

A Neandertal “burial ritual” at Des-Cubierta Cave? “Cave fires and rhino skull used in Neanderthal burial rituals”.

The blackened hearths surround a spot where the jaw and six teeth of a Neanderthal toddler were found in the stony sediment. Puzzlingly, within each of these hearths was the horn or antler of a herbivore, apparently carefully placed there. In total, there were 30 horns from aurochs and bison as well as red deer antlers, and a rhino skull nearby.
Archaeologists believe the fires may have been lit as some sort of funeral ritual around where the toddler, known as the Lozoya Child, was placed around 38,000 to 42,000 years ago.

If that description is accurate, it is hard to imagine this behavior outside of a symbolic culture. This is more than simple mortuary deposition, it requires the construction of an elaborate and consistent series of associations with arbitrary objects.

Ewen Callaway reports on a talk at the European Society for Human Evolution meeting, presenting new human teeth from the ongoing Liang Bua archaeological work: “Human remains found in hobbit cave”. The story is that these remains may document some of the earliest modern human presence in the cave, postdating the last occurrence of H. floresiensis and extinct mammalian fauna. But I am always skeptical about the idea we can clearly diagnose the taxonomic status of unknown hominins from a couple of teeth.

María Martinón-Torres, a palaeoanthropologist at University College London who attended the talk, thinks that the lower molar looks like those of H. sapiens, whereas the premolar seems a bit more primitive. To prove conclusively that the teeth are human, she would like to see comparisons with a wide range of remains from H. sapiens and also from H. erectus (which might have survived in Indonesia until around 50,000 years ago). “I think they have quite a tough job. There are lot of factors to take into account,” she says.

It’s very encouraging that the cave still holds much more evidence to uncover, and I’m sure we’ll hear more as the work progresses.