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paleoanthropology, genetics and evolution

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

Handaxes trailing up the coastline

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

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

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

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

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

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

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 Callao Cave, Philippines, in buccal view
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.

Map of island southeast Asia indicating sites discussed in the text
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

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?

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

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

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

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

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

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

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.