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john hawks weblog

paleoanthropology, genetics and evolution

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

Link: The women behind early anatomical illustration

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

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

“The technique they used is one that's relatively unique to medical illustration, called carbon dust,” says Wooldridge. “To get the tone in, they would rub carbon against sandpaper to get a pile of carbon dust and they would apply that with a paint brush. You would get these lovely even tonal gradations with an amount of contrast that would reproduce really well.”
[Dorothy Foster] Chubb was a master of this technique, he says. “Dorothy Chubb's work is very visually distinctive – I could recognize it immediately… It's really beautifully observed, and has a really strong sense of a light source and a really strong three dimensional sense.”

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

Link: When should academic scientists retire?

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

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

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

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

The naming of X and Y

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

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

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

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

Link: Archaeology of nonhuman tool use

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

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

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

A Denisovan news article

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

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

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

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

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

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

Link: Origins of human languages

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

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

In general, fostering language vitality is one of anthropologist Gwyneira Isaac’s goals as director of the Smithsonian Institution’s Recovering Voices program. Though Isaac does not work specifically with emerging languages, she witnessed how cultural practices can help revive language after meeting a Canadian man who spoke the endangered Anishinaabe language. The man found some of his tribe’s maple syrup–making tools in a cabinet at the Smithsonian and was so excited that when he returned home, he produced a series of videos about syrup-making using phrases from his native tongue.
Young people in his community hear the language when they watch the videos, but they also encounter aspects of their cultural heritage. “This small thing of opening a cabinet turned into this journey,” Isaac says, “building the collective knowledge which is really at the base of language.”

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

Quote: Two competing hypotheses

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

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

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

Black Tudors

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

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

Sounds like an interesting history.

Zebra stripes and flies

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

When it comes to biting insects, zebras are doubly cursed. For one, they’re highly susceptible to a variety of fatal diseases, including trypanosomiasis, African horse sickness, and equine influenza, that are spread by horseflies and tsetse flies. They’re also very vulnerable to insect attacks: Compared with other grazers such as antelopes, the hairs on their coat are unusually short, allowing flies to more easily find blood vessels with their piercing mouthparts.
Stripes, for some reason, seem to help. In 2014, Caro and his colleagues showed that striped horses—three zebra species and the African wild ass with thin stripes on its legs—tend to live in regions with lots of horseflies. And several researchers, over the years, have shown that these flies find it hard to land on striped surfaces. No one, however, had watched the insects trying to bite actual zebras. That’s why Caro’s team went to Hill Livery.

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

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

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

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

Link: On the science of science communication

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

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

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

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

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

In any event, the landscape has changed.

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

That last point is of central importance.

Forest monkey hunters of Late Pleistocene Sri Lanka

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

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

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

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

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

The bone points made from monkey fibulae are amazing:

Monkey fibula bone points from Fa-Hien Lena cave site, Sri Lanka

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

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

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

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

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

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

Link: History of women in computer programming

The New York Times Magazine last week printed a wonderful long article on the history of women as computer programmers: “The Secret History of Women in Coding”.

A great part of the article is the description of the first ENIAC programming team.

When the time came to hire technicians to write instructions for the Eniac, it made sense, to the men in charge, to pick an all-female team: Kathleen McNulty, Jean Jennings, Betty Snyder, Marlyn Wescoff, Frances Bilas and Ruth Lichterman. The men would figure out what they wanted Eniac to do; the women “programmed” it to execute the instructions.
“We could diagnose troubles almost down to the individual vacuum tube,” Jennings later told an interviewer for the IEEE Annals of the History of Computing. Jennings, who grew up as the tomboy daughter of low-income parents near a Missouri community of 104 people, studied math at college. “Since we knew both the application and the machine, we learned to diagnose troubles as well as, if not better than, the engineer.”
The Eniac women were among the first coders to discover that software never works right the first time — and that a programmer’s main work, really, is to find and fix the bugs. Their innovations included some of software’s core concepts. Betty Snyder realized that if you wanted to debug a program that wasn’t running correctly, it would help to have a “break point,” a moment when you could stop a program midway through its run. To this day, break points are a key part of the debugging process.

This is a nice piece to read in combination with the story earlier this month about women who contributed to papers in genetics during the 1970s and 1980s who were not given coauthorships but were listed in acknowledgements: “The Women Who Contributed to Science but Were Buried in Footnotes”.

Over the past few years, a team of students led by Emilia Huerta-Sánchez from Brown University and Rori Rohlfs from San Francisco State University has been searching through two decades’ worth of acknowledgments in genetics papers and discovering women who were never given the credit that would be expected for today’s researchers. They identified dozens of female programmers who made important but unrecognized contributions. Some were repeatedly thanked in the acknowledgments of several papers, but were never recognized as authors. They became literal footnotes in scientific history, despite helping make that history.

How much do scientific societies fear Plan S?

An article in Science looks at some of the debate over a funder-driven initiative to require open access publication of the research they fund: “Scientific societies worry Plan S will make them shutter journals, slash services”.

An existential threat. That's what scientific societies supported by journal subscriptions call Plan S. Introduced in September 2018 by European research funders and endorsed by others since then, the plan will require that grantees' papers be immediately available free of charge. All publishers that charge subscriptions will be affected, but scientific societies fear they could be hit especially hard.

I’ve been following the story of “Plan S” fairly closely. This is the initiative pushed by some large scientific funding organizations to require immediate open access publication of all research that they fund. Most publishers currently have options that allow authors to choose immediate open access, but the fees for this service are predatory—often $3000 or more. “Plan S” would cap the open access fees, thereby making this option more affordable for authors and funders.

The linked article is about scientific societies, which today obtain a fraction of their funding from publishing journals. Critics of for-profit scientific publishing by corporations like Elsevier or Nature Publishing Group often emphasize the extremely high profit margins of these companies, together with the extremely high costs of subscriptions for universities and other organizations. Critics have paid less attention to the role of scientific societies in publishing.

Like for-profit publishers, scientific societies also charge high subscription fees for institutions. Sometimes these fees are necessary for the societies to “break even,” because as small publishers, their costs for staff and journal management computer systems are higher per-article than for large publishers. In other cases, subscription fees are diverted into other activities of the society, such as conferences, student training, staff salaries, or professional development.

Many scientific societies are big businesses. With memberships numbering in the thousands, they often employ professional staffs, maintain large offices, and must be able to establish long-term contracts to support future activities such as conferences. Some have professional lobbyists. Historically, most of them have supported the publication of scientific research through scientific journals, monographs, book series, newsletters, and other venues. Some also publish educational materials, curricula, nonspecialist magazines, and a few have their own training and certification arms.

All of these activities are potentially beneficial for scientists who are members of the societies, and arguably for science as a whole. Most people can understand why members would pay annual dues that include both these activities and support of society publications, including individual scientific research journal subscriptions.

On the other hand, it is not obvious why university libraries should be paying for these activities through their subscription fees.

Some scientists fear that shifting to an open access publication model will shift all costs of publishing to authors, and thereby remove a major source of funding from scientific societies.

I strongly support open access publication. At the same time, I have concerns about the shift of publication costs to authors. In my field, a large fraction of researchers lack institutional or funder support for publication fees. A world where author fees are increasingly charged for publication is one where researchers will have to weigh publication fees against other financial costs of research. For researchers and institutions in the developing world, the cost of publishing a single article may consume student bursaries, field assistant salaries, or research supplies.

There are a few high-quality open access journals publishing work in human origins that do not charge author fees. PaleoAnthropology and the South African Journal of Science are both very important, and both are publishing a higher and higher fraction of premier work in this field. These are both society journals.

I worry that such venues may not be able to sustain their APC-free publishing model as the volume of submissions increases. Meanwhile I know that many junior scientists have faced strong pressure to publish in the for-profit journals in the field, such as the Elsevier-owned Journal of Human Evolution. Can this peer pressure from senior academics continue in a world where authors must also pay APCs to publish in these journals?

Some other society journals in the field of anthropology are already published by for-profit publishers, including the American Journal of Physical Anthropology and American Anthropologist. Such cases have varying levels of difficulty depending on the agreements under which the journals are published. In some instances, societies in the past made short-sighted decisions that left them unable to extricate themselves from relationships with publishers that became increasingly onerous over time.

The article discusses how some journals may cover costs by accepting more articles. Such an idea seems rational, considering that the number of articles published by scientists is increasing every year, and new journals are being founded to pick up the slack. But scaling up also has costs, and some journals argue that growth cannot be sustained:

Science's publisher, Bill Moran, says the journal doesn't want to pursue what he calls "a volume play." He wants Plan S to carve out an exemption for Science and similar selective journals that reflects their unusual circumstances and roles in scholarly communications. Science accepts only about 7% of manuscripts submitted and publishes, in addition, a variety of news, perspectives, and other nonresearch articles. The journal wouldn't be sustainable if author fees had to cover all publication costs, Moran says.
"Science is unique," Moran says. "Not all journals are the same. If your goal is to maintain quality, there has to be an exception" to a one-size-fits-all approach like Plan S.
Still, if more funders demanded solely open-access publication, Science might have to make adjustments, he adds. An option might be to charge subscription fees only for nonresearch content, he says.

I’m a member of the AAAS and thereby have a subscription to Science. It’s a valuable journal and I enjoy much of the news coverage it provides. I have published research articles and technical comments in Science, and am proud of those contributions.

As one of the largest scientific societies with a very high-profile society journal, AAAS has much at stake in the shift to open access publishing. Contributions to Science can be made open access by paying an APC. The society additionally already has a fully-APC-funded journal, Science Advances. The main threat of Plan S to AAAS is therefore the imposition of a cap on APC rates, which limits revenue per published article. This is a problem because both Science and Science Advances (to a lesser extent) have a funding model in which rejected papers cause a high fraction of editorial costs.

One solution may be submission fees to such journals (“Should authors pay to submit their papers?”).

In the long run, I do not think it makes sense for Science to limit scientific research articles to readers who pay subscription fees. Science is a valued place for researchers to publish because of the perception that it publishes groundbreaking work. Yet the journal has been dogged by the observation that its articles are more likely to be retracted, and is less likely to be replicated, than journals with narrower focus.

With this situation, the journal cannot maintain its status over the long term without heightened transparency. Transparency is going to require broader readership, easier responses with critical commentary, and a more representative process of peer review.

A human evolution exhibit in Israel

The biological anthropologist Israel Hershkovitz has a nice essay in Nature discussing a new exhibit at the Steinhardt Museum of Natural History’s Dan David Center for Human Evolution and Biohistory Research at Tel Aviv University: “My hopes for Israel’s human-evolution gallery”.

Hershkovitz helped to create the exhibit together with his colleagues Hila May and Rachel Sarig.

As have other Western countries, Israel has seen conservative religious values increasingly clash with secular ideals. Last year, public schools saw a reduction in teaching hours in science, technology, mathematics and English, but not in Jewish studies. Evolution by natural selection is rarely taught to students at public schools, let alone in the many religious schools. In a poll of Israeli adults run by the Israeli newspaper Haaretz last year, 37% said they don’t believe that humans and apes share a common ancestor. Even more disturbing: that percentage grows to 50% among those aged 18–24, highlighting the increasing hold of conservative religion on Israel’s youth.

The essay gives some perspective on religious creationism in Israel, as well as some of the strategies the team used to communicate some important aspects of human origins.

Link: Transmissible Alzheimer's Disease?

Jennifer Frazer writes on the Scientific American blog site: “The Case for Transmissible Alzheimer’s Grows”.

It’s a very scary story if true:

Indeed, two types of Aβ [beta amyloid peptides] and tau were still present in the vials, even after more than three decades of room temperature storage. Aβ and tau, at least, are survivors too.
This team took their study a step further by injecting a tiny sample of these vintage vials into the brains of mice engineered to be susceptible to human Alzheimer’s. The mice developed both Aβ plaques and cerebral amyloid angiopathy, although they showed no signs of tau. Aβ peptides had not only managed to survive decades of room-temeprature storage, they were also still transmissible. This is concerning.

Among other things, there’s a suggestion that prions and possibly Alzheimer’s-related peptides on surgical equipment might transmit associated disorders by means of surgeries. It’s a scary idea. The medical research establishment unfortunately has poorly in the past at examining the hypothesis that pathogens are associated with chronic disease.