john hawks weblog

Big data approaches to scientific career success

2019-08-30T00:00:00-05:00

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'

2019-08-28T00:00:00-05:00

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

2019-08-27T00:00:00-05:00

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

2019-08-26T00:00:00-05:00

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

2019-08-25T00:00:00-05:00

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

2019-08-24T00:00:00-05:00

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

2019-08-23T00:00:00-05:00

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

2019-08-22T00:00:00-05:00

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

2019-08-21T00:00:00-05:00

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:

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

2019-08-21T00:00:00-05:00

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

2019-08-20T00:00:00-05:00

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

2019-08-20T00:00:00-05:00

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

2019-08-19T00:00:00-05:00

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”.

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.

Biological Anthropology association speaks out on data access

2019-08-18T00:00:00-05:00

For many years, biological anthropologists have been talking about data access.

This month the American Journal of Physical Anthropology is running a commentary: “Data sharing in biological anthropology: Guiding principles and best practices”.

An ad hoc committee on data access and data sharing produced the commentary, which they describe as a consensus of forty participants across the field.

I think that it is very positive that biological anthropologists are having these conversations. There is broad agreement that the data that underlie published studies should be available for replication and meta-analyses.

On the other hand, I’ve noticed over the years that many scientists who agree in principle that data should be available nevertheless find many ways to obfuscate or prevent access. I see some language in the published statement that makes me nervous. For example:

Project design should include a clear data management and sharing plan that is in place prior to the start of the project. Data sharing should be viewed over a time horizon related to the length of the research project, such that different parts of a data set may be shared at different times. For example, timelines in a grant proposal might include specific target dates for making particular data available (e.g., metadata, raw data, etc.).

I get very worried when I see this. In my experience, timelines and target dates in grant proposals do not translate into data access upon publication. In some areas of biological anthropology, projects that have been funded by our major grant agencies are less likely to archive data in ways that other researchers can access, even though they have filled in the mandatory “data access plans”.

It’s also curious that the NSF-funded data repositories for biological anthropology data, such as MorphoSource and PaleoCore, are not included on the list of recommended data repositories. I know that many projects have satisfied NSF data access plan requirements by referring to these repositories. Yet some people have worried that such data repositories are not sustainable in the long term because they rely upon continued funding.

Anyway, I recommend reading the statement and thinking about how the best practices can be improved.

The complexity of paleomagnetic pole flipping

2019-08-12T00:00:00-05:00

Scott Johnson writes at Ars Technica about the Brunhes-Matuyama boundary: “The last magnetic pole flip saw 22,000 years of weirdness”.

The researchers interpret this additional data as showing a major weakening of the magnetic field starting 795,000 years ago before the pole flipped and strengthened slightly. But around 784,000 years ago, it became unstable again—a weak field with a variable pole favoring the southern end of the planet. That phase lasted until about 773,000 years ago, when it regained strength fairly quickly and moved to the northern geographic pole for good.

The Brunhes-Matuyama paleomagnetic reversal is conventionally recognized as the boundary between the Early and Middle Pleistocene. When we talk about recognizing geological time periods, it is important to realize that our understanding of the boundaries is limited by the precision of our geochronological methods, and the physical processes that give rise to geological changes themselves.

This is an example where a boundary has 22,000 years of wiggle room that we might not have expected. In the span of 780,000 years, that’s not a long time, but if we want to examine whether two events are simultaneous or one caused the other, it’s a long time.

Profile: David Reich on ancient DNA

2019-08-02T00:00:00-05:00

Harvard geneticist David Reich recently was awarded a prize in Molecular Biology from the National Academy of Sciences. On the occasion, PNAS has done an interview with him, by journalist Beth Azar: Q and As with David Reich.

The interview may not offer much new for people following human evolution closely, but I thought it was worth sharing Reich’s comments on how the field of ancient DNA might move forward:

PNAS:What are you most excited about moving forward?

Reich: I’d like to help midwife this explosive new field into something that is mature and fully integrated into archeology. One goal is to help generate a lot more data from understudied places in the world, especially outside of Europe, and to build an ancient DNA-based atlas of human migrations all around the world. I would also like to help realize the potential of ancient DNA to provide insights into biology. To understand biological change over time, it is critical to understand how the frequencies of genetic variations change. To do that, large sample sizes of ancient people are needed. In the last two years, due to efforts by our lab and others to scale-up data production, the needed sample sizes are finally becoming available.

Dinosaur property war

2019-07-19T00:00:00-05:00

Phillip Pantuso of the Guardian reports on the legal battle over the ownership of significant dinosaur fossils: “Perhaps the best dinosaur fossil ever discovered. So why has hardly anyone seen it?”

In a test, last November that court ruled that fossils on Montana state and private land could be considered minerals. “Once upon a time, in a place now known as Montana, dinosaurs roamed the land,” begins Judge Eduardo Robreno’s opinion. “On a fateful day, some 66m years ago, two such creatures, a 22ft-long theropod and a 28ft-long ceratopsian, engaged in mortal combat. While history has not recorded the circumstances surrounding this encounter, the remnants of these Cretaceous species, interlocked in combat, became entombed under a pile of sandstone. That was then … this is now.”

This is a well-reported case recently, and the Guardian account provides more detail and background than other stories I’ve seen. It is very different for me as a paleoanthropologist to think about the world of commercial fossil hunters. I can’t disagree with Horner’s opinion expressed in the article:

They contacted natural history museums around the world, including the Smithsonian – where the bones were offered for a reported $15m – and the Museum of the Rockies, in Bozeman, Montana, whose then head paleontologist, Jack Horner (the inspiration for the character played by Sam Neill in Jurassic Park) told them they were scientifically useless.

“In order for a specimen to be of scientific use and publishable, we have to know its exact geographic position, its exact stratigraphic position, and the specimen must also be in the public trust, accessible for study, which this specimen is not,” Horner says.

Fossils are often beautiful objects, and museums are often great showcases for these objects for public engagement and understanding. But today the science requires a lot more detailed examination of the sedimentary context of fossils than the nineteenth century. Not every fossil is of great interest to present scientists. For scientific research today, separating fossils from their context should be a scientific judgement, in which we must weigh the destruction of context against the possibility of collecting and analyzing information.

For the interests of science, the best place for many fossils is to keep them in the ground. When we excavate anything, there is a loss of information and context, a destruction. As technology has developed, it has given us ways to study fossils and their context with less destruction, and to collect information that was once invisible or simply discarded. The future will bring better methods. In every case, we must consider whether today is the right historic time to separate a fossil from its context, balancing the gain to science against the loss of future opportunities—and any risks to the fossil in its present location.

For hominin fossils, the decisions are just as complex. I’m very glad that private ownership and market value of the fossils is not an issue for our work in South Africa.

Are parsimony analyses better than Bayesian methods for phylogenetics?

2019-07-07T00:00:00-05:00

During the past few years, Bayesian approaches to phylogeny reconstruction have become more and more widespread, including analyses of fossil hominins. Among hominins, Bayesian approaches sometimes lead to very different results from parsimony, even when applied to exactly the same datasets.

That’s a problem. As a field, we can put much more effort into building morphological datasets of fossils. The best existing datasets still have enormous holes and gaps—they are highly biased toward cranial and dental traits, and even these traits are underrepresented in published datasets compared to fossils that preserve the traits. Researchers who have tried to include some specimens in their analyses have actually been denied permission to study them, meaning that they must rely on published studies only, which exclude many traits. So there’s much room to better document the fossil record that already exists.

Last year Robert Sansom and coworkers carried out a study to examine what difference it makes to use Bayesian methods versus parsimony upon the same datasets. Their conclusion is stated in their title: “Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees”.

Other scientists have looked at how these methods perform in generating phylogenetic trees for simulated data. In that artificial context, Bayesian methods do better than parsimony. But what about real data? Sansom and colleagues considered it possible that some aspects of real datasets make them different from the usual simulated datasets.

That’s tough to test, because we don’t know the real phylogeny in real datasets. But Sansom and coworkers looked at how the different methods perform with relation to the stratigraphic position of fossils — testing for stratigraphic consistency. They found that Bayesian algorithms don’t do so well:

Bayesian analyses yielded trees that were significantly less congruent with stratigraphic data. Given that the 167 empirical datasets were from a wide range of authors, clades, time periods and taxonomic levels, we can place confidence in the small but significant differences observed. Taking stratigraphic range data as a benchmark independent of morphology, therefore, indicates that parsimony should be preferred over Bayesian analyses, but these empirical results differ from simulation studies. We explore a few possible explanations for this discrepancy.

To be honest, the difference in performance between the two methods in this study is pretty slight. Both methods do badly in generating trees that are stratigraphically consistent. Parsimony was better in a statistical sense but the difference was not large. To me, the bottom line is that some real datasets have features that make Bayesian methods work badly, and others probably have features that make parsimony work badly (and many probably are unsuitable for both).

One thing that the study discusses is whether published trees and methods have already been biased by researchers who were aiming for a particular solution:

Cycles of revision and re-analysis of morphological data matrices during construction could lead practitioners to prioritize phylogenetic solutions that fit some preconceived ideas for final publication (either consciously or subconsciously), including stratigraphic fit. Under such circumstances, parsimony trees might exhibit artificially elevated stratigraphic congruence because parsimony is the historic default method used to evaluate morphological data.

From my experience with hominins, this kind of bias is a real possibility. Until the last few years, paleoanthropologists seemed to aim at a particular kind of phylogenetic hypothesis: one in which successive species in stratigraphic order are progressively more closely related to living humans. That’s an intrinsically unlikely order for relationships to occur. Even though scientists profess to accept that human evolution was a tree, they still tend to arrange them as if they were a straight line.

In conclusion, our analyses demonstrate a clear result: Bayesian searches yield trees that have significantly lower stratigraphic congruence compared with trees from parsimony searches. We find little difference between parsimony using equal and implied character weighting—they are roughly comparable with respect to stratigraphic congruence. If stratigraphic congruence is taken as a benchmark for phylogenetic accuracy, then, maximum parsimony is the preferred method of choice for analysis of morphological data.

I’m not sure that stratigraphic congruence is anything that we should be aiming at. With hominins, it has become clear that relationships between lineages may have little to do with the age of the fossils. I’m also dubious that any change in algorithm is going to bring us closer to the “real” phylogeny. As long as we have substantial missing data from specimens that have already been found, the algorithms are garbage-in-garbage-out.

McKenna and Bell on ranked categories

2019-07-02T00:00:00-05:00

I learned mammalian systematics and cladistics around the same time that Malcolm McKenna and Susan Bell published their 1997 book, Classification of Mammals: Above the Species Level. The movie-title placement of the colon in their book title suggests the epic nature of the task they took on.

McKenna began during the 1960s to undertake the task of updating Simpson’s 1945 mammal classification to accord with the rules of cladistics, and published an interim part of the work in 1975. When I learned mammal paleontology, it was with class notes drawn from mimeograph copies of old notes. McKenna’s 1975 classification had a prominent place in this—sometimes as the only available classification for some groups, sometimes as one among other conflicting alternatives. From it I learned the placement of many extinct branches of early mammals, and saw systematics as an important part of understanding the fossil record.

How can systematists generate a classification that makes sense given the phylogenetic arrangement of mammals? Much of the evolutionary diversity of mammals has historically been recognized at the level of Linnaean orders – Primates, Carnivora, Perissodactyla, and so on. It happens that many of these orders have a very similar time depth, because they originated at or shortly after the Cretaceous-Paleogene impact event 66 million years ago. But relationships below the level of these orders are diverse – some lineages diversified enormously with sudden adaptive radiations at different times, others were more conservative. And when extinct mammals come into the picture, the diversity and time depth expected of “orders” and other higher level groups become less clear.

Today, genomic evidence indicates that the order Primates is a sister to the order Dermoptera (colugos). The group including both is known as Primatomorpha. Rodentia and Lagomorpha (rabbits) are likewise sisters, grouped as Glires, and this group appears to be a sister to Scandentia (tree shrews), although possibly Scandentia is closer to Primatomorpha. All these together form a group with the name Euarchontoglires. There remain several levels above Euarchontoglires but below the class Mammalia. Primates themselves have an extinct group of relatives known as Plesiadapiformes—sometimes included as a stem group within Primates, but sometimes included within Primatomorpha as a sister to Primates. Each of these higher-level branches of the mammal tree belongs to a distinct level of the hierarchy.

To deal with this complexity, systematists must multiply levels. But how many levels? Linnaeus could stack as many orders into a class as he liked, because he was not working with a bifurcating tree. A modern cladistic classification involves many, many bifurcations, each successive bifurcation in the tree representing a distinct level in the hierarchy. To get from one class to 40 orders requires at least six bifurcations: five hierarchical levels of classification between the class and order. Five is not enough for mammals, because of all the extinct stem branches represented by the known fossils. Each new fossil discovery of early mammals potentially introduces another level.

Simpson (1945) had included fifteen levels from class to species; McKenna and Bell (1997) increased this to 25 levels—recognizing categories such as “magnorder” and “supercohort” above the order, and “parvorder” and “subtribe” for lower levels.

They addressed the interesting difference between a classification and a tree, by discussing how prefixes relate to the hierarchy. As I re-read this passage from page 18, I thought it worth sharing:

Certain taxonomic categories came to bear prefixes suggestive of special hierarchical linkage (e.g., in the family-group, subfamilies are always subsumed in families). Others did not (e.g., tribes might alternatively have been dubbed "microfamilies" or some such term connoting subordination). use of a prefixed category implies that the category to which the prefix applies is also used. In the Linnaean system we do not cconstruct superfamilies directly from subfamilies without also employing families. Logically, however, above the species level there is nothing special about sub- or supercategories. They all could have received unprefixed cardinal names or simply be referred to as taxa. Such names are, after all, just labels (recognition symbols) (Mayr 1953:391). That prefixed categories did not receive unprefixed cardinal names, free of reference to another rank, seems to us to be partly a matter of practicality and memorability, and partly a function of their authors' essentialistic belief in the objective reality (beyond a construct of human language) and commensurability of various examples of such taxonomic levels as classes, orders, families, and genera (see Slaughter 1982). We employ prefixed names for the sake of stability, because they have been long in use, but we do not hesitate to allocate to an incertae sedis position some taxa whose names happen to be prefixed. For reasons of stability we might not wish to change their rank or to list the lower-ranked contents but not the valid but prefixed monophyletic taxon containing them.

It is a thoughtful observation. A tree is a logical structure that does not care whether humans can recognize and remember its parts. One advantage of a system of classification is that it is built with human memory in mind. The use of categories that bear a hierarchical relationship not only in definition but also in the form of the category names themselves has utility. Once a student learns that a parvorder is below the level of an infraorder, and a mirorder is above the order but below the grandorder, they’re not likely to confuse them.

Yet.

Any set of taxonomic levels faces a problem as soon as any new stem branch emerges between two adjacent levels of the hierarchy. Taxonomists who recognize lots and lots of levels have a buffer against taxonomic changes, because there will be empty levels. But with new discoveries of stem groups, the empty levels may eventually be filled.

We are in that situation with hominins. Hominini is a “tribe”. The group used to be called “Hominidae”, at the family level, but the discovery of the branching order of the apes argued for recognizing the family at a higher level of the tree, so that Hominidae includes great apes and humans, the subfamily Homininae includes African apes and humans, and the tribe Hominini includes only humans and fossil species closer to humans than to chimpanzees and bonobos. But clearly that still does not leave enough levels. The McKenna and Bell classification only provides family, subfamily, and tribe. The branch including chimpanzees, bonobos, and humans lacks a level in this hierarchy. Some scientists advocate recognizing this branch as the tribe Hominini, which would make humans and their fossil relatives a subtribe, Hominina. A different approach would be to introduce more levels: Historically, below the family level, taxonomists have used categories like “infrafamily”,”hypersubfamily” and “supersubfamily”.

None of this would matter very much to everyday use of these groups, if the names of them were not connected to the level. McKenna and Bell discuss this as well. What I didn’t realize is that the use of level-specific suffixes was itself a post-Linnaean innovation with the laudable aim of making levels more consistent:

With the proliferation of ranked categories that had increased steadily from Linnaeus's original six, came also a perceived need to encode the names of taxa themselves as signifying that the taxa for which they stood were members of some particular rank. In each particular discipline, the names of family-group taxa came to have various standardized inflected suffixes linked to the perceived rank. Thus, in zoology, a name ending in "-idae", signifies a taxon at family rank. Latreille (1796), who introduced the family category to zoology, did not use the suffix "-idae". That modification was provided later by Kirby (1815), and has not only stuck but is now legislated by the ICZN. We think of these inflective conventions as part of the "Linnaean System" but, in fact, they are arbitrary post-Linnaean additions to it, originally added for the mnemonic usefulness but now the occasion of much pedantic drudgery whenever taxonomic rank is changed or organisms are transferred from one kingdom to another.

There has been plenty of pedantic drudgery associated with changing hominin taxonomy, and that’s not counting the many holdouts.

Anyway, what if our taxonomies routinely use more and more levels? Doesn’t that get hard to keep track of? It’s fascinating to me that McKenna and Bell defend their 1997 classification of 25 levels by noting that “it’s no harder to learn than the alphabet”. But this passage really made my jaw drop:

In the present classification of more than 5000 mammalian taxa that are assigned generic or subgeneric rank, additional categories have proven useful in depicting in words a somewhat richer hierarchical arrangement of mammals than that found in Simpson's (1945) classification. There are now many more mammalian taxa to classify than was the case in 1945, both in real terms and because of the efforts of "splitters" and paleontological "apparent lineage choppers". Increasingly, most of these names organisms are made known from fossil materials only, sometimes very poorly represented. Moreover, the cladistic revolution in systematics has resulted in far more attention to phylogeny than was the case in the 1940s. The 25 taxonomic levels used in our classification actually fall closer to the theoretical minimum, 13 (see below for formula) than to the thousands that would be required if the classification reflected a completely pectinate (and very unlikely) sequence of taxa. The hierarchical level sequence is no more difficult (for humans) to learn than the alphabet, or probably less so in that some of the levels are very easy to remember because of meaningful prefixes and suffixes. We see no particular reason why, if useful, additional categories (or simply unranked taxa) should not be proposed (or revived). Computers can remember them for us. Indeed, in the program Unitaxon (TM) used to process the data resulting from this classification, facilities exist to expand and keep track of the names, number and sequence of taxonomic levels indefinitely, if deemed appropriate.

Ha! We don’t need to remember taxonomic categories because the computers can remember them for us!

If you’re interested in outsourcing your taxonomic knowledge to a computer, you can still see the Web 1.0 page for Unitaxon, listed as a “software product from yesteryear”. Here’s an excerpt:

Unitaxon Browser 2.0 is available directly from its developer, Mathemaesthetics, Inc. The application is distributed on CD for both Macintosh (System 8 and 9) and Windows (95 or later) operating systems. The Browser will work in Classic compatibity mode under Mac OS X. For maximum performance reasons, the Browser reads the entire classification into memory when you open the file. Depending on the level of taxon commenting in the database, the overhead is currently about 1MB RAM per 1200 taxa on average.

For instance, the most recent classification of the Mammals has been placed on the net in Unitaxon Browser format. It is our expectation and hope that other large taxonomic databases will follow suit.

The price per copy for the Browser is US $128, plus shipping/handling.

Well, that’s one solution.

The changes in 20 years have enormous. Even the link in the Unitaxon website to “vertebrate paleontologists” at the AMNH no longer connects to vertebrate paleontologists — the AMNH site now redirects the link to its “Center for Biodiversity and Conservation”. Malcolm McKenna passed away in 2008.

Anyway, the McKenna and Bell introduction has a lot of really interesting and useful thoughts about taxonomy and classification. The volume was published at the height of cladistic morphological classification, just as DNA evidence was starting to become a potent source of information about the deep relationships of mammal groups. As such, the McKenna-Bell classification has become outmoded in many details, even if some of the guiding concepts behind their taxonomy remain valuable.

Quote: Blumenbach looking for the horned rabbit

2019-07-02T00:00:00-05:00

I have open Johann Blumbenbach’s A Short System of Comparative Anatomy, in the 1807 English translation by William Lawrence. The full text is on Google Books.

In a footnote to page 24, where Blumenbach described the various horns and antlers of the group known as the Pecora, Blumenbach describes the jackalope!

I have collected about twenty instances, from the middle of the 16th century downwards, in which horned hares are said to have been found, with small branches like those of the roebuck, both in different parts of Europe, and in the East Indies. Were this fact ascertained, it would furnish another striking point in which these animals resemble the pecora. The fact is suspicious, because I have not yet been sufficiently satisfied of a single instance in which the horns were on the hare's head, although every trouble has been taken to procure information; and they appear in the drawings, which I posses [sic], by far too large for a hare.

It seems likely that the source of this idea was the muntjac, or other small cervids. Still, it’s not hard to imagine Americans heading west, thinking that some of the large jackrabbits might turn out to be antelope-like in more ways than one.

Quote: Weidenreich on the resistance to Neandertals as human ancestors

2019-06-26T00:00:00-05:00

Franz Weidenreich, in his 1943 article, “The ‘Neanderthal Man’ and the ancestors of ‘Homo sapiens’” (p. 44):

At the time when Darwin and Huxley first claimed that Man evolved from a primate similar to the anthropoids of today, little evidence substantiated by palaeontological facts was available. In the meantime, however, quite a number of fossil forms have been recovered all of which may justifiably be claimed as “missing links.” Yet, strangely enough, the more such intermediate types came to light, the less was the readiness of acknowledging them as ancestors of Homo sapiens. In many cases the scepticism apparently was the last bastion from which the final acceptance of Darwin’s theory could be warded off with a certain air of scientism. In other cases, it was the pure respect for traditional axioms when advanced by authorities.

Weidenreich is honorary patron of the Neandertal anti-defamation league.

How will ancient proteins change paleoanthropology?

2019-06-26T00:00:00-05:00

Nature has a news feature by Matthew Warren that provides a nice background to recent work on proteomics of fossil hominins: “Move over, DNA: ancient proteins are starting to reveal humanity’s history”.

Like most areas of new technology, news stories are training the public to expect that lab folks will wave a magic wand and soon answer all questions. The reality is more complicated.

Protein sequences from teeth and bones provide tremendous promise for understanding the evolution and relationships of ancient hominins. But it’s important to separate the science from the hype. Protein sequences provide information that is orders of magnitude more limited than genome sequences. A single low-coverage genome sequence built from three Neanderthal specimens led the observation that humans today have Neanderthal ancestry, many of them as much as 2 or 3 percent. That observation—arguably the single most important ancient DNA result—is outside the power of protein work. Another area where ancient DNA has transformed our knowledge is the divergence times of ancient hominin groups. Protein data will provide some information about such divergences in cases where DNA is unobtainable. But the precision of such dates will be very low, because the number of changes in amino acid sequences among hominoids is small.

That being said, those of us who work with fossil hominin material are excited about the potential of proteins. They are already transforming some areas, and they have much to offer in others. For example:

Proteins are great for identifying hominin fragments too small for reliable anatomical identification. In this area, proteins are already prime-time science. This has been one important application of the ZooMS approach, with tremendous success under the leadership of Katerina Douka on the Denisova Cave bone collection.
Along similar lines, ZooMS has started to make important contributions to understanding the species composition of fragmented faunal collections. We could use additional investigation of how comparable such results are to traditional, less-destructive quantification of faunal collections based on identifiable fragments.
As related in Warren’s story, protein sequences have brought new information to phylogenetic questions of extinct groups, such as sloths, South American ungulates, and rhinoceroses. Hominin systematics is a mess. Few studies agree on the shape of the phylogenetic tree of human relatives. This confusion comes from a combination of too little morphological data about some fossil fragments, and too many instances of morphological convergence or parallelism in various hominin lineages. Protein sequences don’t necessarily solve these problems—there will be many lineages with no data, few changes among most species, and convergent amino acid changes are by no means impossible in hominins. But everyone who works on hominins is interested in any approach that can squeeze more information out of the record.

The article spends much time on this third area of future promise, which is the most susceptible to hype. This is partly driven by the recent recognition of the Denisovan affinity of the mandibular fragment from Xiahe, China, based upon protein sequence. That similarity is compelling, but it is based upon very little information—one single change in the collagen sequence that has been observed in a Denisova Cave genome and not in living humans or Neandertals.

The enamel proteome has more information than collagen, and many ancient hominins are more different from us than Neandertals and Denisovans. That means when we look at ancient hominins like Homo erectus, we can expect a bit more information about their evolutionary divergence from us. That’s a time frame during which we know much less about relationships:

Go back one million years or more, and things get even less clear. H. erectus, for example, first emerged in Africa around 1.9 million years ago, but without DNA evidence, it remains uncertain exactly how it is related to later hominins, including H. sapiens.

I think the most likely result of this research is that “it” is going to be “they”. Protein analysis is not the only new approach shedding new light on the relationships of Early and Middle Pleistocene hominins, and all of the new information is raising new questions about how we recognize and understand species and populations.

Work on internal structure of the teeth, involving Maria Martinón-Torres and others, is starting to provide some fascinating evidence that “Homo erectus” in Asia is a complicated story, involving branches that haven’t been previously been recognized. Gross morphological evidence has long suggested that African “Homo erectus”” is likewise complicated, and in Africa work on the internal anatomy of teeth is only just getting started.

The big challenge is this: We live today in a world where “lumping versus splitting” is no longer an interesting question about extinct hominins. We know that populations of hominins existed for hundreds of thousands of years in relative isolation, with very little or no gene flow, and yet still interbred with each other. That interbreeding shaped the evolution of later populations, including people living today, even when it makes up a fairly small proportion of their ancestry.

So, how do we examine the evolution of earlier populations? Even with DNA evidence, there is a limit to our ability to test for layers of hybridization and introgression, because of the small and geographically limited samples we have. With morphology and low-information biomolecules like proteins, we are going to need a new synthesis to understand the connections between biomolecules, morphology, and development.

This is nothing to be afraid of. New sources of evidence are going to make it possible to fill in some broad strokes that are currently monochrome. We’re going to see multiple populations of H. erectus—whether we will call those species, or paleodemes, or populations, is not yet clear, and will depend on their temporal and spatial patterning.

I’m less sure that we will resolve much about hominin phylogeny. It’s very bad now. Three different methods of looking at the phylogenetic placement of Homo naledi have led to three very different results, and similar problems have emerged with Australopithecus sediba, Homo floresiensis, and other species. These are some of the most complete skeletal samples of any hominin species, and our field cannot reliably place them on a tree. Proteomics will provide some new evidence to add to the tree, but it may only deepen some of the problems.

Meanwhile, as the science of proteomics develops, we need to be vigilant to avoid some of the mistakes that have been made by ancient DNA researchers. The Nature article includes a link to last year’s story by Ewen Callaway: “Divided by DNA: The uneasy relationship between archaeology and ancient genomics”. That story went into some details about the conflicts that have arisen between ancient DNA specialists and archaeologists. These groups have different histories, and few ancient DNA specialists have made the effort to understand some of the deeper, darker history of archaeology, with troubling results for their work. Meanwhile, both groups have a history of failure to work effectively with descendant communities and local researchers in many countries.

Although Warren’s story new story about proteomics does not focus on this element, ancient proteins will pose many of the same problems as ancient DNA sampling. The sampling is destructive, and they have possibly greater application to cultural material than to the human remains themselves. Meanwhile, integrating protein results–which are limited–into a more complex picture involving many kinds of information will be a challenge.

I look at those challenges as opportunities. What a single laboratory might perceive as a “problem” of interpretation is a place where leadership from other researchers is most valuable. I know many of the people who are making progress in proteomics, and I think they’re on a good track at the moment to make better science with these kinds of collaborations.

Quote: Keith's awkward analogy for Neanderthal dental anatomy

2019-06-25T00:00:00-05:00

Here’s a painful analogy deployed by Arthur Keith (1924:253) for Neandertal dental anatomy:

The nature of the taurodontal change in tooth formation may be explained by the use of a homely illustration. It is the fashion in Europe to separate the legs of trousers---which correspond to the roots of the teeth up to the fork of the thighs. But there have been fashions where the seat of trousers, corresponding to the floor of the pulp cavity, has been carried down to the level of the knees, or even to the ankles. In teeth of the taurodont form the seat is carried to correspondingly low levels, or, as in this example from Ghar Dalam (Fig. 1, E), carried to the level of the ground and thus turned into a skirt.

Quote: Darwin on the line of progenitors leading to humans

2019-06-24T00:00:00-05:00

In the Descent of Man, Charles Darwin ends his discussion of the relationship of other animals to humans with this evocative paragraph:

Thus we have given to man a pedigree of prodigious length, but not, it may be said, of noble quality. The world, it has often been remarked, appears as if it had long been preparing for the advent of man; and this, in one sense is strictly true, for he owes his birth to a long line of progenitors. If any single link in this chain had never existed, man would not have been exactly what he now is. Unless we wilfully close our eyes, we may, with our present knowledge, approximately recognise our parentage; nor need we feel ashamed of it. The most humble organism is something much higher than the inorganic dust under our feet; and no one with an unbiassed mind can study any living creature, however humble, without being struck with enthusiasm at its marvellous structure and properties.

Why won't Science publish replication studies?

2019-06-23T00:00:00-05:00

An article in Slate by Kevin Arceneaux and coworkers recounts their experiences trying to publish a replication of a high-profile psychology study in Science: “We Tried to Publish a Replication of a Science Paper in Science. The Journal Refused.”

The story concerns a 2008 study in Science that claimed that people react differently to scary pictures depending on whether they are political liberals or conservatives. The study was widely publicized at the time of publication and has become a mainstay of

There’s one problem: It didn’t replicate. Arceneaux and coworkers explain how they got grants to set up expensive equipment in their laboratories and tried to extend the work with hundreds of subjects. And failed. And then they tried to replicate the exact circumstances of the original study, with the input of the original authors, with a larger sample of subjects. And failed.

They wrote it up and submitted it to Science. Desk reject. The story is well worth reading, this is the authors’ bottom line:

We believe that it is bad policy for journals like Science to publish big, bold ideas and then leave it to subfield journals to publish replications showing that those ideas aren’t so accurate after all. Subfield journals are less visible, meaning the message often fails to reach the broader public. They are also less authoritative, meaning the failed replication will have less of an impact on the field if it is not published by Science.

Science is published by the American Association for the Advancement of Science. The cause of science is not advanced by publishing studies that attract huge public attention, but then failing to publish the results when those studies fail to replicate.

I am surprised that the editors of the journal do not see the opportunity here to establish a responsible precedent. Well-powered, pre-registered studies that revisit splashy research findings are the way that future science is going to happen. As it is, Science is appealing to researchers who design underpowered studies that produce counterintuitive results. As we’ve seen in the last few years from the “replication crisis”, those studies are very likely to turn out to be bunk.

I would add one thing. To me, here’s an irritating part of the story that is not getting the attention it deserves:

We had raised funds to create labs with expensive equipment for measuring physiological reactions, because we were excited by the possibilities that the 2008 research opened for us.

That’s the power of a research study published in Science: it changes the funding environment for all scientists in a field. Such studies establish for referees and grant agencies what is worth investing time and resources in.

That’s bad. No single study should have that kind of influence. But the reality is that new research directions often come from just such single cases, and a study like this can start a rush to be in the first wave of researchers investigating a new phenomenon. When those results are bunk, all that time and money—that could have been spent in more promising directions—is wasted.

Quote: Martin on the difficulties of reconstructing human migrations

2019-06-22T00:00:00-05:00

For a writing project, I’ve been looking at some pre-Darwinian accounts of human origins and relationships. One of the most detailed was published in 1841 by William Martin, “A General Introduction to the Natural History of Mammiferous Animals”.This is a haphazard book, something like a rambling Dickensian biology textbook, but I thought it was worth sharing this paragraph on the difficulty of examining the relationships of humans:

Let it also be remembered, that the migrations of Man are, for the most part, not single acts, performed by one tribe, and, so to speak, finished at once; but they have generally been like the waves of the advancing tide---the way once open, swarm has followed swarm, the movement has been general, and years have passed, till, at length, the flood has either ceased to roll on, or has taken some new direction. Meanwhile the invaders have become amalgamated with the more ancient possessors of the soil, and their commingled descendants again with other invaders, in their turn. Most nations, besides, if even relics of their early history be by chance preserved, have fondly claimed for themselves a romantic or heroic origin---a descent from gods, or god-like men---have blended facts with fables, between which it is not a little difficult to separate, and have assigned the most extravagant antiquity to their commencement. Hence, then, the difficulty of forming a clear digest of the subject, and of tracing the branches and offsets to their primitive stocks; hance the uncertainty which attends the most plausible hypotheses.

Scaling data, some hints in dimension reduction methods

2019-06-21T00:00:00-05:00

PLoS Computational Biology has a very helpful article by Lan Huong Nguyen and Susan Holmes meant to help people with statistical visualizations: “Ten quick tips for effective dimensionality reduction”.

Commonly, people examining large datasets with many dimensions will present their results with figures that show only two dimensions. In genetics, most of them will use principal components analysis (PCA) to reduce thousands of dimensions into two. In morphology, PCA is also very common, although some specialists may use Procrustes fitting or other methods. This paper by Nguyen and Holmes runs through several common misconceptions and errors in choosing methods to reduce dimensions and displaying the results of such procedures.

One of the biggest: A PCA plot should be scaled according to the variances of the dimensions, not an arbitrary scale. Otherwise, data that are really normally distributed may look anything but.

Figure 2 from Nguyen and Holmes, 2019. These charts all show the same data, which were generated by selecting two sets of normally distributed (Gaussian) random variables with two centers. The two clusters are red and blue in the final frame, which has an aspect ratio based on the variance in the data. The others show incorrectly scaled data, which are easily misinterpreted. I would add, morphological datasets are based on much smaller samples, and more easily give rise to false interpretations.

It's a frequent irritation to me that for data visualizations we are so often at the mercy of people who write up papers but do not share original data. So in presentations or for secondary work you're left relying upon someone else's PCA plot. These are almost always composed with bad choices of colors, unreadable fonts, and weird scales that make no sense. Don't get me wrong, there are some beautiful data visualizations out there. But the average paper in morphology or genetics is full of stinkers. And it would be so easy to just provide the original data so that those of us who re-use data in other contexts can make your results look better. Share!

Probing ancient pheomelanin

2019-05-26T00:00:00-05:00

Living organisms create spatial patterns of trace elements in their bodies. Clever means of detecting those spatial patterns are arriving. These have given new avenues into the biology of extinct organisms, by pulling information from exceptional fossils.

A new paper in Nature Communications by Phillip Manning and colleagues describes a new way to look at the distribution of the red pigment, pheomelanin, in the preserved fossil soft tissues of ancient organisms: “Pheomelanin pigment remnants mapped in fossils of an extinct mammal”.

They have applied XRF (X-ray fluorescence) and XAS (X-ray absorption spectroscopy) at a very tiny scale by using a synchotron. This provides a way of building a microscopic matrix of trace element distributions across a fossil.

Similar approaches have been looking at eumelanin distributions for some time, exploiting the fact that the process for generating eumelanin relies upon a copper-containing enzyme. Recently, it has become possible to quantify pheomelanin versus eumelanin by focusing on zinc. The results described in this paper focus on a particular fossil mammal, a Pliocene mouse. Those are interesting as a proof of concept but I am more fascinated by their description of the chemistry involved:

Trace metals are key components of melanin and play important roles in melanogenesis. Melanins are complex molecules formed from the aromatic amino acid tyrosine via the action of the Cu-containing enzyme tyrosinase. Because Cu is the metal cofactor in the enzymatic process forming eumelanin, elevated concentrations of organically bound Cu can typically be correlated with eumelanin-rich tissue. After Cu, Zn is the second most abundant metal in mammal melanosomes. Both metals may be complexed within the interior ring structure of eumelanin, attached to the diol functional group of dihydroxyindoles, or attached to terminal carboxylate groups, but in all cases, the Cu and Zn within eumelanin are strictly light-element coordinated (O/N): in eumelanin, there are no sulfur groups to which trace metals can bind. Importantly for this study, pheomelanin synthesis additionally requires the sulfur containing amino acid cysteine as a substrate. Sulfur in pheomelanin is contained within benzothiazole (or benzothiazine) units that are accessible for metal attachment. While Cu is strongly associated with eumelanin, Zn correlates with pheomelanin pigment. Previously, work on fossil integument concluded that organosulfur–Zn complexes may be the residue of pheomelanin; however, detailed coordination chemistry for Zn in extant pheomelanin to use in comparison with the fossils was unavailable. Subsequently, Edwards et al. applied detailed XRF and XAS to extant pheomelanin-rich feathers. The results showed that these feathers possessed a distinct chemical signature for Zn and S, with a significant portion of the Zn inventory bonded to S, almost certainly through the S contained within the pheomelanin molecule. This conclusion was based on the fact that there was a strong, spatially resolvable correlation between Zn and pheomelanin-associated sulfur groups.

Biochemistry is complicated, and bodies do other things with heavy metals besides make melanin. Besides, fossils get trace elements in them from post-depositional processes, not only from the intrinsic biochemistry of the living organism. So it is extremely necessary to validate these kinds of approaches using large samples of tissues from extant organisms as well as various controls from non-fossil bearing sedimentary situations.

That kind of work has so far been pretty light. For understandable reasons, research teams are working to validate their approaches upon exceptional fossils that preserve details of soft tissue anatomy, and preferably tissue microanatomy.

The point of using exceptional fossils in such analyses is that the chemical patterns can be compared to anatomical patterns. When they correspond to each other, that gives some confidence that the chemistry is seeing something real.

My hope would be that once the techniques are validated more widely, they may be able to bring some information out of the much larger samples of less exceptional fossils.

Probabilistic calls of the titi monkeys

2019-05-21T00:00:00-05:00

A fascinating paper in Science Advances today looks at the way that a small platyrrhine monkey species conveys information about predators in its vocal communication system: “Titi monkeys combine alarm calls to create probabilistic meaning”.

The titi monkeys have two kinds of alarm calls, which they can combine together in complex sequences. The research by Mélissa Berthet and coworkers shows that the sequences carry information about not only the type of predator but also the location of the predator. Unlike human sentences, which are comprised of words that have distinct meanings, these titi monkey call sequences are probabilistic, that is, it is not the precise order or number of calls, but their quantity in combination that predict to a feature of the environment.

A couple of paragraphs from the discussion of the paper are enlightening:

Human and nonhuman animals (hereafter referred to as animals) live in environments where most stimuli appear in a continuous form, but perception is often categorical (9). For example, although rainbows consist of continuously changing wavelengths, they are perceived by humans as color bands. Similar effects are found in communication systems, including human speech. Acoustically, the human vocal tract can gradually alter the second formant of the syllable from the sound “b” (as in “beer”) to “d” (as in “deer”) and then to “g” (as in “gear”), although they are perceived in sharply categorical ways by listeners (10). Another example comes from the American Sign Language, where the hand configuration gradually differs between the words “please” (the thumb and all the fingers are selected) and “sorry” (only the thumb is selected) but is perceived categorically by deaf signers (11).

Linguists have focused quite extensively on the categorical encoding of human language. In looking for precursors or analogues of human communication in other animal communication systems, linguists and animal behaviorists have often paid attention to such categorical systems – for example, the alarm calls of vervet monkeys, which seem to form clear categories relating to predator types.

Yet maybe there is more to be seen in the simple call systems of non-human primates than correspondences between calls and features of the environment:

Although the notion of categorical meaning is intuitively compelling, it is not necessarily the default mode of animal perception. Categorical perception has been a major theoretical pillar in animal communication research, particularly because of its intuitive link to linguistic theory. For example, Macedonia and Evans [(16), p. 179] presupposed that external events are processed in categorical terms (“…all eliciting stimuli must belong to a common category”). Although this approach has been fruitful and productive, it has also generated enigmas suggesting that the underlying theory may have to be revised. For example, in a seminal paper, Cheney and Seyfarth (17) were puzzled by the fact that animals appeared to have very few categorical semantic labels, mostly limited to predator classes and a few social events. One possibility is that graded meanings are the default way of animal communication [e.g., (18)], although this hypothesis has been much ignored and considered as less interesting than categorical perception (16). Our study suggests that explaining animal communication on categorical terms alone may be too restrictive and anthropocentric and may explain the struggle to extract meaning from some animal communication systems.

I think this is cool. It suggests that natural language learning systems, which include strongly probabilistic features, might make some headway with animal communication systems.

Quote: Darwin on human variation

2019-05-19T00:00:00-05:00

There is much that could be said about Charles Darwin’s discussion of human races in Descent of Man. In Chapter 7 he embarked on a long discussion of whether races of humans should be considered as different species. Throughout, he argues that they should not, but Darwin presented and weighed the best arguments he can find on either score.

As I read the following quote, I wanted to tweet it, but it’s too long:

Every naturalist who has had the misfortune to undertake the description of a group of highly varying organisms, has encountered cases (I speak after experience) precisely like that of man; and if of a cautious disposition, he will end by uniting all the forms which graduate into each other, under a single species; for he will say to himself that he has no right to give names to objects which he cannot define.

I think that’s a wonderful precept. If every scientist refrained from “giving names to objects” without a clear definition, it would save marvelous confusion.

The immediate context of this sentence is Darwin’s discussion of what he describes as “the most weighty of all the arguments against treating the races of man as distinct species”, namely, that human races grade continuously into each other. As a consequence, he notes:

Man has been studied more carefully than any other animal, and yet there is the greatest possible diversity amongst capable judges whether he should be classed as a single species or race, or as two (Virey), as three (Jacquinot), as four (Kant), five (Blumenbach), six (Buffon), seven (Hunter), eight (Agassiz), eleven (Pickering), fifteen (Bory St. Vincent), sixteen (Desmoulins), twenty-two (Morton), sixty (Crawfurd), or as sixty- three, according to Burke. (18. See a good discussion on this subject in Waitz, 'Introduction to Anthropology,' Eng. translat., 1863, pp. 198-208, 227. I have taken some of the above statements from H. Tuttle's 'Origin and Antiquity of Physical Man,' Boston, 1866, p. 35.) This diversity of judgment does not prove that the races ought not to be ranked as species, but it shews that they graduate into each other, and that it is hardly possible to discover clear distinctive characters between them.

Many of today’s issues in biology were already known to Darwin. It is easy to forget how much his presentation of such issues shaped the way later authors would present them. He sometimes packaged the ideas of others, but the fact that Darwin promoted and gathered such ideas together tended to place them into the biological canon.

Link: Long-read on Cayo Santiago

2019-05-18T00:00:00-05:00

The New York Times Magazine today has a long-read article about Cayo Santiago, the island just off Puerto Rico where a large colony of rhesus macaques was introduced back in the 1930s to supply the medical research trade. The island became a laboratory where researchers could study every aspect of the free-ranging macaques’ lives.

In 2017, Puerto Rico was hit hard by Hurricane Maria, with enormous effects on the people of the island. Cayo Santiago was also hit, stripping much of its forest. The macaques weathered the storm relatively well, but researchers have found longer-term effects. The article explores these effects on the macaques, explains the research and its history, and highlights the struggles of the people of Puerto Rico: “Primal Fear: Can Monkeys Help Unlock the Secrets of Trauma?”

In October 2018, Lauren Brent began analyzing some of the preliminary poststorm observational data and began to notice unexpected patterns. There seemed to be two things going on. One, the monkeys seemed to be expanding their social networks, increasing the number of individuals that they had meaningful relationships with. Two, the monkeys appeared to become more tolerant of one another. They were living under radically diminished circumstances, competing for resources that had never been in such short supply, like edible leaves and the temperature-reducing shade that those leaves produced, but the amount of inter- and intratroop violence had seemed to taper off significantly. It was as if the hurricane had bonded even former foes against a common enemy and made the monkeys much more tolerant of life’s everyday frustrations, at least in the early days.

I’ve chosen to quote a passage that is monkey-centric, but the article really is about the human stories – researchers, local research assistants, and other people caught in an extraordinary and often tragic set of circumstances.

Handaxes trailing up the coastline

2019-05-04T00:00:00-05:00

In The Conversation this week, archaeologist Amanuel Beyin and his colleagues Ahmed Hamid Nassr and Parth Chauhan describe their work surveying the Red Sea coast of Sudan for early archaeological sites: “Red Sea stone tool find hints at hominins’ possible route out of Africa”.

This is valuable work and I’m happy to see the authors sharing it. They are exploring for evidence of ancient hominin activity in a place where hominins should logically have been abundant in the Pleistocene, and they’re finding sites:

Recently we led a research team to fill the existing evidence gap about our ancestors’ route out of Africa. Our focus was on the western periphery of the Red Sea. This area links the fossil-rich Horn of Africa and the Sinai Peninsula, which is the only land bridge that could have facilitated direct hominin movement between Africa and Eurasia in the past two million years.

We found evidence of hominin settlement in the area in the form of stone artifacts that suggests this region was a key early dispersal corridor – and possibly the first. That evidence includes stone tools, colloquially referred to as handaxes or bifaces. These were associated initially with the first fully bipedal (upright walker) hominin species, Homo erectus, and subsequently with other species.

Handaxes are highly recognizable evidence because they were not commonly produced in Africa after 150,000 years ago. For the archaeologist, they give a rapid indicator that sites of Early or Middle Pleistocene antiquity are present—although handaxes can erode out of older sites and lie on the surface for a very long time. In any event, the presence of a network of ancient populations on the Red Sea coast is a logical prediction and great to find. This may be a region that was important to the repeated connections between African and Eurasian populations during the Middle Pleistocene.

I’m skeptical about the concept of “dispersal corridors” for hominins. I’ll reflect on that idea at greater length some other time, I don’t want to detract from the value of these authors sharing their work. All I’ll say is that I was worried when I saw the headline of this piece pointing to the “possible route out of Africa” that the work would have a lot of the usual nonsense about “southern route” and “northern route” possibilities for modern humans. So I was very pleasantly surprised that the authors were taking a broader view and filling in some important unknowns with respect to much earlier archaeological material.

Quote: 'Disciplinary integration' in anthropology is a myth

2019-04-26T00:00:00-05:00

I’ve been reading a new open access book by the anthropologist Rob Borofsky: An Anthropology of Anthropology: Time to Shift Paradigms?. The book is available for free download.

Borofsky has become well known as an advocate for “public anthropology”, the idea that anthropology should interact with a broader public, and be of service to the public.

I may point to a number of passages in the book as I read it. There is a great paragraph on page 23 that I want to highlight. Borofsky looked at several journals including the American Anthropologist and others to assess how many articles involve more than a single subfield – that is, when the research question actually requires core concepts and original data from two or more different kinds of anthropology.

The lack of subfield integration in times past is readily apparent when you read through old issues of the American Anthropologist. So why would anthropologists affirm something about the past—that the subfields previously collaborated in significant ways—that is clearly at variance with established fact? The myth of an earlier “golden age” of disciplinary integration constitutes a “social charter” for today’s departmental structure: It holds up an ideal. Disciplinary integration is imposed on the past—an “invention of tradition,” to quote Eric Hobsbawm and Terence Ranger. But it also does more. It implicitly represents a call for more disciplinary integration to resolve the current problem of departmental fragmentation. The myth allows anthropologists to address a problem of social structure—intellectual fragmentation within a department—without the pain of anyone actually having to change. It allows them to pretend that they all once worked together as a team.

Conspiracy theories in pseudoarchaeology

2019-04-25T00:00:00-05:00

Science magazine has a recent online article by journalist Lizzie Wade looking at the growing influence of ancient aliens and other pseudoarchaeological nonsense in the United States: “Believe in Atlantis? These archaeologists want to win you back to science”.

I’ve selected a passage in the middle of the article to quote:

Adding to archaeologists’ sense of responsibility is that “many of these ideas started within mainstream archaeology,” says Jeb Card, an archaeologist at Miami University in Oxford, Ohio. “We have to own these stories.”

For example, white settlers and early archaeologists in 19th century North America excavated elaborate pre-Columbian burial mounds—but ascribed them to a lost “moundbuilder race” that was killed by the ancestors of Native Americans. Former President Andrew Jackson used those ideas to justify displacing Native Americans from their lands.

Today, white nationalists make similar claims. To argue for Europeans’ deep roots in the Americas, they have latched onto Vinland, a short-lived medieval Viking settlement in eastern Canada, and the “Solutrean hypothesis,” which argues that the Americas were first peopled by arrivals from Western Europe. Neither claim started as pseudoarchaeology—Vinland was real, and the Solutrean hypothesis was proposed by mainstream archaeologists, then tested and ruled out—but they have been twisted for ideological ends. A white supremacist accused of murdering two people on a train in Portland, Oregon, in 2017 included the words “Hail Vinland!!!” in a Facebook post less than a month before the attack.

When it comes to mainstream media figures who are promoting pseudoarchaeology, I think we need to focus on the money. Pseudoarchaeology is a business. The media organizations, actors, and authors who are promoting this nonsense are profiting enormously from it. They’re quacks.

That money is coming, directly and indirectly, from people who often have a genuine and deep interest in knowing about the human past. Pseudoarchaeology is stealing their money and betraying their real quest for knowledge by feeding people nonsense.

Broadening participation in research beyond research jobs

2019-04-23T00:00:00-05:00

The current issue of American Anthropologist has a series of short essays by biological anthropologists, featured as a “Vital Topics Forum” in the journal. The essays come from anthropologists of a diversity of backgrounds and training, including many groups that have been historically underrepresented in this field of science. According to the journal, these are open access, and I may feature several of these essays over coming weeks.

Today I read the essay by Milena Shattuck, “Research in a Non‐Research Position”. One of the ongoing realities of academic institutions in the U.S. and internationally is a shift toward contingent (adjunct and other non-tenure-track) faculty for many teaching and service roles. As PhD scientists finish their degrees and proceed through their early career, they are increasingly finding that research is not part of the jobs they are getting. That reality has important implications for how we train and mentor PhD students, and also for how we conceive of research.

[G]iven the constraints that most people in our field face, it may be time to rethink our idea of who belongs at the table. For starters, given that teaching responsibilities are increasingly shifted onto NTT faculty, we need to acknowledge their importance in training the next generation of scientists. However, we also need to consider their potential role in research. High‐budget projects that produce large datasets are absolutely necessary to advance our field. But we must not conflate the research with the researcher, and those who manage to produce knowledge despite limited means should be valued too. Rather than be sidelined, NTT faculty should be actively sought out for collaborations. Ignoring 70 percent of academics can only harm science.

I would add, at the same time that universities are creating more non-research positions, they are also expecting more and more undergraduate research experience for students who apply to pursue higher degrees. This is a contradiction. I agree that research experience is valuable for students, and to provide it we must value and provide more support for the research roles of many instructors, even those in primarily teaching positions.

Link: Anatomical models

2019-04-22T00:00:00-05:00

The Age has an article describing the work of two anatomists who want to bring new high-fidelity plastic models into medical anatomy training: “Buster, the perfect human made of plastic, is the future of anatomy”.

There are VR simulators and screens that can slice a virtual human body in two with the swipe of a finger. But the secret real secret here is a machine, pioneered by Professor McMenamin, that can print out plastic human bodies. No one else in the world can do this.

First, a high-accuracy CT scan of a donor body is obtained. Then, about half-a-million dollars’ worth of cutting-edge 3D printers build a copy out of soft plastic.

They are so accurate, calling them models does not do them justice. Professor McMenamin prefers “replica”.

I know many anatomy professors very well. All of them attest that the experience of learning anatomy with donor cadavers cannot be matched by any artificial model. The gift that donors give when they will their bodies to medical education is precious and irreplaceable. The linked article shares the Australian professors’ view, which is aligned with mine.

But even though there is no replacement for experience with real human cadavers, I see great promise in 3D models to broaden anatomy education. In undergraduate courses, we cannot match the experience of gross anatomy training in the medical school context. Having high-resolution models like these from real individuals would enable us to bring human variation into a much broader sample of courses. That would be helpful for health sciences training by giving pre-med and pre-nursing students more repetitions with better materials. It would also broaden knowledge and training in human anatomy outside of the health professions.

Link: So easy to match DNA to names

2019-04-12T00:00:00-05:00

Forensic genealogy is now mainstream. From Bloomberg Businessweek, a report by Kristen Brown: “A Researcher Needed Three Hours to Identify Me From My DNA”.

It wasn’t hard. I’d previously sent a DNA sample to the genetic testing company 23andMe Inc. and then uploaded my data anonymously to a genealogy website. Researcher Michelle Trostler was able to access my data from that site and spent an afternoon looking for connections that would help her put a name to my data. The task was so easy that in the meantime she rewatched a season of Game of Thrones.

Seems to me that we are only a few steps in synthetic biology away from people being able to conceive “three-parent” children, where some of the DNA is modeled on the publicly available sequence of someone off the internet.

New species of hominin from Luzon

2019-04-10T00:00:00-05:00

The online journal Sapiens invited me to write up my thoughts about the announcement of Homo luzonensis yesterday. I do have more to say about this cool discovery, but I wanted to share that article here also, for readers who might not have seen it:

This week, anthropologists working in the Philippines unveil new fossils that they say belong to a previously undiscovered species of human relatives. The fossils come from Callao Cave, on the northern island of Luzon, and are at least 50,000 years old.

The team, led by Florent Détroit of the National Museum of Natural History in Paris, have named the new species Homo luzonensis after the island where it lived.

Teeth from the Callao Cave individual that serves as the holotype for Homo luzonensis, CCH6.

With only seven teeth, three foot bones, two finger bones, and a fragment of thigh, the set of Callao fossils doesn’t give much to go on. Their small size is reminiscent of Homo floresiensis, the tiny-bodied species discovered in 2003 on the island of Flores, Indonesia, that lived around the same time. But there aren’t enough remains here to say just how tall Homo luzonensis was. And, unfortunately, the team was unsuccessful in attempts to find DNA. Many people will wonder, on such slim evidence, if the declaration of a new species is warranted.

I was fortunate to be a part of the team that discovered the new hominin species Homo naledi, which lived in South Africa around 250,000 years ago. That work was published in 2015. Such discoveries seemed almost unimaginable 20 years ago, when I was finishing my Ph.D. At that time, some of the most respected anthropologists actually suggested that the hunt for hominin fossils was almost over. Funding agencies directed their efforts away from exploring for new fossils and toward new technologies to wring more precious data from fossils discovered in the past.

Yet the last 20 years have seen an unprecedented burst of new discoveries. Some, like H. naledi and H. floresiensis, represent branches of the human family tree that separated from the modern human line quite early and yet survived until a surprisingly recent time.

Was H. luzonensis another such population? To establish that these fragmentary fossils justify recognition as a new species, a key first step is to exclude their membership to modern humans. Living people of the Philippines include some very small-bodied groups. Small size alone is not enough to place the Callao fossil teeth outside the range of modern people.

To go further, Détroit and colleagues studied the details of the bones and teeth. Together, they represent a mash of features that are confusingly reminiscent of a huge range of other hominins, and together make for something new and hard to classify. The molars, for example, are small compared to every other known species, while the adjacent premolars, bizarrely, are not so small. The molar crowns have a simple, humanlike pattern, but the premolars bear resemblance to the larger teeth more typical in older species, including H. floresiensis and some early specimens of Homo erectus. Some premolars have three roots, as sometimes found in H. erectus and more distant human relatives. The toe and finger bones also seem different from modern humans: One finger bone is curved, and the toe doesn’t seem to have been able to bend upward at the ball of the foot as much as ours. In some ways, these bones resemble hominins that lived more than 2 million years ago, such as Lucy’s species, Australopithecus afarensis. No other known species shares the whole set of features found at Callao.

So, what does this discovery mean? To me, it solidifies the case that ancient human relatives were a lot smarter and more adaptable than we used to give them credit for.

The low sea level stand of the last glaciation is just below 120 m, indicated here on the map. Flores, Sulawesi, and Luzon all have archaeological remains that predate any evidence of modern human presence in the region.

Flores lies about 2,000 miles to the south of Luzon, but both islands share a peculiar geography: Land bridges never connected these islands to the Asian continent. Another large, disconnected island in the region is Sulawesi. There, stone tools from a site called Talepu were made by hominins more than 118,000 years ago, though no fossils have been found yet to indicate who was making them. Some anthropologists have thought that the colonization of such islands over water was due to luck. Maybe ancient storms or tsunamis washed a few unsuspecting survivors onto ancient beaches. But where one strange event might be attributed to luck, three are much more interesting.

The evidence for life on these islands goes back a long way. Some hominins were making stone tools on Flores more than a million years ago, and the oldest hominin fossil on that island is around 700,000 years old. Last year, paleoarchaeologist Thomas Ingicco, from the National Museum of Natural History in Paris, and colleagues reported on work at the site of Kalinga, Luzon. There, they found stone tools and butchered rhinoceros bones, also around 700,000 years old. Very early forms of Homo must have surpassed barriers and found new ways of life in places with very different climates and plant and animal communities than their African ancestors. Meanwhile, within Africa, a diversity of hominin species continued to exist throughout most of the last million years.

It’s too early for us to say whether the earliest inhabitants of Flores and Luzon gave rise to H. floresiensis and H. luzonensis. I wouldn’t bet on it. Many new arrivals may have come between the first occupations and the later appearance of modern people in the region. One such arrival may have been the Denisovans, a mysterious group known from DNA evidence. Today’s people of the Philippines bear genetic traces of Denisovan ancestry, and new analyses of Denisovan genetic contribution in New Guinea suggest deep roots for this ancient group. Could the Denisovans have existed on Flores, Sulawesi, or the Philippines?

To answer such questions, we must reinvest in exploration. The new discoveries of the past decade or so have transformed the field of human origins. New methods of exploration, and more intensive exploration of underrepresented regions, have introduced a new paradigm. Ancient groups of human relatives were varied and adaptable. They sometimes mixed with one another, and that mixing gave rise to new evolutionary solutions. Our species today is the lone survivor of this complicated history. We have replaced or absorbed every other branch of our family tree.

Many more of these branches are surely waiting for us to find them.

This work first appeared on SAPIENS under a CC BY-ND 4.0 license. Read the original here.

Link: The women behind early anatomical illustration

2019-03-09T00:00:00-06:00

The University of Toronto has a really nice article by Romi Levine that looks at the work of anatomical illustrators in the history of Canadian medical science: “Body of work: The pioneering women behind the groundbreaking Grant’s Atlas of Anatomy”.

I was fascinated by the process of creating the large-format illustrations, which began with photographs of dissections, projected from transparencies and sketched, then painted with carbon:

“The technique they used is one that's relatively unique to medical illustration, called carbon dust,” says Wooldridge. “To get the tone in, they would rub carbon against sandpaper to get a pile of carbon dust and they would apply that with a paint brush. You would get these lovely even tonal gradations with an amount of contrast that would reproduce really well.”

[Dorothy Foster] Chubb was a master of this technique, he says. “Dorothy Chubb's work is very visually distinctive – I could recognize it immediately… It's really beautifully observed, and has a really strong sense of a light source and a really strong three dimensional sense.”

The article includes a great story of how the original illustrations were saved from the landfill, then used for a new edition of the atlas.

Link: When should academic scientists retire?

2019-03-08T00:00:00-06:00

The Scientist has a nice piece by Katarina Zimmer on the idea of mandatory retirement ages for academic scientists: “Is Mandatory Retirement the Answer to an Aging Workforce?” The lede covers a scientist at Oxford University who has won a three-year extension on the mandatory retirement age of 68.

I headed my post with “academic scientists” because the problem has different parameters for scientific fields than for humanities and arts.

For [Hagan] Bayley, however, dismissing experienced researchers at the height of their careers isn’t just unfair—it would do more harm than good for science. “I don’t think that firing faculty members at 68 is going to give you the best science,” he says. “And it’s also not good for young people,” as lab members will have to find alternative posts after their PI leaves. “You’re not firing one person, you’re firing an entire research group.”

I wanted to point to the article because it deals with the complexity of the problem at several levels, including individuals, institutions, and grant agencies.

The naming of X and Y

2019-03-04T00:00:00-06:00

The Scientist this month has a nice short article by Joseph Keierleber that recounts some of the early history of scientific investigation of the sex chromosomes: “How Chromosomes X and Y Got Their Names, 1891”.

It begins with the German biologist Hermann Henking, who studied firebug sperm and found a large lump of chromatin that he labeled “x”. It was this “x” that eventually won out in the naming of the sex-determining chromosomes, but not before some additional complexity:

In the early 1900s, Nettie Stevens at Bryn Mawr College and Edmund Beecher Wilson at Columbia University tackled the puzzle of how chromosomes relate to sex differences in insects. Although they worked independently, they followed each other’s research. In 1905, Wilson, the more established scientist, described a pair of unequally sized chromosomes, which segregated in a 50:50 ratio among insect sperm. A month later, Stevens reported a similar discovery in beetle gonads. Half of beetle sperm carried a small chromosome, which Stevens labeled “s,” and half carried its larger companion, “l.” Female somatic cells contained two copies of the large chromosome, while male cells contained one small and one large. “This seems to be a clear case of sex determination,” Stevens wrote, concluding that sperm carrying the small chromosome, not McClung’s large accessory chromosome, determined male sex.

As the story goes on to relate, it was Wilson who went on to name “X” and “Y” by following Henking’s example.

Link: Archaeology of nonhuman tool use

2019-02-27T00:00:00-06:00

Scientific American is previewing an article by Michael Haslam from their March issue, “The Other Tool Users”. The article focuses on the use of archaeological methods to recover information about tool use by nonhuman animals.

This is an archaeological dig, and it looks much like you might imagine, with buckets, sieves, strings, levels, collecting bags and measuring tapes strewn about. Yet the ancient objects that drew me here to the small island of Piak Nam Yai in Laem Son National Park are not typical archaeological finds. I am not looking for coins, or pottery, or the remains of an old settlement, or long-lost human culture. Instead I am after bygone traces of the monkey culture that is on full display up the beach.

Many thoughts in the article about how nutcracking and other uses for stone may have “pre-adapted” early hominins for later stone tool manufacture by the widespread unintended generation of sharp flakes.

A Denisovan news article

2019-02-27T00:00:00-06:00

A nice article by Ewen Callaway has just come out in Nature looking at the current scientific scene regarding the mysterious Denisovans: “Siberia’s ancient ghost clan starts to surrender its secrets”.

It’s a timely piece because there have been quite a few papers on Denisova Cave and its inhabitants during the past year, including the “Denny” individual with both Neandertal and Denisovan parents, a better chronology for the cave system and its deposits, and this unpublished news:

But more material is emerging slowly. Archaeologists excavating Denisova Cave in 2016 discovered a freshly broken chunk of parietal bone — part of the skull — that contains mitochondrial DNA from a Denisovan. The bone is shaped a bit like that of Homo erectus, a species of hominin that most researchers consider to be a close ancestor of humans, Neanderthals and, presumably, Denisovans (see ‘Tangled tree’). “Sadly, it’s not very informative. I expected more of it,” says Viola, who will describe his analysis in March at the annual meeting of the American Association of Physical Anthropologists. He hopes that the other pieces of the parietal bone, or even a complete skull, might soon be found. “It would be nice to have somewhat more,” he adds.

A lot of people are doing great science on the questions related to this ancient population, and that’s neat to see. I am really looking forward to the Denisova symposium at the upcoming American Association of Physical Anthropology meetings next month, organized by Serena Tucci and Eduardo Amorim, where I will be taking part as the discussant.

I think that Callaway’s article is a great summary of the way many people are thinking, and I recommend it. But personally I disagree with the way many scientists are thinking about Denisova.

The series of Denisova discoveries has shown that anthropologists and geneticists were fundamentally wrong in their assumptions about ancient hominin variation and population interactions. “Finding” more Denisovans, or identifying any specimen with substantive skeletal morphology that can be connected to this population would be newsworthy, sure. But we should be clearing the field of this kind of typological thinking. The fact that we did not predict the existence of this population is a pretty clear indication that morphology never had the value that anthropologists once assumed.

Link: Origins of human languages

2019-02-26T00:00:00-06:00

The online magazine Sapiens has a fascinating piece by Elizabeth Svoboda looking at the ways that new languages form: “Where Do “New” Languages Come From?”

I’ll just quote a passage from the middle of the piece that touches on the value of a language for holding together a community with its own history:

In general, fostering language vitality is one of anthropologist Gwyneira Isaac’s goals as director of the Smithsonian Institution’s Recovering Voices program. Though Isaac does not work specifically with emerging languages, she witnessed how cultural practices can help revive language after meeting a Canadian man who spoke the endangered Anishinaabe language. The man found some of his tribe’s maple syrup–making tools in a cabinet at the Smithsonian and was so excited that when he returned home, he produced a series of videos about syrup-making using phrases from his native tongue.

Young people in his community hear the language when they watch the videos, but they also encounter aspects of their cultural heritage. “This small thing of opening a cabinet turned into this journey,” Isaac says, “building the collective knowledge which is really at the base of language.”

Humans have within them the potential to create new languages by recombining elements from different source languages. That amazing generative capacity reflects a deep-seated need for communication in our species.

Quote: Two competing hypotheses

2019-02-23T00:00:00-06:00

A 2015 review paper on archaic human introgression by Fernando Racimo and coworkers has a wonderfully succinct summary of the modern human origins debate:

The relationship between modern humans and other, now extinct, archaic hominin groups has been a subject of controversy since the 1970s. Two competing hypotheses were originally proposed: the multiregional model posited that modern humans evolved in parallel throughout Africa and Eurasia from different archaic groups while exchanging migrants, whereas the out-of-Africa model proposed that all present-day humans had a recent origin in the African continent, from which they expanded across the world. However, over the past 30 years, these two hypotheses were increasingly seen as an over-simplification.

The only quibble I have is that the debate began closer to the 1870s than the 1970s!

Black Tudors

2019-02-22T00:00:00-06:00

Last year Atlas Obscura published a review of the book Black Tudors, by Miranda Kaufmann: “The Africans Who Called Tudor England Home”.

As Black Tudors details, Africans weren’t just members of society but were present during some of the major events of the Tudor era. Jacques Francis, a salvage diver from Guinea in West Africa, worked the wreck of the Mary Rose and Diego the circumnavigator explored the globe with Francis Drake. The aforementioned John Blanke would have certainly enjoyed some celebrity during his time due to his position in the royal court. He even performed at Henry VIII’s coronation and married a London woman. So, what changed? What prompted England to become a key nation in promulgating the Atlantic slave trade?

Sounds like an interesting history.

Zebra stripes and flies

2019-02-21T00:00:00-06:00

A fun story by Ed Yong in The Atlantic looks at an experiment that put horses in zebra suits to test whether the stripes confound biting flies: “The Surprising Reason Zebras Have Stripes”.

When it comes to biting insects, zebras are doubly cursed. For one, they’re highly susceptible to a variety of fatal diseases, including trypanosomiasis, African horse sickness, and equine influenza, that are spread by horseflies and tsetse flies. They’re also very vulnerable to insect attacks: Compared with other grazers such as antelopes, the hairs on their coat are unusually short, allowing flies to more easily find blood vessels with their piercing mouthparts.

Stripes, for some reason, seem to help. In 2014, Caro and his colleagues showed that striped horses—three zebra species and the African wild ass with thin stripes on its legs—tend to live in regions with lots of horseflies. And several researchers, over the years, have shown that these flies find it hard to land on striped surfaces. No one, however, had watched the insects trying to bite actual zebras. That’s why Caro’s team went to Hill Livery.

This is a great story to illustrate how hard it can be to test evolutionary hypotheses. Even this one, which requires people to systematically watch lots of horses, zebras, and horses in an experimental setup, which seems pretty obvious as a test of the hypothesis, required a very special situation and tremendous effort to carry out.

And this works only because the effect is very strong. An effect strong enough to be of paramount importance to natural selection may only be a fitness increase of 1% or less. One percent fewer flies would not probably translate to one percent fitness difference; but then again, who knows? And ten percent fewer flies would require a lot of horses and zebras to show that the sample was different from chance.

And there are reasons to criticize even this setup. Are we really talking about large flies? Do tsetse flies have similar problems with the stripes? If horseflies are a problem solved by stripes, and stripes have no evolutionary cost, then why didn’t European and Asian horses have stripes? Do stripes have evolutionary costs?

Lots of questions still, but this kind of study is rare, and I’m happy to see it!

Link: On the science of science communication

2019-02-20T00:00:00-06:00

The College of Life Sciences here at the University of Wisconsin–Madison has a very strong department of Life Sciences Communication, with some world-leading researchers in the effects and practices of science communication.

I wanted to link to this interesting interview of Dietram Scheufele, who has been working to understand what leads to effective communication of scientific research to the public: “Dietram Scheufele on #scicomm: What scientists can do to promote science and explain their work”.

Much of the interview addresses the fragmentation of the media environment and the increasing “bubble” effect in which people only see stories and news that they already agree with.

Science journalists are translators that speak the language scientists speak and can take years of complex science and rewrite it so it matters to people. Those translators are largely gone. We’re now at a point where fewer than 20 states still have newspapers with science sections. We no longer have the authoritative voice that tells us why science is important, why this finding matters for our personal life. We have to figure it out ourselves.

This is an important phenomenon for those of us engaged with the public to understand. It affects human origins a bit less than many other fields of science. I used to think that human origins research was insulated because the kinds of voices people listened to were always expert; I now suspect that the trendline seems flatter just because our field never did a very good job of communicating its results to the public.

In any event, the landscape has changed.

So, what can scientists and others who want to promote science do instead of just giving people more facts?

The thing that great science communicators are so good at is taking scientific facts and connecting them to things that matter to people. Motivated reasoning can be a problem but it’s also the path to the solution. It basically tells us that if we want to communicate meaningfully with an audience, then we need to communicate where their values and concerns are. We need to say, “This matters to your values and this is why. I, as a scientist, am as excited as you are as a potential user of this.” And we have to remember to speak to what their concerns are, not what we think their concerns or their values should be.

That last point is of central importance.

Forest monkey hunters of Late Pleistocene Sri Lanka

2019-02-19T00:00:00-06:00

Fascinating: “Ancient humans hunted monkeys for tens of thousands of years”.

If you picture early humans dining, you likely imagine them sitting down to a barbecue of mammoth, aurochs, and giant elk meat. But in the rainforests of Sri Lanka, where our ancestors ventured about 45,000 years ago, people hunted more modest fare, primarily monkeys and tree squirrels. Then they turned the bones of these animals into projectiles to hunt more of them. The practice continued for tens of thousands of years, making this the longest known record of humans hunting other primates, archaeologists report today.

That quote comes from the news story by Virginia Morell. The research is by Oshan Wedage and colleagues (it’s shameful that Science didn’t include the first author’s name in their news coverage). The paper is published in Nature Communications: “Specialized rainforest hunting by Homo sapiens ~45,000 years ago”.

This team, including Patrick Roberts, has been very interested in ancient cultural adaptations of people to tropical forest environments. The paper is based on analysis of materials from a cave site called Fa-Hien Lena.

This is not the first or oldest site to present evidence of forest hunters targeting primates and other small mammals. As the paper indicates, the site of Niah Caves, Borneo, also has such evidence. But the Fa-Hien Lena assemblage provides a good indication of the parallel cultural development of such practices in tropical forest environments, which are also shared by many living hunting and gathering peoples around the world.

The bone points made from monkey fibulae are amazing:

I gotta tell you, while there are some cool things in the Upper Paleolithic of Europe, the records of technical innovation in other parts of the world are in most cases more interesting and earlier. Archaeologists are now bringing these other areas of the world more into their thinking about the history of human adaptations, and that’s a very good thing.

The paper emphasizes the continuity of the hunting practices over a long period of time, from the earliest evidence at the site up to 48,000 years ago up into the mid-Holocene. There are a substantial number of bone tools or bone objects inferred to be ornaments in the oldest layers of the site, and the entire bone assemblage is highly fragmented and subjected to grinding in ways that suggest that bone tool production was a common activity.

I would love to have a more highly-resolved record that might reveal changes over time, whether cultural (for example, stylistic changes in ornaments) or subsistence-related. That being said, the long persistence of similar hunting strategies and technical processes documented at Fa-Hien Lena may be similar to what we are seeing in some other parts of the world. For example, a 40,000-year-long practice of hunting small forest game approaches in duration the long evidence for poison arrow hunting in southern Africa. Fairly detailed technical strategies were evidently quite stable in some ancient cultural contexts.

The Late Pleistocene layers at Fa-Hien Lena also include skeletal remains of ancient humans that were described by Ken Kennedy in his book about the evolutionary history of humans in South Asia, God Apes and Fossil Men. This paper doesn’t provide any new information about these specimens but does place them into its chronological context.

Previous excavation in Fa-Hien-lena produced the oldest human fossils so far in Sri Lanka. Remains of a 5.5–6.5 years old child, mixed with remains of at least two infants as well as a young adult female, were dated based on associated charcoal to 30,600 + 360 BP. These remains were found in layer 4 at the rear of the cave during the 1986 excavations (approximately represented by context 179 during our 2010 excavations) (Fig. 2). Overall, our new data confirm Fa-Hien Lena as the oldest site with H. sapiens fossils in Sri Lanka, and wider South Asia. They also indicate that Fa-Hien Lena now represents one of the earliest appearances of microlith toolkits and bone tool technocomplexes outside of Africa.

I think it’s a good question whether living and hunting in forests may have pre-adapted people toward development of projectile technology. It is possible for humans to get within several meters of small arboreal mammals in trees, and darts, arrows, or small thrown spears can be highly effective in this situation. Humans have converged on similar hunting strategies in forests around the world.