john hawks weblog

New footprints from Laetoli and improving the science of fossil context

2016-12-14T00:00:00-06:00

I’m jazzed this morning because eLife has published a paper by Fidelis Masao and colleagues describing new footprint trails from the famous site of Laetoli, Tanzania: “New footprints from Laetoli (Tanzania) provide evidence for marked body size variation in early hominins”.

The scientific theme of the paper is about body size and dimorphism. The species presumed to have made all the trackways is Australopithecus afarensis, the only species that has so far been reported from fossil remains at Laetoli, although the tracks at 3.66 million years old are a bit more ancient than any of the fossils. This is the same species as the Lucy skeleton, which was found at Hadar, Ethiopia, and the “First Family” series of fossils from Hadar in the locality known as A.L. 333. In 2010, Yohannes Haile-Selassie and colleagues reported a partial skeleton from Woranso-Mille, Ethiopia, some 3.6 million years old, which also seems to represent a large male individual, that stood just under 160 cm tall. Based on a regression of foot size to stature, the new footprint trail in test pit L8 represents an individual that probably stood around 165 cm, with 10 cm or so error either way.

Here’s a neat graphic showing stature estimates for early hominins up through early H. erectus:

Figure 12 from Masao et al. 2016. Original caption: "Estimates of predicted stature of fossil hominin individuals by species over time for the interval 4–1 Ma. Solid symbols (or crosses in bold) refer to stature estimates based on actual femur length; open symbols refer to stature estimates based on estimated femur length, in turn based on femur head diameter. For Laetoli and Ileret, stature estimates are based on footprint length (see Materials and methods). For Laetoli, Ileret and Woranso-Mille, the average value and range of predicted stature are shown. Colours are associated to the geographical location of each fossil/ footprint site on the map."

That’s a bit complicated but the point is pretty clear. A. afarensis overlaps with H. erectus substantially in stature. If we consider only the tiny Lucy skeleton (the lowest “x” in the figure at less than 110 cm), we get a misleading view of body size in this early hominin species. But at the same time, Lucy and some other specimens of A. afarensis really are quite a lot smaller than any H. erectus specimens. The conclusion made by Masao and colleagues, applying some statistics, is that A. afarensis was more variable and sexually dimorphic than humans and H. erectus.

This idea of higher dimorphism in early hominins has been the subject of pointed debate over the past fifteen years, a debate that has been driven by insufficient fossil data. One group of authors has, through the use of increasingly complicated statistical games, tried to show that a tiny sample of fossils are not really as variable as they look to the eye.

These new data don’t revolutionize the question, they just move the ball downfield slightly. Adding a few more data points, even very large individuals, doesn’t vastly narrow the confidence limits on second- and higher moments of a size distribution. But what these footprints should remind us is that discovering new fossils is a lot more valuable than statistical games. With that in mind, I think we should also be skeptical about whether these footprints were really produced by A. afarensis. That species already has problems at Hadar and at Woranso-Mille, where some researchers now recognize multiple species are present. At Laetoli, we should probably apply a level of skepticism to the idea that only one fossil species could be present.

As I was reading this new paper, what struck me was that the authors had some difficulty being certain that the new footprints represent the same “Footprint Tuff” in which the older track G hominin footprints were found back in the 1970s. They found that the original scientists involved in describing the footprints, including Tim White, Mary Leakey, and Richard Hay, had been very thorough in describing the footprints themselves and some aspects of the geological setting. But those original descriptions just did not present sufficient detail about some geological aspects essential to recognizing the geological layers in the field setting. There were no published photographs of the stratigraphic sequence, for example, and no description of the color or “eye-scale characteristics” of the tuffs. Without such details, it is difficult to do replicable work on new aspects of the geology. That is, the level of detail sufficient to publish fossils in the 1980s does not meet the basic needs of scientists today. We need better descriptions of the context of fossils, and we need to know when those fossils are really in situ like these footprints.

We have come a long way in understanding aspects of microstratigraphy and taphonomy, and we have come to demand greater contextual detail in addition to the basic description of fossils. You can see that shift manifested in this paper by Masao and colleagues, which includes clear field descriptions of all the geological units they encountered.

Figure 3 from Masao and colleagues (2016), illustrating footprint trail L8 with an elevation map applied.

What we demand in descriptions today is also much more detailed than forty years ago. Then, it was sufficient to publish line drawings of footprints, with a few topographic views. But even then, researchers recognized that publications didn’t provide all the detail that was necessary to really evaluate the science. So they made casts available to allow other researchers to compare the evidence. Of course we all know that some scientists have stopped exercising such care, but for the rest of us, we place higher demands on the evidence we’re willing to accept.

Today, we can make three-dimensional models available instantly. So in addition to the different modes of visualization used in the research paper, Masao and colleagues have placed research-grade models of the footprint trails on Morphosource for anyone to download. That’s the same mechanism we used to distribute 3D surface models of the Homo naledi discovery, and it is great to see more and more scientists taking advantage of the opportunity to increase the replicability and quality of their science in this way.

It’s just really exciting to see researchers around the world engaging with new discoveries like this, getting them out to the public in open access journals, and building the global support for our science.

References

Masao F, Ichumbaki EB, Cherin M, Barili A, Boschian G, Iurino DA, Menconero S, Moggi-Cecchi J, Manzi G. 2016. New footprints from Laetoli (Tanzania) provide evidence for marked body size variation in early hominins. eLife 2016;5:e19568. doi:10.7554/eLife.19568

Jungers WL. 2016. Paleontology: These feet were made for walking. eLife 2016;5:e22886. doi:10.7554/eLife.22886

Haile-Selassie, Y., Latimer, B. M., Alene, M., Deino, A. L., Gibert, L., Melillo, S. M., ... & Lovejoy, C. O. (2010). An early Australopithecus afarensis postcranium from Woranso-Mille, Ethiopia. Proceedings of the National Academy of Sciences, 107(27), 12121-12126.

Link: A deep dive into Cahokia

2016-12-13T00:00:00-06:00

Annalee Newitz has a detailed and fascinating story in Ars Technica about the Cahokia site, on the Illinois side of the Mississippi River from St. Louis: “Finding North America’s lost medieval city”.

At the city's apex in 1100, the population exploded to as many as 30 thousand people. It was the largest pre-Columbian city in North America, bigger than London or Paris at the time. Its colorful wooden homes and monuments rose along the eastern side of the Mississippi, eventually spreading across the river to St. Louis. One particularly magnificent structure, known today as Monk’s Mound, marked the center of downtown. It towered 30 meters over an enormous central plaza and had three dramatic ascending levels, each covered in ceremonial buildings. Standing on the highest level, a person speaking loudly could be heard all the way across the Grand Plaza below. Flanking Monk’s Mound to the west was a circle of tall wooden poles, dubbed Woodhenge, that marked the solstices.

Despite its greatness, the city’s name has been lost to time. Its culture is known simply as Mississippian. When Europeans explored Illinois in the 17th century, the city had been abandoned for hundreds of years. At that time, the region was inhabited by the Cahokia, a tribe from the Illinois Confederation. Europeans decided to name the ancient city after them, despite the fact that the Cahokia themselves claimed no connection to it.

She reports from the scene where she participated in some archaeological work, including some of my favorite bits: digging in the houses and structures used by ordinary people, on the outskirts of the monumental area.

Link: A consideration of religion and Neandertals

2016-12-07T00:00:00-06:00

Barbara King asks, “Were Neanderthals religious?”

Given their intelligence, it seems to me likely that the Neanderthals contemplated, in some way, the mysteries of life. Wouldn't they have wondered not only about unexpected and surprising weather events and sky events but also what happens when our lives comes to an end? If they thought about these questions, did they do so with awe, dread or reverence?

I provided a quote for the piece, which discusses what kinds of evidence archaeologists consider. I have come to recognize that the recognition of mortality and cultural practices associated with death may be among the deepest behavioral aspects of human evolutionary history.

Third molar agenesis: a puzzling case of recent human evolution

2016-12-03T00:00:00-06:00

One of the most obvious cases of recent human evolution is the increasing frequency with which individuals don’t develop third molars, what is called “M3 agenesis”. This condition is when the third molars, or wisdom teeth, don’t form at all – the individual never developed them.

I could be wrong, and I’m sure that a reader will remind me if I am, but I cannot think of an instance of M3 agenesis in hominins outside of modern humans. It was entirely typical for most hominins throughout our evolutionary history to develop and erupt third molars into normal occlusion.

Agenesis of the third molars is different from cases where the M3 fails to erupt normally or remains impacted within the jaw. It is also different from the dental or surgical removal of third molars, which is now carried out on a very high proportion of people in the United States and many other countries. The number of students in my courses at the University of Wisconsin that still have their third molars is pretty small, generally less than 20 percent and often less than 10 percent. The majority of third molar removal is for orthodontic purposes. When third molars erupt, they exert forces on the rest of the teeth that can cause crowding and malocclusion, and more rarely, severe pain. One of the easiest ways to maintain straight teeth is to pull the ones in the back.

The problems with crowding of the anterior teeth points to the reason that anthropologists have traditionally given for the change toward a higher incidence of agenesis. Our Pleistocene ancestors very rarely had malocclusions due to dental crowding. The development of our jaws and teeth evolved within a context where people lived hunter-gatherer lifestyles and ate fairly tough foods, even as young children. By contrast, crowding of the dentition and resulting malocclusion have been very common in many Holocene populations, mostly those with agricultural subsistence. Agriculturalists don’t eat as many tough foods; they eat a large fraction of cooked grains and easy-to-chew cooked plants, milk, and meats. The idea is that the development of the jaw is plastic, and a reduction of the forces exerted on the dentition during early childhood can alter the developmental trajectory of the mandible and maxilla. If the jaws don’t develop as to as large an adult size, the teeth will tend to be crowded, and the last teeth to initiate development, the third molars, may not form at all.

This is an elegant story in some ways, but in fact we don’t know whether it’s true.

We do know that the teeth develop from an embryonic tissue sheet, which is divided into segments by genes during early development. Those segments expand and wrinkle into the form of tooth germs in a characteristic pattern, which is retained across most mammal orders, although many of the orders have come to have different numbers of teeth, which result from evolution of this early developmental pattern. Within a species, if an individual ends up with a segment that is too small or doesn’t develop quite right, that tooth will not form. The most common change is to the extreme tooth, which is the third molar. Less commonly, individual teeth within the other types may fail to develop – P4 agenesis is fairly frequent, sometimes I2 agenesis. Some of these kinds of agenesis are syndromic, meaning that other biological traits covary strongly with them.

How jaw forces might influence the pattern of tooth development is not well understood. Nor is it well understood how heritable M3 agenesis may be – to the extent it seems to run in families, this might reflect similar environments or similar genetics.

We do know quite a bit about the incidence of M3 agenesis in different human populations. The trait is nearly universal – it occurs everywhere in large enough samples of people, even in hunter-gatherer peoples who have recently continued eating “wild” food diets. But it differs greatly in frequencies.

Carter and Worthington (2015) did a meta-analysis of studies that have estimated M3 agenesis frequencies in particular human populations. By looking at 92 studies in different regions of the world, they give a global picture of where humans are more or less likely to have agenesis of the third molars. They limited their analysis to include studies of living human populations with radiographic evidence, so the agenesis was clearly documented.

Here’s the picture summarizing the frequencies in different regions:

Figure 3 from Carter and Worthington (2015). Original caption: "Bean plot of the proportion of individuals with agenesis of at least 1 third molar, partitioned by geographic provenience (92 studies, 100 effect sizes). Solid diamonds and error bars denote the means (inverse variance weighted) and 95% confidence intervals (CIs) of proportions for each region. Dark gray circles are individual studies, while light gray polygons are kernel density estimates of the distribution of proportions within each region. Analysis was performed on logit-transformed proportions, but means and 95% CIs are back-transformed for easier interpretation. LRT, likelihood ratio test."

The incidence of M3 agenesis is lowest in African populations today. This chart represents only two studies in Africans, but the observation of a very low frequency of M3 agenesis is in accord with studies of skeletal samples in my experience. Other populations have a higher frequency, although the study does not include any populations indigenous to Australia, New Guinea or the nearby areas of Melanesia, which in my experience also have low frequencies of M3 agenesis. Some of the highest population frequencies are observed in Asia; these are sampled broadly, including one sample from South India, several studies of Japanese, Turkish, Israeli and Iraqi. So it’s not specifically East Asian, but more broadly some population samples across the continent.

The most common M3 agenesis is a single missing third molar, and that is what is illustrated in the chart. It is less common to be missing two molars, and very uncommon to be missing three or all four of them. Women are slightly more likely to be missing an M3 than men (Carter and Worthington found a 14 percent greater likelihood in women).

I know that many anthropologists lecture about M3 agenesis as a recent evolutionary change, but it is a complicated one. Few look deeply into the pattern, which is strongly parallel across many human populations, not regionalized. In a broad sense, the frequencies of M3 agenesis across populations covary with molar sizes, and it may simply be that the evolution of smaller tooth size has M3 agenesis as a frequent side effect. The greater incidence of agenesis in women also might be expected as a correlate of smaller molar sizes.

There is no evidence that M3 agenesis is itself an adaptation that has been favored by natural or sexual selection. The possibility of sexual selection presents itself in this context because of the possible effects of a crowded dentition on mating preferences in past populations. But if M3 agenesis owes its recent high frequency to selection, it is likely as a side effect of selection for smaller teeth. However, even that is hardly so simple, as the pattern of size reduction in teeth was not uniform in Holocene populations, and the frequencies of M3 agenesis fluctuate substantially among studies.

And we do not know how much of M3 agenesis may be explained by plasticity of development within current environments. Some studies show a difference within a geographic sample between people who have originated from different immigrant populations (for example, in Singapore between people of Chinese, Malay, and Indian ethnicity), but none have really evaluated the frequencies in second-generation and third-generation immigrants. The genetics of the trait, even heritability, is basically an open question. Of course, if it were entirely explained by environment, M3 agenesis would not be an example of evolutionary change at all.

So M3 agenesis is a fascinating example of recent biological change in human populations, and we know very little about how and why it has changed.

Reference

Carter, K., & Worthington, S. (2015). Morphologic and Demographic Predictors of Third Molar Agenesis A Systematic Review and Meta-analysis. Journal of dental research, 94(7), 886-894. doi:10.1177/0022034515581644

Link: Geese hybridization

2016-11-01T00:00:00-05:00

Just a note that ducks provide many great examples of hybridization dynamics, particularly invasive ducks. This recent paper on geese by Jente Ottenburghs and colleagues (“Hybridization in geese: a review”) shows that they are much the same. Lots of geese species, lots of hybridization, including cross-generic hybridization.

Most hybrid geese are fertile; only in crosses between distantly related species do female hybrids become sterile. This fertility pattern, which is in line with Haldane’s Rule, may facilitate interspecific gene flow between closely related species. The knowledge on hybrid geese should be used, in combination with the information available on hybridization in ducks, to study the process of avian speciation.

Link: Swartkrans site formation

2016-10-29T00:00:00-05:00

Travis Pickering and colleagues have a paper presenting new teeth from Swartkrans, which they attribute to Paranthropus robustus: “New early Pleistocene hominin teeth from the Swartkrans Formation, South Africa”. I’m pointing to the paper because it has a long and clear review of the complex history of site formation in this ancient cave.

Neandertal anti-defamation files, 22

2016-10-26T00:00:00-05:00

This, from ScienceAlert:

We caught modern genital warts because our ancestors were banging Neanderthals

Nothing like this story as been such a race to the bottom for headlines for a long time.

I will note that Annalee Newitz has a much better version of the story with this winning quote:

[A]lways practice safer sex, even if you're getting down with a Denisovan.

There is, by the way, the interesting question of whether Neandertal immune variants might influence susceptibility to the strain in question, which has made little inroad into sub-Saharan Africa.

Race and the medical student

2016-10-25T00:00:00-05:00

Ike Swetlitz in Stat has an article about the ways that some medical educators are trying to build a more anthropological knowledge of race and health in their students: “Teaching medical students to challenge ‘unscientific’ racial categories”. Unfortunately both the headline and article get a bit snarled in their use of language. Maybe that’s inevitable.

“You see ‘African American,’ automatically just circle ‘sickle cell,’” said Nermine Abdelwahab, a first-year student at the University of Minnesota Medical School, recounting tips she’s heard from older classmates describing the “sad reality” of the tests.

Medical school curricula traditionally leave little room for nuanced discussions about the impact of race and racism on health, physicians and sociologists say. Instead, students learn to see race as a diagnostic shortcut, as lectures, textbooks, and scientific journal articles divide patients by racial categories, reinforcing the idea that race is biological. That mind-set can lead to misdiagnoses, such as treating sickle cell anemia as a largely “black” disease.

In an episode of M*A*S*H from the early 1980s, Corporal Klinger starts suffering from a rare side effect of the anti-malarial drug primaquine. The doctors know that the drug has the potential of negative side effects in blacks, but issue it to everyone else. Hawkeye and the other doctors assume Klinger is just goldbricking. But another soldier, Private Goldman, starts to exhibit the same symptoms. The doctors determine that both Klinger and Goldman are suffering anemia, and take them off the primaquine. At the end of the program, it is revealed that people of Levantine origin (like Klinger) and Ashkenazi Jews (like Goldman) also may have the same susceptibility to primaquine side effects owing to their ancestry.

The side effect in question is a breakdown of blood cells and consequent anemia in people with G6PD deficiency, which is indeed very common in sub-Saharan and North Africans, and less common but still notable in people of broader Mediterranean descent.

I like the program quite a lot, and I remember it from the first time it was broadcast. It is a well-scripted way illustration of how a physician can make erroneous assumptions about ancestry and genetics that lead to bad treatment. But it also goes to show that there’s very little new in today’s attempts to improve medical school training with respect to race and medicine. These are all ideas that were well-known more than forty years ago and have been staples of anthropology.

Of course today we can know from anyone’s genotype data whether they have a susceptibility to some adverse drug reactions, and that includes many that do not have much higher frequencies in one population or another. Whatever there is to be said for genotyping, it beats census categories if you are looking to diagnose most common traits influenced by Mendelian genes. If we are training medical students for the world of five or ten years from now, allowing them to make effective use of this information should be the priority.

Will virtual reality compete with museums or help them?

2016-10-25T00:00:00-05:00

Linking to a provocative piece that “VR Will Break Museums”.

The article discusses many issues with museums both large and small. The best museums add context to the objects that they display, putting them into a story that builds knowledge in the museum-goer. But some concepts are incredibly difficult to communicate in that fashion, and others rely so much on place that removing objects to a museum does not convey their context accurately.

And the crowds suck. Nothing is better than a huge museum on a very empty day, and those don’t happen very often.

The problem is, museums don’t scale well. The British Museum sees almost 7 million visitors a year. What would it take to accommodate double that number? Ten times that number? It simply cannot be done, not for any reasonable amount of money.

The Internet, on the other hand, is built for scale. The marginal cost of an extra YouTube viewer or app download is practically zero. That’s how a video about the history of Japan can be made for free, distributed for free, and enjoyed for free by more people in a single month than who walk through the doors of the Louvre in an entire year.

Museums are a very important part of human evolution research, both by serving as repositories for the objects we study and for helping the public to understand the importance of our science. I’ve consulted with many museums over the years and have visited a large fraction of the major museums of natural history in the world.

Human genetics is more and more important to how we understand human evolution. Yet this is one of the most difficult parts of science to illustrate in a museum setting. Museums excel at visual material and unique objects. While it is possible to do video or virtual content for genetics, whenever I encounter videos at a museum, I groan. They’re always a chore and rarely hit the mark as well as simple text accompanying an object.

Honestly, I think that museums face much the same problem as movies. Studios invest tremendous sums of money in movies that have bad scripts. There are many reasons for this – sometimes the director has too much power and keeps shifting the script, sometimes the original idea relied upon visuals that cannot be realized, sometimes studio executives ruin a cohesive script by committee. Whatever is the case, the ultimate reason why this situation happens so often is the same: Audience demand for certain kinds of movies is just not very responsive to script quality.

Likewise, public visitation to certain museums doesn’t respond much to the quality of stories they can effectively tell. A museum exhibition with bad videos is regrettable, but most people skip the videos anyway. Especially if the first few seconds of the first one doesn’t connect.

The great thing about the idea of virtual experiences is that they may be laboratories for real innovation in storytelling. The stories that work should be translated into the museums that audiences already value. As someone who has done a lot of museum consulting, I can really imagine having a lot of fun helping make virtual experiences that educate and convey exciting science.

Incidental capuchin flake manufacture

2016-10-22T00:00:00-05:00

This is a nice article by Ed Yong about Michael Haslam’s research documenting how capuchin monkeys incidentally make stone flakes as a side effect of their nut smashing: “Rock-Smashing Monkeys Unintentionally Make Sharp Stone Tools”.

The interesting thing is that many of the flakes are indistinguishable on technical grounds from Oldowan flakes. That raises the possibility that intermittent, possibly local traditions of nut-cracking among some forms of primates might create the appearance of localized flake assemblages.

He also thinks that archaeologists should spend more time looking for the works of ancient monkeys and apes. “[We should] consider what other non-human primates in Africa and elsewhere may have been up to for the past tens of millions of years,” he says. “There is no reason why stone flakes may not be littered throughout primate history, at unknown places and times.”

Actually, I think there is nothing materially different about what these capuchins are doing and what early hominins were doing when they made flakes. One may say that the hominins made flakes “intentionally”, or with a goal in mind to use the flake. But the difference here is not cognitive, it that the capuchins have not learned socially to use flakes for anything.

Primatologists already observe capuchin monkeys learning socially to lift rocks nearly half their body weight, thrust them down onto a platform with a fruit, and repeat this until yummy bits of nutmeat scatter everywhere. It would not take any great cognitive advance for them to learn how to use flakes, if there were something useful for them to do. The ability to generalize is simply the ability to emulate others.

Notable: Modern human origins and Ethiopian volcanoes

2016-10-19T00:00:00-05:00

Notable paper: William Hutchison et al. (2016) A pulse of mid-Pleistocene rift volcanism in Ethiopia at the dawn of modern humans. Nature Communications 7, 13192. doi:10.1038/ncomms13192

Synopsis: Many of today’s lakes and volcanic calderas of the central Ethiopian rift were the outcome of a cluster of volcanic activity between 320,000 and 170,000 years ago.

Interesting because: Early examples of Middle Stone Age (MSA) archaeological industries were developing at this time, and possibly the immediate ancestors of most of today’s gene pool were making some of them. Volcanoes might have affected the local environment.

KILL THIS QUOTE WITH FIRE: “current evidence overwhelming [sic] suggests that all major events in hominin evolution occurred in East Africa”. No. Just no.

Bottom line: It is very hard to test how local environmental shifts may have affected hominin populations; either prompting adaptation or creating population sinks. My guess would be that a region full of active volcanoes probably acted either as a sink or a barrier to gene flow. As an extreme, these volcanoes may have impeded migration from the Afar region further south along the African rift during the later Middle Pleistocene, making this fossil-rich region a relative cul-de-sac. However, in my opinion a 30-km zone of unpleasantness surrounding a volcanic caldera is not much of a barrier to mobile and interconnected hominin populations. Ancient people probably looked in wonder at the great forces within the earth, and watched their children played in the snowing ash.

Quote: Dobzhansky on borderline cases of species and races

2016-10-16T00:00:00-05:00

Theodosius Dobzhansky, in his essay, “On species and races of living and fossil man” (1944):

The opinion is often expressed that species and races are arbitrary categories. This opinion is false. If given the opportunity to secure the necessary data, a biologist is able in a majority of cases to decide beyond a reasonable doubt whether the forms under study are distinct species or only distinct races. Lion, tiger, leopard, and domestic cat are species ; Angora cat and alley cat are surely not species but races. However, “borderline cases”, in which it is impossible to decide whether one is dealing with species or with races, do exist. Indeed, their existence was used by Darwin to demonstrate organic evolution. If species are the primordial units of creation, or else if they arise by sudden leaps (as thought by G. St. Hilaire and recently by Goldschmidt), then we should be able to find methods to decide whether any two forms are still races or already species. If, on the other hand, species evolve gradually from races, then the decision will be possible only in some, perhaps in a majority, of cases, but at least some instances must be found in which forms are too distinct to be races but not distinct enough to be species. Evolutionists have concentrated their efforts on proving that such borderline cases do exist; by indirection they conveyed to biologists in general the impression that there are no other but borderline cases.

Misuse of statistics

2016-10-15T00:00:00-05:00

This essay should be required reading for graduate students: “The problem with p-values”. David Colquhoun writes extensively about science and statistics, and in this essay he brings out many of the biggest misconceptions that drive poor conclusions in scientific practice.

Even quite respectable sources will tell you that the p-value is the probability that your observations occurred by chance. And that is plain wrong.

Paleoanthropology is one field in which papers that point out poor use of statistics are publishable. The primary fossil data are very sparse, and we work hard to establish what little we can say with confidence. There are generally scientists willing to criticize statistically misleading attempts to answer the unanswerable.

Personally, I’ve spent a good amount of time looking into the basic statistical underpinnings of human evolution datasets. For example, my paper “How much can cladistics tell us about early hominid relationships?” showed that the datasets of most hominin species are simply not big enough to yield confident conclusions about how they are related to each other. A later paper, “No brain expansion in Australopithecus boisei”, worked through statistical issues with time-series data on which paleoanthropologists have often based conclusions about trends in morphological features over time.

My all-time favorite paper outlining statistical problems in human evolution research is by Richard Smith, “Biology and body size in human evolution: statistical inference misapplied.” Smith shows a systematic problem with the most common comparisons of ancient human relatives. Now, twenty years after that paper was first published, most papers that consider body masses of fossil hominins still get this wrong.

That’s a well-worn tale in science. Pointing out statistical errors is sisyphean. Many recent papers in human evolution reflect poor statistical practice. And a good number of “classic” results are based on datasets that today would be statistically doubtful. Science is self-correcting, but it is going to take some hard work to get this stuff straight.

References

Hawks, J. (2004). How much can cladistics tell us about early hominid relationships?. American journal of physical anthropology, 125(3), 207-219. doi:10.1002/ajpa.10280

Hawks, J. (2011). No brain expansion in Australopithecus boisei. American journal of physical anthropology, 146(2), 155-160. doi:10.1002/ajpa.21420

Smith, R. J. (1996). Biology and body size in human evolution: statistical inference misapplied. Current Anthropology, 37(3), 451-481. JSTOR

Everything Neandertal is not bad

2016-10-14T00:00:00-05:00

This is not a bad story about Neandertals by Melissa Hogenboom: “What Neanderthals’ healthy teeth tell us about their minds”. It’s an overview of what scientists learn from various kinds of dental studies.

But I wanted to comment on one thing:

"We realised nobody had directly compared Neanderthal [teeth loss] to modern humans, so we didn't realise Neanderthals had [slightly less] tooth loss," says Weaver.

This flies in the face of previous studies, which suggested that several Neanderthals lived long after losing all, or nearly all, their teeth.

But bizarrely, the finding that Neanderthals apparently had healthy teeth actually suggests something rather negative about them.

I don’t disagree that there is a slight difference in tooth loss. That does not contradict the real observation that some Neandertal individuals had extensive premortem tooth loss.

Mandible of the Neandertal with the most premortem tooth loss, La Chapelle-aux-Saints. Photo by Milford Wolpoff.

I agree that some people have made more cultural conclusions from the observation of tooth loss than the data warrant. I wrote about this back in 2005, when the subject of discussion was total premortem tooth loss in the Dmanisi skull D3444: “Caring for the edentulous”. My conclusions today don’t differ from then:

In the case of life history variation, I think that the survival of a small number of individuals under extraordinary circumstances says little about the habitual capabilities of a species.

A handful of Neandertals lived with fairly extensive loss of dental function, but that probably doesn’t tell us much about Neandertals that we do not already know about many primates.

What I really object to in the linked article is the way this topic is framed: This good thing about Neandertals “bizarrely suggests something negative about them.”

Often in human evolution, research is presented with a simple storyline that goes like this: “This bad thing everybody knows about, well, guess what—it’s actually good when you think about it from the evolutionary perspective.”

That’s the storyline of the sickle cell mutation. It causes disease, but it is an adaptation to malaria. It’s also the storyline of the “thrifty genotype” idea: Diabetes is bad, but its occurrence today may be a side effect of ancient adaptations to food scarcity.

That framing doesn’t erase the bad aspects of such biological traits, but it does give people a different way of thinking about why bad things happen. “Everything bad is actually good” is a fairly useful frame for teaching human evolution.

The opposite storyline is also pretty common. “That good thing that everybody knows about? Well, guess what—it’s actually bad when you think about it from the evolutionary perspective.”

This is how the invention of agriculture gets portrayed nowadays. Jared Diamond famously called it, “The worst mistake in the history of the human race.” The idea is that once upon a time, humans were adapted to a hunter-gatherer existence, and agricultural subsistence caused scores of bad unforeseen effects.

This “everything good is actually bad” storyline is especially common when it comes to studying Neandertals. For example, Neandertals seem to have eaten lots of meat. Does that mean they were successful hunters optimizing resources in a harsh environment? No, it means they failed to build knowledge of plant foods, putting them at extreme risk of extinction when times got tough.

Another example: Some Neandertal sites seem to have different assemblages of tools that may be suited to different functional tasks, for example some toolkits include many scrapers for preparing hides, while others lack such a dominance of scrapers. Is this evidence of clever and flexible Neandertals? No, to some archaeologists it was evidence that Neandertals must have behaved like herd animals, with women and children in some camps, and small groups of bachelor males in others.

My favorite essay on such stereotypes is by the archaeologist John Speth: “News Flash: Negative Evidence Convicts Neanderthals of Gross Mental Incompetence”. He humorously reviews a series of extravagant claims about what Neandertals couldn’t do, mostly tests that would fail when applied to some groups of modern humans.

Every so often, new evidence convincingly debunks one of these Neandertal stereotypes. For example, over the past ten years, a series of papers describing starches and phytoliths in Neandertal dental calculus have documented their use of plant resources, including cooking of some grains and the possible use of medicinal plants. In this case and many others, the press has reported the “surprising” conclusion that Neandertals were very much like modern human subsistence foragers.

Just once, I would like to see a journalist report such results as unsurprising evidence that past archaeologists were incompetent.

Now I don’t want to go overboard in the opposite direction. There probably really were some strange things about some Neandertals. Culture did evolve, and the evolutionary history of Neandertals probably yielded cultural abilities that humans lack, just as modern humans may have abilities that they lacked. In other words, I do not assume that they were merely modern humans with browridges.

But these are among the hardest ideas to test with archaeological evidence. At the same time, ideas about Neandertal cognitive difference align with persistent stereotypes about Neandertals. For that reason, I maintain an attitude of skepticism.

We know a good amount. Some of the cultural behaviors of recent and living modern humans have never been noted in Neandertal sites. But their tools, the traces of animals and plants that they ate, and their use of space show that Neandertal subsistence behavior had a lot in common with modern human subsistence foragers.

Many modern human subsistence foraging groups have left little or no evidence of “symbolic” artifacts, “complex site structure”, musical instruments, projectile weapons or similar trappings. We now know that Neandertals used pigments, engraved objects and rock surfaces, wore ornaments, made and used many kinds of bone tools, used shellfish, birds and small mammals—basically all things that past stereotypes held they didn’t do.

The point is, the difference between Neandertal and modern human behavior is clearly not a yawning chasm. They overlapped.

Studying Neandertal biological traits in combination with archaeology has a lot to offer to understanding their behavior. Dental pathology is a great avenue to understand how their health relates to their subsistence behavior. For example, Neandertals were once believed to have a much higher incidence of developmental dental pathologies than modern humans, traits like linear enamel hypoplasias that result from stress on the developing teeth from nutritional shortfalls or disease. It turns out that many modern human groups have just as high an incidence of such dental traits as Neandertals, including children from many agricultural groups.

Both Neandertals and prehistoric modern human subsistence foragers have vastly lower incidence of dental pathologies like caries when compared to most agricultural peoples, so it’s interesting to see that tooth loss was actually less among Neandertals than in the prehistoric modern human groups.

Better teeth may reflect the basic fact that Neandertals died faster than the Upper Paleolithic modern humans that followed them. By our best estimates (provided by Rachel Caspari and Sang-Hee Lee), Neandertal mortality was greater across the adult life span. Most known Neandertal dental remains come from relatively young adults, less than thirty or so years old.

Such high mortality probably does indicate something about Neandertal social relationships. Today’s human cultures owe much to the knowledge and experience of older adults, common in human societies. If those older adults were rarer, with some groups lacking older adults altogether, Neandertal cultures must have been poorer for it.

But adults in their twenties and thirties are not poor caregivers today. In fact, they are the primary caregivers toward both children and the most aged adults in our societies.

For that reason, I resist the framing that Neandertals good teeth may have meant they took less care of the sick. It may well have been true that sick Neandertals did not live as long, or have as good a chance of recovery. But I attribute that to the basic challenges of subsistence, not social incompetence.

References

Caspari, R., & Lee, S. H. (2004). Older age becomes common late in human evolution. Proceedings of the National Academy of Sciences of the United States of America, 101(30), 10895-10900. doi:10.1073/pnas.0402857101

Speth, J. (2004). News flash: negative evidence convicts Neanderthals of gross mental incompetence. World archaeology, 36(4), 519-526. doi:10.1080/0043824042000303692

Link: A new prehistoric footprint site in Tanzania

2016-10-13T00:00:00-05:00

National Geographic has a neat story by Michael Greshko about ancient footprints near Lake Natron, in Tanzania: “Treasure Trove of Ancient Human Footprints Found Near Volcano.

Local villager Kongo Sakkae found some of the footprints prior to 2006, but the site didn’t reach scientists’ attention until 2008, when Pennsylvania-based conservationist Jim Brett happened to be staying at the Lake Natron Tented Camp, just a few hundred yards from the footprints. Stunned by what he saw, Brett snapped as many pictures as he could and resolved to pass them along to a scientist he knew he could trust: Liutkus-Pierce, whom he had met when she was a postdoctoral researcher.

The trouble was, Brett picked the worst possible day to call.

“It was April Fool’s Day, I kid you not,” says Liutkus-Price. “He called me and said, ‘I think I have found some really cool hominid footprints.’ And I said, ‘Jim, can you call me tomorrow, so I know that this is not a joke?’”

The article gives a very nice account of the realization that these are fossil footprints, notes that they had been known to some local people earlier, discusses how collaborators were brought into the project, does not avoid mentioning a big problem with one of the researchers, and generally does a great job of showing how science is done.

Talking to the public is essential to the future of science

2016-10-09T00:00:00-05:00

Susanna Martinez-Conde, Stephen Macknik and Devin Powell have a short article with advice for would-be science popularizers: “How Scientists Can Engage the Public without Risking Their Careers”.

Daniel Kahneman, who published Thinking, Fast and Slow nearly a decade after he won the Nobel Memorial Prize in Economics, went to almost heroic lengths to ensure that traditional academics would approve of his book. “It took me four years to write my book—four exceedingly miserable years because I was explicitly trying to do two things,” he says. “I wanted to write a popular book, without losing the respect of my colleagues. I paid a lot of money to have my book reviewed anonymously by young associate professors, four of them, I paid them two thousand dollars each, to tell me whether this would damage my reputation. And interestingly enough, it did damage my reputation among a subset of my colleagues.” Even so, Kahneman feels that the academic reaction to his book was by and large, very positive

I admire scientists like Kahneman who make the decision to reallocate their time toward public activities. By doing so, they advance the work of their colleagues and their field in general. His solution seems a little extreme, but I am glad to see how he values the referee work and the opinions of other scientific colleagues.

Interacting with the public is hard work. Being effective at public communication is a skill that scientists develop only through extensive practice, talking and writing honestly about the value of scientific work and its implications. Being an effective teacher is equally challenging, and while the skillsets do overlap, they are not identical.

I do a lot of public writing, blogging, documentary consulting, and filming. This work has made me a better scientist. I see the effects throughout my research. I make discoveries, and as much as possible, I get to take lots of other people with me. I don’t want to work any other way.

Most academics in my field have been totally supportive of the way I work. I do everything I can to promote the great work of friends and colleagues around the world. It’s always great to hear about connections made, and I’ve found so many friends in unexpected places.

I can’t deny that I’ve heard some criticism over the years. That kind of criticism is what stops many young scientists from even trying to engage outside their narrow subdiscipline. It’s entirely rational to keep your head down and stick to academic journal articles.

But honestly, most critical comments come from a small number of professionals who spend a lot of effort trying to become “academic celebrities” themselves. Some people assume that a certain degree of success in science will automatically cause people to listen to everything they say. The world doesn’t work that way, nor would anyone sensible want it to.

I’ve learned a lot from those interactions. I’m still finding out new ways to persuade people that our origins matter, to show them how our scientific work makes a difference.

Brief thoughts on Upper Paleolithic 'hybrids'

2016-10-09T00:00:00-05:00

Science News has a long feature article by Bruce Bower that recounts the new wave of examining hybridization in human origins: “Animal hybrids may hold clues to Neandertal-human interbreeding”. He features the symposium at the AAPA meetings this spring organized by Rebecca Ackermann, which involved many scientists researching hybridization in primates and other mammals.

The big idea is that the biological consequences of hybridization are often recognizable in the skeleton. Fossil human populations may include individuals with ancestry from diverse populations, like Neandertals and Denisovans, much more genetically different than any living populations are. Paleontologists might use insights from hybridization in other mammals to understand which fossils show evidence of such population mixture. The big success story is the Oase 1 mandible, which has a high proportion of Neandertal ancestry:

Since the fossil’s discovery in 2002, paleoanthropologist Erik Trinkaus of Washington University in St. Louis has argued that it displays signs of Neandertal influence, including a wide jaw and large teeth that get bigger toward the back of the mouth. In other ways, such as a distinct chin and narrow, high-set nose, a skull later found in Oase Cave looks more like that of a late Stone Age human than a Neandertal.

Roughly 6 to 9 percent of DNA extracted from the Romanian jaw comes from Neandertals, the team found.

“That study gave me great happiness,” Ackermann says. Genetic evidence of hybridization finally appeared in a fossil that had already been proposed as an example of what happened when humans dallied with Neandertals.

Not only does the Oase mandible have a high fraction of Neandertal ancestry, roughly 3 times higher than any living people today, but also that Neandertal-like DNA occurs in large chunks, indicating a recent Neandertal ancestry. This individual may have had a Neandertal great-great grandparent.

Such a recent potential Neandertal ancestor means that the population mixture in this real-life case is not too far from what occurs in some natural and laboratory experiments on hybridization. The models from the present day have great relevance to this past case.

I will add, the Oase individual is not a singular case. Many early Upper Paleolithic skeletal remains from Europe have comparable evidence of anatomical features that are common in Neandertals but very rare or absent in other populations. David Frayer has documented many of these in detail, joined by other scientists, especially Milford Wolpoff.

It just happens that Oase 1 is the first specimen with ancient DNA evidence showing substantially elevated Neandertal ancestry beyond that observed in later populations. The ‘Ust-Ishim femur does not have more Neandertal ancestry than recent humans, and although the value for Kostenki 14 is high, it is not an outlier. Both those specimens have Neandertal DNA in relatively longer linkage tracts than today’s people, allowing us to see that mixture had preceded the birth of these individuals by only 10,000–15,000 years or so. But Oase 1 was nearly on the scene; where this individual lived, population mixture was probably still underway.

We know from ancient DNA evidence of later specimens. The earlier Upper Paleolithic populations had more genetic influence from Neandertals than populations from the Mesolithic and later. In part, this reduction of Neandertal ancestry reflects natural selection against functional parts of the Neandertal genome; in part it probably reflects repeated immigration into Europe of people from West Asia or other parts of the world. A pattern that appears in morphological traits, with Neandertal resemblance declining over time in European Upper Paleolithic and later populations, is paralleled by genetics.

Link: A comment on replicability by a psychologist

2016-10-03T00:00:00-05:00

Joe Simmons on psychology: “What I Want Our Field To Prioritize”.

I am writing all of this because it’s hard to resolve a conflict when you don’t know what the other side wants. I honestly don’t know what those who are resistant to change want, but at least now they know what I want. I want to be in a field that prioritizes replicability over everything else. Maybe those who are resistant to change believe this too, and their resistance is about the means (e.g., public criticism) rather than the ends. Or maybe they don’t believe this, and think that concerns about replicability should take a back seat to something else. It would be helpful for those who are resistant to change to articulate their position. What do you want our field to prioritize, and why?

Simmons gives an example of his past work being shown false by non-replication in a vast sample, and makes some important points. Probably most salient, description of methods should allow other researchers to build on results.

Lichens did not grow on Homo naledi

2016-10-02T00:00:00-05:00

Earlier this summer, Francis Thackeray published a short paper in the South African Journal of Science suggesting that lichens had deposited manganese upon the surfaces of hominin bone from the Dinaledi Chamber. Knowing that lichens depend upon light for their growth, Thackeray suggested that the Dinaledi bones had once been exposed to light for long enough to explain the lichen growth and manganese deposition.

Thackeray proposed that the geological evidence was somehow wrong, and that the Dinaledi Chamber had once been open to the surface. He elaborated on this view in an essay written for The Conversation:

I strongly believe that there was possibly a temporary entrance into the chamber, in addition to the one used by explorers today. This temporary entrance may been covered up by a rock fall that also trapped the individuals whose bones were found some time later.

Our team, including geologists and geochemists, has now published a response to Thackeray. We review some of the ways that manganese and other trace elements from dolomitic limestone can be deposited on fossil bone, and present additional evidence from the bone surfaces that rules out lichen involvement.

The Dinaledi bones bear traces of manganese and iron oxides. Some of the staining is dendritic, with very tiny features that suggest microbial involvement. The deposition process happens within sediment, in the dark

Several of the hominin fossils have linear tide marks of manganese or iron oxides. These mark an interface of air and sediment in which these bones were embedded.

Detail of DH2 skull, showing tide marks of manganese and iron deposition on surface

Looking through a microscope, the bones bear many different patterns of mineral staining and calcite deposition. Some of the fossils have calcium carbonate deposition on top of manganese staining; others have manganese deposition on top of calcium carbonate. Some have successive encrustations of iron oxide, manganese, and iron oxide, as visible in this photo:

Figure 4F from Randolph-Quinney et al. 2016, showing manganese stain formed on surface of iron oxide staining, with additional iron oxide encrustation overlying the manganese.

Additionally, some fossils have manganese deposits that have been removed by gastropod activity; others have manganese formed on top of old gastropod markings. All of this evidence is consistent with a long history of manganese and iron oxide deposition on the fossils within their current sedimentary environment.

None of this geochemical activity requires light.

One of the things that we have kept at the forefront of our papers describing the Rising Star cave system is that we must not set aside or ignore any of the geological evidence.

The geological evidence from the Dinaledi Chamber shows that it was an isolated depositional environment during and after the bones of Homo naledi entered the chamber. The sediments with the bones of H. naledi are very different in their chemical composition and particle characteristics from the neighboring Dragon’s Back Chamber. Dragon’s Back sediments have some input of surface material, the Dinaledi Chamber doesn’t. With articulated skeletal parts, complete representation of skeletons, and abundant fragile juvenile material, the bones of Homo naledi reject the hypothesis that the Dinaledi deposit could be a secondary accumulation from some other source. This is all compatible with the ceiling of the chamber, which is a chert layer with at most small thin fissures and no substantial openings, except for the vertical crack called the “Chute”.

Although the bone has been within the Dinaledi Chamber, that doesn’t mean it has been static. There has been erosion of the deposit since it began to form, with sediment and other material exiting the chamber through floor drains and some of the hominin bone being reworked along with the chamber’s surface. Bone within the Dinaledi Chamber was modified by gastropods and other cave-dwelling organisms, and minerals were deposited on its surfaces. The surfaces of many bones have been etched by the slightly acidic groundwater. Within parts of the deposit that are mere centimeters apart, the chemical circumstances differ.

It’s a very complicated picture, and whenever we make a new observation we must integrate it into the entire body of evidence. That work continues. This summer, members of our team published a review of the team’s 3D data collection strategies, including some mapping data from the cave. And our original research article on the context of the fossil assemblage remains open access in eLife, with detailed maps and analyses.

From earlier this year: “Deliberate deposition and Homo naledi”

References

Dirks, P. H., Berger, L. R., Roberts, E. M., Kramers, J. D., Hawks, J., Randolph-Quinney, P. S., ... & Schmid, P. (2015). Geological and taphonomic context for the new hominin species Homo naledi from the Dinaledi Chamber, South Africa. eLife, 4, e09561.

Dirks, P. H. G. M., Berger, L. R., Hawks, J., Randolph-Quinney, P. S., Backwell, L. R., & Roberts, E. M. (2016). Deliberate body disposal by hominins in the Dinaledi Chamber, Cradle of Humankind, South Africa?. Journal of human evolution 96: 149-153. doi:10.1016/j.jhevol.2016.04.007

Kruger, A., Randolph-Quinney, P. S., & Elliott, M. (2016). Multimodal spatial mapping and visualisation of Dinaledi Chamber and Rising Star Cave. South African Journal of Science, 112(5/6) doi:10.17159/sajs.2016/20160032

Randolph-Quinney, P. S., L. R. Backwell, L. R. Berger, J. Hawks, P. H. G. M Dirks, E. M. Roberts, G. Nhauro, J. Kramers. 2016. Response to Thackeray (2016) – The possibility of lichen growth on bones of Homo naledi: Were they exposed to light? South African Journal of Science doi:10.17159/sajs.2016/a0177

Thackeray, J. F. (2016). The possibility of lichen growth on bones of Homo naledi: Were they exposed to light?: scientific correspondence. South African Journal of Science, 112(7-8), 1-5. doi:10.17159/sajs.2016/a0167

Val, A. (2016). Deliberate body disposal by hominins in the Dinaledi Chamber, Cradle of Humankind, South Africa? Journal of Human Evolution 96: 145-148. doi:10.1016/j.jhevol.2016.02.004

Link: Neandertal burial ritual with antler hearths

2016-10-01T00:00:00-05:00

A Neandertal “burial ritual” at Des-Cubierta Cave? “Cave fires and rhino skull used in Neanderthal burial rituals”.

The blackened hearths surround a spot where the jaw and six teeth of a Neanderthal toddler were found in the stony sediment. Puzzlingly, within each of these hearths was the horn or antler of a herbivore, apparently carefully placed there. In total, there were 30 horns from aurochs and bison as well as red deer antlers, and a rhino skull nearby.

Archaeologists believe the fires may have been lit as some sort of funeral ritual around where the toddler, known as the Lozoya Child, was placed around 38,000 to 42,000 years ago.

If that description is accurate, it is hard to imagine this behavior outside of a symbolic culture. This is more than simple mortuary deposition, it requires the construction of an elaborate and consistent series of associations with arbitrary objects.

Link: Modern human teeth from Liang Bua, Flores

2016-09-30T00:00:00-05:00

Ewen Callaway reports on a talk at the European Society for Human Evolution meeting, presenting new human teeth from the ongoing Liang Bua archaeological work: “Human remains found in hobbit cave”. The story is that these remains may document some of the earliest modern human presence in the cave, postdating the last occurrence of H. floresiensis and extinct mammalian fauna. But I am always skeptical about the idea we can clearly diagnose the taxonomic status of unknown hominins from a couple of teeth.

María Martinón-Torres, a palaeoanthropologist at University College London who attended the talk, thinks that the lower molar looks like those of H. sapiens, whereas the premolar seems a bit more primitive. To prove conclusively that the teeth are human, she would like to see comparisons with a wide range of remains from H. sapiens and also from H. erectus (which might have survived in Indonesia until around 50,000 years ago). “I think they have quite a tough job. There are lot of factors to take into account,” she says.

It’s very encouraging that the cave still holds much more evidence to uncover, and I’m sure we’ll hear more as the work progresses.

Link: Replication crisis and status competition in psychology

2016-09-30T00:00:00-05:00

The ongoing “replication crisis” in psychology has become an interesting study in the sociology of science. I don’t have anything especially deep to say about it, but I found this long update by the statistician Andrew Gelman very interesting: “What has happened down here is the winds have changed”. He focuses on a recent op-ed by Susan Fiske, who decries what she terms “mob rule” by other scientists who are questioning the statistical basis of some dearly-held theories in social psychology.

Gelman gives a history of the current “crisis”, pointing out that the statistical problems were apparent to some scientists in the 1960s. The current recognition of those problems has been long unfolding, and has yet to really change the practice of science. But it is raising uncomfortable questions for many established scientists who have built reputations on what many critics now describe as p-hacking. Fiske describes this criticism as “methodological terrorism”. The drama is ratcheting up.

I bring this up not in the spirit of gotcha, but rather to emphasize what a difficult position Fiske is in. She’s seeing her professional world collapsing—not at a personal level, I assume she’ll keep her title as the Eugene Higgins Professor of Psychology and Professor of Public Affairs at Princeton University for as long as she wants—but her work and the work of her friends and colleagues is being questioned in a way that no one could’ve imagined ten years ago. It’s scary, and it’s gotta be a lot easier for her to blame some unnamed “terrorists” than to confront the gaps in her own understanding of research methods.

To put it another way, Fiske and her friends and students followed a certain path which has given them fame, fortune, and acclaim. Question the path, and you question the legitimacy of all that came from it. And that can’t be pleasant.

Today’s established leaders attained their status under old rules that simply do not work for early and midcareer researchers today. Yet those established players have the power to allocate tenure, grants, and recognition, and they have mostly been relying upon the old rules to do so. As a result, early and midcareer scientists are justifiably frightened. They have to play the game by obsolete rules to get ahead, but it is increasingly clear that this game cannot lead to accurate and replicable science in the long term.

The best and most obvious way to make scientific progress is to tear down the nonreplicable edifice, but this inevitably requires attacking the cherished ideas of long-established players – many of whom have lucrative book and speaking careers based upon their social psychology “discoveries”.

And that’s why the authors’ claim that fixing the errors “does not change the conclusion of the paper” is both ridiculous and all too true. It’s ridiculous because one of the key claims is entirely based on a statistically significant p-value that is no longer there. But the claim is true because the real “conclusion of the paper” doesn’t depend on any of its details—all that matters is that there’s something, somewhere, that has p less than .05, because that’s enough to make publishable, promotable claims about “the pervasiveness and persistence of the elderly stereotype” or whatever else they want to publish that day.

When the authors protest that none of the errors really matter, it makes you realize that, in these projects, the data hardly matter at all.

What a mess.

Link: A short Sterkfontein history on its 80th anniversary

2016-09-26T00:00:00-05:00

The discovery of hominin fossils at Sterkfontein, South Africa, was eighty years ago this year. Recognizing the occasion, Jason Heaton, Travis Pickering and Dominic Stratford have a post on the Scientific American website: “The Fossil That Rewrote Human Prehistory”.

In August 1936, Robert Broom, a Scottish doctor with a keen interest in paleontology, visited a lime quarry in South Africa called Sterkfontein. In a guidebook at the time, the owner of the site, wrote, “Come to Sterkfontein and find the ‘missing link.’” It would not be long before Broom did just that.

It’s a nice short summary of the history of excavations at the site, which continues to produce new evidence about human origins.

Link: Sleeping sickness hides in human skin

2016-09-25T00:00:00-05:00

A news story by Michael Price in Science: “Sleeping sickness hides in human skin”.

[Annette MacLeod] examined the samples for the sleeping sickness parasites and found them in a handful of people, even though they showed no symptoms of the disease at the time. Further testing revealed that mice with parasites in their skin, but undetectable levels of the parasite in their blood, can easily transmit the disease to tsetse flies. Taken together, these results indicate that human skin is likely an “unappreciated reservoir of infection,” MacLeod and colleagues report this week in eLife. People who display no symptoms and have virtually no parasites in their bloodstream can still carry the disease and transmit it to others if they’re bitten by tsetse flies, she says. Skin-to-skin transmission between humans is technically possible, she adds, but is likely rare because it would have to get into broken skin.

The upshot is that if health agencies only test people’s blood for African sleeping sickness—the most common practice—they’re going to miss remnants of the disease that prevent it from being completely eradicated. “These asymptomatic people are the secret reservoirs that keep the disease going,” MacLeod says.

This makes a lot of sense. A reservoir in asymptomatic individuals, with long-term possibility of infecting new hosts, is an essential for human pathogens of the Pleistocene.

Quote: Tobias describes an endocast

2016-09-24T00:00:00-05:00

Classic Phillip Tobias:

During embryonic, foetal and post-natal life, the form of the calvaria becomes accurately moulded over the surface of the expanding brain. Pulsating, as the brain does with the beating of the heart, the outer surface of the brain imprints itself upon the interior of the brain case. In some areas, the convolutions or gyri leave hollow impressiones gyrorum on the endocranial surface, separated by areas where endocranial ossification has penetrated, to varying degrees, into the sulci between the gyri. With care, one may be able to read off from the surface of an endocranial cast some of the markings that had originally bedizenned the surface of the brain.

Yes, he really wrote “bedizzened.” Unfortunately in a context too long to tweet!

Reference

Tobias, P. V. (1987). The brain of Homo habilis: A new level of organization in cerebral evolution. Journal of Human Evolution, 16(7-8), 741-761.

Link: The problem with 'basal' in phylogenetic trees

2016-09-23T00:00:00-05:00

Stacey Smith summarizes the problems with using the term “basal” when discussing phylogenetic positions of organisms: “The ancestors are not among us”.

Basal is a term that refers to the position of a node near the root of a phylogenetic tree. It’s a perfectly good term, it just doesn’t describe the branches that come from that node. To understand why, I find the following paragraph makes the problem with “basal” especially clear:

Every branching in a (phylogenetic) tree is rotatable (see Fig. 1). Of course, the tree has a base, and there is a most basal branching and a next most basal branching, but there is no such thing as the most basal clade. Because branchings are rotatable, there are always two most basal clades (if the most basal branching is completely resolved, Fig. 1) or even more most basal clades (if the most basal branching is not completely resolved, e.g. in Polyneoptera in Fig. 1). Both branches originating from a node (i.e. the two sister groups) are of equal age and have undergone equivalent evolutionary change. Whether a group has branched off early (basal) or later in the phylogeny contains no information about this particular group, but information about both this group and its sister group, because both branched off at the same time.

That is from an editorial from 2004 by Frank Krell and Peter Cranston in the journal Systematic Entomology, “Which side of the tree is more basal? Smith points to the editorial in her post, and I found this discussion helpful.

I’ve thought a good amount about this issue as I’ve been working on an undated assemblage. Reading the literature in this light, I am amazed at how often anthropologists cover up uncertainty about the relationships within Homo with the term “early Homo”. I admit to being guilty of using this term myself, it seems like such a convenient way to forget about all the problems applying species concepts.

Reading these articles about “basal” reminded me that “basal” is no substitute. Phylogeny doesn’t give us an easy way to refer to these lineages from deep time, and that is probably for the best. It’s important to keep our trees straight.

References

Krell, F. T., & Cranston, P. S. (2004). Which side of the tree is more basal?. Systematic Entomology, 29(3), 279-281. doi:10.1111/j.0307-6970.2004.00262.x

Some thoughts on Dorothy Garrod and celebrity fossils

2016-09-17T00:00:00-05:00

Lydia Pyne’s new book, Seven Skeletons: The Evolution of the World’s Most Famous Human Fossils is a reflection on how fossils become worldwide celebrities. I’m not entirely through the book but I like it quite a lot so far.

No one can write about the history of discoveries of these “famous” hominin specimens without taking note of the absence of women from the history of paleaonthropology. This week, Pyne published an essay reflecting on this gendered history: “Writing About Fossils Found By Men”.

Interestingly, women who show up in early paleoanthropology generally come from different background disciplines than do their male counterparts. Women tended to come to paleoanthropology from archaeology or anthropology, rather than from anatomy or paleontology – sciences that were less about spectacular discoveries of “things” (fossils) and more about understanding processes. But those sorts of research questions are hard to canonize in a science’s historical mythos. The discovery of some really cool fossil, traditional science storytelling goes, is so much more exciting to read and write about.

Accordingly, the traditional histories of paleoanthropology don’t have a whole lot of women in them. Dart’s student, Josephine Salmons, occasionally makes an appearance. Lady Smith Woodward shows up here and there in various stories of the Piltdown hoax, since her husband Sir Arthur Smith Woodward was so involved in Piltdown’s excavation and study. By and large, however, these women are ladies in the early fossil stories, not scientists. The big names in anthropological research, like Mary Leakey or Jacquetta Hawkes, tend to be researchers who focus more on the behaviors associated with early Homo than finding new hominin fossils. And this is pretty much the canon of paleoanthropology’s history of science as it currently stands.

As Pyne reflects on these famous fossils, she suggests that it is the “celebrity” nature of the fossils that tends to push women out of the story.

I found Pyne’s mention of Jacquetta Hawkes interesting in this context. Hawkes is not typically discussed in histories of paleoanthropology, because most of her work concerned the archaeology of the last few thousand years. In that area, she was a towering figure in the mid-twentieth century. But Hawkes herself did fieldwork as a student with Dorothy Garrod, and drew inspiration that set her on the path toward a career in archaeology (as discussed by the University of Bradford).

A skeleton of a Neanderthal woman was found, named Tabun 1 from the cave in which she was discovered. Jacquetta felt a strange kinship with this ancestral figure whose fragile skull she held. Despite their very different minds and experiences, both were part of the same stream of consciousness, “two atoms” in the millennial growth of the human brain.

Dorothy Garrod directed excavations that resulted in some of the epochal discoveries in the origin of modern humans and their interactions with the Neandertals. She didn’t make Pyne’s list because the Skhul and Tabun skeletal remains don’t fit her criteria of a single, “celebrity” skeleton. But that series of discoveries was much more important to the theoretical development of the field than most of the “celebrity” fossils.

If we consider the Skhul and Tabun discoveries, there’s no question that Garrod belongs in the pantheon of major fieldworkers in human origins. The Tabun archaeological sequence forms the basis for understanding the chronology of the Levant, with evidence for a quarter-million years of human habitation. To this we can add the excavation at Devil’s Tower, Gibraltar, and the Neandertal specimen it uncovered. Many archaeologists working today are frustrated with Garrod because her excavation methods left many unanswerable questions. Today no one would excavate a site like Tabun in the way that Garrod did. But this is true of almost every historical figure in the field.

Probably others would be more critical of Garrod than I am. I view her as one of the first prehistoric archaeologists to supervise massively interdisciplinary research. As she put it in her inaugural lecture as Disney Professor at Cambridge,

The prehistory of the Old Stone Age is far more closely bound up with certain branches of natural science—geology, palaeontology, palaeobotany—and the formation of a prehistorian in this sense calls for a scientific discipline to which the later stages of Man's story is not normally submitted.

It is noteworthy that among those who have built up the study of Early Man nearly all the outstanding names belong to men who have approached it from one or other of the natural sciences. This recruitment is to be expected in a subject which touches those sciences at so many points, and it has been of the highest value in the development and systematisation of human palaeontology in the widest sense. On the strictly archaeological side, however—that is, in the study of artefacts of fossil man—it has had certain results which are perhaps not quite so happy. It is time, I think, that these tendencies should be critically examined, and that we should ask ourselves whether they are not in part responsible for the present divorce between the student of the Old Stone Age and the archaeologist in the popular sense of the word.

With these words she introduced why archaeological knowledge is essential to understanding prehistory. Natural scientists, in her view, tended to treat artifacts as if they themselves were fossils, evolving under the laws of evolution, complete with hybridization and mutation. This in her view was wrong, leading to an exaggerated and typological view of cultural traditions. She was speaking to archaeologists about the importance of the archaeological approach.

As I read her, Garrod fully appreciated the role of different scientific disciplines in their own proper spheres, all of which had to be appreciated by the prehistorian. Certainly she followed that approach in her management of the excavation and study of material, in which she was strikingly modern in comparison to her scientific contemporaries. Like all modern discoveries of any importance, the Mount Carmel work in the 1920s and 1930s was a large-scale project that relied upon many collaborators. Theodore McCown, still a PhD student at the time, had responsibility for excavating the Skhul skeletons and transporting them to the U.K., where he worked to prepare them under the supervision of Arthur Keith. The resulting anatomical interpretation was one of the most important monographic descriptions of any fossil hominin sample, which faced up to the challenge of how to understand “transitional” patterns of anatomical features. It’s probably not an accident that Garrod, herself the daughter of a named professor of medicine, knew how to effectively work with experts in this area for this part of the work.

Thinking about McCown and Keith, they both influenced the interpretation of the fossils in such a way as to downplay their potential as “celebrity” fossils, notwithstanding Jacquetta Hawkes writing poems about the Tabun skeleton. Had Keith realized that the Skhul fossils were among were the earliest modern humans outside Africa, he might have created a mythos for Skhul V, but on this he missed the boat. Instead, he conceived them as transitional between earlier humans with more modern anatomy and later Neandertals. For his part, McCown refused to see the fossils as representatives a “type”, insisting that each was a mere sample of diversity within a population. The resulting description broke ground in how to conceive of variation in fossil human populations. Their science was a landmark, and the fossils did not take on mythological status in the process. I count that a scientific success.

I should point out that one consistent aspect of Garrod’s work is that her publications and reports all appeared “promptly” (as Jane Smith put it in a short biography). She was able to accomplish much, because she was effective in describing the science.

I don’t know how much Garrod’s approach to directing interdisciplinary work might have influenced Louis Leakey, who knew her. Looking at Leakey’s record it is clear that he conceived his and Mary’s roles differently than other earlier workers other than Garrod. The way that he recruited and delegated anatomical work to Phillip Tobias, John Napier, and other anatomical experts is reminiscent of how Garrod organized the Mount Carmel work. Maybe he would have taken this approach in any event.

At any rate, these are just a few of my thoughts. This seems like a fertile area for a historian to explore in more detail.

Link: Article on the life and death of George Price

2016-09-16T00:00:00-05:00

Michael Regnier has an article in Mosaic about the exceptional life and tragic end of George Price: “The man who gave himself away”.

I found it interesting that Mosaic commissioned the story in light of Oren Harman’s recent book about Price, The Price of Altruism, which is also an excellent account. But for a good short read, or for assigning in classes, Regnier’s article is a great one.

Châtelperronian bone fragments identified as Neandertal based on protein residues

2016-09-16T00:00:00-05:00

Frido Welker and colleagues have applied a new method to identify tiny bone fragments as Neandertal remains, based on the protein residues that they contain.

The study uses a fairly simple concept—take a lot of unidentifiable bone fragments and test them with a protein mass spectrometry toolkit (ZooMS) to identify them to genus if possible. They were pretty successful. The real innovation is that they were able to identify a protein polymorphism for which 99% of living humans have a derived amino acid, and all known Neandertals have the ancestral amino acid. In the context of a Châtelperronian archaeological layer, finding the ancestral allele gives a strong indication (but not an infallible one) that a bone fragment probably has a Neandertal heritage.

I think the result is pretty cool because Welker and colleagues were able to identify a large number of bone fragments that probably belong to an infant skeleton, which they already knew was in the site based on a handful of identifiable remains.

Despite their spatial proximity within Layer X and squares C7 and C8, none of the newly described specimens could be fitted together to form larger fragments. The morphologically informative specimens, however, seem to represent small fragments of an immature cranium and an unfused vertebral hemiarch of neonatal age (SI Appendix, Fig. S10 and Table S13). This is supported by isotopic evidence suggesting that these fragments belonged to a nonweaned infant and by proteomic evidence in the form of proteins present in bone before bone remodeling has started. All the newly identified specimens were found in close spatial association with a previously described hominin temporal bone from square C7, Layer Xb, assigned to an infant around 1 y old, as well as 10 dental specimens from squares C7 and C8 (6, 7). These dental specimens overlap in developmental age, suggesting they represent one or possibly two individuals between 6 and 18 mo old (7). The 28 newly identified specimens, together with already described specimens, may therefore represent the skeletal remains of a single infant.

Châtelperronian makers

The reporting on this paper has emphasized the conclusion that the bones are Neandertal, which in addition to the protein evidence is also indicated by some mtDNA sequence fragments from some of the remains. To me this is basically a failure to reject a long-substantiated association: Neandertals made the Châtelperronian industry.

The Châtelperronian has been found across much of France and into the Pyrenées of Spain, and dates to around 40,000 years ago. It is termed a “transitional” industry because although it is based upon flaking strategies typical of earlier Mousterian assemblages, the Châtelperronian includes elements usually attributed to Upper Paleolithic toolkits including many bone artifacts and elongated flake tools that share many details with the blades of later Aurignacian assemblages.

The identity of the makers of the Châtelperronian has been a white whale for some archaeologists. The only diagnostic skeletal remains ever found with Châtelperronian tools have been Neandertals, notably the Saint-Césaire skeleton but also more fragmentary skeletal remains from Arcy-sur-Cure. Yet despite this association, some archaeologists have doubted that Neandertals made such apparently “sophisticated” tools. They have examined whether Châtelperronian assemblages are a palimpsest or mixture of elements from earlier Mousterian and later Upper Paleolithic contexts, whether Neandertal remains might have moved out of stratigraphic position, whether Châtelperronian layers may have slumped in a way not recognized in old excavations.

Today it would be truly surprising if an unambiguous modern human skeleton turned up in a Châtelperronian archaeological layer. If a specimen with modern human traits emerged, or a tooth that shared traits with modern humans, I would not be surprised, but that’s because I expect there was likely population mixture in Europe at the time of the Châtelperronian some 40,000 years ago.

Ten years ago, a debate erupted about the type locality of the Châtelperronian industry, Grotte des Fées du Châtelperron. I wrote about that episode here (Interstratified palimpsests), and it was never really satisfactorily resolved.

Why was it such a big deal? The last refuge of scoundrels has been the notion that Neandertals were incapable of making Châtelperronian artifacts on their own and needed the enculturating influence of modern humans to do so. This idea was popularized by Jared Diamond in his book, The Third Chimpanzee and has hung around within European archaeology for more than thirty years. The importance of possible interstratification of Châtelperronian and Aurignacian industries is a test that Neandertals who made Châtelperronian artifacts and modern humans who made Aurignacian artifacts might really have encountered each other on the same landscape. Without the possibility of such contact, it is hard to conceive of the idea that Neandertals were “acculturated” by their encounters with modern humans.

What is my opinion? I have to say, two or three thousand years is a lot of time, and it is hard for me to imagine that populations did not exchange a good amount of information across Europe during that time, whether they lived in overlapping areas or not. I doubt that the early Aurignacian people were very much different from late Neandertals in their cultural and technical abilities. Even if they were different on average for some cognitive abilities, which I can well imagine, I expect their abilities would have overlapped to a substantial degree.

The conclusion of the paper sums up my feelings fairly well.

Our biomolecular data provide evidence that hominins contemporaneous with the Châtelperronian layers have archaic nuclear and Neandertal mitochondrial ancestry, supporting previous morphological studies (6, 7). They are therefore among some of the latest Neandertals in western Eurasia, and possible candidates to be involved in gene flow from Neandertals into AMHs (or vice versa) (48). Future analysis of the nuclear genome of these or other Châtelperronian specimens might be able to provide further insights into the direction, extent, and age of gene flow between Late Pleistocene Western European Neandertals and “incoming” AMHs (49, 50).

More results coming

Doing more to uncover the hominin remains at a site is valuable even if the anatomical information to be gained is minimal, and even if genetic information cannot be reliably obtained from the fragments with today’s techniques.

Still, in the short term at many sites, what the method reveals about the fauna will be even more interesting. Identifying rare species in faunal assemblages from non-diagnostic fragments should greatly increase the representativeness of the archaeological record. As reported by Welker and colleagues in an earlier paper (2015), they can reliably identify bone fragments to genus in a large fraction of cases, even for bone fragments that have passed through a carnivore’s digestive tract.

This result is published this week just after a number of studies were presented in talks at an international conference on ancient biomolecules. That other work is reported by Ann Gibbons (“Oldest-ever proteins extracted from 3.8-million-year-old ostrich shells”), which includes a statement that protein has now been recovered from tooth enamel of extinct fauna from Dmanisi. Protein analysis of ancient fossils suddenly looks like a very big deal.

References

Brown, S., Higham, T., Slon, V., Pääbo, S., Meyer, M., Douka, K., ... & Derevianko, A. (2016). Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Scientific reports, 6. doi:10.1038/srep23559

Welker, F and others. 2016. Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne. Proceedings of the National Academy of Sciences, U.S.A. (early edition). doi:10.1073/pnas.1605834113

Welker, F., Soressi, M., Rendu, W., Hublin, J. J., & Collins, M. (2015). Using ZooMS to identify fragmentary bone from the late Middle/Early Upper Palaeolithic sequence of Les Cottes, France. Journal of Archaeological Science, 54, 279-286. doi:10.1016/j.jas.2014.12.010

Some dissatisfaction with review articles

2016-09-13T00:00:00-05:00

John Ioannidis often speaks out on abuses of confidence and statistics in science. He recently did an interview with Retraction Watch in which he commented upon the proliferation of “systematic reviews and meta-analyses” in science: “We have an epidemic of deeply flawed meta-analyses, says John Ioannidis”.

Retraction Watch: You say that the numbers of systematic reviews and meta-analyses have reached “epidemic proportions,” and that there is currently a “massive production of unnecessary, misleading, and conflicted systematic reviews and meta-analyses.” Indeed, you note the number of each has risen more than 2500% since 1991, often with more than 20 meta-analyses on the same topic. Why the massive increase, and why is it a problem?

John Ioannidis: The increase is a consequence of the higher prestige that systematic reviews and meta-analyses have acquired over the years, since they are (justifiably) considered to represent the highest level of evidence. Many scientists now want to do them, leading journals want to publish them, and sponsors and other conflicted stakeholders want to exploit them to promote their products, beliefs, and agendas. Systematic reviews and meta-analyses that are carefully done and that are done by players who do not have conflicts and pre-determined agendas are not a problem, quite the opposite. The problem is that most of them are not carefully done and/or are done with pre-determined agendas on what to find and report.

This comment resonated with me. This year has seen an explosion of review papers on hominin diversity.

The review papers that have appeared so far this year mostly seem to reflect symposium contributions that were presented in 2014 or 2015. Few of them have significant updates since they entered review sometime in 2015, and so they do not discuss findings of the last couple of years except very superficially. Most do not integrate findings from across different time intervals in human origins.

So, for example there have been three or four review papers this year summarizing hominin diversity in the Middle Pliocene. This is the time period that has produced evidence of Australopithecus afarensis, as well as a bunch of other species represented by a few fossils each, including A. bahrelghazali, Kenyanthropus platyops, and most recently A. deyiremeda.

Each of the review articles this year reads basically like a position paper by its authors about Australopithecus deyiremeda, either for or against.

This is a difficult area to review right now. The fossil evidence is sparse. Many of the authors consider the “best” evidence of species diversity to be the partial foot skeleton from Burtele, Ethiopia, which has not been assigned to a species. Few scientists have studied all the relevant material.

A real answer to the question of Middle Pliocene hominin diversity should start from a full and free examination of the variation found within the largest fossil samples, not excluding any specimens, and without any prior assumptions about their taxonomic status. We would need to revisit and test ideas from the 1980s about the taxonomy of Hadar fossils, relying upon the larger dataset that has since accumulated from Hadar and other sites. This would require us to seriously examine the idea that the cranial and dental fossils may represent more than a single species, and the postcranial fossils may represent more than a single adaptive pattern.

This kind of open examination would have many beneficial outcomes. Not least, it would provide some clear idea of what kind of evidence should be supplied to support the diagnosis of new species.

I recognize the root of my dissatisfaction in Ioannidis’ comments. The current crop of review articles, which serve the purposes of journals and players with pre-determined agendas, does little to advance the science. It is one thing when such a review is in a journal dedicated to review for non-specialists, like Annual Reviews in Anthropology or the Yearbook of Physical Anthropology. But it’s depressing to realize how little actual synthesis we are seeing in other contexts.

Link: Privacy and sharing genomic data for research

2016-09-13T00:00:00-05:00

Good article in Undark about privacy and genome sequencing in the era of data sharing, by Adam Tanner: “The Promise and Perils of Sharing Your DNA”.

President Obama echoed this sentiment in February. “I would like to think that if somebody does a test on me or my genes, that that’s mine,” he said.

STILL, IT’S OFTEN HARD to know if you have signed away your ownership rights because of lengthy and obtuse privacy policies. “If you look at enough terms of service and privacy policies you will see the word ‘may’ or ‘might’ being used a lot — as in we ‘may share’ — which leaves the door open,” says Jan Charbonneau, a PhD candidate at the Centre for Law and Genetics at the University of Tasmania in Australia.

Link: Earliest cancer in the fossil hominin record

2016-09-12T00:00:00-05:00

A nice piece in The Conversation by Edward Odes and Patrick Randolph-Quinney describing their research into the tumors afflicting ancient specimens from Swartkrans and Malapa: “Fossil evidence reveals that cancer in humans goes back 1.7 million years”.

Tumours and cancers are collectively known as neoplastic diseases. Until now, the oldest evidence of neoplasia in the hominin fossil record dated back 120,000 years. This was found in a rib fragment of a Neanderthal from Krapina in Croatia.

But our discovery, in two South African cave sites, offers definitive evidence of cancer in hominins – human ancestors – as far back as 1.7 million years ago.

Combating 'ivory tower' syndrome

2016-09-12T00:00:00-05:00

There is much in this editorial by Andrew Hoffman that merits broadcasting more widely: “Why academics are losing relevance in society – and how to stop it”. I have been tweeting part of the article with a quote from University of Michigan President Mark Schlissel.

We forget the privilege it is to have lifelong security of employment at a spectacular university. And I don’t think we use it for its intended purpose. I think that faculty on average through the generations are becoming a bit careerist and staying inside our comfort zones. [But] If we’re perceived as being an ivory tower and talking to one another and being proud of our discoveries and our awards and our accomplishments and the letters after our name, I think in the long run the enterprise is going to suffer in society’s eyes, and our potential for impact will diminish. The willingness of society to support us will decrease.

In these comments, Schlissel encapsulated one perspective on the “ivory tower” problem. It’s hard to run a state university in today’s budget and political climate when many faculty appear to have little interest in serving the public. Within the U.S., state funding of universities is declining. They depend increasingly on federal research funding, which has remained steadier, but with an increasing proportion sucked up by overhead. Universities’ share of federal research funding has increased even as individual research grants become more difficult to obtain, but this cannot be sustainable in the long run. Particularly if the public interest in academic work is not sustained.

Many academics would respond that it is wrong to expect research to be useful or to have an impact on society. Or they might say that the topics of research are irrelevant to the purpose of the university, which is to advance learning and provide students with the tools to push the boundaries of knowledge.

But as it turns out, today’s students enter academic training hoping to make a difference in the world, not within a cloister:

Many graduate students report that they have chosen a research career precisely because they want to contribute to the real world: to offer their knowledge and expertise in order to make a difference. And many report that if academia doesn’t value engagement or worse discourages it, they will follow a different route, either toward schools that reward such behavior or leave academia for think tanks, NGOs, the government or other organizations that value practical relevance and impact.

The frustration is such that some no longer tell their advisors that they are involved in any form of public engagement, whether it be writing blogs or editorials, working with local communities or organizing training for their peers on public engagement. Will academia eventually spit these emergent scholars out, or will they remain and change academia? Many senior academics hope for the latter, fearing a worrying trend toward a reduction in the level of diversity and quality in the next generation of faculty.

These trends make me worry about the future. Students are clever and come into academic work with energy and goals to expand the importance of their fields. But so many established academic advisors actually diminish students’ abilities to reach out to the public.

Worse, the students who are successful at public engagement are often selected out of academia. What matters in tenure-track job competition is research funding, not engagement or broader impacts. Federal grants have included a “broader impacts” criterion for a long time. But in my experience reviewing grant applications, a negative assessment of a broader impacts plan has never resulted in a failure to fund the grant. I just do not see this criterion making any difference at all to the level of engagement expected for funding. As long as public engagement remains unimportant in the process of hiring, tenure, and grant funding, the students and early career academics who are most out of touch will continue to win positions and prestige, and students who succeed at engagement and public impact will continue to seek other opportunities.

Link: Getting students to act like givers instead of takers

2016-09-11T00:00:00-05:00

Interesting approach to getting students to collaborate in a course, from Adam Grant:

The most difficult section of my final exam was multiple choice. I told the students that they could pick the one question about which they were most unsure, and write down the name of a classmate who might know the answer — the equivalent of a lifeline on the game show “Who Wants to Be a Millionaire?” If the classmate got it right, they would both earn the points.

Essentially, I was trying to build a collaborative culture with a reward system where one person’s success benefited someone else. It was a small offering — two points on a 120-point exam — but it made a big difference. More students started studying together in small groups, then the groups started pooling their knowledge.

Link: Bonobo female coalitions

2016-09-10T00:00:00-05:00

Nice article by Natalie Angier about recent work on bonobo social behavior: “Beware the Bonds of Female Bonobos”.

The latest research indicates that the nature of the bonobos’ sororal bonds shifts depending on circumstances, and that the most effective deterrent to male harassment may be a cross-generational pact.

“I sometimes think that bonobos sit up late at night reading papers about primates, and then decide to do the opposite,” said Joan Silk, a primatologist at Arizona State University. “They’re unusual in so many ways.”

Link: Watch evolution of antibiotic resistance in action

2016-09-08T00:00:00-05:00

This is awesome:

The problem of drug-resistant infections is terrifying but also abstract; by their nature, microbes are invisible to the naked eye, and the process by which they defy our drugs is even harder to visualise.

But now you can: just watch that video again. You’re seeing evolution in action. You’re watching living things facing down new challenges, dying, competing, thriving, invading, and adapting—all in a two-minute movie.

An experimental setup in which bacteria colonize progressively more antibiotic-laced environments when they have favorable mutations, all put on video.

Link: Exoplanet fatigue

2016-09-02T00:00:00-05:00

Oliver Morton thought that the recent Proxima Centauri exoplanet news would be bigger; he ponders why he was wrong: “It will be a long time before you see another exoplanet on a front page”.

Various people suggested to me on twitter that the public has become a little blase about exoplanets, possibly because they have been a bit oversold. (One person suggested that astronomers may have cried wolf too often, which I mention mainly in order to link to this bit of brilliance from Mitchell and Webb). With regular announcements of planets more “earthlike” than the last — but with no evidence that any of them is actually remotely like the Earth — the fact that this one was nearer than any of the others hardly seemed like that big of a step forward.

It is a real challenge in the public communication of science to explain the interesting parts of incremental progress.

Sequencing new animal genomes is no longer newsworthy absent some additional and surprising scientific finding from them. Technology has progressed and new data are coming in, but each incremental data point is not advancing theory.

When the buildup of data starts leading to new scientific predictions and insights, that will make much more of an impact.

Link: People on the receiving end of misaimed vigilante justice due to poor database design

2016-08-30T00:00:00-05:00

This is a fascinating story of the age of massive databases and loss of human privacy: “How an internet mapping glitch turned a random Kansas farm into a digital hell”.

For the last decade, Taylor and her renters have been visited by all kinds of mysterious trouble. They’ve been accused of being identity thieves, spammers, scammers and fraudsters. They’ve gotten visited by FBI agents, federal marshals, IRS collectors, ambulances searching for suicidal veterans, and police officers searching for runaway children. They’ve found people scrounging around in their barn. The renters have been doxxed, their names and addresses posted on the internet by vigilantes. Once, someone left a broken toilet in the driveway as a strange, indefinite threat.

All in all, the residents of the Taylor property have been treated like criminals for a decade. And until I called them this week, they had no idea why.

Link: Captive monkey microbiomes are more like humans

2016-08-29T00:00:00-05:00

Ed Yong writes about an examination of the microbiomes of different monkey species in captivity versus wild populations: “Captivity Makes Monkey Microbiomes More Human-Like”.

In the wild, both monkeys host different and distinctive communities of gut microbes. But in captivity, these communities converge, so they become harder to tell apart. Even though doucs and howlers come from different continents and naturally eat different kinds of plants, and even though those specific captive individuals lived in three zoos across three different countries, their gut microbiomes ended up looking very similar. They were closer to each other than to their wild counterparts, and oddly similar to the microbiomes of humans.

Why the changes? Zoo animals often get antibiotics, but Clayton found that even untreated animals had different microbiomes from wild ones. Instead, these changes were most likely due to diet.

This is not too surprising but raises many interesting questions about microbiome evolution. Clearly there is a rapid shift in the microbiome based on dietary environment in primates. How much of this is caused by the colonization of the guts of these primates by microbes from humans (or other captive animals)? How much change can be attributed to selection within the microbiomes of these primates? And what does the pace of colonization by microbes of primate guts imply about the evolutionary dynamics of these microbiomes in wild populations?

Why I'm skeptical about Lucy in the Skyfall

2016-08-29T00:00:00-05:00

I have no trouble believing that Lucy might have fallen to her death. Why not? The Lucy skeleton has several features compatible with a lifetime of climbing, and other fossils attributed to her species, A. afarensis, have even more. So I am not primed to be skeptical of the conclusion of the new paper by John Kappelman and colleagues in Nature.

But I’m struggling to figure out why the authors decided to publish without addressing basic questions that any paleontologist would ask.

Lucy skeleton. Credit: John Hawks CC-BY-NC-ND

The Lucy skeleton was recently on tour in the United States, beginning at the Houston Museum of Natural Science, and on this tour the bones were scanned in a high-resolution CT machine at the University of Texas. Studying the scans, Kappelman and his team decided that some of the fracture patterns are consistent with injury near the time of death, called perimortem trauma.

Their strongest evidence is the fracture pattern of the right humerus. The surface of the humeral head was crushed downward, with large chunks of the neighboring bone shattered outward and fossilized in place. Previous scientists have interpreted this damage as the product of fossilization and crushing under layers of sediment. Kappelman and colleagues examined the fragments and found two aspects that are indicative of a “green” fracture, made while the tissue was still fresh. Putting the fragments back together like a jigsaw puzzle, they saw that the entire proximal end of the bone first sheared off diagonally in a pattern called a spiral fracture. The fracture left some small shards of bone, only millimeters in size, still adhering to the fractured fossil. Kappelman and colleagues argue that if this breakage had happened with fossilization, after the soft tissue of the shoulder joint was completely gone, then these tiny shards of bone should be missing. Their presence suggests that the bone was broken near the time of death, buried with soft tissue still present, and fossilized in place.

It is not hard to find comparable proximal humerus fractures in modern clinical cases. For example, this one is from a paper on treating humeral fractures by Shane Nho and colleagues:

Radiograph of proximal humerus fracture from Nho et al. 2007.

Here is a diagram of the fragments of the Lucy proximal humerus from Kappelman and colleagues:

Extended data figure 1 from Kappelman and colleagues (2016), showing fragments of humerus as distinct colors.

Comparing those images, you can see how the proximal humerus of Lucy resembles a fracture injury. Kappelman and colleagues build a broader case involving many other bones. Of the rest of the skeleton, the other obvious instance of damage from compression is the left distal femur, which has condyles that were jammed upward and laterally. Kappelman and colleagues show that the contour of the damaged bone is a mirror-image to the proximal end of the right tibia, the left being missing from the skeleton.

In all, they argue that some 20 bones of Lucy’s skeleton present evidence of perimortem fractures. Nearly every break present on the bones, including the broken edges of preserved fragments like the clavicle, they interpret as perimortem.

On the surface, it might seem like a watertight case. But as my Facebook feed began to pulse with messages from other anthropologists this morning, the authors defined perimortem fractures so loosely, every break in any fossil might be described as perimortem. If Lucy really had fractures on more than 75% of her preserved bones, she didn’t fall out of a tree, she fell out of an airplane.

As an example, consider the first rib. The authors do not illustrate this rib, but they argue that the rib has a “hinge fracture” at the neck, and several fractures at midshaft that were made at the time of death. They note that the first rib is almost never fractured, even in accidents where the other ribs suffer many fractures, because of the extensive soft tissue around it–dramatically, they call it a “a hallmark of severe trauma”. Their scenario for Lucy is that the extreme stresses on the shoulder at impact caused the clavicle to break, deflecting downward into the first rib and breaking it in multiple places.

But there is another process that breaks first ribs very commonly in the fossil record: Becoming a fossil.

I am not aware of any first rib from a Plio-Pleistocene hominin that is intact. The Nariokotome Homo erectus first rib appears to have a very similar pattern of breakage to the Lucy first rib. The first ribs from Dmanisi are broken, as are first ribs from Malapa and Sterkfontein. The first hypothesis to turn to for all these broken ribs is damage in the process of natural deposition and fossilization. Fossil bones are usually broken, and Lucy is no exception.

Does it matter that the authors describe some of these breaks as “hinge fractures”? Dry bones lacking the strength of their organic matrix often fracture in a straight line, like broken Greek columns, while a hinge fracture is one that changes in direction at one edge. When people see such a fracture that deflects in direction, they often attribute the fracture to fresh bone instead of dry bone.

But in reality, a fracture that passes through a cortical bone layer may deflect in a direction more perpendicular to the bone surface even if the bone is dry, beneath sediment, or mineralized. The paper uses the term “hinge fracture” many times, but neither defines it nor gives examples of how this evidences perimortem fracturing. If they examined a large collection of faunal fossils from the same context, they would find similar patterns, not from falling out of a tree but from simple post-depositional breakage.

The lack of comparison is a fatal deficit of the paper. The authors make no attempt to show that the pattern of fractures in the Lucy skeleton is different from that found in non-hominin bones from similar contexts. How many of the faunal remains from Hadar have similar fracture patterns? What about hominin bones from other sites?

In comments to Science News, Tim White provides a clear illustration of why comparisons are necessary to support the authors’ conclusion. Here in a photo is Lucy’s right proximal humerus compared to a fossil horse humerus:

The horse did not fall from a tree.

Now, to be fair the horse doesn’t show the same degree of compression of the humeral head as Lucy. But like most paleontologists I’ve seen plenty of fossils that are much more deformed than the Lucy humerus and femur. Understanding whether that deformation is perimortem requires a close comparison with many other fossil specimens from similar contexts. None of that comparison is in this paper. No data concerning the preservation of non-hominin remains from Hadar or any other site are in this paper. If the authors want anyone to believe their analysis of the Lucy skeleton, they need to demonstrate that the fractures on the Lucy skeleton are different from those present on other fossils.

As it stands today, those paleontologists who are most knowledgeable about the Hadar fauna have been vocal: Similar fractures are common on other animal fossils including rhinos and elephants.

The paper provides no answer to this obvious criticism. It lacks minimal basic comparisons and therefore gives little reason to believe the authors’ conclusions.

The lack of data does not mean the authors’ hypothesis is necessarily wrong. I still think it is credible that Lucy may have had perimortem fractures, and I consider it possible that the humerus and femur may have compressive fracture damage consistent with a fall. But the authors frame their hypothesis as a just-so story, and only examine evidence consistent with it instead of looking for contrary evidence.

Skilled forensic anthropologists have only a limited degree of accuracy assessing perimortem versus postmortem fractures, when they are looking at buried skeletal remains that are only a few years old. With Lucy, we are talking about fractures that have been evident since the skeleton was found, and every previous scientist who examined them has concluded that they are likely postmortem damage consistent with the pattern on other fossils from Hadar. Showing that these fractures came from a particular traumatic event is going to take much better data than this paper provides.

References

Kappelman, John, Richard A. Ketcham, Stephen Pearce, Lawrence Todd, Wiley Akins, Matthew W. Colbert, Mulugeta Feseha, Jessica A. Maisano and Adrienne Witzel. 2016. Perimortem fractures in Lucy suggest mortality from fall out of tall tree. Nature doi:10.1038/nature19332

Nho, S.J., Brophy, R.H., Barker, J.U., Cornell, C.N. and MacGillivray, J.D., 2007. Management of proximal humeral fractures based on current literature. The Journal of Bone & Joint Surgery, 89(suppl 3), pp.44-58. doi:10.2106/JBJS.G.00648

Photo: An early Neandertal life rendering

2016-08-11T00:00:00-05:00

One of the earliest artist renderings of a Neanderthal (1887), published in a magazine called The Open Court, which was dedicated to the dialogue between religion and science. The artist was Guernsey Mitchell.

From the collection of the Internet Archive.

Link: Desert kites from ancient hunters

2016-08-11T00:00:00-05:00

National Geographic is running a fascinating story about “desert kites”, ancient structures dating to the Iron Age or earlier in Central Asia and the Levant: “Giant ‘Arrows’ Seen From Space Point to a Vanished World”. They are hunting traps that work on the psychology of herding antelopes, who will avoid a low wall or ditch and can thereby be herded into traps.

Equally striking, Amirov’s team found dozens of desert kites arrayed like a giant net across a hundred miles of tablelands east of the Aral Sea. Such a huge construction project hints at a collective hunting effort by large numbers of ancient nomads. They could have harvested entire antelope herds, Amirov writes. The haul of meat must have far exceeded the needs of immediate consumption. The excess was probably traded away. Today these kites still stand with their V-shaped mouths gaping northward, awaiting a ghostly migration that never comes.

Link: Science reports on public knowledge of science

2016-08-10T00:00:00-05:00

Science magazine: “Americans may know more than you think about science”. Looking at a more expansive view of knowledge that tries to get at how people actually process knowledge into action. But there’s “bad news” – people may know plenty about science, but this doesn’t make them support spending a lot of public money on new scientific research:

But the bad news is that researchers may have misled policymakers and educators about the connection between literacy and support for science. “Available research does not support the claim that increasing science literacy will lead to appreciably greater support for science in general,” the report concludes. Scientists are partly to blame for that misconception, it adds, because the metrics they typically use to assess literacy “are only weakly correlated” with how people behave.

This is related to the “deficit model” for science communication; the idea that people will support the same policies supported by scientists if the people only know enough about science.

Some early uses of the term 'missing link' in anthropology

2016-08-09T00:00:00-05:00

I’ve been tracing some early uses of the term “missing link”. Paleontologists really hate this term today. It conjures the pre-evolutionary idea of a “Great Chain of Being”, and fails to recognize that the evolutionary process generates a tree of species from common ancestors, not a succession of species one after another.

But paleontologists in the old days used the term “missing link” quite often. They used it in the straightforward sense of an evolutionary intermediate that was not yet known from the fossil record. Google’s Ngram Viewer shows the usage of the term over time, which recently has been as great as ever:

The idea of “missing link” has always been applied far beyond biology. It is an evocative metaphor that is widely useful and understood, and has long been a cliché. One hears of “the missing link in international finance” and other monstrosities. It’s also a very English-specific metaphor; the equivalent phrase in German and French never gained much historical currency. Today, biological uses of the term are rare and probably a small minority of uses, but science writers still bring it into news stories about fossil discoveries.

“Missing link” was still scientifically respectable in the 1980s as applied to other lineages of organisms, but it seemed an anachronism to apply it to fossil hominins by that time. So it looks on the surface like anthropologists were the leading wave of “missing link” rejection. I’m interested in exactly when and how anthropologists turned against it. This post doesn’t answer that question, I’m just collecting some instances.

From the beginning, “missing link” was a metaphor that cut both ways. Darwin claimed that species share common origins, and that demands that there must have once been intermediates between today’s species and their distant common ancestors. This was very easy to believe in cases where forms still exist today that are intermediates between two different species. Darwin used many such forms as arguments in favor of the general idea of evolutionary transformation. But for species like humans, there are no living forms that are apparent intermediates between us and our closest living relatives, the great apes.

During the initial years after Darwin’s Origin of Species, some of the more learned critics of Darwin used the term “missing link” in a derisive sense, noting that intermediates bridging the apparent gap between humans and other animals had never been found. But it was not only used by critics of Darwin, the term “missing link” was a widely-understood metaphor for something anthropologists should be seeking out; an evolutionary forerunner of humans that must have shared many characteristics of apes.

Anthropologists were an odd set of characters in 1860s London. Many of them had social relationships with naturalists and geologists like Lyell and Owen, but they considered the anatomy of humans as a distinct enterprise. For the anthropologists, the highest part of their work was understanding the features that set apart human races. Some of them had been students of phrenologists, and still believed that the shape of the skull was a window into the mind. All were committed to the idea of deep and intrinsic differences between human races, some actively believed that the races should be considered as distinct species. This group included many who believed in the separate creation of different races, an idea known as polygenism.

In 1865, Barnard Davis read a paper on the Neanderthal skull and the questions and commentary after the reading were taken down and published in the Journal of the Anthropological Society of London. The comment by C. Carter Blake uses the term “missing link” to apply to the idea that Neandertals are an evolutionary intermediate between apes and humans. I’ve cited the whole passage to put the phrase into context, as one among many theories to account for the morphology of the Neanderthal specimen (emphasis added by me).

Mr. C. Carter Blake said he felt considerable diffidence in speaking on the subject once more, since, on the 16th of February last, he laid before a meeting of the Society the evidence then possessed respecting the characteristics and probable antiquity of the Neanderthal skull. He begged to call to mind that he then stated the several theories that had been propouncled. One of those theories, advocated by Professor Huxley, was that it resembled the skulls of existing Australians. Another theory was, that the skull represented a distinct species--Professor King said, a distinct genus of mankind. In the opinion of Dr. Pruner Bey, it was merely the skull of a powerfully organised Celt, somewhat resembling the skull of a modern Irishman with low mental organisation. An anonymous writer in the Medical Times and Gazette, to whom they were indebted for a most satisfactory theory, expressed the opinion that it was the skull of an inividual [sic] who had been affected with idiocy and rickets. They had also had more theories since he had the honour to read his paper in February. Dr. Gibb, in a paper read during the last session, suggested that the thickening of the skull was compatible with the theory that the individual was an example of hypertrophic deformation. Professer Mayer of Bonn, in a recent excellent Memoir, took a very different view of the origin of the skull, and instead of ascribing to it great antiquity, conceived that the Neanderthal skull, which had been found in a cave, covered with two feet of mud, was possibly that of one of the Cossacks who came from Russia in 1814. The last thory [sic] he should notice--and certainly the most absurd one--was one which gave the Neanderthal skull still more essentially an abnormal character, for it supposed it to be that of an extinct race who formed the missing link between man and the lower animals. There were other characters in which the Neanderthal skull was supposed to differ, first of all from man in an abnormal condition; and, secondly, from healthy man : and it had been pronounced to be a wonderful pathological conformation. That evening, however, the mythological period was past; they had had the skull taken out of the domain of theory, and once more placed upon the substantial ground of plain anatomical facts, from which those who were desirous of eliciting popular notoriety had warped it. He confessed he felt some gratification at that result, as it had been his duty, in a publication printed in 1861, to protest against the supposition that the Neanderthal skull possessed any race character, on grounds which he then thought sufficient, and he now found that Dr. Davis fully corroborated his opinion.

This is a great example, showing how the idea of the “missing link” was immediately part of the scientific discussion of the Neandertals.

Robert Dunn at the end of 1866 read a paper for the Ethnological Society of London in which he considered how discoveries from prehistoric archaeology might affect the interpretation of observations from ethnography. In this, he referred to the Neanderthal discovery and to contemporary theories of the origin of human races, in both cases making reference to the idea of a missing link. The first passage is from page 315 of the contribution:

But it is not to be forgotten, or overlooked, that another, once celebrated fossil skull of a very different character, is in existence, found in a cave in the Neanderthal, near Dusseldorf, and for which, at first, not only an antiquity was claimed, equally as great as that of the Engis man, but an importance infinitely greater ; for it was looked upon, by some, as "the missing link," in the chain of continuity between the monkey and man, and for which the advocates of the ape origin of the human species had been so earnestly in search. A scrutinising inquiry, however, into its locale and the history of its discovery, and a strict and rigid anatomical examination of its structural peculiarities, have, alas ! for advocates of the ape theory of man, deprived it altogether of its prestige and importance

The Engis skull is now recognized as a Neandertal, in fact the earliest to have been unearthed, although at the time Dunn wrote this was not yet evident. So again, this is a discussion about an actual ancient fossil specimen where the key question is whether it may be an evolutionary intermediate.

On the following page, Dunn refers to the idea that the human races had separate origins from different primate species, one version of the obsolete but then-common scientific idea of human polygenesis:

Need I here remark that "the missing link" is still wanting, and that, as I opine, it never will be found. But, I ought rather to have said the missing links, for according to the ape theory of the origin of the human species, as expounded by Dr. Carl Vogt, of Geneva, and others, the different typical human races are the descendants from different ape ancestors. Now on this subject, I do most heartily join issue with what has so emphatically been said by our venerable President, however I may differ in opinion from him as to whether there may have been more creations than one ; indeed, I need scarcely here observe, that the monogenetic and the polygenetic origin of man is still, and is likely to remain, an open question among ethnologists

Today it is common to hear scientists say that the idea of a “missing link” is a misnomer, because whenever we discover a fossil intermediate between two forms, we create two new gaps on either side of it, both of which now have a “missing link”. Dunn’s formulation here is the first time I can find the same rhetorical objection – that it is not one missing link but many – but here he applies it in the service of polygenism! That is, Dunn implies that a single “missing link” cannot account for the diversity of human races, so there must in fact be several. For Dunn, this was a reason to reject the evolutionary hypothesis. He deploys the idea of the “missing link” in very much the same way that some creationists have done in recent times.

A later edition of the Journal of the Anthropological Society of London recounts a similar discussion following the reading of a paper by W. C. Dendy in 1869. Dendy’s paper presented a polygenist account of human origins, in which he argued that despite the diversity of humankind, the “chasm” between apes and humans had never been bridged over. Again, Dr. Carter Blake was involved in the discussion, and Denby’s reply to his comments included the term “missing link” in a derisive context:

Regarding the Neanderthal and other skulls (casts of which were before him), there had been very great exaggeration. We might light on crania of equal deformity in men of the present day; and with respect to palaeontological "finds", there was often much suspicion. The quarrymen of France were known to practise [sic] frauds--for instance, their own manufactures of them, langues du chat, were often offered and accepted as flint-arrow heads. Mr. Dendy then exhibited the skeleton of a rickety abortion, which he himself had delivered, and which, he believed, had it been found in strata associated with the relics of extinct mammalia, would have been readily accepted as the "missing link". But even if we found the treasure, it would not prove the Transmutation Theory. It might indicate degradation of species, as well as exaltation, the regress as well as the progress of man; favoring the notion of the Oceanic savage that the ape is a dwindled and degraded man.

That’s a horrifying scene.

Still, paleoanthropologists remain pretty rude today.

References

Blake, C. C. (1865) Comments on: The Neanderthal Skull: Its Formation Considered Anatomically by Barnard Davis. Journal of the Anthropological Society of London, 3: xv-xix.

Dendy, W. C. (1869) Comments on: On Anthropogenesis. Journal of the Anthropological Society of London, 7: xxix-xxxviii.

Dunn, R. (1867) Archaeology and Ethnology: Remarks on Some of the Bearings of Archaeology upon Certain Ethnological Problems and Researches. Transactions of the Ethnological Society of London, 5: 305-317

Link: Biologists working for political initiative on anti-extinction

2016-08-09T00:00:00-05:00

“Making a Mass Anti-Extinction Movement” in Pacific Standard covers some of the concerns that led a group of 49 biologists to pen an open letter calling for a new political consensus on worldwide extinctions. I appreciated this passage that pointed beyond the ecosystem aspects of extinction into the cultural system aspects:

Consider the baboon raids of Africa, for instance. Researchers report baboon populations can skyrocket when an ecosystem loses top predators like lions or leopards. In search of limited food supplies, the overpopulated baboons sometimes raid local farmers’ crops, and a family can thereby lose crucial calories. As a result, people keep their children home from school to guard the food plot. The baboons also bring parasites and other disease into the human communities they frequent. The absence of top predators on the landscape leads to a cascade of unforeseen and unfortunate consequences: The lions are gone so the kids get gut parasites and lose out on education.

The open letter, “Saving the World’s Terrestrial Megafauna” was published in the journal BioScience last month.

Link: Referee troubles

2016-08-08T00:00:00-05:00

Leonid Schneider posts a fairly typically depressing story from a peer referee from Frontiers in Neuroscience. The story is basically an editor pressuring the referee to accept a paper, and the go-rounds are described by the referee.

I thought the story worth linking for this passage from the introduction to the story, which put some concerns succinctly:

In a kind of a vicious circle, this peer review secrecy is a direct invitation to rig it even more. Editors tend to assign friendly reviewers according to authors’ eminence, while peer reviewer conflicts of interests are routinely disregarded, since no one will ever find out anyway. In the same vein, scientists who made themselves some powerful enemies will see their manuscripts destroyed by unreasonable and aggressive peer review. They often naively hope the editor was decent enough not to invite those same adversaries whom the authors specifically asked to be excluded.

Photo: Hadar reconstruction from the North Carolina School of Science and Mathematics

2016-08-08T00:00:00-05:00

The North Carolina School of Science and Mathematics (NCSSM) is a science-focused high school. They have put on Flickr a large series of Creative Commons (CC-BY-SA-NC) licensed photos of their cast collection, including skulls of many hominins. I find it awesome to see a public high school taking this initiative, and I really appreciate the work behind this. Here’s a photo of the old Hadar A. afarensis reconstruction from their collection.

Their photos are also available at their school’s webpage, including the ability to render them as 3-D rotations.

Photo: Sangiran Museum

2016-08-07T00:00:00-05:00

The museum and research center at Sangiran, Indonesia is capped by a large copper conical roof. The surrounding countryside is the source of Early and Middle Pleistocene fossils of many vertebrates, including Homo. It is intensively farmed with many small plots, rice, teak plantations and other crops.

Link: Sustaining open access databases

2016-08-06T00:00:00-05:00

Cameron Neylon considers some of the challenges in keeping open data access initiatives sustainable over the long term: “Squaring Circles: The economics and governance of scholarly infrastructures”. He examines some proposals for supporting scholarly “goods”, and emphasizes that they are usually initiated without much planning for what to do if support eventually is lost:

Second, we can look at stable long standing infrastructures (Crossref, Protein Data Bank, NCBI, arXiv, SSRN) and note that in most cases governance arrangements are an accident of history and were not explicitly planned. Crises of financial sustainability (or challenges of expansion) for these organisations are often coupled to or lead to a crisis in governance, and in some cases a breakdown of community trust. Changes are therefore often made to governance in response to a specific crisis.

Where there is governance planning it frequently adopts a “best practice” model which looks for successful examples to draw from. It is not often based on “worse case scenario” planning. We suggest that this is a problem. We can learn as much from failures of sustainability and their relationship to governance arrangements as from successes.

The Social Science Research Network is a potent example. Initiated as an open repository, it was recently taken over by Elsevier, which changed some policies and began to take down some user-contributed content. Many projects that are started by small groups of founders, or funded initially by grants from a single source, are risky over the long term because in some cases the only way to sustain them is to change their policies or accessibility.

I would observe that the open source software movement is a good source of examples for how to ensure that data will be sustained in the open in the event that funding to a project is lost, or a project is acquired by a private entity. Many open software projects have been acquired or developed by private entities, and when they want to change the license terms, the projects are often subject to forking, where the original project may change but a community maintains an open version. The key is that communities of people must coordinate action and be prepared to mount an equivalent project. Widespread public mirroring of source code by individuals and institutions is a major part of what makes this possible.

To me, this suggests that any open data initiatives should be working closely with universities to ensure that their data are mirrored in an open manner.

Large-scale academic and scientific projects sometimes generate so much data that a large number of redundant mirrors are impractical. But it is exactly these instances that we should focus attention upon and ensure that national or international funding bodies are involved in their maintenance.

Link: High-energy physics and the non-discovery of new particles

2016-08-06T00:00:00-05:00

Dennis Overbye in the New York Times covers this week’s news from the Large Hadron Collider at CERN, where hopes of “new physics” beyond the Higgs boson are not panning out: “The Particle That Wasn’t”.

The Higgs, one of the heaviest elementary particles known, weighs about 125 billion electron volts, in the units of mass and energy favored by particle physicists — about as much as an entire iodine atom. That, however, is way too light by a factor of trillions according to standard quantum calculations, physicists say, unless there is some new phenomenon, some new physics, exerting its influence on the universe and keeping the Higgs mass from zooming to cataclysmic scales. That would mean new particles.

Sabine Hossenfelder shares her perspective on this story of non-discovery, as a theoretical physicist: “The LHC ‘nightmare scenario’ has come true”.

That the LHC hasn’t seen evidence for new physics is to me a clear signal that we’ve been doing something wrong, that our experience from constructing the standard model is no longer a promising direction to continue. We’ve maneuvered ourselves into a dead end by relying on aesthetic guidance to decide which experiments are the most promising. I hope that this latest null result will send a clear message that you can’t trust the judgement of scientists whose future funding depends on their continued optimism.

My reaction was that a few billion dollars spent on human origins research would produce a much higher rate of discovery than the LHC.