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paleoanthropology, genetics and evolution

Photo Credit: Okladnikov Cave. John Hawks CC-BY-NC-ND

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.

Neanderthal reconstruction in profile by Guernsey Mitchell

From the collection of the Internet Archive.

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.

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

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:

Google Ngram viewer output for 'missing link'

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.


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

“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.

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.

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.

Cast of A. afarensis reconstruction, from NCSSM

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

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.

Sangiran Museum from a distance

Link: Sustaining open access databases

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.

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.

This is a Daemonelix, burrow of the ancient beaver relative Palaeocastor. There is a nice exposure of Miocene deposits at Agate Fossil Beds National Monument. The surface of the bluffside displays dozens of natural casts of these ancient corkscrew burrows.

Daemonelix burrow at Agate Fossil Beds National Monument

This is SK 15, a lower jaw from Swartkrans, South Africa. Most scientists today attribute it to Homo erectus, but when Robert Broom and John Robinson found it, they named a new genus, Telanthropus capensis. This was the first solid demonstration that two different kinds of hominins were found at the same African fossil site. The very humanlike SK 15 contrasted with the “robust” australopithecines that make up most of the Swartkrans fossil collection.

SK 15 mandible in lateral view

However, the story is a bit more complicated. Some specialists long questioned whether SK 15 might be a small, presumably female, individual within a population where males had the form and size of the robust mandibles. That argument lost some force when later sites also demonstrated the coexistence of Homo and robust australopiths, but the variation of specimens attributed to Paranthropus robustus remains extremely extensive.

Meanwhile, a number of scientists more recently have referred SK 15 mandible to Homo habilis. Some have considered that it might represent a distinct species of Homo, more basal on the hominin phylogeny than H. habilis and H. erectus.

In other words, the taxonomic status of this specimen is really confused. To me, this is a great illustration of the problems of working with a single mandible, even though in this case the mandible is relatively complete. When you hear people talking with great confidence about the taxonomic identity of a partial mandible, SK 15 is a good case to keep in mind.

Last September, Aeon published a useful essay by science writer Jacob Mikanowski, touching on many of the ways that ancient DNA is changing the way we look at ancient population movements: “Origins: Paleogenetics is helping to solve the great mystery of prehistory: how did humans spread out over the earth?”

Mikanowski hits upon a big theme:

Before the Second World War, prehistory was seen as a series of invasions, with proto-Celts and Indo-Aryans swooping down on unsuspecting swaths of Europe and Asia like so many Vikings, while megalith builders wandered between continents in indecisive meanders. After the Second World War, this view was replaced by the processual school, which attributed cultural changes to internal adaptations. Ideas and technologies might travel, but people by and large stayed put. Today, however, migration is making a comeback.

If there is one overarching finding from these ancient DNA studies, it is that many prehistoric archaeological transitions really did involve the large-scale mass migration of groups of people.

Annalee Newitz describes a study in Science that examines a semi-legendary flood at the dawn of Chinese civilization, which turns out to have been a real event: “Incredible discovery reveals the truth behind an ancient Chinese legend”.

Purdue geoscientist Darryl Granger, who worked with the research team in China, described the flood at a press conference earlier this week. The flood waters, he said, "reached up to 38 meters above the modern river level." We know that because the scientists found distinctive sediments released by the flood in the Jishi Gorge and elsewhere downriver. Knowing the water levels helped the group figure out the volume of water, which, Dr. Granger said, "tells us that the flood was [traveling] about 300 to 50,000 cubic meters per second... It's among the largest known floods to have happened on Earth during the past 10,000 years."

These are more petroglyphs from Hawaii Volcanoes National Park, part of the Pu’u Loa group. During historic times, when a child was born, a small cupule would be engraved for the umbilical cord and covered with a stone. There are more than 20,000 of these in the grouping.

Petroglyphs umbilical dots from Hawaii Volcanoes National Park