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paleoanthropology, genetics and evolution

Photo Credit: The Taung fossil cranium. John Hawks CC-BY-NC-ND

Darren Naish has a very nice post about one aspect of the saga of Piltdown Man: the scientists who never believed that the jaw and calvaria of the specimen actually belonged to a single individual. The post, “Piltdown Man and the Dualist Contention”, mentions several scientists including Franz Weidenreich and William King Gregory, but spends the most time reviewing the reactions of Gerrit Smith Miller and Aleš Hrdlička.

Long prior to 1953 however, certain other anthropologists, primatologists and mammalogists were of the opinion that the cranium and jaw of Piltdown I did not go together, and that while the cranium was human, the jaw was from a chimpanzee or some other non-human ape. In fact, some workers voiced doubts about the authenticity of Woodward’s reconstruction within just two or three years of 1912. We might even go as far as saying that quite a few anthropologists and mammalogists of the early 1900s would not have been surprised on learning that it was a hoax, and some might even have suspected that this is exactly what it was.

Synthetic DNA with extra 'unnatural' bases

Yesterday at the Radcliffe Symposium on the Present and Future of DNA, I got to hear a lecture by Floyd Romesberg, whose lab has been working to create DNA with two novel “unnatural” bases.

The main idea is that natural DNA with its four bases is limited to a total genetic code that has only 64 possible codons. In nature, these 64 include substantial redundancy, so that only 20 amino acids are used to create proteins. But there are many additional amino acids that are chemically possible that organisms do not use in protein manufacture. If biochemists had an easy way of synthesizing proteins using these additional amino acids, they might find therapeutically useful polypeptides or proteins that could never exist in nature. In other words, it would be like taking a standard Lego kit and adding hundreds of new blocks.

Romesberg’s solution is to add two new bases to DNA to enlarge the number of possible codons. Then, synthetic transfer RNA that binds to the new codons would enable the incorporation into protein sequences of any amino acid that can be synthesized.

But there’s a problem: The Watson-Crick base pairing mechanism functions in a way that makes it hard to add new variations on the same theme. Previous attempts to work in possible synthetic nucleotides that use the same manner of hydrogen bonding have failed, mainly because DNA polymerase doesn’t distinguish them well enough from the existing nucleotides.

So Romesberg turned to a large-scale systematic testing of hydrophobic (oily) molecules to see if they could be turned into synthetic nucleotides that would work within the natural DNA sequence and still allow DNA polymerase to function. As he explained, he took a “medical biochemistry” approach of systematically testing hundreds of molecules using cheap assays to find the ones that might work. It was a real scientific detective story, and the product is a new pair of synthetic DNA bases that bind in a fundamentally different way than the A-T G-C pairings of natural DNA, but that still allow DNA polymerase to do its job.

Last year the News-Medical website did a nice interview with Romesberg that helps to give perspective on the research: “Unnatural DNA bases: an interview with Professor Floyd E. Romesberg, The Scripps Research Institute”.

[I]f you look around nature anywhere in the world, in all the diversity that you see, from the lowest, simplest single-celled organisms all the way up to the most complex organisms like you and me, all of the information is encoded in a four-letter alphabet. That’s all the information that nature has to draw upon. That’s all that evolution has to draw upon.
Evolutionary biologists have a way of looking back in time and it appears that, all the way back to the last common ancestor of all life on Earth, it had a four letter alphabet. Going to six letters and showing that it’s possible has conceptual implications for our understanding of information storage in a cell and, therefore, our understanding of what life can be, because the information stored in a genome defines what life can be. I hope it impacts people thinking in that way, and I hope that some evolutionary biologists and people who think about evolution will consider it.
For people who think about the origins of life or why life evolved the way it evolved, this is a rare piece of experimental data that actually addresses that question.

The most recent phase of the research has involved making bacterial cells work with the synthetic DNA sequences. The lab has overcome many interesting challenges, and it is such an interesting story in how science works, and how the products of evolution are really quite different from the products of systematic experimentation by human synthetic biologists.

Is Dryopithecus an ancient gorilla?

I pass along with little comment this New Scientist article in which David Begun is claiming that the fossil ape Dryopithecus may actually be an extinct member of the gorilla clade: “Ape fossils put the origin of humanity at 10 million years ago”.

“What if Dryopithecus – that looks like a little gorilla – really was a little gorilla that had already branched off from humans?” Begun says. We know the relative times of divergence between gorillas, chimps and humans, he says, so we can use the split of gorillas from the others to recalibrate the fossil clock.

The title and article are pitching the idea that if a 12.5-million-year-old gorilla existed, then the divergence of hominin and gorilla lineages must have been earlier than that time. Which means the divergence of hominin and chimpanzee-bonobo lineages was also fairly early.

But the molecular clock is not actually a story here. We’ve known for several years now that the mutation rate is substantially lower than assumed before 2008. For example, I review the situation in my 2012 article, “A longer timescale for human evolution”).

As Langergraber et al. report (2012), a slower rate places the human–chimpanzee common ancestor at more than 7 Mya and possibly as early as 13 Mya, reopening the case for these and other fossils.
A longer time scale has many other consequences. The 10.5-million-year-old Chororapithecus abyssinicus may really be an early member of the gorilla lineage, as its dental anatomy suggests (Suwa et al. 2007). For the orangutan lineage, the prospect of a much deeper genetic estimate of divergence illuminates the relation between phylogenetics and population genetics. Genetic divergence between two species is a function not only of the time that the species became isolated, but also of the genetic variation within their ancient common ancestral population. Whole-genome analysis of apes and humans has uncovered abundant evidence of complex population structure in the common ancestors of living species (Siepel 2009). Hobolth et al. (2011) assessed incomplete lineage sorting of orangutan similarity in human and chimpanzee genomes, showing that the ancestral population of the orangutans and African apes must have been large and diverse. A fast mutation rate and this complex ancient structure made the origin of the orangutan branch uncomfortably recent, only 9 to 13 Mya, barely old enough to accommodate the earliest known orangutan-like fossil evidence, the 12.5-million-year-old Sivapithecus indicus. A slower mutation rate appears to be a better fit to fossil evidence and the genetic structure of this ancient population.

Gorillas splitting from us 13 million years ago is really not a problem with our current understanding of mutation rates. If Dryopithecus is part of the gorilla clade, it is just an incrementally earlier fossil gorilla than already exists in Chororapithecus from Ethiopia. (I wrote about the import of that discovery in 2007: “Did Gen Suwa just save paleoanthropology?”).

So maybe we’re ripe for an expansion of the gorilla clade to include some European fossil apes as well—assuming that there is a reasonable morphological case for it. Living gorillas are morphologically more generalized in some respects than chimpanzees, yet they have a long evolutionary history after the existence of forms like Dryopithecus. Gorillas and Dryopithecus may share many primitive characters that were lost in the hominin and chimpanzee-bonobo lineages. Any shared derived features will be very difficult to distinguish from the background of primitive characters, especially if we look beyond the cranium and teeth and try to examine postcranial morphology, which is varied in Dryopithecus.

I’ll be interested to see Begun’s morphological case. Begun’s views from around 10 years ago are well expressed in his 2005 article, “Sivapithecus is east and Dryopithecus is west, and never the twain shall meet”. He then favored the view that Dryopithecus could be attributed to the clade of African apes including chimpanzees, bonobos, gorillas and hominins, but not particularly as a gorilla relative. The alternative view up until now has been that these European Miocene apes were stem hominoids, branching from our evolutionary history before the divergence of African apes from orangutan ancestors. So placing one of the European apes into the gorilla lineage looks like something of a surprise.


Begun, D. R. (2005). Sivapithecus is east and Dryopithecus is west, and never the twain shall meet. Anthropological Science, 113(1), 53-64. doi:10.1537/ase.04S008

Hawks, J. (2012). Longer time scale for human evolution. Proceedings of the National Academy of Sciences, 109(39), 15531-15532. doi:10.1073/pnas.1212718109

Hobolth, A., Dutheil, J. Y., Hawks, J., Schierup, M. H., & Mailund, T. (2011). Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome research, 21(3), 349-356. doi:10.1101/gr.114751.110

Langergraber, K. E., Prüfer, K., Rowney, C., Boesch, C., Crockford, C., Fawcett, K., ... & Vigilant, L. (2012). Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proceedings of the National Academy of Sciences, 109(39), 15716-15721. doi:10.1073/pnas.1211740109

Siepel, A. (2009). Phylogenomics of primates and their ancestral populations. Genome research, 19(11), 1929-1941. doi:10.1101/gr.084228.108

Suwa, G., Kono, R. T., Katoh, S., Asfaw, B., & Beyene, Y. (2007). A new species of great ape from the late Miocene epoch in Ethiopia. Nature, 448(7156), 921-924. doi:10.1038/nature06113

UnboxScience has done an incredible infographic treatment of the excavation process of Homo naledi.


I need to get a poster-sized version of that for our lab! Fortunately, larger versions and printable PDF can be downloaded from the UnboxScience site.

From PC World: “Neanderthals vs. Homo sapiens - Lessons Learned”

CNN recently reported that Neanderthals were as smart as Homo sapiens. Sure, they were as smart, but they routinely shipped their products two years after Homo sapiens did, with a minimum of usability testing. And Neanderthals depended on income from previous products, such as bowls, when fire first came out. Neanderthals' VP of Marketing freely admitted as much: “We didn't see fire coming. We were so focused on our new model of bowls, we missed fire completely.”

This is too charming for the Neandertal anti-defamation files. And yes, I’ve corrected all the species names in this; I cannot abide miscapitalization of Linnaean binomials.

From my trip to Gibraltar last week for the 2015 Calpe Conference, a photo from deep within Gorham’s Cave of the famous engraving from Mousterian layers attributable to Neandertals:

Neandertal 'hashtag' engraving from Gorham's Cave, Gibraltar

From The Conversation: 'Homo naledi: determining the age of fossils is not an exact science'

This is a reblog of my recent article on the Africa edition of The Conversation, “Homo naledi: determining the age of fossils is not an exact science”, which is under a Creative Commons license.

Age is nothing but a number when it comes to unravelling the relationships of species from our past. We do not know the actual geological age of the Dinaledi fossils, the single largest fossil hominin find in Africa, but the discovery of Homo naledi still provides insight into how our ancestors evolved.

The Dinaledi fossil collection is one of the most complete ever discovered, representing nearly the entire anatomy of a previously unknown species. Yet our team made no statement or conclusion about the fossils' geological age. I reviewed with Ed Yong some of the reasons why it is difficult to determine the age of the fossils.

The bottom line is that, for now, we have little idea how old the fossils may be.

Most fossil hominins are found in association with extinct animals, which give us at least a general indication of their age. Famous fossil discoveries from more than a century ago, such as the Spy Neanderthal skeletons from Belgium and the first Homo erectus from Java, were found together with long-extinct creatures that indicated they were of great antiquity. This won’t work for Homo naledi because we have found no other animals in association with the hominin bones.

Even today, with methods that rely upon radioactive isotopes to determine the absolute ages of rock layers, geologists often have to revise their initial ideas of the ages of fossils.

Across the last 45 years, the age of the famous KNM-ER 1470 skull of Homo rudolfensis, from Koobi Fora, Kenya, has swung upward and down by more than a half million years as geologists revised age estimates of the famous KBS Tuff. The age of the Sterkfontein Member 4 fossils has been notoriously difficult to determine. Different teams have produced very different ages for the famous Little Foot skeleton from the Silberberg Grotto of Sterkfontein, ranging over more than a million years.

In other words, it pays to be cautious about geology.

But how old is it?

Our lack of a geological age for the fossils caught some other experts by surprise. Carol Ward, of the University of Missouri, commented to The Atlantic:

“Without dates, the fossils reveal almost nothing about hominin evolution, beyond supporting the growing realisation that there was much more species diversity than previously thought.”

William Jungers, from Stony Brook University, said in The Guardian.

“If they are as old as two million years, then they might be early South African versions of Homo erectus, a species already known from that region. If much more recent, they could be a relic species that persisted in isolation. In other words, they are more curiosities than game-changers for now.”

Whether it turns out to be 20 000 years or 2 million years old, Homo naledi is equally distinct from Homo erectus either way. The age of the fossils is simply not relevant to their relationships with other hominins. In the study of anatomy, we focus on the shared features of different species, not their age.

Indeed, so-called relic species can be among the most important indicators of biological relationships, survivors that carry anatomical features from deep time. The coelacanth is much more than a curiosity: its anatomy provides vital clues that helped scientists understand how early land creatures could evolve from lobe-finned fish ancestors.

How our ancestors evolved

No matter its geological age, Homo naledi may provide vital clues about the way our ancestors stepped along a humanlike evolutionary path. This is where the real mystery comes in.

When we look across the skeleton of Homo naledi, we see some puzzling combinations of features. Homo naledi has a foot nearly the same as our own, much more humanlike than any early hominin we’ve discovered so far. Yet its hip and thighbone seem more primitive.

Likewise, Homo naledi had a hand and wrist that were largely humanlike, suitable for manipulating objects and possibly making tools. Yet powerful thumbs, curved finger bones and a shoulder canted upward like an ape’s shoulder suggest that its arms were used for climbing much more than any human today.

The skull of Homo naledi is built like those of early Homo species, especially Homo erectus, but its brain was just more than half the size of the average Homo erectus brain. Meanwhile, Homo naledi had teeth that were smaller than average for any early Homo species, a trait we have usually linked to eating better, more calorie-rich foods like meat or starchy tubers.

It’s almost as if Homo naledi evolved from the outside in.

DH3 compared to KNM-ER 3733
Homo naledi skulls DH1 and DH3 compared with KNM-ER 3733, an example of Homo erectus from East Africa.

The traits in direct contact with its environment, used for walking, handling things, and eating, are the most humanlike. The core of Homo naledi’s body, its brain, ribcage and hips, were more like our very distant relatives, the australopiths.

These combinations make it hard to be sure exactly where Homo naledi fits on our family tree. If we trust the humanlike foot and hand, and the Homo erectus-like cranial form, then Homo naledi looks like it may be closer to us than Homo habilis, the famous handy man.

Whether it is closer or not, Homo naledi’s features show that the key changes leading to our genus may have had nothing to do with a large brain. Testing this will bring us closer to understanding the causes that made us human.

This article was originally published on The Conversation. Read the original article.

Rich Borschelt is the communication director for science at the Department of Energy, and recently attended a science communication workshop. He describes at some length his frustration at the failed model of science communication, in which every meeting hashes over the same futile set of assumptions: “Communication, Literacy, Policy: Thoughts on SciComm in a Democracy. After several other issues, he turns to the conferences’ attitude about scientists:

And for good measure, we whip the scientists a little too, lest we be accused of favoritism. Scientists don’t understand how to talk to normal people. Scientists put the stink eye on any of their fraternity who deign to popularize science. Scientists have to be dragged kicking and screaming away from the bench to talk to the unwashed masses. Scientists need to be taught how to tell a story rather than recite a thesis.
These conversations are about 90 percent of the discussion at conferences on science communication — usually all but the last 15 minutes of a two-day talk-fest. Granted, there’s usually one evidence-based outlier invited in to talk social science findings, but that’s usually sandwiched somewhere between lunch and the time the first folks start heading for the door for an early airplane flight.

The sad thing is that such workshops and conferences are funded again and again by organizations on the logic that they are going to do something about science literacy.

Melissa Hogenboom of BBC Earth asks, “Why are we the only human species still alive?” The article features Jean-Jacques Hublin, John Shea and Nicholas Conard, and covers the usual behavioral angles. Much in this hangs on the meaning we assume for “species” and whether it applies to Neandertals, Denisovans and other populations with the force we assume.

Data sharing and the 'gift culture' of science

Some paleoanthropologists claim that they share data very widely, because they are exchanging datasets with other researchers to accomplish particular research aims. When I’ve talked to such people, they often do not understand where I am coming from when I talk about data access. “What’s the problem?” they might say, “I’ve always been able to get data about fossils I needed for my question.”

A few investigators even go so far as hoarding datasets that they gather from other scientists. Imagine scientists trading illicit CT scans….

Wouldn’t it be much easier just to deposit datasets into open access repositories when the work is published?

A number of researchers have examined this question in other branches of science by doing surveys and case studies of research in practice. This is a quote from a paper by Wallis, Rolando and Borgman (2013), who looked at scientific practices among the Center for Embedded Network Sensing, an interdisciplinary research center funded by NSF.

Much more is known about why researchers do not share data than about why they do share. Among the many reasons for not making data available are a lack of appropriate infrastructure, concerns about protecting the researcher's right to publish their results first, incentive systems that favor publishing articles over publishing data, difficulty in establishing trust in others' data, and the individual investment needed to preserve and manage data in ways that will be understandable and useful to others. This is not to suggest that researchers are selfish, lazy, or greedy. Rather, these findings suggest that despite the current interest in managing, sharing, and reusing research data, the infrastructure and incentives to do so do not yet exist.
Another explanation for the lack of sharing is the “gift culture” of scholarship. Researchers exchange data, documents, specimens, and other intellectual resources with each other through trusted relationships. Data often are closely held, as they can be bartered for other data or resources. If openly deposited for anyone to use, researchers may lose the ability to barter data privately, thus creating a disincentive for deposit.

But for various reasons, scientists hesitate to make data public. They may think that others will misuse the data, by misunderstanding the precise conditions under which it was gathered and thereby drawing incorrect conclusions.

I’ve participated in many formal meetings and conversations about data access in anthropology, and they nearly always end in bickering about the precise conventions for “metadata”—the description of the precise way that the data were gathered. Metadata are necessary for researchers to make intelligent choices about whether and how data gathered by different observers are comparable. But the metadata problem in practice is an excuse for no one to make their own data available to anyone else.

Of course researchers are not only driven by altruistic motives to keep other scientists from making errors. They may want to reserve the ability to publish further studies on the same data, instead of allowing others to benefit from their work. If they can share data very selectively, they may be able to get other useful data in exchange, thereby increasing the value of further publications using the same observations. In other words, they want to cash in.

The “gift culture” is an ideal description of some corners of paleoanthropology as practiced since the 1980s. The term doesn’t blame the participants in data exchanges, who have a broad range of motivations and willingness to share their own data. It just recognizes that data are being shared reciprocally within established networks of scientists, which are based on reputation, access and power. Always within this gift culture some individuals and institutions have shared data and access to information broadly with respect to the power or position of recipients. But others have been extremely reluctant to share any information at all, even questions about their own published research, and never share data unless they can exert control over the direction of the science.

At its worst the gift culture is not science at all, it’s sycophancy. Scientific analyses critical of some previous studies can never be performed, because data are shared only with scientists who will support the conclusions of prior work.

Ability to perform an unbiased replication is by far the most important scientific reason for open data access. Even if no replication is ever performed, the availability of the data provides a minimal assurance that the conclusions are based on real observations. In paleoanthropology, the widespread use of reconstructions and corrections for distorted fossils make this a real concern. How can we know that the seventeenth attempt at reconstruction is the anatomically correct one, if we cannot independently evaluate the data that underlie it?

But a widespread gift culture not only raises questions about the practice of science, it can damage the future of the science. Consider:

  1. An informal network of data sharing, outside of recognized repositories, does nothing to advance the institutions that curate hominin fossil remains. They have no ability to track this informal data sharing, nor do they develop a connection with the recipients of data from their collections. This denies those institutions opportunities to receive public and donor funding for their work. By contrast, recognized repositories allow a citation trail to be established between uses of data and the institutions that curate fossils.

  2. Informal “gift culture” networks cut early career researchers out of the system as independent scholars. If early career researchers can only access data through existing networks of senior scholars, then they may simply not be able to ask certain questions without connections through an academic advisor or other senior investigator. For some research questions this may look like patronage, for many it is peonage.

  3. The gift culture keeps data out of the hands of teachers who are training the next generation of students. Open sharing of data enables teachers to create valuable teaching resources that show how human evolution happened. When data are held close by researchers and traded in secret, students will not have these opportunities to see how science works. Teachers are the biggest losers, and opponents of teaching evolution are the biggest beneficiaries of the gift culture of paleoanthropological data.

It doesn’t have to be this way. Paleoanthropologists are drawn into the gift culture ultimately as a way of managing their reputations. A better way of building a reputation is to provide data freely. The data have contributed to some piece of work, and sharing data with the world is a hard-to-fake way of demonstrating the rigor of the work.

In other words, we need to move from a gift culture to a potlatch culture.

Some excellent institutions and individuals curate and share data broadly, and they deserve more recognition for what they are doing. The University of the Witwatersrand is getting some attention for open access this week because of the Rising Star collection on MorphoSource. Teachers all over the world have been printing out the fossils and sharing them with their classes! Our team is building upon the long-term efforts of many others. More and more paleoanthropologists are using open access repositories like MorphoSource and Figshare, or are depositing datasets in supplementary material of journal publications.


Wallis JC, Rolando E, Borgman CL (2013) If We Share Data, Will Anyone Use Them? Data Sharing and Reuse in the Long Tail of Science and Technology. PLoS ONE 8(7): e67332. doi:10.1371/journal.pone.0067332

From The Conversation: 'Homo naledi fossil discovery a triumph for open access and education'

This is a reblog of my current article on the Africa edition of The Conversation, “Homo naledi fossil discovery a triumph for open access and education”, which is under a Creative Commons license.

Homo naledi has made headlines around the world as one of the most significant fossil discoveries ever made.

The unprecedented sample of fossils represents a rich record of an ancient population of human relatives, preserving nearly every part of the skeleton and spanning the lifespan.

Many people around the world have been following the compelling story of discovery from the first days of the excavation.

Using social media to tell the story

As our cavers and scientists worked underground in challenging conditions, we kept the world up to date on Twitter, Facebook and with our Rising Star Expedition blog.

Since those first days, the team has worked to build open access into every stage of the project. People can now share not only in the discovery but also in the process of understanding these ancient hominins.

After nearly two years of work, on September 10 we published our first scientific papers on this discovery in the journal eLIFE. These original scientific descriptions of these fossils and their geological context are free for anyone in the world to download and share.

In the week following the publication of these papers, the lead paper describing Homo naledi was viewed more than 170,000 times – an extraordinary figure for any scientific paper.

Our team has also moved quickly to make our data available to anyone in the world. Many of our fossils are now represented by research-quality 3D scans on MorphoSource.

This online archive of data from skeletal and fossil discoveries, maintained by Duke University, provides a way to share large data sets both for scientific work and teaching.

3D technology used in classrooms

Our team has generated virtual reams of scans that enable anyone to visualise these fossils, and even to use 3D printing technology to create their own physical copies.

Right now, teachers and researchers all around the world are printing 3D models of the fossils of Homo naledi. Kristina Killgrove, a leader in applying 3D printing technology in her anthropology classroom, wrote:

I downloaded the model as an .STL file…and then printed it using my trusty old MakerBot. It took 20 minutes, tops. Then I gave the model to a grad student who was heading in to teach the undergraduate lab in biological anthropology. Bam! Species-announcement-to-teaching-cast in under 12 hours.

Since the announcement, more than 3300 copies of these data sets have been downloaded, with makers proudly showing off their printed models on Facebook and Twitter.

Find broke boundaries

Paleoanthropology has often been caricatured as the lone pursuit of fossils by Indiana-Jones-like characters. But in the 21st century, making new discoveries in paleoanthropology – as in all other areas of science – requires collaboration across many disciplines.

This project has involved a team of more than 60 scientists, each bringing their own distinctive expertise and data sets together to help solve the problems posed by these fossils.

The project is led from South Africa and stretches across international boundaries to impact the world.

At the event announcing Homo naledi at Maropeng, the Vice-Chancellor of the University of the Witwatersrand, Adam Habib, remarked on the importance of open access for building a 21st century science:

We often talk about science as having no boundaries, but in our world scientific knowledge has become commodified, and too often, what should be the bequest of the world, the bequest of a common humanity, is locked up under paywalls that postgraduate students and researchers cannot get access to. So what we did when we made this discovery, was we put cameras in the cave, and we streamed it live from day one.

We partnered with eLIFE, an open access journal, to make sure that the discovery was available to all of humanity. And what we did in that practice, is create the first elements of a common global academy….We are not simply going to be beneficiaries of open access, but we are going to be contributors to open access, to the knowledge of a common humanity.

eLIFE editor Randy Schekman wrote about the benefits of open access publishing in 2013 when he won the Nobel Prize. His article, entitled How to break free from the stifling grip of luxury journals, emphasised that by limiting access to publishing, traditional journals create artificial scarcity to distort the process of scientific communication. Open access makes for better science.

Public engagement

The open access philosophy has driven our work on Homo naledi from the beginning. Instead of keeping these discoveries veiled behind locked doors, we have tried to bring them to the public in ways that will drive greater curiosity and engagement with science.

We are proud to be able to share the original fossils with the public at Maropeng, where they will be on display until October 11.

Not only the public benefits from scientific open access; science itself benefits. Showing the process of science in action, we create better tools for educators to equip students with the scientific method.

As we train a new generation of scientists, we must give them the tools to build collaborations and work with massive data. By sharing data openly, we build a worldwide community of practice as we attempt to understand this and other future discoveries.

This article was originally published on The Conversation. Read the original article.

Is Homo naledi just a primitive version of Homo erectus?

We’ve gotten lots of feedback on the new species Homo naledi. Most has been enormously positive, a little bit has been critical. In particular, a few scientists have come forward with criticism of the idea that H. naledi is really a new species. Fortunately I can address those criticisms easily by pointing to some easy-to-find answers.

Is H. naledi really two species?

On one side, Jeffrey Schwartz has argued that the H. naledi remains actually represent two or more different species. Newsweek gave him an op-ed platform to make his case, “Why the Homo Naledi Discovery May Not Be Quite What it Seems”.

Viewed from the side, two partial skulls are long and low, with a long gently sloping forehead that flows smoothly into the brow – nothing like us, or most specimens regarded as Homo. A third partial skull is very short and rounded, with a high-rising forehead that is distinguished from a distinct, well-defined brow by a shallow gutter – not like the other skulls, and not like us or most specimens regarded as Homo. The femur has a small head (the ball end that fits in the hip socket) that is connected to the shaft of the bone by a long neck, and, below the neck, is a "bump" of bone that points backward. These features are seen in every australopith femur. In us, and all other living primates, the head of the femur is large and the neck short, and the "bump" points inward. Further, the teeth are very similar to those from a nearby fossil site that has yielded various kinds of australopith. Even at this stage of their being publicized, the "Homo naledi" specimens reflect even greater diversity in the human fossil record than their discoverers will admit.

Homo naledi has a mosaic of features that include some that compare most closely to more primitive australopiths, and others that compare more closely to Homo. How do we know that this is one species rather than a jumble of species mixed together? Simple: every feature that is repeated in the sample is nearly identical in all individuals that preserve it. It would be very strange to have a mix of different species where all seven proximal femora come from one species, while all of a dozen lower third premolars come from a different species.

Schwartz is also totally wrong about the crania: All the frontal bones in the collection have a similar morphology with a thin supraorbital torus and slight but distinct supratoral sulcus. The variation within the collection is not high, it is extraordinarily low—in fact, the tooth size varies less than half as much as is usual in most human populations. Schwartz seems to imply in his argument that some of the Swartkrans teeth attributed to Homo are similar to H. naledi. There are some superficial similarities, but in fact we cannot find a good comparable example within the Swartkrans collection, particularly for the distinctive premolar crown and root morphology, the lower canine crown morphology, and the small molar sizes of H. naledi.

All of that is in the paper, which is open access for anyone to read anywhere in the world: Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa”. It is not really a mystery why someone like Schwartz would come forward in such a public way with criticisms that are easily answered by the open access paper—after all, it’s not every day that an anthropologist is asked to write a full-page piece for Newsweek.

DH1 and DH3 of Homo naledi compared to KNM-ER 3733 of Homo erectus
DH1 (left) and DH3 (center) of Homo naledi compared to KNM-ER 3733 from the Turkana Basin, usually attributed to Homo erectus. These skulls, shown to scale, illustrate the very small size of the Homo naledi cranium compared to African Homo erectus.

The “primitive small Homo erectus” story

Another criticism of Homo naledi has come from a prominent paleoanthropologist and member of the National Academy of Sciences, Tim White. White has been publicizing his theory about Homo naledi in many press interviews (e.g., “Some bones to pick”):

White: Dating is irrelevant; these are a small, primitive H. erectus, whatever the date turns out to be. This is because they are not biologically different, in any significant way, from already known H. erectus found in places like Swartkrans (800m away), eastern Africa, or the Georgian republic. Of the 80+ traits listed in the e-LIFE supplemental material, only a small fraction of them are even claimed to differentiate these fossils from earlier described H. erectus, and that fraction of characters is known to vary among members of the same species (even population) of both H. erectus and H. sapiens. In other words, the newly described "species" is an example of artificial species inflation in palaeoanthropology.

Of course, Homo erectus is a very well-known species, and we compared the Dinaledi fossils to every specimen available to us. Many of our team have studied the originals of most Homo erectus remains around the world, and I have personally examined the key cranial and postcranial specimens from Dmanisi. So we examined this question in great detail as we studied the Homo naledi material.

How are we to know that Homo naledi is not the same as a primitive, small Homo erectus? Well, for one thing, at least two H. naledi individuals have endocranial volumes around 460 cc, much smaller than any H. erectus cranium ever found. There is barely any overlap between the larger individuals and H. erectus, with only a single H. erectus specimen coming close to the H. naledi range of variation in volume.

White doesn’t specify how many features would be sufficient in his view to define a species. It should be obvious that if we list 80 cranial and dental traits that are informative among all hominins, that most species will differ in only a relatively small fraction of those. Nevertheless our open access paper lists many clear differences between H. naledi and H. erectus, including aspects of premolar crown and root morphology, the crown morphology of the molars (simplified in H. naledi, invariably crenulated and complex in H. erectus), vault shape (H. naledi does not have the elongated, low cranium of H. erectus) and mandibular shape—all listed on page 10 of our open access paper. Even setting aside the postcranial skeleton and the very small endocranial volume, these show H. naledi to be distinct from H. erectus.

When we look at the postcranial skeleton, there is simply no way that H. naledi could be confused for H. erectus. H. naledi has a long, anteroposteriorally flattened and anteverted femur neck, which looks very different from African and Dmanisi femora attributed to H. erectus. The H. naledi tibia is exceptionally mediolaterally thin and long, with a rounded anterior border and tubercle for the pes anserinus tendon, all traits that we could not find in known tibiae attributed to H. erectus including Dmanisi. The H. naledi scapula has a superiorly oriented glenoid, very different from the Dmanisi scapula specimen or the Nariokotome H. erectus skeleton. The vertebrae of H. naledi do not match in proportions or morphology the comparable examples from Nariokotome or Dmanisi, and the pelvis of H. naledi exhibits a short, flared ilium unlike those known for H. erectus, including the Gona pelvic specimen.

It’s just a poor match to H. erectus, so that the only way to make the H. naledi fossils fit within Homo erectus is to stretch that species beyond any other ever defined in the human lineage. There are clearly some similarities, which to us indicate something about the evolutionary relationships of H. naledi and H. erectus—but we are hesitant to go so far as to posit a unique relationship of these two species because many of their similarities also overlap with species such as H. habilis, H. rudolfensis, and even Australopithecus sediba. Figuring out those relationships will take additional research and analysis.

What a species diagnosis does

The purpose of a species diagnosis is to enable other researchers to distinguish the new species from other species they already know. The diagnosis is a taxonomic act, creating a name that can be recognized in the future by agreed-upon rules of nomenclature. The species diagnosis provides a basis for later descriptive work, which can go into much more detail about the morphology of the fossils and include comparisons with all specimens of other species rather than merely differential traits.

It has been tradition in paleoanthropology for the first diagnosis of a new hominin species to be very brief. For example, the diagnosis and description of Australopithecus ramidus (White et al. 1994) included dental, cranial and postcranial material, and was only 6 pages long. The diagnosis and description of Australopithecus garhi (Asfaw et al. 1999) was also 6 pages. The diagnosis and description of the new species Australopithecus deyiremeda (Haile-Selassie et al. 2015) is 5 pages.

Of course there is a problem with such short descriptions. How were we really to know that Australopithecus ramidus was different from Australopithecus afarensis? More to the point, a year later, when White and colleagues published an erratum to their article that named a new genus for the material, which they called Ardipithecus, how were we to know that was justifiable based on evidence? Well, in that case we waited 15 years for the publication of additional descriptive material. The description of Au. garhi is still, 16 years later, the only scientific document on those fossil remains. The description of Au. deyiremeda this spring (Haile-Selassie et al. 2015) was met with immediate criticism by Tim White, who seemingly has no time for species that he himself has not named.

Some people have become jaded about the entire idea of hominin species, cynically concluding that every new species name is just an exercise in glorifying the discoverer, or is stoked by nationalist pride. In my experience, that’s rarely true. Paleoanthropologists are careful scientists who want their work to stand the test of public attention. But the field’s convention of brief species diagnosis followed by long delays for more information has led to confusion and criticism.

We hope that a more open approach will lead to more productive conversations about hominin species.

With 35 text pages, not counting supplementary data, the species description of Homo naledi is around 6 times longer than has been typical in paleoanthropology. We worked to give a much broader perspective on the anatomy across the skeleton than is typical of species descriptions in our field, and we have described the differences between H. naledi and other species with much greater specificity than has been done before.

There is much work to do in describing the Homo naledi collection, and we have several publications forthcoming and in review that give more descriptive detail about the H. naledi fossils. This is just the beginning of a conversation about the form and place of this species in our evolutionary history. But we think that the data we have provided in this initial publication will allow people to know with some confidence that H. naledi is really quite different from other previously-known species.

Download them yourself!

Of course, no one has to trust what we have written about the fossils, because we have made the 3D shape files for many of them available open access through MorphoSource. Anyone can sign up for a free login and download the shape files, even print them out. It’s been exciting to see anthropology departments and seminars printing the fossils and discussing them all week long!

Some senior paleoanthropologists have unfortunately been accustomed to secretive practices. They may think that people will trust their authoritative pronouncements about fossil remains because no one will ever see the data. That’s an unscientific approach, and it leads to bad practices.

What we’re seeing now from senior scientists like Tim White and Jeffrey Schwartz is an unfortunate pattern. These scientists are used to being able to immediately talk to their cronies in the press with a knee-jerk reaction to new fossil publications, secure in the knowledge that the authors won’t release the data to contradict them. Even White, who has famously written (White 2000) that no one should publish on a fossil without seeing the original, has twice this year chased attention for his own fringe views about new species.

I hope that he’ll print out the fossils and take a careful look side-by-side with his own data. Maybe someday he’ll share his data with other scientists and the world so that we can have a real conversation.


Asfaw, Berhane, et al. "Australopithecus garhi: a new species of early hominid from Ethiopia." Science 284.5414 (1999): 629-635.

Berger, Lee R., et al. "Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa." eLife 4 (2015): e09560.

Haile-Selassie, Yohannes, et al. "New species from Ethiopia further expands Middle Pliocene hominin diversity." Nature 521.7553 (2015): 483-488.

White, Tim D., Gen Suwa, and Berhane Asfaw. "Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia." Nature 371 (1994): 306-312.

White, Tim D., Gen Suwa, and Berhane Asfaw. "Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia." Nature 375.6526 (1995): 88.

White, Tim D. News and Views: A View on the Science: Physical Anthropology at the Millennium. American Journal of Physical Anthropology 113 (2000):287–292.

Link: Announcement of Homo naledi

Last week Lee Berger and our team announced the first series of findings from the Rising Star Expedition and subsequent analyses of the hominin fossil remains. I’ll have more to write about that in the upcoming weeks, but for the time being I want to provide a link to the announcement at Maropeng in the Cradle of Humankind World Heritage Site:

The leading dignitary at the event was the Deputy President of South Africa, Cyril Ramaphosa, whose remarks on the discovery were just wonderful. The Vice Chancellor of Wits University, Dr. Adam Habib, delivered a really thoughtful speech about the importance of open access publication for Africa.

The presentation of Homo naledi begins around 40 minutes in, with short presentations by Lee Berger, myself and Paul Dirks, finishing with the unveiling of a substantial portion of the fossil collection. These fossils will be on public display at Maropeng until October 11.

Upcoming event: 'The Past, Present, and Future of DNA' at Harvard

On October 2, I will be participating in a public symposium at the Radcliffe Institute for Advanced Study at Harvard University, titled “The Past, Present, and Future of DNA”. From the website:

The one-day science symposium will focus on the explosion of knowledge about past and present DNA, and will include discussions about possible directions and applications for future research. The event will include experts in ancient DNA, de-extinction, human origins, population genetics, forensic science, ethics, business, future synthetic life, and the personal genome.
This event is free and open to the public.

I’ll be part of a session talking about the science of ancient DNA, moderated by George Church, and with Beth Shapiro and Spencer Wells as the other presenters. I’m looking forward to it, and I think the entire event will be a really timely and provocative look at where DNA technology and society are going. If you are in the Boston area and want to attend, the event is free but does require pre-registration, so check it out!

Quote: Cowgill on statistical methods

George Cowgill is an archaeologist with a long interest in promoting the unfortunately rare good use of statistics by archaeologists. He has a paper within the current Annual Review of Anthropology, titled “Some Things I Hope You Will Find Useful Even if Statistics Isn’t Your Thing”, which is full not only of wisdom but also highly quotable paragraphs.

Some are even useful for biologists, such as:

If you are worried about data quality, reducing data to “present” and “absent” just makes the problem worse, unless you are sure that absence in the sample unambiguously implies absence in the relevant population. But a category that is scarce but present in the population will be totally absent in many samples from that population. The chance that it is absent in any one sample strongly depends on the size of that sample. This makes “presence versus absence” a very unstable statistic. If you want to be intentionally vague and conservative, it would be much better to use terms such as “way below average,” “about average,” and “way above average.”

Paleoanthropologists use an awful lot of “present” and “absent” when assessing the relationships of fossil samples, often based on a single individual. Of course, I wrote something about that myself (Hawks 2004), showing that small fossil samples scored as “present” or “absent” for traits lead much of the time to incorrect phylogenetic conclusions.

Back to Cowgill, there is also this wonderful paragraph:

In fact, archaeologists have been astonishingly ready to assume that their findings are highly reliable (repeated studies would get almost the same results) and very valid (their findings are a nearly unbiased sample of the population of interest). Leaving these assumptions unchallenged is nothing short of a conspiracy of silence, and it is not going too far to call it a dirty little secret. Over the years I have compiled a bibliography of more than 4,000 publications on a wide variety of archaeological topics. Among other things, I have been on the lookout for publications reporting studies of reliability and/or validity, wherein sites were recollected or resurveyed or different observers independently classified the objects in a collection. I have located just 20, of which the most recent and most telling is that by Heilen & Altschul (2013). The bad news is that the level of reliability and/or validity is often shockingly low. If you believe your results can be trusted without any checking, you are fooling yourself and doing the profession a disservice.

He emphasizes the ethical need to make and curate collections as an essential matter of allowing repeated observations and checking:

To be sure, not all sites can be redug or resurveyed. Some sites can be, and even when that is not possible, curated collections can be restudied; the frequent need for restudying them is a major reason why it is essential to make collections and is irresponsible to imagine that recording observations without making collections is adequate.

In archaeology, it is usually observers and not machines that produce the data. While you can reverse-engineer the way a machine scores observations, it is much less easy to do so for a human observer, and impossible without ready access to the collections that human observer has studied.


Cowgill GL. 2015. Some Things I Hope You Will Find Useful Even if Statistics Isn’t Your Thing. Annual Review of Anthropology 44:1–14 doi:10.1146/annurev-anthro-102214-013814

Hawks J. 2004. How much can cladistics tell us about hominid relationships? American Journal of Physical Anthropology 125: 207-219. doi:10.1002/ajpa.10280