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john hawks weblog

paleoanthropology, genetics and evolution

Photo Credit: Pre-Clovis Gault Assemblage artifacts. Thomas Williams et al. (2018) CC-BY-NC

Thalamus in the spotlight

Knowable magazine, which covers research published in Annual Reviews journals, has a nice interview by writer Emily Underwod of Michael Halassa, an expert on the functional neuroscience of the thalamus: “A long-overlooked brain region may be key to complex thought”.

In the interview, Halassa emphasizes that the thalamus has often been assumed to function basically as a relay station between the senses and the cortex, based mainly on visual processing as a model for the rest:

What’s so interesting about primate vision and visual cognition is that when we interact with the world, we’re not just interacting with pixel intensities, we’re building internal representations of objects. That’s why you can categorize any cup you see, even if you've never actually seen that particular cup before, and it looks different from other cups. Neurons that can specifically recognize male or female faces, or respond only to a photo of Jennifer Aniston — all that exciting stuff happens in the cortex, which is part of the reason that the thalamus has been sort of shoved to the side.
But there are many other areas of the thalamus besides the LGN and other sensory areas that interact with the cortex, including areas involved in motor control and cognition. Now we are studying those too.

If you did purely imagine the thalamus as a relay station, that would not mean it was unlikely to be important to cognition. In the real-world telecommunications network, relays have to work fast and flawlessly. But to evolution, noise in a relay system is potentially a source of adaptive variation. A small change to the relay, like a slightly greater or lesser degree of crosstalk to one or another region, might often be a negative, but once in a great while might have an effect on cognition that enhanced survival or reproductive fitness. Even if the relay functions are strongly conserved among species, getting these connections slightly wrong would occasionally be useful in one or another lineage.

Humans, with a rapidly evolving brain and vastly larger cortex, might be just the lineage in which “wrong” connections might have a positive effect once in a while.

Nobel Wikipedia lapse points to the holes in science journalism

This story from Marina Koren in The Atlantic about new Nobel laureate Donna Strickland has an important message: “One Wikipedia Page Is a Metaphor for the Nobel Prize’s Record With Women”.

Unlike her fellow winners, Strickland did not have a Wikipedia page at the time of the announcement. A Wikipedia user tried to set up a page in May, but it was denied by a moderator with the message: “This submission’s references do not show that the subject qualifies for a Wikipedia article.” Strickland, it was determined, had not received enough dedicated coverage elsewhere on the internet to warrant a page.

As a science writer friend pointed out, this is a hole in science journalism. Here we have Nobel-Prize-winning work, and before the Prize was awarded this week, there were not enough stories to justify a page.

The vast majority of wonderful and important work in science will never win a Nobel. Far more good science, I’m sure, than there are writers who write about science. To have a Nobel-winning area that hasn’t been covered in depth by science writers since the 1980s is far from an unthinkable circumstance.

But clearly in this case the science press has had different priorities from physicists who judge the long-term significance of research. That means the public isn’t seeing the spectrum of highly-significant work. How many pages have been printed, and internet virtual ink spilled, on string theorists and untestable ideas? In the meantime, how much of the real empirical record of physics has gone unheralded by any journalists at all?

This is equally true in most fields of science, probably all of them. There are amazing, rich discoveries in human evolution that I think are really cool that don’t get the attention they should. I do what I can to bring attention to many of them, and I’ll keep on trying to do so.

Looking at linguistic echoes of extinct species

Priscilla Wehi and coworkers have a neat article in The Conversation describing a recent research paper that looked at traditional sayings in Māori, to try to understand whether they contain a trace of how the Māori ancestors interacted with bird species that the first encountered when reaching New Zealand: “Dead as the moa: oral traditions show that early Māori recognised extinction”.

It takes all kinds to study the past. Our team includes a conservation biologist, a linguist, a bioinformaticist and experts in Māori culture. Together, we delved into the wealth of ecological knowledge embedded in Māori oral traditions. We unpicked language cues, historical events and cultural contexts to understand habitats, animals, landscapes and the relationships between them.
Many whakataukī (pithy sayings like English proverbs) reveal intimate observations about nature. The link between flowering times and animal activity expose seasonal cycles. Whakataukī note the abundance of food resources.
Of those that refer to birds, a disproportionate number talk about moa. What they looked like. How they trampled through the forest with their heads in the air. How best to eat them.

This really is a fascinating concept, that the way that ancient people interacted with different species may be recorded in subtle ways by oral traditions. For those people who are curious about the stories of “ancients” in various parts of the world, this is the kind of linguistic research that might open a crack into unrecognized histories.

Remembering King Leopold's human zoo

National Public Radio (U.S.) has a story about one of the evils of Belgian colonization of the Congo: King Leopold brought hundreds of Congolese to Belgium to live in a mock African village for public display: “Where ‘Human Zoos’ Once Stood, A Belgian Museum Now Faces Its Colonial Past”.

The site near Tervuren is now part of the current grounds of the Royal Museum for Central Africa. As the story details, it wasn’t a one-off:

Fifty years later, Belgium built another mock African village at the 1958 Brussels world's fair. The Congolese who traveled to Belgium for the exposition thought it would be a cultural exchange, says Zana Etambala, a historian at the Royal Museum for Central Africa.
Instead, they found themselves standing behind a bamboo fence, on live display for Europeans, some of whom made monkey noises to get their attention.
"They were throwing bananas and peanuts to [the Congolese]," says Etambala, who grew up in Belgium and Congo. "And the Congolese protested against that. They wanted to be respected and not seen as animals in a zoo."

The Royal Museum today is undergoing a renovation that will bring some of the horrific stories of colonial abuses into the public displays.

The postmortem grandchild

What???

The British couple’s only child, a son, had died suddenly in a motorcycle accident, at the young age of 26. Somehow, the son’s body wasn’t recovered for two full days.
But after the discovery of the body, his parents apparently jumped into action quickly; they had their son’s sperm extracted from his body. Once extracted, the parents began the process of trying to use the sperm to bring into the world their own grandchild. Oh boy.

With a donor egg and a surrogate, the couple now has a three-year-old biological grandchild. The linked article goes into the legal aspects, including the problem that this was all impossible in the U.K., where the couple lives, and so they brought their grandchild into the world in the U.S.

Engaging scientists from indigenous communities in genomic data

This is an important news article by Lizzie Wade in Science, covering the Summer Internship for Indigenous Peoples in Genomics: “To overcome decades of mistrust, a workshop aims to train Indigenous researchers to be their own genome experts”.

The internship is a program that provides training and information about genomic research for scientists who are members of indigenous groups around the world. The idea is to bridge the mistrust that has emerged from past interactions, where scientists took samples from communities without sharing anything back.

The article gives some background on the anthropological geneticist Ripan Malhi, who has helped to organize the program. I wanted to share this paragraph describing one of his early career experiences that epitomizes why such an effort is important.

[In Malhi's early career] he kicked off his effort with a lecture at a reservation in Northern California. It was the first time he had spoken with a Native American community, despite years of studying their genetics. Expecting to gather dozens of DNA samples, "I brought a bunch of cheek swabs with me," he recalls. But at the end of his talk on DNA variation and the importance of filling in sampling gaps, the room fell uncomfortably silent. "Then one person stood up and said, ‘Why should we trust you?’" Malhi remembers. "That's a formative memory. I had not learned about anthropologists going to communities, taking samples, and just leaving."
He got no samples that day.

As Kim TallBear, quoted in the article, puts it: “If you’re going to work with Indigenous communities collaboratively on genetics, you have to be willing to make lifelong relations”.

The point is, you cannot engage people as research subjects and then just disappear. The approach of scientists in the past to indigenous groups has been fundamentally exploitative: Scientists went to communities and got samples, then did analyses, published papers, and built careers, but provided no opportunity for research subjects to shape the research, and gave nothing of value back to the people who volunteered their time and genetic information.

Changing that bad history means making real collaborations in which the research subjects have agency and influence on the study design and research questions. I would add something not reflected in this article: Descendant communities should equally have the ability to influence the shape of research on DNA from ancient remains.

This is an article that has many observations and stories worth reading, and I plan to distribute it to my classes. I highly recommend it.

Upcoming lecture: Michigan State University

For readers and friends in the Lansing area, I’ll be giving a lecture at Michigan State University on Thursday, October 4.. The talk is in the International Center room 115, at 2:15 pm.

Here’s a promo:

Hybrids and Ghosts: How ancient DNA and new fossils are changing the science of human origins.

John Hawks is delivering a lecture on Ancient DNA & Human Origins. The rapidly changing field of ancient DNA has settled into a kind of normal science, as several teams of researchers have coalesced around a set of approaches to discover the genetic relationships among ancient peoples.

I’ll be talking about Neandertals, Denisovans, and various signatures of other ancestral human populations, as well as the increasingly complex fossil record.

A better track of contamination in ancient DNA

A new paper from Anja Furtwängler and coworkers finds that the usual way of estimating contamination fraction in ancient DNA samples may fall short: “Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis”.

The upshot is summarized in the abstract:

We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.

DNA from living or recently dead people can enter ancient samples at many different stages of recovery, conservation, and curation of remains. Some laboratory methods preferentially amplify modern DNA, which is a problem for researchers who want to reduce the cost of sequencing runs. So the cost-effectiveness of ancient DNA research depends upon finding ways to increase the fraction of endogenous DNA in sequencing runs.

Reducing costs is the main reason why ancient DNA labs have thrown so much effort into obtaining petrous bones. It is not a matter of better preservation so much as a matter of higher endogenous DNA content, which makes sequencing with today’s approaches relatively cheaper. The finding in this paper that petrosal samples have a more stable relation of mitochondrial and nuclear contamination rates will probably be cited as another point in favor of the predictability of petrosal versus other sampling approaches.

Brexit fears affecting U.K. archaeologists

I have no political position on the impending departure of Britain from the European Union. Nevertheless, I wanted to point to this article in The Guardian that discusses the way that “Brexit” is affecting archaeologists and museums in the U.K.: “Archaeologists and curators leaving UK over Brexit fears”.

Kate Geary, from the Chartered Institute for Archaeologists, said EU nationals made up to 60% of workers on some projects. She said the obligation to carry out such work may be scrapped due to staff shortages, which would be “detrimental to the country’s heritage”.

A number of early career archaeologists on Twitter have added their voices, saying that they are planning to leave Britain, or have already left, to maintain their access to European Research Council funding. Hiring for academic posts in the U.K. over the past 20 years has brought many European nationals into positions in U.K. universities, and the future of many of these scientists is uncertain.

ZooMS finds more Denisovans

A nice news article in Nature about the “zooarchaeology by mass spectrometry”, or ZooMS work being done at Denisova Cave by Katerina Douka and coworkers: “Denisovan hybrid cave yields four more hominin bones”.

This approach uses the slight variations in amino acid sequence of the collagen protein to identify the mammal species represented by a small sample of bone. Within many archaeological sites, the average bone fragment is an unidentifiable piece of bone shaft that even the most skilled anatomist is unlikely to identify to species. That means the “faunal collection” of the average Paleolithic archaeological site may contain hominin pieces that cannot be identified.

Excavation at Denisova Cave, credit John Hawks CC-BY-NC-ND
Excavation at Denisova Cave, credit John Hawks CC-BY-NC-ND

The ZooMS technique allows a basic identification of a bone specimen to biological family or in some cases species. It relies upon differences in the amino acid sequence of the collagen protein in different animals.

Archaeologists can use this information on bone fragments to add resolution about prey species exploited at a site. Being able to quantify bovid, cervid, or equid from fragments might help show which species hyenas were bringing into a site, and which the hominins were hunting. But the most newsworthy use of the method has been to find hominin fragments, which then can be moved into a queue for ancient DNA sampling.

ZooMS was how Samantha Brown and coworkers identified the Denisova 11 specimen, whose DNA sequence was reported earlier this year. The Vindija 33.16 specimen originally targeted for sequencing by Pääbo’s research group was not found using collagen chemistry, but it had a similar history: a barely-identifiable bone fragment, it was assigned to the faunal collection and later identified by an anthropologist as hominin.

This week’s story, reporting on a conference presentation by Brown at the European Society for Human Evolution, is that the Denisova ZooMS sampling has uncovered an additional four hominin fragments. The work goes on, systematically going through thousands of bone fragments:

Meanwhile, Douka, Brown and a handful of volunteers will continue to sift through thousands more bone fragments.
So far, they have found 1 hominin bone for about every 1,000 animal ones in this cache. At this rate, they could find as many as 400 more hominin specimens.

If you could open up any museum drawer and find one previously-unidentified hominin bone in every 1000 bone fragments, it would be a massive advance by any measure. If you could identify such bone fragments at every archaeological site, the resulting sample would provide an unparalleled record of hominin populations in the past–not to mention, we’d find a few ghosts in the process.

Most fossil settings are dominated by fragments, and most bone fragments within mixed assemblages are not identifiable to species. An advance like ZooMS should remind everyone of just how much useful biological information has been lost from sites excavated in historic times when archaeologists simply did not collect unidentifiable bone fragments. The backdirt of old archaeological sites is full of bone fragments and stone artifacts that were “not good enough” to bother cataloging and collecting. In a few cases, recent archaeologists have returned to those backfill deposits, finding bone fragments–even refitting them to broken specimens that made it into museums. Without such extraordinary luck, those massive backdirt piles remain contextless, drifting flotsam of bad archaeology. ZooMS can’t fix that problem now; the context is already gone.

Digging sites responsibly means recording and preserving context for the future. Archaeology is inevitably an act of destruction and it is not possible to retain every microscopic detail or chemical trace, especially since what makes those traces meaningful is their position and situation within a site. Recording every site at a microscopic level is not possible with today’s approaches.

Tomorrow’s approaches will be better. Testing every bone fragment has just come into the realm of possibility, but remains incredibly time and resource-intensive. It can yield huge dividends at a site like Denisova where the information can catalyze ancient DNA recovery. This kind of large-scale chemical testing may not presently justify the cost for most archaeological sites, but it will be cheaper in the future–or may help to justify a reduced intensity of digging and a higher intensity of sampling at some sites.

Recognizing how technology brings the potential for better information recovery, archaeologists must sample sites deliberately, with an eye toward what is possible today with time-intensive methods, and what must remain for the science of future generations.

The ZooMS method, as exciting as it is, relies upon collagen preserved in bone fragments, and so archaeologists can apply it only to sites where collagen is preserved, which are mostly within the past 100,000 years or so. Will we ever have a method that will allow paleontologists to make use of the fragments of bone within older sedimentary contexts? I think we will.

Related:

“A visit to La Grotte de Cotencher”

“Identifying the species used to make bone arrowheads”

Link: Identifying the species used to make bone arrowheads

The Conversation is running a neat story by Justin Bradfield that details the use of the ZooMS protein-barcoding technique on bone arrowheads from Late Stone Age archaeological sites in South Africa: “New technology tells us which animal bones were used to make ancient tools”.

The results indicate that farmers used fewer species for tool manufacture than they hunted for food. We also found that certain animal species were used for tools that didn’t appear to have been hunted for food.
We identified a narrow range of antelope from the bone tools from nine archaeological sites from Gauteng and Limpopo. Of particular interest is the presence of sable, roan, zebra and rhino. Until now, we didn’t know that these species’ bones were used to make tools in southern Africa.

The story is a popular rendering of results from a research paper out last week in Archaeological and Anthropological Sciences: “Identifying the animal species used to manufacture bone arrowheads in South Africa”.

Although this particular research doesn’t strike into the deeper-time use of bone as a raw material, such as by Neanderthals, it does show the potential of the ZooMS bone-identification method to address some of the (in my opinion fallacious) arguments about bone tools. I’ll look forward to seeing more ancient work on the species that earlier hominins used for toolmaking.

BRICS leaders meet Homo naledi

Last week, the leaders of the BRICS nations (Brazil, Russia, India, China, and South Africa) met in a joint summit in Johannesburg, South Africa, along with other leaders and government representatives. One of the unique events during the summit was a “virtual” visit to the Maropeng Visitor Centre of the Cradle of Humankind World Heritage Site.

The SA News agency wrote up a story about the visit: “BRICS leaders get a taste of Cradle of Humankind”.

The Cradle WHS is home to many famous hominin fossil sites, including Sterkfontein, Swartkrans, Cooper’s Cave, Malapa, and Rising Star. For the last year, Maropeng has been the host to an extraordinary public exhibition of the Rising Star fossil material, including the new fossils from the Lesedi Chamber. For last week’s BRICS meeting, these were joined at Maropeng by some other significant skeletal remains from the Cradle, including the STW 573 “Little Foot” skeleton from Sterkfontein, and the MH1 “Karabo” skeleton from Malapa.

The South African minister of Higher Education and Training, Naledi Pandor, led the virtual tour.

Pandor went on to give the BRICS leaders an exclusive view of three types of specimen hominin fossils that were on display. These were Homo naledi, “Little Foot” (Australopithecus prometheus) and “Karabo” (Australopithecus sediba).
It was the first time that “Little Foot” was on public display, after having been recovered from the rock in which it has lain buried for the past 3.67 million years at Sterkfontein.
The BRICS leaders were first taken through the origins of Homo naledi, one of the fascinating discoveries in human origins.
Consisting of more than 1 550 numbered fossil elements, the discovery is the single largest fossil hominid find yet made in Africa.

It’s really exciting that the South African government is so proud of the fossil discoveries, and that South African scientific work can shine in this way.

Heritage and science development are much more central to the conversation at meetings like BRICS, compared to the political and economic focus of the G7. I’d say that the larger economies have misplaced—or, maybe, shorter-term—priorities. Taking the long view might help us all find greater common ground.

'Museum of Man' to change name

This came across my feed this morning: “San Diego Museum of Man In Balboa Park Wants Your Help Deciding New Name”.

It’s a good idea—the name is confusing:

But one tourist from Europe said he thought the museum was literally just about males.
"When I was there I thought it’s only for men," Intan Devreies said. "In the Dutch language, "man" means man not humankind."
A spokeswoman for the Museum of Man said a new name will not be unveiled until 2020.

The thing is, in the twenty-first century, “Museum of Man” sounds like somebody’s idea of a hip, ironic name for a museum actually devoted to men.

Link: A visit to La Grotte de Cotencher

The SwissInfo news site has a nice article about a Neandertal site in Switzerland: “Meet a Neanderthal woman from one of Europe’s oldest cave sites”.

Now you can see the exact spot where the woman was discovered. Since early June, this cave, “La Grotte de Cotencher” – just a short drive and walk from the town of Neuchâtel – has been open to the public for guided tours. The cave is the oldest archeological site in this part of Switzerland showing human habitation. The woman’s jaw was found on a little shelf of earth the size of a dinner plate.
“We call her ‘La Dame de Cotencher”, says archeologist François-Xavier Chauvière, who has been in charge of excavations at the cave since 2016.

It’s always neat for me to see human evolution heritage tourism and public communication expanding into countries where they have not been as prominent historically. Switzerland has a history of great research in human origins, and it’s great to see expansion of Paleolithic archaeology in the country itself.

Still, I always hate to hear about the sheer amount of material removed in early twentieth-century excavations:

Those explorers had to crawl in on their bellies, bumping their heads on the low ceiling. Between 1916 and 1918, they removed some 300 cubic meters of soil and rock (and animal teeth and bones).
But now you can stand up and easily move around the 1375-cubic meter cavern. Yet, this space is still smaller than what the nomad cave clans found more than 72,000 years ago. In the Pleistocene Epoch when hunter-gatherer Neanderthals sheltered here, this cave above a stream, was considerably larger than what we see today, because, since then, millennia of earth, rock, leaf litter and the sands of time have accumulated.

Modern excavations remove very little material, and leave as much of the original profile as possible.

Three hundred cubic meters is a lane of an Olympic swimming pool. Archaeologists today have to work around the destruction of past generations, and must do their best to avoid destroying evidence that future generations might recover with new technologies.

DNA genealogy and forensic cold cases

This year there have been some amazing new leads in “cold cases” by using a new kind of DNA approach, using public genealogy websites to look for people who are similar to samples from crime scenes and thereby identifying suspects by finding their genetic relatives.

Today NBC News is running an article that reports on a new case solved with genealogy, and gives some broader perspective: “‘This is just the beginning’: Using DNA and genealogy to crack years-old cold cases”.

Then, this spring, that company, Parabon NanoLabs, called back, offering to perform a new type of DNA testing that went far beyond the traditional biometric match police labs use. Fort Wayne agreed, and six weeks later the company’s lead researcher reported that she’d narrowed the list of potential suspects to two brothers. On Sunday, detectives arrested one of the brothers, who confessed.
This seemingly rapid resolution to a long-stalled murder case is becoming something of a trend: It is the fifth cold case solved by Parabon and their researcher, CeCe Moore, since early May, meshing high-tech DNA analysis, traditional genealogical work and the soaring popularity of online ancestry databases. A sixth, involving an accused serial killer in California, was solved in a similar manner.

Some people think this is the next big step in restoring justice to victims, others think is it a major potential invasion of genetic privacy.

I haven’t written about these cases yet, but I have to say this forensic approach may be the most significant story in human genetics this year.