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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Dental chipping in Homo naledi. Ian Towle and colleagues

Can methylation of DNA in ancient bones really predict the morphology of Denisovans?

Last week, Cell published a new paper by David Gokhman and coworkers that tries to infer the skeletal form of Denisovans from signatures of methylation in the Denisovan genome data. The paper is here: “Reconstructing Denisovan Anatomy Using DNA Methylation Maps”.

I’m a skeptic about the paper. The authors follow an approach that has not been shown to predict the morphology of any living humans or any other species.

The study tries to justify its method by looking at Neanderthal methylation and saying that the methylation pattern can accurately predict Neanderthal bone shapes. This may look convincing on the surface. But it’s actually not. This is a case where “researcher degrees of freedom” are very high.

I am working on a comment to submit to Cell about the study, focusing on some technical issues. I hope that the editors will be interested in publishing a critical exchange on the approach.

In the meantime, I want to point readers to a related study by another group of researchers that has been mostly ignored in the press coverage on this new paper.

Genevieve Housman and coworkers released a preprint earlier this year on biorXiv that looked at methylation patterns in several primate species (chimpanzees, macaques, vervet monkeys, baboons, and marmosets) to see if methylation could predict skeletal morphology within species or between species.

The preprint is here: “Intra- and Inter-Specific Investigations of Skeletal DNA Methylation and Femur Morphology in Primates”.

Housman and coworkers carried out a careful study that includes several analyses that are not in the new Cell paper by Gokhman and colleagues. Housman and coworkers measured DNA methylation in bone cells taken from the femur of each primate individual, and they actually took caliper measurements on the femur of each individual. This means that in every case they compared like with like. That’s different from what Gokhman and colleagues could do with ancient DNA, where the samples are coming from different parts of the skeleton from a mixture of different cell types.

Housman and coworkers found some methylation differences that seemed to associate with morphology in their samples. But these were small effects that they could not separate from other possible influences (genetic and environmental differences). I would add that the small sample sizes in the study (only 4 chimpanzees, for example) make it possible that the observed effects might be spurious effects of small samples.

When they looked between species, Housman and colleagues found differences in methylation, similar to Gokhman and coworkers in this new study. Some of those differences in methylation are near genes that matter to skeletal form. Gokhman and coworkers found the same thing for Denisovans and Neanderthals. But in the living primates, the methylation differences actually did not correlate well to the phylogenetic relationships of the primate species. While Housman and coworkers suggest that the methylation differences between species might make some difference to the evolution of their traits, they did not try to predict what those differences were. That’s very reasonable considering the lack of clear signatures within species and the small proportion of the genome included in these regions with different methylation.

What I think: Studying methylation differences is a promising avenue of research, but we are a long way from understanding how differences in methylation may relate to differences in the skeleton. It is important to match like with like – in the Housman study, the methylation of femur bone cells was used to study femur form.

It’s not outlandish to think that the pattern of methylation across promoters in the genome might give a clue about morphology. But there are huge gaps in our knowledge. And there are things we know about methylation in bone that this study doesn’t seem to represent. Those make me skeptical that this study is doing much more than presenting an interesting hypothesis.

I’ve seen a number of geneticists quoted in news stories, saying that now paleoanthropologists will have to test what methylation has told us about Denisovan morphology. That’s only partly correct. A test with paleontology cannot be valid until comparative evidence supports the proposed mechanism connecting differential methylation to morphology—remember, based here upon indirect functional inference for only 2.2 genes per trait.

But if we’re looking for a paleontological test, the Xiahe mandible may already provide one. Gokhman and coworkers predict that the Denisovan dental arch should be longer than modern humans and also longer than Neandertals. The Xiahe mandible, with its complete M3 agenesis, does not have a long dental arch.

When peer review turns to trolling

In University Affairs, environmental scientist Ryan Bullock looks at his career-worth of experience subjecting his research to peer review: “The trolls have infested academic peer review”.

It’s a worthwhile perspective and many scientists will recognize their own experiences.

After much consideration, I believe that current peer-review processes often do the opposite of what they are supposed to achieve. That is, the double-blind system provides no assurance to me – and, by extension, the readers – that reviewers are qualified professionals. The blind review process can reduce accountability, leading to poor-quality service work, which reviewers can no doubt still count on in their annual evaluations without having properly served their journal, their discipline or their colleagues. The blinded format can encourage boorish and unethical behaviour. To top it off, troll reviews waste an incredible amount of professional time and energy of authors, editors and colleagues who reviewed earlier drafts.

I agree that the system of anonymity is harmful. I sign my reviews for journals that permit it. I think that an open system would be much fairer to authors and referees. I also think openness would do much to reduce the overhyping of research articles upon their release.

Big data approaches to scientific career success

Undark recently published an article by Viviane Callier, looking at recent research on scientific career trajectories: “What Matters Most on the Road to Scientific Success?”.

For many people, the most salient (and potentially troubling) findings coming out of this research are that publication in “prestige” journals is transmitted through training networks, from supervisors to trainees. That, and there’s a selection effect at work:

“The prestige of your doctorate does matter insofar as it helps you get a more prestigious job,” Larremore explained. “But what we’ve found is, once you’re in the door to a faculty job, the training then doesn’t matter.” In other words, once in the same department, the productivity of faculty members who trained at more prestigious universities was indistinguishable from that of their colleagues who trained at less prestigious universities.

Relevant to me:

<blockquote.They also found that scientists were more likely to succeed if they trained with graduate and postdoctoral mentors with disparate expertise that they could incorporate into their own work.</blockquote>

David said he suspects that building connections that had not previously existed might be key to success. “There’s an intellectual space that hasn’t really been occupied before,” he said. “And if you can draw on two different areas of expertise and take something that’s kind of unique to each of them and bring them together into a problem of your own, then you can stake out some territory that hasn’t been explored before.”

Most successful scientists today will work in teams. Moving between teams seamlessly is very important to anyone who wants to continue to do exciting, cutting-edge work.

Stopping 'wasteful recollection of data already held by other research groups'

Last week I commented on the American Association of Physical Anthropologists’ recent statement on access to data: “Biological Anthropology association speaks out on data access”.

This is a big issue to which many voices have contributed. I’d like to bring attention to a broader selection of those views—not just the loudest or most widely read.

Three years ago, Lynn Copes and coworkers published a Scientific Data descriptive paper for a dataset of CT scans of non-human primate skeletal material. The paper is open access: “A collection of non-human primate computed tomography scans housed in MorphoSource, a repository for 3D data.”

The sample consists of 489 scans taken from 431 specimens, representing 59 species of most Primate families. These data have transformative reuse potential as such datasets are necessary for conducting high power research into primate evolution, but require significant time and funding to collect. Similar datasets were previously only available to select research groups across the world.

This has been a groundbreaking data release, providing an irreplaceable source of data not only for comparative analyses with other primate collections but also for education. The Harvard Museum of Comparative Zoology, which houses the primate material in the study, is to be congratulated for its forward thinking.

In the Scientific Data paper, Copes and colleagues commented on the overall situation with data access in biological anthropology. One paragraph is especially worth sharing:

Despite this rush to digitize, comparative morphology is experiencing a crisis as a mode of addressing large-scale evolutionary questions due to the difficulty involved in accruing datasets large enough to have high explanatory power, and the small community of researchers that can participate effectively. This presents a paradox: If so many researchers are putting large efforts into scanning, where are the massive samples? Though a few research groups have managed to generate large samples of scans comprehensively representing diversity in one clade or another, this work has been time consuming, and expensive: as a result these scans are not made widely accessible to non-collaborating researchers. This inequality in access to what is now essential, basic data clearly falls short of scientific ideals for meritocracy. Furthermore, a significant component of the unmanageable demand for 3D scan data experienced by museums may represent wasteful recollection of data already held by other research groups.

We are in an age where scientists must recognize the risk of destruction, damage, and loss of physical specimens held by museums around the world. Creating high-fidelity digital models of the physical objects and distributing those models widely is increasingly essential as a strategy for protecting objects with scientific and heritage value.

Of course researchers cannot answer every possible question from a digital model. But even for questions that must be addressed from original specimens, providing high-resolution digital data is essential for future researchers to see the details of analyses and use them as comparative data for analysis of other objects.

Natural areas going to the dogs

Human presence has changed the natural environment in many ways. One of the most important is the spread of species that do well in the presence of humans, many of which we tolerate and tacitly (or explicitly) encourage. Like Canis familiaris.

Last week, the Washington Post ran a short article describing research into the destructiveness of feral dogs in Brazil’s national parks and other natural areas: “The dog is one of the world’s most destructive mammals. Brazil proves it.”

It was found that the closer humans lived to a nature preserve, the more likely dogs had penetrated it.
But perhaps most striking? The dogs were neither feral nor domestic — but somewhere in between.
“All the dogs we detected had an ‘owner’ or a person that the animal has a bond with,” Paschoal said. “The species population increases following human populations, exacerbating their potential impact on wildlife.”

This is why many farms have dogs, to deter or kill small carnivores and other animals that would otherwise damage crops or kill small domesticates (especially chickens and other fowl). In communities where neutering and spaying are not practiced, large semi-feral dog populations often exist at the edges of human societies. They can rely upon discarded human foods during times when wild foods are scarce, which gives them a buffer that wild predators lack.

This process must have been important in the prehistoric past also. It may have contributed to a certain brittleness of human societies in the face of environmental change, since dogs would have reduced small herbivore biodiversity in the areas of human settlement, with longer-term consequences for forest and grassland plant community composition.

Looking at the importance of art in astronomical sciences

I’d like to point to a recent article from Undark by writer Mara Johnson-Groh, looking at the way that artistic visualization methods have been important to astronomy in recent years: “Sketching the Stars: How Art Can Advance Astronomy”

The article profiles several real-world examples where scientists have applied art techniques to build a better means of visualizing and understanding large astronomical datasets. This one was trippy:

With the aid of a specialized loom, they have also created woven installations nearly the size of a van that visualize the interconnectivity of the cosmic web. “We believe that art, as much as science, seeks to say something true about the nature of existence,” they wrote in a 2017 paper on their collaboration, “and that end is best served by artistic representation that grapples with real data and not only with allegorical concepts.”

The bottom line of the article is encompassed in the last paragraph:

“Applying the techniques from art definitely influences the way astronomers see and interact with their data,” English said. “I don’t think [techniques from art] in astronomy visualization can be relegated to a sidebar any longer. It really does enhance discovery science.”

Human genetics is always a step or two behind astronomy in terms of data processing and visualization. I see a lot of promise over the next few years in developing new ways of visualizing and understanding genetic datasets from humans and other creatures.

A story of Australian repatriation

The September issue of Smithsonian magazine has a feature article by Tony Perrottet recounting the burial ceremony for the “Mungo Man” skeleton, which happened in late 2017. The article includes perspectives from Aboriginal people, scientists, and museum professionals, and gives an idea of the scope of the repatriation issue in Australia. I will be looking at assigning this for my courses: “A 42,000-Year-Old Man Finally Goes Home”.

The article tells many stories that are part of the broader issue of repatriation. One section recounts a visit to the Repatriation Program of the National Museum of Australia, with director Michael Pickering. In this passage, he recounts the problems of inadequate curation of Aboriginal (and other) skeletal material in the past:

“We had 3,000 individuals, all indigenous, in the ’80s,” Pickering marveled. “Rooms full of bones.” Locating the Aboriginal communities to return them to involved serious detective work. Many of the skeletons were mixed up, their labels faded or eaten by silverfish, and their origins were only traced through century-old correspondence and fading ledgers.
The unit’s centerpiece is a table where skeletons are laid out for tribal elders, who wrap the remains in kangaroo skin or wafer-thin paperbark to take back to Country. But not all of them want to handle the remains, Pickering said, often asking staff to do it instead. “It can be a harrowing experience for the elders,” says heritage officer Robert Kelly, who has worked in repatriation since 2003. “To see the skulls of their ancestors with serial numbers written on them, holes drilled for DNA tests, wires that were used for display mounts. They break down. They start crying when they see these things.”

Later in the article, there are two paragraphs juxtaposed back-to-back with each other that express a deep contrast in views of the past. I cannot share the article without commenting on them.

Just as revolutionary was what Mungo Man meant for the understanding of Aboriginal culture. “Up until Mungo, Aboriginals had been frequently denigrated,” Bowler said bluntly. “They were ignorant savages, treacherous. Suddenly here was a new indication of extraordinary sophistication.” The reverent treatment of the body—the oldest ritual burial site ever found—revealed a concern for the afterlife eons before the Egyptian pyramids. Two of Mungo Man’s canine teeth, in the lower jaw, were also missing, possibly the result of an adolescent initiation ceremony, and there were the remains of a circular fireplace found nearby. “It took me a long time to digest the implications,” Bowler said. Today, Aboriginal people still use smoke to cleanse the dead. “It’s the same ritual, and there it was 40,000 years ago.” All the evidence pointed to a spectacular conclusion: Aboriginal people belong to the oldest continuous culture on the planet.
News of Mungo Man’s discovery, presented as a triumph by scientists, provoked outrage in the Aboriginal communities; they were furious that they had not been consulted about their ancestor’s removal from his homeland. “I read about it in the newspaper like everybody else,” recalls Mary Pappin, a Mutthi Mutthi elder. “We were really upset.” The first quiet protests over archaeological work had begun years earlier over Mungo Lady, led by her mother, Alice Kelly, who would turn up with other women at new digs and demand an explanation, carrying a dictionary so she could understand the jargon. “My mum wrote letters,” recalls her daughter. “So many letters!” Removing Mungo Man seemed the height of scientific arrogance. Tensions reached such a point by the end of the 1970s that the 3TTs placed an embargo on excavation at Lake Mungo.

I work to build a better scientific understanding of the past. When we look at past people, we often come to understand their inventiveness and creativity, the depth of their cultures, and the way they overcame challenges. Building a richer picture of ancient people can be inspiring.

But the first paragraph here illustrates a self-serving narrative by archaeologists. “Suddenly here was a new indication of extraordinary sophistication.” The notion suggests that we should recognize the past achievements of ancient people as a reason for respecting their descendants today. That’s wrong. It’s backwards.

Treating living people with respect does not require understanding their ancestors. Treating living people with respect is basic humanity. It is wrong for archaeologists (and geneticists and other scientists) to work without effective consultation with communities of descendants and relatives.

In fact, there was nothing “sudden” about the shift in archaeological practice. The stories told before the 1970s were created by colonial Europeans—including archaeologists and anthropologists—to control and subjugate Aboriginal people.

The Mungo archaeological work began at a time when colonial assumptions were newly questioned within archaeology, by a generation of researchers coming of age during the 1960s and 1970s. The interpretation of the Mungo discoveries incorporated ethnographic insights in ways that were rare in earlier archaeological work, part of a shift in archaeological practice globally. The work was important scientifically, it led to new ways of looking at the past. That much is true.

But the work itself still reflected colonial practices and structures. Archaeology might have been shifting its interpretations of past peoples, but it hadn’t yet found its way to full respect of descendant communities in conceiving and carrying out the work.

Archaeological discoveries about ancient Aboriginal people are fascinating. I hope that such discoveries will continue, because they bring a perspective on the development and history of human societies not only within Australia but as a comparison for many other parts of the world.

But discoveries cannot continue without the participation and engagement of local and descendant communities. Science developed without such participation is bad science—ethically wrong, and almost certainly factually wrong.

Self-citation quantified

I always feel a little bit bad when I have to cite my own prior work for a new research paper. As scientists develop career trajectories, self-citation becomes inevitable. Early work often becomes a foundation for later work. The point of citation is to credit the work that allows you to advance; we track citations so that we can see more clearly which research efforts have led to further advances.

And so, most successful scientists will often cite their own earlier work. The more entrenched an individual’s research trajectory becomes, the higher ratio of self-citation to citation of other research will be.

A new study in PLoS Biology by John Ioannidis and coworkers develops a citation metrics author database that facilitates seeing which authors cite themselves the most often: “A standardized citation metrics author database annotated for scientific field”.

Nature comments on the study, focusing on the issue of self-citation: “Hundreds of extreme self-citing scientists revealed in new database”

The data set, which lists around 100,000 researchers, shows that at least 250 scientists have amassed more than 50% of their citations from themselves or their co-authors, while the median self-citation rate is 12.7%.
...
The data are by far the largest collection of self-citation metrics ever published. And they arrive at a time when funding agencies, journals and others are focusing more on the potential problems caused by excessive self-citation. In July, the Committee on Publication Ethics (COPE), a publisher-advisory body in London, highlighted extreme self-citation as one of the main forms of citation manipulation. This issue fits into broader concerns about an over-reliance on citation metrics for making decisions about hiring, promotions and research funding.
“When we link professional advancement and pay attention too strongly to citation-based metrics, we incentivize self-citation,” says psychologist Sanjay Srivastava at the University of Oregon in Eugene.

When it comes to judging the impact of individual scientists, people are very sensitive to possible ways of “cheating the system”, and self-citation is widely perceived to be one of those ways. But actually Ioannidis and coworkers find that separating self-citation from total citation counts doesn’t change much when it comes to highly-cited researchers. There are some outliers, but they are focused in particular countries, fields, and institutions.

Another aspect of Ioannidis and colleagues’ study is quantifying the citation practices in different fields of study. Anthropology as a field is not separated out in their table, but social sciences generally have low citation numbers—less than half the numbers of biology or clinical sciences. The 90th percentile for total citations in the social sciences is 423, meaning that only 10% of researchers have career citation totals of more than that.

As a result, methods of judging scientific output that rely upon citation counts tend to underestimate the impact of social scientists. Most kinds of scientific assessment look within fields rather than across them, but in some of the cross-disciplinary organizations (like national academies) social scientists are under-represented compared to their impact in ways other than citations.

Laser surface scan accuracy tested

This is encouraging for those of us who rely upon 3D surface data collected with laser scanners: “Dimensional accuracy and repeatability of the NextEngine laser scanner for use in osteology and forensic anthropology”.

Second, as an application to osteology we examined intra-observer scanning protocol variability, using the coefficient of variation (CV) to quantify surface area and volume variance between repeated scans of eight porcine capital femoral epiphyses with undulating mammillary processes on one surface with amplitudes covering the range of the test block bas-relief offset values. The CoR showed each test-retest measurement from each instrument differed by no more than their CoR: 0.010 mm, 0.137 mm, 0.068 mm, 0.193 mm for the VHX, NE, HP and CMM, respectively. There was agreement between the instruments, but each instrument (NE, HP and CMM) overestimated bas-relief features as reported by the VHX, on average (bias) by 0.046 ± 0.038 mm, 0.025 ± 0.033 mm, 0.026 ± 0.033 mm for the NE, HP and CMM, respectively. Both scanners captured surface features as small as 0.1 m

Porcine capital femoral epiphyses – that’s a pretty great test of some of the small bone fragments that we study in the fossil record. Errors of less than 0.1 mm are less than I would have expected.

The research is by Ronald Perrone, Jr. and John L. Williams in Journal of Archaeological Science: Reports.

Quote: Sherwood Washburn on intellectual traditions in human origins

Sherwood Washburn was a prominent biological anthropologist of the mid-twentieth century, best known as the architect of the “New Physical Anthropology” movement to bring population thinking and primate behavioral ecology into the study of human origins. In the early 1950s, he became involved in an exchange of views about the import of the Piltdown hoax on thinking about modern human origins. The following paragraphs are from a 1954 commentary in American Anthropologist: “An old theory is supported by new evidence and new methods”.

Just before this passage, Washburn details that “There have been two major theories concerning the origin of men anatomically like ourselves” – one theory positing a very recent appearance of modern people during the last glaciation, and a second theory positing a very ancient appearance of modern people and their long coexistence with Neanderthals and other extinct forms.

The Piltdown specimen was a primary buttress for the idea of a long existence of modern humans. When the hoax was revealed, other supposed evidence for the existence of modern humans at a very early time was subject to doubt, and the antiquity of skeletal remains like the Galley Hill material was shown to be erroneous.

Washburn comments on the intellectual traditions that guided various scientists’ reactions to the Piltdown evidence:

Since 1946 events have moved so rapidly that everyone is readjusting and what one said even a few years ago may be quite different from present belief. But it is necessary to look at the past a little more to understand subsequent events. I have mentioned Weidenreich and Hooton, not in the spirit of praise or blame, but as representatives of different traditions. In general, the Germans never accepted early Homo sapiens or Piltdown. The English accepted early sapiens, and the Americans have followed the English tradition. One might put the matter this way: apparently it was as hard for a German to believe in early Homo sapiens as it was for an Englishman to be a skeptic. Hrdlička followed the German tradition. I am no intellectual historian and make no pretense of having read the vast literature on fossil man, but the influence of the intellectual tradition on the interpretation of human fossils is so great that the record makes little sense without considering it. As a part of these traditions, we all have built-in preconceived notions. Was it dogmatic for Weidenreich to accept the result of Friederich’s study, showing that the Piltdown jaw was that of an ape? Or was it dogmatic for Hooton to reject this conclusion? Each acted in accord with previous belief and in accord with the tradition to which he belonged. Both were right. The jaw was that of an ape, but it was impossible that such a jaw should be associated with a sapiens skull by chance. Both were wrong in that neither saw the possibility of a fake as the explanation.
It is easy to refer to the other person’s guesses as preconceived and dogmatic, but from the point of view of the developing science of human evolution the essential point is that progress comes when the area open for personal debate is narrowed. The development of chemical dating methods makes it possible to settle some of the problems which up to now have been matters of personal opinion. Frequently human bones have been found under circumstances in which there is real doubt about their associations and the more such problems can be settled by methods which are independent of intellectual traditions the more rapidly our understanding of human evolution will progress.

In textbooks and popular accounts of the history of paleoanthropology, Piltdown takes a very prominent place.

These popular accounts usually elide other supposed evidence of the great antiquity of modern humans in Europe, like the Galley Hill and Fontéchevade fossil remains, or the contribution of Louis Leakey’s Kanam and Kanjera discoveries in Africa.

A complicated story with various forms of incomplete evidence and competing intellectual traditions is harder to tell than a simple story of a hoax. But the complicated story provides a better model for understanding the ways that fossil and archaeological evidence can contribute to long-lasting scientific debates.

UPDATE (2019-08-22): It strikes me upon re-reading that Washburn is not very fair here to Gerrit Smith Miller, the American who concluded that the jaw and skull of the Piltdown “specimen” could not represent a single species. Miller also didn’t get it right, but he certainly didn’t “follow the English tradition”.

I wrote previously about the doubters: “Lessons of Piltdown doubters”.

Skeletons from the Himalayan lake

Yesterday a fascinating story came out in Nature Communications about the skeletons of Roopkund Lake, in northern India: “Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India”. The research was authored by Éadaoin Harney and coworkers. Some background about the site is provided by the introduction of the study:

Roopkund Lake is a small body of water (~40 m in diameter) that is colloquially referred to as Skeleton Lake due to the remains of several hundred ancient humans scattered around its shores (Fig. 1). Little is known about the origin of these skeletons, as they have never been subjected to systematic anthropological or archaeological scrutiny, in part due to the disturbed nature of the site, which is frequently affected by rockslides, and which is often visited by local pilgrims and hikers who have manipulated the skeletons and removed many of the artifacts.

The Atlantic has a nice article by Rachel Gutman that reviews the research: “The Mystery of ‘Skeleton Lake’ Gets Deeper”.

Since a forest ranger stumbled across the ghostly scene during World War II, explanations for why hundreds of people died there have abounded. These unfortunates were invading Japanese soldiers; they were an Indian army returning from war; they were a king and his party of dancers, struck down by a righteous deity. A few years ago, a group of archaeologists suggested, after inspecting the bones and dating the carbon within, that the dead were travelers caught in a lethal hailstorm around the ninth century.

It turns out that the skeletons accumulated over at least three different episodes, and they reflect entirely different groups of people, one from as far away as the Eastern Mediterranean. This deepens the historical mystery: how did groups of people from three different places and times end up dead in this one place?

What I really like about the study is the multidisciplinary approach relying upon ancient DNA, stable isotopes, and radiocarbon to develop lines of evidence about the origin of the individuals. I wish that these had been combined with a deeper analysis of the skeletal biology of the individuals, including what can be said about their anatomical features, age, sex, and health status.

The study does include some information from a report on the physical anthropology of the skeletons, placed into a supplementary note (Supplementary Note 2). The note explains the connection between the work and a National Geographic documentary that was produced in 2004.

The following section is an edited version of an unpublished report generated before genetic data were available by co-author Prof. Subhash Walimbe. The goal of our edits is to synthesize the anthropological discussions included in that report with the genetic findings. Newly added statements dealing directly with the genetic results are shown in italics. Some of the content of the original reports was used as part of the script of a National Geographic television documentary that was made describing the Roopkund Lake Site, so there are similarities between parts of the text that follows and that script.

One reason why I’m interested in the skeletal information is that this case raises important questions about archaeological sites more broadly. Here’s a case where the context of the skeletal remains led scientists naturally to assume that they represented a single event or group. Now we know that the remains come from different groups who lived more than a thousand years apart, and some of whom came from very far away.

As scientists, we’re conditioned to assume that such coincidences don’t happen. Skeletal remains in one place with an ostensibly similar depositional situation should represent similar individuals. Yet more and more sites are revealing two situations that challenge the usual assumptions:

  1. Cemetery distributions that actually represent diverse people who have migrated to a single location, integrating (to varied extents) into a single society.

  2. Multiple depositional situations that occur within the same landscape or space, sometimes guided by geographic or geological conditions, but representing entirely different groups of people.

The first situation has become a widespread subject in stable isotope biology, as strontium and other stable isotopes have revealed individuals who originated far from the cemeteries where they ended up. The second situation is also being revealed more and more by technology as skeletal remains and genetic data show big differences between individuals from single archaeological sites. The recent analysis of the skulls from Apidima—one very Neanderthal-like in morphology, the other much more modern in what is preserved—is a great example of this.

Coincidences of body deposition from different times and cultures are cropping up. With a large enough record, of course, coincidences are inevitable. But my feeling is that they are turning out to be more common than we have assumed, and that means we need to apply extra critical analysis to many archaeological sites.

So a close study of the skeletal biology is very much in order. The supplementary note mentions a difference in “robusticity” among the skulls. Quantifying whether this actually reflects the population differences in the genetics, whether there are health differences that might have been noticed between groups, and whether there are other clues of different populations would be very worthwhile.

Because other cases are out there, and we’ve likely missed them by assuming that bodies found together must sample variation within a single group.

One more note on this study: This analysis included DNA sampling of 71 individuals, 35 based on whole-genome approaches. This is a huge study in terms of the history of ancient DNA analysis, but today it is a moderate sample size for an analysis of new data. We’ve come to the point where dozens of samples of genome-wide data are within the bounds of a single paper in a speciality journal, to answer a fairly specialized historical question. That’s a great thing from the standpoint of replicability of studies and building a more powerful understanding of the past. But it’s a concern if this is a standard that other studies of the past will be forced to meet. It is not always appropriate to require such large sample sizes, even if a skeletal sample numbers that many individuals.

In this case, the sample size of skeletal material was large, the skeletons themselves are in an unsecured situation where they are subject to looting, and the connection to possible descendant communities was previously unknown. It would be valuable to use this paper for a case study of how confident we can be of conclusions at varied sample sizes—-possibly in combination with deeper skeletal analyses.

Quote: Loren Eiseley on Neanderthal hybridization

Loren Eiseley was an anthropologist well known in the mid-twentieth century for his popular writing about human evolution and science more generally.

In the Winter 1946 issue of Prairie Schooner, Eiseley had an essay recounting the discoveries of the Skhūl and Tabun fossil material from Mount Carmel, Israel. In 1939, Theodore McCown and Arthur Keith had published their analysis of the fossil remains, suggesting a population in the “throes of evolution” with characters of both modern humans and Neanderthals. They rejected an alternative hypothesis, that the skeletons might reflect hybridization between two anatomically divergent populations, but this hypothesis was later taken up by other authors including the geneticist Theodosius Dobzhansky.

Eiseley’s discussion of the situation is worth reading in full as a picture of its time. I wanted to share some paragraphs as examples of his use of language and his standing as a contemporary observer of a moment in science when hybridization was seen as an important topic in human evolution.

Another explanation inevitably comes to mind as we survey this assemblage of beings who dwelt on the slopes of Mount Carmel---an explanation which, though intriguing in its own right, would illuminate but little the origins of that creature in which we are intensely interested, namely, ourselves. Can it be---so runs the little disturbing thought which will not be quieted---can it be that we are dealing with a group of mixed bloods, of hybrids between Neanderthal and a type already essentially modern?

Lest anyone think that it was silly for Eiseley to describe the idea of hybridization as “a disturbing thought”: Even well into the 1990s some serious professional anthropologists were still claiming that hybridization was unlikely or impossible because these ancient populations would have been disgusted at the thought of mating with each other. Scientists carried with them an intense bias from their own social experiences and preferences, and they were unapologetic about playing upon the biases of others in their popular writings.

Eiseley ends his essay with a paragraph that could be a nice example of the “jury is out” statements at the end of many popular science articles.

The fault does not lie in this unique and invaluable discovery which, among other things, has demonstrated that an essentially modern brain and facial structure already existed in the Riss-Wurm Interglacial. It lies in our inadequate knowledge of human genetics and the processes which influence or determine the rapidity of human evolution. Only as our knowledge of the Ice Age population of Palestine increases and the science of genetics grows more sure will the vistas of human prehistory opened by the sleepers in the cave of Mugharet es Skhul be capable of interpretation by modern eyes.

Epstein's science posse

I have been following the story of the late Jeffrey Epstein very closely. The combination of politics and money for this billionaire alleged child sex trafficker continues to command huge press and public attention. I have been appalled by the sheer number of prominent scientists and intellectuals who have been revealed to be on Epstein’s private plane flight logs, or guests of his salons privées, or grantees of his various charitable foundations.

The Observer has an article by Luke Darby that looks at this aspect of the Epstein story: “Private jets, parties and eugenics: Jeffrey Epstein’s bizarre world of scientists”.

Lawrence Krauss, a physicist who retired from Arizona State University, even continued defending Epstein after his 2008 conviction, telling the Daily Beast in 2011: “As a scientist I always judge things on empirical evidence and he always has women ages 19 to 23 around him, but I’ve never seen anything else, so as a scientist, my presumption is that whatever the problems were I would believe him over other people.” He added, “I don’t feel tarnished in any way by my relationship with Jeffrey; I feel raised by it.”
Other scientists seem to have been drawn to the attention and spotlight that Epstein gave them. Evolutionary biologist George Church, one of the few researchers who has apologized for having contact with Epstein, which he attributes to “nerd tunnel vision”, told STAT News that “he is used to financiers, technologists, and celebrities seeking him out, and has become a quasi-celebrity himself”.

A year ago, I was in a discussion with a number of prominent science journalists about how universities monitor conflicts of interest. One thing that they emphasized was the vulnerability of the enterprise of science to the appearance of being bought by moneyed interests. There is no shortage of people and companies looking to buy credibility.

In the case of Epstein, it seems clear that one reason he paid the bills for various scientists is to buy himself social respectability in a certain circle. The list of scientists willing to sell themselves for this purpose is depressing.

Supplementary data loss

My inbox this morning has an article by Diana Kwon in The Scientist, looking into the data decay from the supplementary materials of published scientific articles: “The Push to Replace Journal Supplements with Repositories”.

The story leads with Vaughn Cooper, an evolutionary biologist who published a recent paper on a secondary school biology curriculum in the journal Evolution: Education and Outreach. Readers quickly discovered that the supplementary files were inaccessible.

Supplementary information for journal articles is a bad idea. It has always been a bad idea. Journals at the dawn of the World Wide Web, faced with the opportunity to publish infinite pages at low cost, chose instead to create proprietary non-edited slush piles for methods and analyses totally separate from the standard distribution format of their articles. It’s a near-miracle twenty years later that any supplementary information can still be read by today’s software.

Instead of becoming standardized rich media for data distribution, supplements became a bloated morgue where Excel spreadsheets go to die.

But it’s not just broken hyperlinks that frustrate scientists. As papers get more data-intensive and complex, supplementary files often become many times longer than the manuscript itself—in some extreme cases, ballooning to more than 100 pages. Because these files are typically published as PDFs, they can be a pain to navigate, so even if they are available, the information within them can get overlooked. “Most supplementary materials are just one big block and not very useful,” Cooper says.
Another issue is that these files are home to most of a study’s published data, and “you can’t extract data from PDFs except using complex software—and it’s a slow process that has errors,” Murray-Rust tells The Scientist. “This data is often deposited as a token of depositing data, rather than people actually wanting to reuse it.”

That is a super phrase: “Token of depositing data”. It’s exactly the concern I raised earlier this week: “Biological Anthropology association speaks out on data access”.

Going through the motions of providing data instead of actually creating a useful foundation for further work is a universal problem. After all, work is work. As the software industry has long known, there’s no substitute for full and adequate documentation of code, but still everyone is under pressure to produce outputs right now, with less incentive for doing the work for everyone else.

To their credit, the biological anthropologists reference several online data repositories, which grant agencies and publishers are increasingly encouraging. The Scientist article introduces the subject of repositories as a substitute for supplementary information:

Mark Hahnel, the CEO and founder of figshare, says that he started the company during his doctoral studies out of frustration with the limitations of supplemental files. “We expected to play this role for people who were producing outputs of research that didn’t fit into the model of publishing PDFs,” he tells The Scientist. But increasingly, academics also are using figshare for other reasons, he adds, such as being able to freely reuse material associated with a published paper without worrying about infringing upon copyrights. (While research outputs such as figures in a traditional journal may be subject to a publisher’s copyright policies, those deposited to repositories like figshare are usually published with a creative commons license that allows others to use the material without restrictions.)

Data repositories are a partial solution for only one of the problems of data access — providing a way for readers to get the data and code that underlie a published analysis. Building a durable foundation for further work is another task that should be recognized and valued much more.

Part of that task is publishing texts that actually provide the details of analyses. This comes back to supplements. Today, too many published scientific papers are little more than glorified abstracts. Details are hidden in hundred-page supplements, where they are poorly reviewed (if they are reviewed at all) and rarely replicable.

Some papers should be broken up into independent units. Multidisciplinary work that actually consumes hundreds of pages of detail should be formatted and published in a way that recognizes the detail, not hides it. Scientists working on multidisciplinary problems need to model good writing to enable readers to follow how the details from many analyses fit together. That would be vastly more valuable as a foundation for later work than a citation in a weekly science journal.

Making photogrammetry better with spectral imaging

Three-dimensional scanning of teeth and bones has become a bigger and bigger part of morphological analysis. When it comes to teeth, microfocus CT is the most prominent approach. This is in part because the CT can reveal internal structures such as the enamel-dentin junction, and in part because the translucency of enamel makes it very difficult to get accurate scans from other techniques, including laser surface scanning, photogrammetry, and structured light scanning.

Researchers have long dealt with the translucency of enamel in photography by spraying the teeth with substances that temporarily render them opaque, like chalk dust. Nowadays we realize that many kinds of trace evidence can persist on fossill teeth, and subjecting them to repeated surface treatments for the purposes of scanning and photography is a bad idea.

A new paper by Aurore Mathys and coworkers tries something new: dividing the spectrum for scanning the surfaces of teeth: “Improving 3D photogrammetry models through spectral imaging: Tooth enamel as a case study”.

Spy 2B taken at many wavelengths, from Mathys et al. 2019

Enamel is relatively less translucent to ultraviolet wavelengths, and so Mathys and coworkers were able to obtain better scans by breaking down to ultraviolet scanning. I’m not sure this is the wave of the future, but it is a clever idea.