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paleoanthropology, genetics and evolution

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

Should people lay off social psychologists with unreplicable ideas?

Pardis Sabeti has written an op/ed for the Boston Globe addressing the scientific casualties of the “replication crisis” in social psychology: “For better science, call off the revolutionaries”.

After naming a number of psychologists whose work has come under criticism for overhyped claims and underpowered samples, she decries the level of public criticism that these scientists have received:

Good science requires a spirit of collaboration, not domination. The debate in social psychology involves some essential criticism of past scientific practice, but revolutions can also lead to a bandwagon effect, in which bullies pile on and bystanders fearfully turn a blind eye. Especially as more disagreements among researchers surface in social media rather than professional publications, there is an insidious temptation to mistake being critical for being right, and to subordinate humility and decency to a “gloating sense of ‘gotcha,’” as the journal Nature put it.
There is a better way forward: through evolution, not revolution.

Sabeti contrasts the current situation in social psychology with genomics. In her account, much work in human genetics came under similar criticism in the early 2000s for relying upon underpowered samples, finding gene-trait associations that didn’t satisfy rigorous statistical requirements.

According to Sabeti, human genetics did not take the path of strong public criticism of underpowered studies, or of vilification of the researchers trying to find gene-trait associations with too little data. Instead, human geneticists built upon the imperfect results, revising them as samples got better and technology accelerated.

But there are many additional reasons why human genetics in the early 2000s was different from social psychology today.

The Human Genome Project during the late 1990s presented an enormous series of challenges to mainstream academic human geneticists. Scientists in government and in universities, led at first by James Watson and later by Francis Collins, rose to collective action, racing with Craig Venter’s private Celera venture to complete a draft of the human genome.

In doing so, they established a pattern of work that was unprecedented in biological science—in the process, building new expectations and protocols for sharing data. These scientists forged a collective understanding of the “big challenges” facing human genetics in the next decade. This included the critical need greatly increase knowledge of variation across the genome, to bring additional populations into human genetic samples, and to increase understanding of the genetic architecture of traits, especially disease traits.

That project established a hierarchy of scientists recognized as leaders, embedded within or experienced working with NIH, DOE, and other major funders. Some became directors of newly-founded major research institutes, among the first creations of the burgeoning philanthropic and government funding that moved into genome sequencing.

Few fields of science have ever seen the increase in money, power, and prestige poured into human genetics during the early 2000s. It’s not accurate to say this was a world free of conflict. Many of the disagreements within the field were acrimonious, and theoretical paradigms like common disease/common variant provoked strong debates. But none of these really compared to the rivalry between the public HGP and Celera during the 1990s. Meanwhile, prestige within the field came from directing and coordinating the Big Science efforts. That enabled project leaders to cultivate early career talent and select the most promising ideas from young people.

By contrast, social psychology has relatively little funding and no “Big Science” project. The competition for prestige and attention is very different than in human genetics. Psychologists write popular books, pen op/eds, and give Ted talks.

It’s like the Wild West, compared to human genetics. And where genetics was in the middle of a huge technological shift enabling vastly larger samples and more data for less money, samples in social psychology have been getting more expensive over time, not cheaper.

It will take a shock to the academic system to change the culture in such fields, toward pre-registered studies, vastly larger samples, and open data approaches.

Making the Mesolithic population of Scandinavia

A short article in The Conversation by Jan Apel describes some new research from Mattias Jakobsson’s lab on the population mixture that gave rise to the Mesolithic people of Scandinavia: “Ancient DNA sheds light on the mysterious origins of the first Scandinavians”.

This contradiction between genetics and geography can only be explained by two main migrations into Scandinavia. It would have started with an initial pulse from the south – modern day Denmark and Germany – that took place just after 11,700 years ago. Then there would have been an additional migration from the northeast, following the Atlantic coast in northern Finland and Norway becoming free of ice.

I think this work is exciting. The retreat of the European ice sheet left an opportunity for ancestral hunter-gatherers to colonize Scandinavia. The genetic data show that even this very simple biogeographic setting nonetheless gave rise to a complex mixture of populations from multiple sources, over a few thousand years of time.

Later, the introduction of farming into the region led to its own complex series of genetic migrations and interactions.

I can’t wait until we have equivalent or larger samples of individuals from other parts of the world of the same age.

Reference

Günther T, Malmström H, Svensson EM, Omrak A, Sánchez-Quinto F, Kılınç GM, et al. (2018) Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS Biol 16(1): e2003703. https://doi.org/10.1371/journal.pbio.2003703

What's the deal with the Sahelanthropus femur?

The species most often named as the earliest evidence for human evolution is Sahelanthropus tchadensis. The species is known from a skull and several mandibular specimens, found in Chad in 2001 by a team led by the French scientist Michel Brunet. These fossils are thought to date to between 6 million and 7 million years ago, approximately the time that our branch of the primate family tree diverged from the ancestors of chimpanzees and gorillas.

It has been called a “missing link”. It undergirds our best current timeline of human origins. It has been claimed as the earliest evidence for upright posture and bipedal locomotion in our lineage.

But there’s a mystery about Sahelanthropus. Some scientists claim that a fossil femur was found with the skull, a femur that they say is unlikely to be from an upright-walking ape.

Nature News has just published an article by Ewen Callaway investigating this mystery: “Controversial femur could belong to ancient human relative”.

The occasion for the article is that two scientists, Roberto Macchiarelli and Aude Bergeret, attempted to present a talk describing this femur at the annual meeting of the Societé d’Anthropologie de Paris this month. The society rejected their abstract, which has triggered some professional criticism.

The fossil may belong to the earliest known hominin, the group that includes humans and their extinct relatives. Few people have had access to it, but two scientists who analysed the bone briefly in 2004 have prepared a preliminary description of it. They had hoped to present their analysis at the meeting, which is organized by the Anthropological Society of Paris and is taking place in Poitiers. But the proposal by Roberto Macchiarelli, a palaeoanthropologist at the University of Poitiers and France's National Museum of Natural History in Paris, and Aude Bergeret, director of the Museum of Natural History Victor-Brun in Montauban, France, was rejected by the conference organizers.

Look, I’ve been following and writing about this case for a long time. I have been a scientific critic of the interpretation that Sahelanthropus was an upright hominin. I don’t think the cranial or dental evidence is persuasive, and I was a coauthor of both a peer-reviewed paper and a comment on the original description.

If a femoral specimen was found with the Sahelanthropus cranial remains, it is important evidence. If the femur preserves anatomy that would test the hypothesis of upright posture or bipedal locomotion, no one should pretend that the evidence does not exist. Secrecy was ridiculous from the start, now it is inexcusable.

The femur was discussed in La Recherche in 2009, and I reviewed what had been made public at the time: Sahelanthropus: ‘The femur of Toumaï?’”

My post included photographs of the femur in question:

Purported primate femur found at TM 266
The primate femur found at the TM 266 locality, originally numbered TM 266-01-63. Photo credit: Aude Bergeret

As I wrote at the time, the photographs do not provide clear-cut evidence that this is a hominoid femur and I would not make any conclusion based on them myself. I assume that Macchiarelli and Bergeret, with the opportunity to examine the specimen, are confident in their conclusion and I have no reason to doubt them.

There have been several other strange irregularities with the interpretation of Sahelanthropus. Most have involved one of the scientists who assisted with the original research, Alain Beauvilain, who wrote several critical articles questioning the discovery’s context and date. I reviewed this record in 2009, after Beauvilain’s published claim that the fossils had been found in a secondary context disturbed by local people at some point in the past: Sahelanthropus: Did camelherders bury Toumaï facing Mecca?”.

I have no direct knowledge about any of the supposed irregularities. One of the claims, that a left molar was mistaken for a right, was renounced in a letter signed by 29 scientists external to the team, a singular case in the history of paleoanthropology.

But what amazes me is just how long this has all gone on. All of the critics could be silenced within hours by data and evidence. Instead, silence about these key fossils has reigned for fifteen years.

Callaway got no new details about this fossil. Nevertheless, his article changes the situation substantially.

For example, this passage raises serious questions about the quality of the research:

David Pilbeam, a palaeoanthropologist at Harvard University in Cambridge, Massachusetts, who was a co-author on the 2002 and 2005 papers describing Toumaï’s skull and jaw, says that he saw the femur briefly while visiting Brunet in Poitiers more than a decade ago, but that he is not involved in any analysis. “All I can recall is that it lacked ends and was very black,” he says.

The major thesis of these research papers was that the skull reflects upright posture. A possible femur is obviously relevant to this hypothesis. If a coauthor was in a position that prevented him from either examining this key evidence or getting answers about it, it is very troubling.

It is time for Nature’s editors to investigate. Nature published the original description of the Sahelanthropus fossils in 2002, and two 2005 papers providing analyses of the skull and descriptions of new mandibular fossils.

Now Nature’s news division has revealed the existence of the specimen, and has quoted senior scientists who say that it may not be a hominin. Can this go on any longer?

Link: Remembering a dinosaur dictionary

I really like this post from Matt Wedel, reminiscing about a book that made a big difference to his start on the path toward paleontology: The New Dinosaur Dictionary, Mark Hallett, and the best Christmas present ever”.

“By Mark Hallett.” I didn’t know who this Hallett guy was, but his art was all over the book, along with William Stout and some guy named Robert T. Bakker and a host of others who were exploding my conception of what paleo art could even be. Anyway, this Mark Hallett was someone to watch, not only because he got mentioned by name a lot, but because his art had a crisp quality that teetered on some hypercanny ridge between photorealism and scribbling. His sketches looked like they might just walk off the page.

It’s a nice reminder of how important art can be to scientists. The comments include other scientists remembering some other valuable books.

A look at the history of Mormon archaeology in Mexico

Science magazine this week has a feature article by Lizzie Wade, looking at some of the history of archaeological research in Mexico supported by the Church of Jesus Christ of Latter Day Saints: “How a Mormon lawyer transformed archaeology in Mexico—and ended up losing his faith”.

The story is fascinating, focused on Thomas Stuart Ferguson and his efforts to fund and carry out research in Mexico starting in the 1940s.

Ferguson, a lawyer by training, did go on to open an important new window on Mesoamerica's past. His quest eventually spurred expeditions that transformed Mesoamerican archaeology by unearthing traces of the region's earliest complex societies and exploring an unstudied area that turned out to be a crucial cultural crossroads. Even today, the institute he founded hums with research. But proof of Mormon beliefs eluded him. His mission led him further and further from his faith, eventually sapping him of religious conviction entirely. Ferguson placed his faith in the hands of science, not realizing they were the lion's jaws.

It’s interesting to see this kind of feature in Science. It is a long piece that brings light to an underexamined period of the history of American archaeology, one that illuminates both faith and loss of faith within scientific work.

The importance of kindness in scientific work

Nature has a “Career Feature” by Kendall Powell recounting a recent scientific meeting in New Zealand meant to promote the idea of kindness in scientific work: “Should we steer clear of the winner-takes-all approach?”

While working on another topic, I was just thinking of how much more valuable kind researchers are. I believe that promoting kind behavior and rewarding cooperation are essential in training the next generation of scientists. In paleoanthropology, we have to break a cycle of bad behavior that existed in the aging population of senior scientists.

One thing that interested me in the linked article is that some researchers recognize the explicit connection between kindness in science and effectiveness within in communities where we work.

This is from James Ataria, a Maori researcher:

Kindness is quite an evocative term, but I see it come through when researchers experience how their work is changing a community. Likewise, from the community’s perspective, being at the decision-making table and co-generating research is empowering, and is a form of kindness. We’ve got these concerns, you’ve got expertise: how can we pair them together? Collaboration with communities can both create conditions for kind science and produce good scientific outcomes.

There is a place in scientific work for healthy, good-spirited competition. Science today is a team sport, and teams work together well when the players have a team spirit. And we need to be making the communities where we work part of the team.

Congress looking to investigate why so much federal grant money has gone to serial sexual harassers and abusers

Two years ago this month, I asked, “Why do universities cover up high-profile harassment? Look for the money”.

Now the U.S. Congress seems to be asking the same question: “Congress Is Demanding Answers About Why Federal Grants Are Given To Harassers In Science”.

The letter asks NIH, NSF, USDA, DOE, and NASA to report: how many cases of sexual harassment or assault have actually been investigated at their agencies; what they do when they receive complaints about a grantee; and whether they require grantees to inform them of allegations of sexual harassment or gender discrimination.

This appears to be a bipartisan request from the House Committee on Science, Space, and Technology. In the field of anthropology, we know enough from the Survey of Academic Fieldwork Experiences study to know that millions of federal dollars have been directed toward field research programs where sexual harassment and assault, bullying, and hazing have been frighteningly routine.

As I wrote last year:

We know from the 2014 SAFE study that harassment and assault have been very common in recent and existing field programs in archaeology and anthropology. Millions of dollars of funding have gone to researchers who maintain field projects that are widely rumored to be sites where abuses have happened for years. Researchers have used this support to intimidate and silence the targets of their abuse, and have evaded scrutiny from institutions because of the federal dollars they bring in (“Why do universities cover up high-profile harassment? Look for the money”). Meanwhile, the institutions who received 50% or more overhead on these NSF grants did not maintain minimal levels of professional standards by the site directors.

More details about these abuses need to be brought to light.

Are these moustached monkeys a species unto themselves?

I ran across a news article from the BBC by Paul Rincon, about a proposed taxonomic revision to patas monkeys in northeastern Africa: “Moustached monkey is separate species”.

Scientists took a fresh look at the distribution and physical appearance of patas monkeys in Ethiopia, confirming there were two species rather than one.
It was originally described as a separate species in 1862, but was later folded in - incorrectly - with other patas monkeys to form a single species.

This is not “a new species being discovered” as some might expect from a news story. It’s one researcher, Spartaco Gippoliti, who has written a paper presenting some history of the taxonomy of patas monkeys. He suggests that a species name (Erythrocebus poliophaeus), first given in 1862 but later discarded, now be revived to apply to a geographic population of patas monkeys in Ethiopia. The paper is in the journal Primate Conservation and is available online: “On the Taxonomy of Erythrocebus with a Re-evaluation of Erythrocebus poliophaeus (Reichenbach, 1862) from the Blue Nile Region of Sudan and Ethiopia”.

In the paper, Gippoliti refers directly to the possible importance of this species to broader issues of conservation in Ethiopia:

Monkeys of the genus Erythrocebus are potential flagships for important African ecosystems, and may well be at greater risk than is generally believed.

Recognizing more monkey species would cause greater awareness of the threat to regional populations. Patas monkeys are not listed as threatened, but the populations in Ethiopia are at much greater risk than patas monkeys in other parts of Africa.

But is it scientifically valid to name species for conservation reasons?

I don’t want to criticize this specific proposal about patas monkeys. I agree with Gippoliti that scientists need to know a lot more about them, and this is an urgent conservation concern. They should be conserved where they are at risk.

What surprised me when I followed up the original research paper, is just how little evidence it presents about the variation in patas monkeys and how this population compares to other patas monkey populations.

Truth is, I’ve become accustomed to seeing genetic evidence about population divergences. Most recent papers that claim evidence to support a novel distinction at the species level between primate populations include some evidence about genetic variation within and between populations. Genetic evidence is valuable because it can demonstrate that populations have been evolving along separate trajectories with little gene flow between them for a long time.

That’s not to say that genetic data is always sufficient to establish that a species is valid. Even large genetic differences may not be enough demonstrate that speciation has taken place between two populations. Two populations may exchange genes rarely, yet often enough to prevent the evolution of reduced hybrid fertility or viability.

The paper does discuss coat and skin coloration as evidence for a distinction. But it doesn’t present evidence about the variation of these traits in either population, nor does it present other morphological data about their variation. Mainly, the paper presents a case that scientists don’t know enough about the patas monkey variation.

Considering the geographic separation and distinctive external appearance, I have no hesitation in considering poliophaeus to be a distinct species. Its closest taxon in appearance seems to be baumstarki, for which species’ status is also warranted. The recognition of these patas monkeys as species, highlights the need for field surveys to assess their geographic range and conservation status in both Ethiopia and Sudan.

To me, this is a very sharp example of the old debate between splitters and lumpers as applied to conservation.

Gippoliti discusses the history of the naming of these monkeys, and suggests that prior workers who lumped the monkey populations may have been overly influenced toward lumping them together, by variation and developmental changes to the skin color and coat changes. For him, the geographic separation and differences in appearance are enough to justify a separate species designation.

My philosophical inclination is toward lumping groups together, and recognizing geographic variation below the level of species. Occasional gene flow between genetically differentiated groups has been important to the evolution of ancient humans and other primates. Since long-range gene flow can make such a difference to adaptation within species, and since it has happened so often, I’m inclined to be conservative in naming such groups. Ideally, I’d like have some evidence of reduced fertility before recognizing them as different species.

Yet biologists have come to accept more and more that hybridization and introgression between populations are common in mammal evolution, even when hybrids have reduced fertility. Speciation is much less of a barrier to adaptive gene flow than biologists once assumed.

For those of us who care about the mechanism of adaptation and the particular history of adaptation in hominins, that makes species names much less important than they once seemed. Morphological traits don’t predict evolutionary potential in the way many anthropologists used to think.

For scientists who are deeply engaged in conservation biology, species names make a lot more difference.

Still, with genetics, we’ve become accustomed to having actual data on diversity, rather than the often-subjective assessments of taxonomists. Hopefully some further genetic information from patas monkeys will help to clarify the variation in these populations.

UPDATE (2018-01-19): Reflecting on this, I realized what is bothering me about this instance. We should have many more short papers discussing the history of taxonomies and their problems matching current data on species’ natural distributions. That’s helpful to advancing new data collection and research. I learned a lot about patas monkeys from this paper I didn’t know.

But those kinds of papers, lacking any new empirical data, should not be trumpeted in the press as “discoveries”.

Scientific discussion about species is valuable, and recognizing underappreciated diversity can advance conservation goals. But when a data-free paper is reported in the press as a “discovery of a new primate species”, it damages the credibility of conservation efforts. Such publicity makes it appear that scientific judgments about species are merely arbitrary, motivated by politics and not data.

Linking out to a book review on sociogenomics

The journal Nature has a review of the new book, Social by Nature: The Promise and Peril of Sociogenomics, by Catherine Bliss. The review is written by Nathaniel Comfort: “Nature still battles nurture in the haunting world of social genomics”.

After reading the review I plan to read the book and bring some of this topic into my genetics course this semester.

Comfort’s review presents Bliss’ book as a critical survey of work in social genomics. I can’t assess from Comfort’s review whether the book is really accurate about the genomics research that it describes, and that’s my main interest.

That’s because a historian of science writing about a sociologist uses a hecka lot of jargon.

For instance, the “genomic gaze”:

What the historian Andrew Hogan has called the “genomic gaze” isn’t the fault of individual bad-guy researchers: it’s structural. Bliss is careful to acknowledge the good, even noble intentions of many of the scientists she spoke to (as a sociologist, she keeps the names of her ‘informants’ confidential). But she finds that the funding and publicity mechanisms integral to biology drive it towards genes-first explanations. The stakes are high: finding an SNP associated with a risk increase from 0.01% to 0.03% (a threefold rise) for a disease such as breast cancer could make a career. “While researchers do not intend to lift the focus off of the environment,” Bliss writes, “they are forced to recast social phenomena as ‘evolutionary phenotypes’ so that they can make scientific claims” that sound relevant to biomedical funders.

It seems like sociologists always disappoint me when they talk about the motivations of geneticists. “Finding a SNP” is hardly likely to “make a career” these days.

To be sure, like other areas of science, genetics has a publication bias toward positive findings. But during the last fifteen years genomics has raised the standard of evidence necessary to publish positive associations. A good discussion of this subject would describe the candidate gene approach, still heavily used in some areas of behavior genetics. The candidate gene approach has been strongly criticized within genomics, as genome-wide association studies demand vastly larger sample sizes and result in stronger evidence of association.

This is relevant because today many of the most interesting findings in human behavior genetics are coming from large GWAS-scale samples of tens or hundreds of thousands of research subjects.

The paragraph I’ve selected from Comfort’s review uses as its example a fictitious example chosen to illustrate a very small effect size (“a risk increase from 0.01% to 0.03%”). But “breast cancer” is a pretty poor fit to this fiction. The lifetime incidence of breast cancer in women in the U.S. today is more than 12 percent, three orders of magnitude higher!

Numbers matter. A risk of 0.02% is two cases in every ten thousand people. A study of a candidate gene with 80% power to find a significant difference between 0.01% and 0.03% would have more than 60,000 cases and controls. Geneticists who study rare disorders that actually have such low incidences make extensive use of pedigree data to find genetic regions of interest. Finding a genetic influence so small out of a genome-wide association study is not statistically credible.

In other words, if it seems ridiculous to focus on such a small difference, that’s because the contrived example is nonsensical.

Comfort’s general point has some truth to it. Human genomics has led to the discovery of many genetic variations that have small effects on traits. The “one gene one trait” model, such a wide misconception among the public, is wrong. Meanwhile, the best summaries of genetic associations today still leave a large fraction of heritable variation unexplained.

But those issues have been advanced by professional geneticists, not sociologists. During the last year, one of the most important theoretical questions in quantitative genomics has been whether such small effect size mutations actually matter to anything. They may simply be evolutionary noise. And still, the variation in many human traits is the sum of hundreds of such small genetic effects. Those genetic effects make people different from each other. Some of them seem to have been targets of natural selection in the last couple of generations.

I’ll be reading Bliss’ book carefully to see how she describes the results of behavior genomics. Also I’m curious to see how she describes the origin of the term, “sociogenomics”. It’s not one I’d ever heard before seeing this review.

UPDATE (2018-01-17): As I was writing this, I saw a tweetstream by Jeremy Freese, a social scientist who is quoted in the book. He notes numerous apparent errors of fact in the text, from misspelled names and incorrect dates, to paraphrases of quotes that differ from their sources.

I have no further information but it is a point of concern.

When genomic ancestry tests lead to confusion

An article in Gizmodo by Kristen Brown asks an uncomfortable question about today’s proliferating genomic ancestry industry: “How DNA Testing Botched My Family’s Heritage, and Probably Yours, Too”.

Her family thought their ancestry was mostly Syrian, and they were surprised to get a very different assortment of results from different genome tests for ancestry. That’s not unusual, it happens a lot.

Brown accentuates the explanation that the tests seem to work better for people with predominantly European ancestry because the comparative samples are much larger and pose a limited set of problems compared to other regions.

In my opinion, that’s really not true; it’s just that the issues appear on a different scale. People who derive their ancestry from different parts of Europe are often given results that don’t correspond to their genealogical history.

The article does a good job of discussing the way that people’s expectations of these tests doesn’t match what the scientists are trying to provide.

A big problem is that many of us have a basic misunderstanding of what exactly we’re reading when Ancestry or 23andMe or National Geographic sends us colorful infographics about how British or Irish or Scandinavian we are. It’s not that the science is bad. It’s that it’s inherently imperfect, an estimation based on how much our DNA matches up with people in other places around the world, in a world where people have been mixing and matching and getting it on since the beginning of human history.

But right now the science really is bad.

To me, the great promise of personal genomics is that people can advance the science by engaging with their place in this history. Naturally people are most interested in their own places in the human genealogical web. Anyone can be forgiven if they see this genealogical web as a tree of populations with names like French, German, Italian, or Hausa, Bengal, or Syrian.

So a person’s place in the history seems like it should be some combination of these names, like a pedigree.

It’s very easy for genetics to deliver a combination of names. Trouble is, a single combination of genes may map pretty closely to several different combinations of population names.

Geneticists study samples of human genomes from many different parts of the world as a basis for these ancestry assessments. Those samples of human genomes are simply too small in most regions of the world and most ethnic groups. As much as we know, we are still learning about how today’s groups have originated, and today’s nation-states have come together from ethnic groups in many different ways.

Samples are of adequate size in much of Europe, but still, humans across hundreds of years have not behaved in ways that make it easy to reliably apportion ancestry into geographic bins.

In other words, our knowledge of recent human genetic history is a work in progress. Any one individual’s place in recent history is contingent on the whole story. We know some parts better than others, but even the well-traveled parts of human genetic history have hidden chapters.

Populations did sort of behave like a tree during much of human prehistory–but a tree with millions of interconnections between branches. Anthropologists and geneticists are trying to reconstruct that tree with greater accuracy. They are also using ancient DNA to rediscover branches that are missing from conventional histories.

Braided stream
A braided stream. Photo Credit: Sam Beebe, Ecotrust via Compfight cc

Even though individuals belonged to populations, the genealogies of individuals do not reduce well to a tree of populations. Populations are loosely defined by swarms of individuals with similar genealogies for a few hundred years. Any one individual’s genealogy may diverge quickly from the mainstream of the swarm.

I’d like to promote a broader view of genealogy, one that celebrates the differences between individuals and the populations that some of their ancestors identified with. That has more genetic reality than the alternative, in which people are defined into hardened populations.

See also: “The surprising connectedness of human genealogies over centuries”

Link: Gendered academic space in political science

Macartan Humphreys, of Columbia University, has written a short essay on “Gender discrimination in political science and the problem of poor allies”. It begins with a personal story, then moves into broader issues in his field of political science.

Looking back I think I found it easy to explain things away because at bottom I thought of myself as someone who does not discriminate and so there must be reasonable explanations for things that others might see as discrimination.
With quite a bit of distance though I can see problems with my self explanations.

These are important issues to be conscious of.

Link: On the importance of altruism in starting academic careers

Jenny Martin has recounted a personal story about her first highly cited paper, which followed an altruistic decision from her postdoctoral supervisor, and includes a nice tribute to the late Ben Barres: “selfless in seattle”

Actually, this post has nothing to do with Seattle. I just liked the title. The theme, eventually, is science leadership through altruism. But to get there, first I need to relate a story that has been on my mind the past week or two.

It’s a good story, and a good lesson about the sources of discoveries.

Testing the sex of ancient individuals from their enamel proteins

A recent paper by Nicolas Stewart and colleagues presents a way to determine the sex of ancient individuals by examining the composition of their tooth enamel: “Sex determination of human remains from peptides in tooth enamel”.

Amelogenin is a protein component of tooth enamel. Humans have two different genes for amelogenin, AMELX on the X chromosome, and AMELY on the Y chromosome. The protein products of these genes have slightly different amino acid sequences. Enamel from males, who have both X and Y chromosomes, has a mix of the two proteins, while females have only the AMELX product.

Stewart and coworkers etch the ancient enamel with an acid, freeing protein fragments, or peptides. They use a mass spectrometer to detect the signatures of the Y chromosome and X chromosome specific peptide variations.

The ability to determine the sex of infant and juvenile remains completely revolutionizes studies of growth, child care, epidemiology, and demography in the past. For the first time, it will allow osteologists to examine sex-specific cultural treatment and differentiate between the health of boys and girls, as well as sex-specific growth trajectories and past developmental milestones, such as age of puberty and subsequent repercussions for fertility. Sites with poor preservation are common in archaeological contexts, and at such sites teeth generally survive better than bone, and thus sex can be established for adults as well as juvenile skeletons in the absence of key skeletal identifiers. In addition, the dimorphic peptide sequence is identical in apes (Fig. S1) and so should be present in all hominins.

This is potentially very important for a number of questions that cannot be answered from archaeological sites without direct evidence of sex. The sex of young children in particular is almost impossible to establish reliably from skeletal indicators. In some recent contexts, sex can be inferred from grave goods or from inscriptions. But for most ancient people–including Neandertals and other Paleolithic populations–the sex of young children is unknown.

Amelogenin has previously been used as a forensic sex determination test in humans and in other mammal species. In humans, this test fails to identify males a small fraction of the time because the Y chromosome sometimes has large deletions that include the Y amelogenin (AMELY) gene. That implies that a small fraction of misidentification (biased toward misidentifying males as females) should result from this test applied to ancient samples.

It’s not known whether this difference between males and females has any functional consequences for enamel. Some researchers have been interested in whether the presence of an additional amelogenin variant in males might influence caries. In some populations, females are more likely to have caries than males. The AMELY protein makes up only around 10 percent of the total amelogenin in a tooth, as the Y chromosome version of the gene is not expressed as highly as the X version, but the presence of an alternative form of the protein might make some difference. However, it is very hard to test whether sex-specific life history traits, such as diet differences during development, pregnancy, or other environmental factors, might instead lead to a difference in caries risk.

At any rate, caries incidence was very, very low during most of our evolutionary history compared to the past 20,000 years (and is low in nearly all other mammals). The amelogenin in both sexes did its job pretty well for most of our existence.

Reference

Stewart, N. A., Gerlach, R. F., Gowland, R. L., Gron, K. J., & Montgomery, J. (2017). Sex determination of human remains from peptides in tooth enamel. Proceedings of the National Academy of Sciences, 114(52), 13649-13654.

Link: Article on changing perspectives on Neandertals

A couple of years ago I pointed to a news article about archaeological work at Descubierta Cave, Spain: “Link: Neandertal burial ritual with antler hearths”. Last year Juan-Luis Arsuaga and coworkers presented on the work at the European Society for Human Evolution conference.

It sounds like a very interesting case because of the overall context – human remains, with nearby small hearths, horn cores and antlers of numerous animals.

Sandra Ackerman has written an article for American Scientist that reports on the conference talk, as well as other recent work on Neandertals: “Neanderthals Reenvisioned”.

How to explain such a bizarre assemblage? In a presentation at the conference, Arsuaga laid out his research team’s reasoning: “This association could have been produced by chance, but we consider this improbable, given the preponderance of horns; also, the presence of fire points to an anthropogenic origin.” He continued, “Could it have been subsistence? There is no evidence of human consumption.” As another possibility, it might perhaps have been functional—but we know Neanderthals didn´t use organic substances such as horn, antler, or bone as raw material for implements or ornaments. Moreover, there’s no evidence, such as partly worked bones or a concentration of bone fragments, to indicate that this was a site of industry. To the researchers who discovered them, these carefully arranged horns and skulls looked almost like modern-day hunting trophies. Indeed, at 40,000 to 45,000 years old, Descubierta Cave may contain “possibly the strongest evidence yet for symbolic behavior in Neanderthals,” Arsuaga concludes—although, he says, alternative explanations are welcome.

I’ll be looking forward to hearing more about these discoveries.

Is this better evidence for symbolic culture than the long record of ornaments made and worn by Neandertals? How we answer that question depends on the fine details of defining “symbolic culture”.

A site described as Descubierta has been described has tremendous potential information about cultural ritual. An ornament carries similar information about repeated visual communication. These are different things, and they may inform about different cultural abilities. They certainly inform us about different cultural functions.

I don’t want to minimize the other aspects of the American Scientist article, including the great shout-out to the work of Zenobia Jacobs on dating some of these sites with luminescence methods.

A look at the glacial lakes of Siberia

Many readers in North America have heard of Glacial Lake Agassiz, Glacial Lake Missoula, Glacial Lake Bonneville, and many other large bodies of water in North America during the last Ice Age. Less well known are the large bodies of fresh water that once existed in northern Eurasia.

I was especially impressed to learn about the glacial lake that extended across parts of the West Siberian Plain, in the Ob and Yenesei drainages. Here’s an image showing the extent of this lake around 90,000 years ago:

Illustration showing location and extent of the glacial lake in West Siberia
Figure 2 from Mangerud et al. 2004. Original caption: "Reconstruction of ice-dammed lakes and rerouting of rivers during the Early Weichselian, about 90–80 ka. Ice margins are taken from Svendsen et al. (2004). In the hatched area the ice margin position is unknown, probably because it was overrun by the 60 ka ice advance. Stippled line on Taimyr shows a retreat phase damming a lake. Blue arrows show outlets. The arrow in the Barents Sea shows the longest modelled outburst route for Lake Komi, and the corresponding western ice margin. The shorter and more probable routes have the same starting point. See text for discussion. Sea level is lowered 50 m (Chappell et al., 1996) without considering any isostatic depression."

The glacial lakes on the northern tier of Eurasia changed markedly over time during the last glaciation, as the position of the ice sheet and eustatic sea level changed. According to Mangerud and coworkers (2004), the West Siberian glacial lake was near its maximum between 90,000 and 80,000 years ago, a bit lower by 50,000 years ago, and by the Last Glacial Maximum this lake had drained entirely.

During the LGM, lakes in the northern tier were more prominent in the White Sea embayment and further to the west. There were other glacial lakes in the mountainous regions to the southeast, some of which may have had massive outflows.

I thought the West Siberian glacial lake very interesting because of its sheer surface area. At its maximum extent, geologists think that it drained to the south into the Aral Sea basin (and ultimately into the Caspian and Black Seas). Neandertals were this far north in the European part of Russia, but it is not clear what extent of habitation they had at this latitude.

Still, I wonder whether this lake may have posed a substantial biogeographic barrier to their movement, or whether they sometimes saw its shores.