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john hawks weblog

paleoanthropology, genetics and evolution

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

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.

Link: Writing about science in an African language

Sibusiso Biyela has a great essay in The Open Notebook recounting the challenges faced in communicating science about a South African dinosaur discovery in one of the major languages of South Africa: “Decolonizing Science Writing in South Africa”.

My job was to write about the discovery for the South African website SciBraai—and to do so in my native language of Zulu.
But there’s no word for “dinosaur” in Zulu. Nor are there words for “Jurassic,” “fossilization,” or “evolution.” Despite the fact that Zulu—or isiZulu, as the language is called in South Africa—is spoken by some 10 million people, it simply doesn’t have the words for communicating science.
So my news piece wasn’t just a news piece. It was an attempt to tell a science story in a language that science overlooked—to help right a societal wrong. It was a small contribution among an increasing number that aim to help decolonize South African science writing. And it was rife with more pitfalls than I could have imagined. The task of describing science clearly, concisely, and accurately—already challenging in English—became exponentially more difficult in my native tongue.

I absolutely love how creating new translations and terminology provides the opportunity to escape the bad thinking of the past. For example, on “dinosaur”:

I encountered trouble, however, with the word dinosaur, which comes from the Greek for “terrifying lizard.” The term is a misnomer: Many dinosaurs bear little resemblance to lizards, and some ancient animals that looked like terrifying lizards, such as the dimetrodon, are actually more closely related to mammals than to dinosaurs. I didn’t want to introduce into Zulu the same misconceptions that already plagued so many English speakers.

It is one of the hardest challenges in writing about science to escape the worn ruts of past writers, which may be easier to follow, but lead readers off in wrong directions. The great opportunity of starting fresh is that a writer can build a new way of representing the science that aligns with today’s concepts and ideas.

Link: Scientists and 'science denial'

A short essay by Kari Fischer from the New York Academy of Sciences, in The Scientist: “Opinion: What You Believe about “Science Denial” May Be All Wrong”.

Scientists should receive more institutional support, training, and career incentives to engage in proactive communication with the public. And when we do speak out, we must remember that we represent not only ourselves, but our institutions, and science as a whole. We should resist the temptation to engage with trolls, or become them ourselves by berating “non-believers.” Ridicule will not foster trust.

Obviously I’m more familiar with my corner of science than with others. Anthropologists in the U.S. live in a bubble. Few listen to non-academic voices, or engage the public in a way that has any direct effect on their research agenda.

These kinds of academic meetings encouraging better methods of speaking to the public have some value. But what is really needed is a wholesale change to the incentive and reward system in science and academia.

Long-distance weather 'teleconnections'

Last week Nature released an intriguing paper that demonstrates super-long-distance correlations in rainfall patterns, showing how the South Asian monsoon is synchronized with East Asia, Africa, and even events in North America. The paper, by Niklas Boers and coworkers, is titled, “Complex networks reveal global pattern of extreme-rainfall teleconnections”.

According to the statistics provided with the paper, it has one of the longest submission-to-acceptance times I’ve ever seen. It was received August 7, 2016, and finally accepted December 4, 2018.

The basic idea is that weather patterns are correlated over short distances, but become less and less correlated as distance increases. Over distances less than 2500 km, the loss of correlation is approximately linear with distance, but over longer distances the loss of correlation is faster than linear—a power law with exponent greater than one. But against this pattern of rapid loss of correlation at long distances, some events stand out as being much more correlated than expected. These types of correlations are identified in the paper as “teleconnections”.

Finding such teleconnections is a big data problem, where the datasets involve weather observations in a dense worldwide matrix. As geneticists would recognize, this gives rise to a problem of multiple comparisons. The paper includes a fun discussion of the multiple comparisons problem as applied to weather network data:

Before proceeding, however, a statistical problem needs to be solved, which arises in all data-driven interdependency analyses, and in particular in networks that are constructed on the basis of statistical similarities. Such approaches are generally biased because of multiple comparisons. In this case, we compare each timeseries with 575,999 other timeseries, which amounts to more than 1011 comparisons in total. Therefore, the network will contain links that—despite corresponding to statistically significant pairwise synchronization values—are present only because of random coincidences, and not because of physical mechanisms.

The method used to address this problem in the paper is to reduce the problem to “bundles” of spatial links, thereby identifying channels of long-distance interaction above the noise of incidental similarities. This method lies behind the identification of long-distance couplings:

After applying our correction technique, a concise teleconnection pattern associated with the northern part of the South Asian monsoon is revealed: in addition to regional links covering most of the Indian subcontinent, we observe pronounced link bundles connecting SCA with eastern Asia, the African tropics, large parts of Europe and the eastern coast of North America, as well as the Southern Hemisphere extratropics. The break between regional and teleconnection scales (Fig. 2) is not affected by this correction (Extended Data Fig. 2).

By examining the time lags separating these correlated patterns in different parts of the world, the authors conclude that Rossby waves are the most important mechanism driving long-distance weather correlations. I didn’t know anything about Rossby waves before reading this paper, and they seem like an interesting phenomenon.

One implication of such long-distance correlations is that what seem like “clusters” of extreme events may actually be a single event with long distance results. That has importance for studying the frequency of extreme weather events of all kinds, which have been suggested as a consequence of a warming climate.

We hope that our results will inspire further work on the predictability of EREs arising from these large-scale teleconnection patterns and on their representation in weather and climate models. Many studies have recently raised the concern that the characteristics of extreme events will change under ongoing climate change. A particular challenge in this regard is the discrimination between natural variability and anthropogenic influences6,7. With the increasing temporal lengths of global, high-resolution rainfall datasets, investigating changes of the global rainfall teleconnection structure along the lines of this study should become possible in the near future.

It is possible that the long-distance correlations are actually present within current climate models, and themselves give rise to the increase in extreme weather events in models. Or the Rossby wave-driven correlations might be a mechanism not yet replicated in climate models.

Scientific meetings should happen where research happens

In Nature Evolution and Ecology, Zeresenay Alemseged, Jackson Njau, Brianna Pobiner and Emmanuel Ndiema have a comment that reports on the 2017 conference of the East African Association for Palaeoanthropology and Palaeontology: “Connecting palaeoscientists in eastern Africa and the wider world”. This is a valuable essay and is accessible through the online PDF reader that the Nature journals have started using.

The commentary begins with a strong statement of the injustice of the paleoanthropological enterprise at the end of the last century:

[I]n spite of the undisputed importance of the region to the understanding of human evolution, there was no regional scientific forum that facilitated scientific discourse locally until the birth of the East African Association for Palaeoanthropology and Palaeontology (EAAPP) in 2005. As such, eastern Africa largely served as a data-mining hub in which local research, training and public education saw few of the benefits of the worldwide fame and international funding efforts that the region attracted. A very small number of senior local scholars managed to travel overseas to attend scientific meetings, but most east African scientists, especially students and early-career researchers, were scientifically isolated owing to the prohibitive costs of travel, accommodation and conference registration and cumbersome visa procurement for travel to Western countries. Moreover, there was a complete absence of a platform where international scientists undertaking research in the region could engage with local decision-makers and stakeholders managing research, conservation and curation of palaeoanthropological resources, leading to haphazard and non-strategic collaboration. The rationale behind establishing the EAAPP emanated from these realizations and aimed at addressing these issues.

I added the emphasis to the sentence that mentions “data mining”.

It is sad how little value anthropologists of the past have created for the many nations where they have collected data. The essay points to the funding efforts of the past, but even these have been anemic compared to the scientific value and future potential of fossil discoveries in Africa. The future of discoveries crucially depends on the ability of scientists and other stakeholders to translate heritage into jobs, economic value, and international prestige for nations that face enormous development challenges.

Today’s scientists have to build what the previous generations did not. Previous generations too often acted as if fossil discoveries were like diamond mining. They spoke of “fossil fields being nearly exhausted” and acted like De Beers, creating scarcity of scientific value by limiting access.

That’s a great strategy if you want to keep selling diamonds, but it is a terrible way to build science. Building science means creating value at many levels, not only traditional academic outputs, but building scientific capacity, tourism, and heritage management.

On Twitter over the last few days I have pointed out the analogous situation happening in human genomics and paleogenomics, with a number of scientific meetings this year devoted to the genetics of Africa but being hosted at research institutes in Europe. It is so short-sighted to try to organize a meeting to show an institute is “engaged in Africa” and think that the best way to show this is to pay airfare for Americans to visit Europe.

Link: Falsifiable science and good science

Sabine Hossenfelder has become an outspoken skeptic of the idea that a new, even-bigger-than-the-LHC particle collider will achieve any breakthrough in high energy physics.

Yet many physicists are arguing strongly for a new collider, one that would attain higher energies than the current Large Hadron Collider. They point out the many theoretical models that make predictions about particles within the energy range of a new collider. In response to this argument, Hossenfelder writes: “Just because it’s falsifiable doesn’t mean it’s good science.”.

The other day I got an email from a science writer asking me to clarify a statement he had gotten from another physicist. That other physicist had explained a next larger particle collider, if built, would be able to falsify the predictions of certain dark matter models.
That is correct of course. A next larger collider would be able to falsify a huge amount of predictions. Indeed, if you count precisely, it would falsify infinitely many predictions. That’s more than even particle physicists can write papers about.
You may think that’s a truly remarkable achievement. But the question you should ask is: What reason did the physicist have to think that any of those predictions are good predictions? And when it comes to the discovery of dark matter with particle colliders, the answer currently is: There is no reason.

The current Standard Model in physics explains existing experimental data. Many physicists don’t like the Standard Model because it doesn’t seem natural—it violates their intuition that physical models should be mathematically simple, symmetrical, and “beautiful”. But the Standard Model works. While it might stop working at slightly higher energies, according to Hossenfelder there’s “no reason” to suppose that the particular energies in range of a next-generation collider will lead to new unexplained violations, any more than the LHC has.

Meanwhile, the price tag of a new collider will be extremely high. This price is a reckless gamble on predictions that nearly all physicists believe will be falsified by a collider.

The question is, what could be done instead?

I watch the high energy physics community because they are much better organized to mobilize public funding than evolutionary biologists. They are talking about building a collider that may cost 10 billion dollars. The Human Genome Project cost less than 3 billion.

The Human Genome Project cost less than 3 billion.

The operating budget of the current Large Hadron Collider is approximately 1 billion dollars per year.

The bison bone bed at Gran Dolina

In an earlier post, I looked at work by Mark White, Paul Pettitt, and Danielle Schreve, which considered evidence for Neandertal prey selectivity at five sites. One of those, Mauran, France, was a site where Neandertals repeatedly killed groups of bison, amounting to more than 130 animals over many years.

A 2017 paper by Antonio Rodríguez-Hidalgo and colleagues demonstrated a similar pattern of bison hunting in the TD 10.2 layer of Gran Dolina, Atapuerca, Spain: “Human predatory behavior and the social implications of communal hunting based on evidence from the TD10.2 bison bone bed at Gran Dolina (Atapuerca, Spain)”. There, around 400,000 years ago, hominins left the partial remains of more than 60 bison, forming a bone bed of more than 22,000 specimens.

The results indicate a monospecific assemblage heavily dominated by axial bison elements. The abundance of anthropogenic modifications and the anatomical profile are in concordance with early primary access to carcasses and the development of systematic butchering focused on the exploitation of meat and fat for transportation of high-yield elements to somewhere out of the cave. Together with a catastrophic and seasonal mortality pattern, the results indicate the procurement of bison by communal hunting as early as circa 400 kyr. This suggests that the cognitive, social, and technological capabilities required for successful communal hunting were at least fully developed among the pre-Neanderthal paleodeme of Atapuerca during the Lower Paleolithic. Similarly, the early existence of mass communal hunting as a predation technique informs our understanding of the early emergence of predatory skills similar to those exhibited by modern communal hunters.

It’s not clear whether the hominins at Gran Dolina were early Neandertals like those represented approximately 450,000 years ago in the Sima de los Huesos, or whether they may instead have belonged to some other population. Whoever they were, they must have had a place somewhere nearby where they could kill small groups of bison at two different times of year.

Why nearby? Because they transported basically whole bison bodies into Gran Dolina, where they butchered the animals further and then carried most of the long bones somewhere else. What was left was mostly skulls, vertebrae, and ribs—an unusual proportion of ribs compared to most faunal assemblages. The hominins paused as they butchered to break the ribs and “snack” on red bone marrow.

Why two seasons? Because newborn bison are born at a single time of year, making it possible to work out what season first-year juveniles must have been killed, and the bone bed includes first-year juveniles of at least two different seasons.

Also, there’s this detail:

Human tooth marks on the bison-set have been identified on 192 specimens (Table 5). They are predominantly located on ribs (76.3%) and, to a lesser degree, on unidentified flat bones (7.3%) and hyoids (5.7%), 48.4% of which are associated with other anthropogenic modifications, such as cut marks (Supplementary Online Material [SOM] Table S1). A large range of human tooth marks produced during the consumption of the carcasses have been characterized and recorded, although scored and pits are the most abundant.

The authors emphasize that the bison bone bed is a distinct pattern of evidence about hominin hunting. There are non-bison bones in the layer from many different animals, but these constitute only a small fraction of the total, and none of them have clear evidence of human modifications such as cutmarks. Both the bison and non-bison material has evidence of carnivore modifications. But the representation of large parts of the axial skeleton and the evidence for human butchery show that humans had primary access to the bison carcasses, and carnivores ravaged the bones later, after the humans were done with them. The ribs bear abundant evidence for removal of the viscera, which is rare at other sites mainly because ribs are much less likely to be present.

In total, these show that effective communal hunting of large mammals was part of the behavior of hominins in Europe well before the appearance of Middle Paleolithic toolkits. Rodríguez-Hidalgo and colleagues compare the site to others across western Eurasia:

This is fully consistent with other well-documented and thoroughly taphonomically investigated assemblages from the Middle Pleistocene, such as Bolomor, Cuesta de la Bajada, and Gran Dolina TD10.1 and Gran Dolina TD6 in Spain (Blasco, 2011; Saladié et al., 2011; Domínguez-Rodrigo et al., 2015; Rodríguez-Hidalgo et al., 2015) Schöningen in Germany (Voormolen, 2008; Starkovich and Conard, 2015; Van Kolfschoten et al., 2015) and Gesher Benot Ya'aqov and Qesem in the Near East (Rabinovich et al., 2008; Stiner et al., 2009); in which hunting emerges as the main method to acquire animal carcasses.

As such, these particular hominin-accumulated sites have a very different profile than carnivore-accumulated sites, in that the hominins have been much more selective on a few prey species. That’s compared in this figure from Rodríguez-Hidalgo and coworkers, which looks at the number of individuals of prey species represented (on the x-axis) compared to “evenness”, which is a measure of how equally represented different prey species are. The carnivores here do not focus their attention on single species as often as these hominin accumulations have done:

Prey species evenness from Rodríguez-Hidalgo et al. 2017.

This is notable again for the similarity between the Gran Dolina bison bone bed and the Mauran bison accumulation, from the last interglacial.

The bison bone bed also differs from both earlier and later layers of Gran Dolina. This suggests that the cultural and environmental conditions that gave rise to bison kills near the site were localized in time.

Obviously these kinds of sites where dozens of kills give sufficient information to look at the entire process of hunting and butchery across a limited period of time are relatively rare in the archaeological record.

A site like Gran Dolina tells us that such kill-dense sites cannot be strictly representative, because over hundreds of thousands of years of hominin activity at the site, the bison bone bed represents only a limited time, and very different hunting preferences predominated at other times.

Link: The tension between telling a story and telling readers what is going on

An article by Chip Scanlan at Nieman Storyboard displays an insider’s knowledge of the nut graf, the part of a journalistic article that explains to the reader what the rest of an article is about: “Nut grafs: Overused, misused — or merely misunderstood?”.

The big idea in the article is the tension between writers who want to create a kind of suspense in their stories, and readers who want to know what the heck a story is about before they commit to reading all of it. The so-called “nut graf” is an invention to enable readers to get the gist of an article early on, so that if they choose not to read the rest, they’ll know more or less what they missed. It’s not exactly Cliff’s Notes, but it helps.

Evidently some writers hate the idea because the nut graf is usually written in an omniscient voice that pulls readers out of a narrative.

We toss out the word “story” every day. “Great story!” “Why wasn’t my story on the cover?” And the highest praise, “I wish I could write that story.” But as the legendary writing coach Jack Hart noted, most journalistic pieces are not stories, but articles, well reported and organized, accurate and fair. But no child ever looked up from their pillow at night, eyes wide with excitement, and beseeched, “Daddy, tell me an article!”
Stories have characters, not sources; settings, not addresses; dialogue, not quotes. Instead of nut grafs, they use transitions—a term from the musical world— subtle, elegant turns that mark the passage from one scene, subject, or place to another.

This is a tension that often occurs in science writing. When I teach, I like to assign narrative pieces by writers that tell human stories. But I also like to assign textbook chapters and scientific articles.

Stories are valuable, and they can do things that more neutrally written articles cannot. But a story can be the ultimate cop-out for a writer who is addressing scientific subjects. And the idea that an article must be “well reported and organized, accurate and fair” belongs to a mythological world that probably never existed.

A written piece is a machine for thinking. There will be no single right way to write, because readers are rightly suspicious of any writer’s motives and abilities. Narrative can be an effective way to convey some information, but readers should be wary of the biases hidden in stories about individuals, especially when the stories are a sugar-coated way of introducing a scientific subject.