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john hawks weblog

paleoanthropology, genetics and evolution

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

'Stand Up Science' in Madison Tuesday, January 29

On Tuesday evening, January 29, I’ll be taking part in a show at Comedy on State here in Madison, with comedian Shane Mauss: “Stand-up comedians + scientists = Stand Up Science”.

Award-winning stand-up comedian and science podcast host Shane Mauss presents Stand Up Science!
Learn and laugh as local scientists, comedians and other special guests join Shane to bring you an unforgettable 2 hour show that is equal parts ahas and hahas
Stand-up comedy and science have a lot in common. They both reveal truth, change our perceptions, and challenge the status quo. So why are they so underappreciated? Admittedly, comedy sometimes underestimates the intelligence of their audience, catering to the lowest common denominator. And science has the stigma of being overly complicated, unrelatable or boring. Until now.

Should be a fun evening, and if you’re in Madison, you should check it out!

Will biological anthropologists start publishing in American Anthropologist again?

Adam Van Arsdale and Mary Shenk put out a call in American Anthropologist for more biological anthropologists to submit their work to American Anthropologist: “Biological and Evolutionary Perspectives in American Anthropologist: An Editorial Provocation”.

As sections of AAA, the Biological Anthropology section and the Evolutionary Anthropology section have seen declining membership over the past decade, collectively representing fewer than six hundred active members. This decline can be seen within the pages of American Anthropologist as well. Ironically, the past two biological anthropology year‐in‐review pieces published in the journal (Gokcumen 2018; Nelson 2017) cite a total of just three articles published in American Anthropologist, two of which are themselves reflections of the kind of mixture of introspection and identity crisis that have come to dominate many of the conversations around biological anthropology's place within anthropology since the time of Boas: a copy of Alan Goodman's AAA presidential address, “Bringing Culture into Human Biology and Biology Back into Anthropology” (2013), and Wiley and Cullin's “What Do Anthropologists Mean When They Use the Term Biocultural?” (2016).

During the 1990s, American Anthropologist published some of the most important papers on modern human origins. I’m proud of my 2003 article in the journal that reviewed this history, which was an important contribution to my early career record. It was especially neat to have this article included in the “virtual issue” last fall, “Genetics, Biology, and Race: Understanding Human Difference”.

With that kind of innovative publishing, the journal has a chance of recovering some of the attention of biological anthropologists. It’s a pity that the American Anthropological Association has not taken the chance to move this journal to an open access policy, but I can’t see it being very long before that change happens.

Link: The academic battles of ancient DNA

This week the talk of archaeology and human genetics is a long feature article in the New York Times Magazine about the academic struggles of ancient DNA: “Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?”

Of course the answer to the title question is, “Both”. Ancient DNA evidence has generated enormous advances in our understanding of past human societies, and the relationships of present-day peoples.

The author of the article, Gideon Lewis-Kraus, gives the broad context of the science for readers who haven’t been following advances closely. He also focuses on a recent series of papers looking at the population genetics and ancestry of people in Vanuatu. So there is the intersection of studying the ancestral bones of people who are not represented in industrialized DNA labs, the rivalry between competing labs who are publishing on other archaeological samples addressing the same “big questions” about the peopling of the Pacific, and the complex interactions between archaeologists and geneticists in their attempts to understand the past.

It is a long article with much complexity.

I want to quote a passage from the middle, which helps to explain why David Reich has become such a focus of attention and controversy in this field. It is the avowed establishment of a “factory” approach:

So in 2013, Reich, along with a veteran of Paabo’s lab and a longtime mathematician collaborator, retooled his shop at Harvard Medical School as one of the country’s first dedicated ancient-DNA labs. The idea, he writes in his book, “was to make ancient DNA industrial — to build an American-style genomics factory” that would liberate such fields as archaeology, history and anthropology from hitherto insoluble debates.
He was more successful than even he anticipated. By the end of 2010, only five ancient genomes had been sequenced in total, but in 2014, 38 were done in one year. Soon the number will be close to 2,000. Reich’s lab alone is responsible for at least half of the published output, which doesn’t include some 5,500 more bones in the process of being analyzed and 3,000 more in storage. “Ancient DNA and the genome revolution,” he declares in his book’s introductory overture, “can now answer a previously unresolvable question about the deep past: the question of what happened.

I have many thoughts about the current state of this field. I think it has gone too far in destroying bone samples that are irreplaceable, and it has done so in a way that is unsustaintable in scientific terms.

Using the language of industrial processes is appropriate. In ten years, the factory will be outmoded, the resource depleted, and scientists who remain genuinely interested in broadening participation in understanding ancient people will be picking up the pieces. Maybe there will be a new factory.

It will take me some time to write up those thoughts in a more concrete way.

In the meantime, the one thing that disturbs me the most about this article, which I have pointed out on Twitter, is the sheer number of scientists who were willing to give insight on this field, but who requested to remain anonymous.

There thus reigns, in the world of ancient DNA, an atmosphere of intense suspicion, anxiety and paranoia, among archaeologists and geneticists alike. In dozens of interviews with practitioners of both disciplines, almost everyone requested anonymity for fear of professional reprisal. Many archaeologists described a “smash and grab” culture in which hopeful co-authors source their bones by any means necessary. Among teams at work on any given excavation, it takes only a single colleague to deliver a bone to one of the industrial giants for the entire group to lose control of their findings. Museums, too, are being swept up by the perverse incentives: One of the geneticists told me stories about having brokered an agreement to sample a particular collection, only to arrive and discover that someone else showed up the previous day to claim the same bones under a false pretense. The weaker the institutions of the country, the harder it is for local researchers to have a fighting chance. Scientists in Turkey and Mexico told me that museum curators routinely had to explain that they had promised their native bone collections elsewhere. As one ancient-DNA researcher in Turkey put it to me, “Certain geneticists see the rest of world as the 19th-century colonialists saw Africa — as raw-material opportunities and nothing else.”

I want to be clear. This passage describes my experience of this field. I also personally know dozens of archaeologists and geneticists working with ancient DNA who share this experience.

How capable were early hominins of crossing water?

Last summer I published a piece on Medium about the possible ancient existence of hominins on Luzon: “This is where scientists may find the next hobbits”.

For people who may not be familiar with this story yet, a study in Nature last year by Ingicco and colleagues (http://dx.doi.org/10.1038/s41586-018-0072-8) reports on the butchered remains of an ancient rhinoceros from a place called Kalinga, on the island of Luzon. The bones have cutmarks and at least one percussion mark, and were found with some stone flakes, and one hammerstone. The remains are around 700,000 years old.

A reader asked me to dig back into the behavior issue:

I have a question for Prof Hawks. Given the recent discovery of hominin presence in the Philippines, do you think that paleoanthropologists have been underestimating the extent of behaviour possible by archaic humans as far as possibly Homo erectus?

The islands of Indonesia had very different geographic connections in the past. Java, Borneo, and Sumatra are large islands that were connected to the Asian mainland during periods when the sea level was 120 meters lower than today. That’s why they had (and still have) animals like rhinoceros, tigers, and orangutans that were also common in Southeast Asia.

Philippines ancient sea level map
Philippines and neighboring areas. Present land areas are shown in green, also shown is the 120-meter depth line marking ancient land areas during the last glaciation.

Java, at least, also had Homo erectus populations starting as early as 1.5 million years ago, and lasting up to a half million years ago. We do not have evidence of any other hominins on Java at this time or earlier, but there is some good evidence now that the Homo floresiensis population may be a descendant of an earlier branch than even H. erectus. So maybe we’re talking about a hominin with an even more distant relationship to humans today.

The Philippines were never connected to the Asian mainland. The animal species there must all have crossed water at some point to get there. This was definitely possible for many non-human species, and the Philippines had both extinct forms like rhinoceroses and stegodonts, and surviving forms like tarsiers. All of them must at some point in the past have made one or more water crossings to get to these islands. The tarsiers have been there for more than 30 million years, so we’re not looking at one pulse of events leading to today’s species, at all – ancient humans and modern humans were both part of a much longer story.

This seems like a parallel case to the island of Flores, where hominins were living and making stone tools by a million years ago. Some of those Flores hominins survived, and we find their remains as Homo floresiensis, with one fragment of jaw 800,000 years old, and more skeletal remains in the period leading up to 65,000 years ago from Liang Bua cave.

Many archaeologists doubt that any hominins 700,000 years ago, or a million years ago, or even Neandertals 100,000 years ago, had the cultural and cognitive ability to make boats. They think it is more likely that some “lucky” individuals were caught up in a tsunami, and washed across the sea from Java or Borneo to these islands.

To support this idea, they point to the 2004 tsunami that affected Aceh, Sumatra, and washed many people far out to sea. Some of them survived for many days before being rescued:

https://www.telegraph.co.uk/news/worldnews/asia/indonesia/11309717/Boxing-Day-tsunami-I-survived-nine-days-alone-in-the-Indian-Ocean.html

Nothing about that idea is impossible. Maybe some ancient hominins were lucky survivors. But the idea gives early hominins very little credit for knowledge of their environment.

Some scientists start from the notion that we cannot assume “complex” behavior without extraordinary evidence. But what is “complex”? Is it hard to imagine that a medium-sized mammal species, which relies on foraging across 100 square kilometers or more for high-energy foods, would be aware of islands that are in sight?

Personally, I have a different opinion. I think we have to recognize a continuum of abilities. Extraordinary ideas and abilities probably existed in most ancient populations. Today, in our very large population with huge economic and social incentives for innovation and discovery, those abilities can change the world. But in the past, in low-density populations living on the edge of survival, most innovations could never have become sustained, long-term traditions that leave an abundance of archaeological evidence.

Nonetheless, they changed the world for an individual, or a group.

When it comes to colonizing a new island, it is the exceptional that matters. In fact, if crossings were regular, island populations could never evolve to be very different from nearby mainland populations. It is the very fact that crossing is rare that allows island adaptations to emerge after the population is established.

But it is also the group that matters. A single individual cannot found a new population.

When you look at these places in island Southeast Asia with early hominin activity, ancient sea levels were much lower and all these islands are one or two small hops across narrow straits. Palawan is an island between Borneo and the Philippines, and today these water crossings are hundreds of kilometers, but in the past they may have been as narrow as ten kilometers.

That’s not very far to imagine hominin individuals making crossings, if they were already playing with very basic ways of crossing rivers and using near-beach water resources.

How much did Y chromosome haplogroups shape our current picture of early modern humans?

Earlier this month I published a piece on Medium about our changing picture of modern human origins in Africa: “Three big insights into our African origins”. There really have been amazing changes during the last few years, and those comments–directed at geneticists–raise many questions about the way forward.

Last year, after the announcement of redating of hominin material from Jebel Irhoud, Morocco, I had a reader question that is very relevant to this topic:

Is the recent redating of "anatomically modern humans" and the reclassification of North African Archaics (like Jebel Irhoud) in part a response to the finding of the introgressed A00 haplogroup?

This is a great question. It’s hard to say exactly what goes into the background of people’s thinking. The data that tell us something about “early modern” humans has just changed enormously in the last five years.

The A00 haplogroup was described by Fernando Mendez and colleagues back in 2013 (https://doi.org/10.1016/j.ajhg.2013.02.002). It is a Y chromosome branch that seems to diverge from the rest of the modern human Y chromosome tree between 240,000 and 580,000 years ago. It’s found today in some Mbo men from present-day Cameroon, and some African-American men.

That’s very early compared to the rest of the Y chromosome tree. It is not very early compared to the autosomal genome, which shows that African populations started to become genetically differentiated around 300,000 years ago or so.

There’s a suspicion that this haplogroup may have entered recent human populations by interbreeding with a more ancient, diverged branch of archaic humans. It’s possible. The story of African “archaic” humans today is intricate, because we have just enough data to raise questions and not enough data to answer those questions.

For example, the Iwo Eleru skull fragment, from Nigeria, is a specimen that we now recognize is less than 16,000 years old, but is archaic-looking in some details of its anatomy (https://doi.org/10.1371/journal.pone.0024024). Maybe this is a late-surviving pre-modern human population in West Africa that contributed to today’s people in some degree.

There is evidence for “ghost population” contributions to West African people, and central African hunter-gatherers. All of this evidence comes from statistical examination of genomes of living people, and different research groups have come to different conclusions – some point to multiple admixtures, from very ancient, diverged groups that may have been as different as today’s people from Neanderthals, but all within Africa.

Others point to a possible “pre-modern” population, an outgroup to all of today’s modern people but maybe only 400,000 or 500,000 years diverged, that contributed a much bigger fraction of West African genetic ancestry today. I think there’s a good chance that the Jebel Irhoud hominins belonged to such a “pre-modern ghost” population. The anatomy of these crania is not what I think the common ancestor of all of today’s African populations probably looked like. But that’s a guess.

It’s going to be a while before these studies start to converge on a single picture, because they’ve been using different samples and different methodologies.

Honestly, I think the Y chromosome haplotypes are not coming into people’s thinking. The reason for this is that most people now recognize that the uniparental lineages, the mtDNA and Y chromosome, are not very helpful once you get back into the initial stages of diversification of today’s African populations.

The A00 haplogroup does not seem to mark that early diversification, because it isn’t present in Khoesan as far as we know. And if our mtDNA mutational timeline is correct, the autosomal differentiation of Africans started long before the mtDNA “Eve” lived.

Personally, I think these uniparental systems are probably reflecting natural selection on various haplogroups, and the introgression dynamics are driven by their fitness in different environments and genetic backgrounds.

Link: 'Africa' in the desert? Stop it now

This is going around from people who think it’s hipster and cool and ought to know better: “Africa by Toto to play ‘for all eternity’ in Namib desert - video”.

'I … wanted to pay the song the ultimate homage and physically exhibit 'Africa' in Africa,' Siedentopf told NPR. 'The Namibian desert — which is, with 55 million years, the oldest desert in the world — seemed to be the perfect spot for this.'

I like Toto’s “Africa”, but this is graffiti on the Mona Lisa. I hope somebody finds this thing and eliminates it with extreme prejudice.

Link: Field Museum Native American collection

This is an important article in Chicago magazine, “An Artist Addresses the Field Museum’s Problematic Native American Hall”. The article is a review of a new art installation happening at the Field, by artist Chris Pappan and it includes many nice images with the story of the exhibit.

For me, the most significant part is near the beginning of the article, looking at the way that the Field is planning how to exhibit its collections moving forward into the next century:

The case labeled “Indians of the Chicago Region,” for instance, makes no mention that the greater metropolitan area now has the nation’s third largest Native American urban population. This restricted view can be traced back to the museum’s beginning. Native American objects acquired for the 1893 World’s Columbian Exposition by anthropologist Franz Boas — who believed he was salvaging remains of disappearing cultures — were part of its founding collections.
After six decades of this static display, the tribal nations connected to these objects will finally have a voice in their presentation, emphasizing their place in living culture. In October, the museum announced a three-year renovation of the hall. When it reopens in 2021, it will not just represent a new direction for the Field Museum but will reconsider what natural history museum ethnographic galleries can, and should, be in the 21st century. The challenge is in recognizing the colonialism in their roots while involving indigenous voices that have long been left out.

It is valuable and critically important to include the diversity of cultural experiences in museums. But the creation of these exhibits and collections in the past was based upon incorrect views, often racist and Eurocentric. I cannot even express how many exhibits I have seen that were created during the 1960s to the 1980s, that describe cultures as if they stopped in time when the objects were collected.

The Field has a remarkable collection, and I am glad they are moving to find new ways to tell the stories, including the voices of descendant populations.


Notable paper: Zanolli, C., Pan, L., Dumoncel, J., Kullmer, O., Kundrat, M., Liu, W., … & Tuniz, C. (2018). Inner tooth morphology of Homo erectus from Zhoukoudian. New evidence from an old collection housed at Uppsala University, Sweden. Journal of human evolution, 116, 1-13. doi:10.1016/j.jhevol.2017.11.002

Synopsis: Zanolli and coworkers studied a small sample of teeth in Uppsala that had been taken to Sweden by Otto Zdansky in the 1920s. Being held in Sweden, these teeth escaped the loss of the rest of the Zhoukoudian fossils during the Second World War. Zanolli’s team carried out CT scanning of the fossils and studied their enamel-dentine junction (EDJ). This part of the internal structure of the tooth reflects the initial stages of development of the tooth crown, and can preserve evidence of anatomy even as the occlusal surface of the tooth develops wear.

Interesting because: The results suggest that Chinese H. erectus may have been taking a different evolutionary pathway from H. erectus in Indonesia. Zanolli and coworkers emphasize that an Indonesian H. erectus sample from later in the Middle Pleistocene, from Ngandong, has “simplified” EDJ morphology compared to earlier Indonesian samples. Zhoukoudian teeth have a more similar form to earlier Indonesian teeth than to Ngandong teeth, even though the Ngandong teeth are more similar in age. That difference might just be teeth, although the cranial and mandibular morphology also shows some consistent differences between Zhoukoudian and Ngandong, as evident since Franz Weidenreich studied the samples. This may be a sign of deep population divergences and history within the sample long known as Asian H. erectus.

Evolutionary connections: As pointed out in this paper, Yousuke Kaifu and colleagues (2015) examined the EDJ morphology of Homo floresiensis teeth, and concluded that they reflected a very simplified form compared to H. erectus. That seems to be a similarity with later H. erectus specimens from Java like Ngandong. That’s interesting in light of the observations by Debbie Argue and coworkers (2017) and Mana Dembo and colleagues (2016) that H. floresiensis seems to be deeply rooted in the phylogeny of Homo and not closely related to Indonesian H. erectus.

Link: A historic mystery about blue specks on teeth

A new article in The Atlantic by Sarah Zhang looks at some fascinating detective work on ancient teeth by Christina Warriner and Anita Radini: “Why a Medieval Woman Had Lapis Lazuli Hidden in Her Teeth”.

The study of microscopic and chemical remains that are embedded in ancient dental calculus has become very important to understanding prehistoric diets, health, and lifestyles. What a lot of readers might be less aware of is the way that they can inform about much more recent, historic populations.

If pigments can be preserved in tartar—the gunky yellow stuff on teeth that dental plaque hardens into—that means that fibers, metals, and other dyes could be, too. “This is genuinely a big deal,” says Mark Clarke, a technical art historian at Nova University Lisbon who was not involved in the new study. You could imagine identifying metalworkers, carpenters, and other artisans from the particles embedded in tartar, Clarke says. “It’s opening up a new avenue in archaeology.”

How much do X-rays and CT scans affect ESR dating?

The electron spin resonance (ESR) method of geological dating relies upon the idea that newly-formed solids (such as tooth enamel or igneous rock) are affected by natural radiation over time, resulting in unpaired electrons that give rise to a paramagnetic signal. Groundwater and sediments contain low levels of uranium and other radioactive elements, many of which are part of the uranium decay chain. Also, cosmic radiation impacts materials that are buried at shallow depths. Laboratory equipment can measure the signature that results from this natural radiation over long periods of time, and if the rate of natural radiation is known, the present signature can be used to estimate the age.

More and more, ESR has become important to understanding the ages of hominin fossils. It is one of the few methodologies that can apply to biological material older than around 50,000 years. But the technique is complicated for many reasons. The level of uranium in the immediate environment of a fossil tooth can vary greatly over time. The uranium that is absorbed within a fossil matters a lot, and this can be absorbed quickly or slowly.

So any estimate of geological age is based on an assumption that the present-day measurement of radiation is relevant to the past. To understand the uranium history, ESR analysis is usually carried out in conjunction with direct measurements of uranium and its decay products (usually thorium) in the fossil tooth. Results are often reported using a series of different statistical models, including “early uptake”, “linear uptake”, or others.

But ESR on teeth is not just a method for geological dating. It’s also a method for measuring radiation doses experienced by people who have been exposed to X-rays and other artificial forms of radiation.

For example, Ishii and colleagues (1990) examined teeth extracted from people who lived near Chernobyl and were exposed to radiation. Similar approaches have been used to examine the accumulated dose from dental X-rays. Scientists have even applied ESR to assess irradiation of food.

Those applications hint at a big problem for archaeologists who want to know the geological age of fossils. Newly-uncovered fossils straight from the ground are one thing. But when scientists uncover fossils, they often start to subject the fossils to human-induced high-energy radiation. The most common and important of these is X-ray radiation from radiography and CT-scanning. These methods have been very important to studying the morphology of fossil material, but they have strong effects on the overall radiation dose suffered by a fossil.

How much?

Recently, scientists have been concerned whether X-ray radiation from CT scanning may damage the preservation of DNA or other ancient biomolecules. Medical devices have long been tuned to lower radiation levels, but examination of fossils has often been done with industrial or research microCT devices that exert higher radiation doses. Some fossil tooth enamel has been visibly darkened in color by such scanning.

Alexander Immel and coworkers in 2016 investigated the effects of such scanning on ancient DNA preservation in subfossil material. They found that conventional exposures to X-ray radiation used in synchotron scanning caused significant degradation of ancient DNA. Doses in those cases could exceed 2000 Gray. Doses below 200 Gray did not have a substantial effect, and they judged that micro-CT devices would not normally result in doses that damage ancient DNA to an appreciable degree.

That’s good news for most studies of ancient DNA. But it’s sobering to realize that a high enough dose of radiation used in morphological analysis can actually chemically damage ancient DNA. ESR relies upon a much more subtle signal of energy in ancient fossil remains. What effect will smaller radiation doses have on this signal?

A couple of months ago, Science published an exchange of comments responding to a paper published early last year on the hominin fossil from Misliya Cave, Israel. This maxilla was published by Israel Hershkovitz and coworkers with an ESR age estimate between 177,000 and 194,000 years: “The earliest modern humans outside Africa”.

Misliya maxilla, mirrored in a CT rendering
Misliya-1 maxilla, the rendering based on CT data from Gerhard Weber, distributed to the media.

That result was challenged by Warren Sharp and James Paces, who wrote a “Comment on ‘The earliest modern humans outside Africa’”. They raised their challenge based upon a sampling of carbonate crust on the fossil used to calibrate the U-series age and thereby the ESR age.

But Hershkovitz and colleagues, “Response to Comment on ‘The earliest modern humans outside Africa’”, responded more broadly to issues besides the narrow question of the carbonate. In their comment, they observe that the radiation dose of CT-scanning was a significant element of doubt that they did not previously report:

Direct dating of Misliya-1 provided a U-series age of 70.2 ± 1.6 ka and a combined U-series and electron spin resonance (US-ESR) age of 174 ± 20 ka. Because uranium uptake may be delayed after the death of the organism, and because it is difficult to accurately evaluate the radiation effects from previous computed tomography (CT) scanning, these two ages should be regarded as the minimum and maximum age brackets for the fossil, respectively. Misliya-1 was CT-scanned three times prior to the ESR dating analysis (1). The x-ray dose during CT scanning is highly variable (6–8). On the basis of our recent study (7), we could roughly estimate that the total x-ray dose was approximately 30 Gy, resulting in an effective equivalent dose (DE) value of 98.3 ± 5.3 Gy. The corresponding US-ESR age would thus be 152 ± 24 ka (i.e., agreeing within error with the TL results). However, considering the significant uncertainty in the true x-ray dose absorbed by the tooth sample, regarding the cited date of 174 ± 20 ka as a maximum age is the most straightforward and reasonable interpretation of the combined US-ESR result.

That’s an interesting analysis of error, and one that deserves attention. In this case, three CT scans of the Misliya-1 fossil were done. Multiple scans are not uncommon in morphological analysis. It is not at all uncommon to do a medical-resolution CT and then later follow up with higher-resolution micro-CT. Also, it is often difficult to estimate what radiation level will be effective in producing images, because the circumstances of mineralization and preservation vary within a fossil. If the first scan doesn’t produce good results, it may take several trials.

Here, the exact dose of X-rays could not be determined. So Hershkovitz and coworkers provide a “rough estimate” of 30 Gray. The “effective equivalent dose” is an attempt to examine how damaging the actual radiation dose was for the purposes of ESR – this is higher than the total dose because the energy of the X-rays is disproportionately damaging to the ESR signal. In their estimation, the CT scanning results in an overestimate of the age of the fossil by some 15 percent (from 152 ± 24 ka to 174 ± 20 ka).

In this case, even though the ESR estimate must be younger that originally reported, the biological interpretation is not very different. The ESR age estimate is augmented by thermoluminescence results on stone artifacts from the Misliya site that have roughly similar and overlapping age estimates as the maxilla. The interpretation of the fossil depends on the accuracy of its association with this archaeological layer, and the exact value of the ESR estimate makes little difference.

That being said, Misliya-1 is a much better situation than many fossils. Many of the fossils in today’s textbooks were unearthed in the early twentieth century. At that time X-rays themselves were cutting-edge science, and not well understood. Early radiographs used high radiation doses and very slow film, which required long exposures to record an image.

Some of those early fossils were subjected to radiographs many, many times. As the specimens have retained their importance in morphological comparisons, every new advance in measuring morphology required that they be re-studied with the newest methodologies. Countless radiographs from the dawn of roentgenography, medical radiographs, early medical CT-scans, high-resolution medical CT-scans, micro-CT scans.

We’re talking about the pre-1960 era when shoe salesmen used X-rays to fit their customers, and ended up with horrible radiation consequences.

I’m surprised that some fossils aren’t glowing by now. Most scientists do realize this, and it’s why no one has attempted to do ESR dating on some important fossils. The context and subsequent history of them after excavation just has not been recorded to a standard that would allow any accuracy at all.

But no doubt in the future some scientists will irresponsibly attempt to apply ESR methods on fossils without accurate context or full records of radiation subsequent to discovery. As the Misliya case shows, a dose from modern CT-scanning results in the overestimate of the age by 15% or more. A history with many X-rays and CT-scans of unrecorded dosage would have a much greater effect.

I take from this another lesson: It is tremendously important to the future of the science that we share CT data widely and freely. There should be no excuse to replicate unnecessary high radiation doses on fossil material. Institutions should demand that CT scans be lodged in repositories where other researchers can use them freely.


Notable paper: DiNapoli RJ, Lipo CP, Brosnan T, Hunt TL, Hixon S, Morrison AE, et al. (2019) Rapa Nui (Easter Island) monument (ahu) locations explained by freshwater sources. PLoS ONE 14(1): e0210409. doi:10.1371/journal.pone.0210409

Synopsis: DiNapoli and coworkers show that the monumental platforms on Rapa Nui (often known as Easter Island) are distributed around the island in ways that relate to freshwater seeps, which are important water sources. By contrast, they do not correspond as well to other important resources on the island including gardens and marine foraging locations.

Interesting because: Construction of monuments by all kinds of ancient people was an incredibly important social activity. The placement of monuments may tell us about social ideology or relationships; or alternatively it may reflect more prosaic environmental issues that had importance to ancient lifeways—in this case, the availability of water.

Evolutionary connections: This might just seem like common sense. But it’s often not so easy to demonstrate common sense in the archaeological record. The location of monuments on Rapa Nui illustrates how it can be difficult to get at the interaction of local environmental variation and ancient human behavior. Our cultures tend to adapt us to environments, and environments will have echoes on many behaviors that can be examined with archaeology. But understanding how environment shaped behavior, and how the ideologies and cultures of people were products of environment, requires mapping well-documented manifestations of behavior at a scale large enough that environments substantially varied in the past. From this kind of example, it is possible to see how to build better “social landscape” maps in prehistoric environments.

Should authors pay to submit their papers?

An article by Tim Vines in The Scholarly Kitchen looks at the pay-to-submit model of open access publication: “Plan T: Scrap APCs and Fund Open Access with Submission Fees”.

Why? APCs have the unfortunate feature that the authors pay for the assessment of all the other submissions that ended up being rejected. Manuscripts rejected from multiple OA journals thus contribute to the APCs of several different authors. Is it fair for authors of good articles to pay for the peer review of others’ lower quality work?

In other words, journals have an incentive to appear to be “exclusive” by rejecting lots of papers; but this means that any paper they accept and publish must carry all the freight of the rejections. If you have an open access model where the authors of published papers must pay for the privilege, they will pay much more in these “exclusive” journals.

Hence, Nature Communications has a $5200 publication fee.

The article is worth considering. Articles cost money to publish. If we insist upon journal publication, that money needs to come from somewhere. I would be happy if my university subsidized submission of papers to open-access journals instead of subscriptions to closed-access journals.

However, I tend to agree with Richard Sever, who tweeted a link to the article and commented:

Plan U: just mandate preprint deposition and let a downstream ecosystem of overlays/journals with various business models evolve in response to community needs. Side benefit: speeding up science massively...

Publication in an academic journal is a system of endorsement in which the journal (and its editors) stand in as proxies for academic referees, who remain anonymous. The endorsement is tied to multiple quality assessments by those referees, but the tie is indirect. Editors may ignore the opinions of referees, and those opinions are suppressed at the time of publication.

Personally I think the system would be better if endorsement were disintermediated. A curation system where journals choose what to publish from work already available in preprint form would be one way to attain this disintermediation. Editors would be more valuable to this process because they could pursue a vision of what was worth having peer referees engage with. They would be drawing from work that authors are already willing to stand behind in public.

Those journals might even be worth paying for.

This wouldn’t work well for the “big journals” that profit from embargoes. But we’ve seen very clearly how these journals have worse records when it comes to replication and accuracy.

Quote: 'The modern view of species'

The University of Michigan has done a release for a new paper studying speciation between black and mantled howler monkeys, by Marcella Baiz and coworkers: “U-M howler monkey study examines mechanisms of new species formation”.

It’s a very nice paper.

I’ve been following research on hybridization between these species for a long time, because one hypothesis for their history involves possible adaptation to colder conditions by one of the species: “Howler hybrid hunting”.

I’m linking the release because I found the following passage to be written very clearly:

A species was once defined as a group of actually or potentially interbreeding individuals that are reproductively isolated from other such groups. The concept of reproductive isolation is key to that definition and means that despite any hybridization, true species maintain their uniqueness.
However, the modern view of what a species is does not require full reproductive isolation, and hybridization has been discovered to be quite common in nature.

This is such a clever way of phrasing. “A species was once defined as…”.

Of course this phrasing is the biological species concept, which everyone learns in introductory biology, still today. It’s not a thing of the past. It’s just that biologists who work with closely-related animal species cannot define them based on postzygotic isolation. The instrumental examples that most people think about when they think of species are all instances of hybrid sterility or inviability.

Most people are less familiar with the hard cases, yet that’s what biologists who focus on speciation must study. During the last fifteen years, the growth of genetic sampling of wild populations has made it possible to examine hybridization to a greater extent. Biologists are finding hybridization almost everywhere.

That message hasn’t gotten out to the public as widely as it should.

Ancient DNA findings have brought hybridization to the foreground with humans, elephants, bears, and a few other groups. Findings about hybridization have really been the low-hanging fruit for ancient DNA, because with our present statistical approaches, ancient hybridization is of the things that can be examined with very small or unique samples. The statistical ease of testing the hypothesis of hybridization has shaped people’s research agendas – they are choosing museum specimens and geographic locations where hybridization is a relevant hypothesis to test.

Link: South African Daily Maverick reports on Little Foot

Elsabe Brits has written a long article covering the recent releases of preprints and papers about the StW 573 “Little Foot” skeleton: “SA’s most complete human ancestor — a bone of contention”.

This is a good article that details the scientific importance of the specimen, the history of its discovery, and features the new published work on the endocast of the specimen by Amélie Beaudet and coworkers.

I usually disapprove of articles that try to push the idea of “controversy” about scientific findings in human origins. Such articles usually set up a false equivalence between experts who have worked for years on something, and scientists outside a research project who may just be seeing the results for the first time. Here, the only new dispute is about the assignment of the skeleton to Au. prometheus, and in my view the article avoids “false equivalence” by giving fairly long and contextualized statements from scientists (including me).

That approach helps to explain why scientists don’t agree in this case. I’ll just quote one short passage from the end of the article:

“I am not concerned about what others ‘think.’ It is I who have worked for 20 years on extracting, cleaning and reconstructing the specimen and thus I understand it better than they do.”
Little Foot may well turn out to become one of the most interesting debates in science for years to come. She is exceptionally well preserved, very complete and yet again a beautiful example from South Africa’s rich fossil heritage.

I think that is a totally appropriate final word outlining the importance and enduring value of the discovery.

Quote: The importance of skeletons

For a research paper, I was re-reading some parts of the edited volume that describes the “Kadanuumuu” skeleton from Woranso-Mille, KSD-VP-1/1. This quote from a chapter by Owen Lovejoy and coworkers is worth sharing:

Articulated fossil specimens are now known to be the key elements that preserve sufficient information with which to solve major human evolutionary issues that cannot be resolved using only the typical single, isolated anatomical site (e.g., femur or humerus).

Paleoanthropology has a rich fossil record, but that record samples some ancient populations and species much more than others, and many ancient populations remain to be discovered.

It has become abundantly clear during the last fifteen years that single anatomical features mislead us about the overall pattern of human evolution. Mosaic evolution is the norm in human origins. That’s not a surprising finding; the idea of mosaic evolution can be found in publications about hominins ever since Wilfred Le Gros Clark discussed the idea in 1958. But for some reason many anthropologists have not taken this lesson on board.

Reference

Lovejoy, C. O., Latimer, B. M., Spurlock, L., & Haile-Selassie, Y. (2016). The pelvic girdle and limb bones of KSD-VP-1/1. In The Postcranial Anatomy of Australopithecus afarensis (pp. 155-178). Springer, Dordrecht.