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paleoanthropology, genetics and evolution

Photo Credit: From the catwalk at Sterkfontein. John Hawks CC-BY-NC-ND


I’m citing this 2011 opinion piece by Hidde Ploegh (“End the wasteful tyranny of reviewer experiments”) in a later post, but I wanted to single out this part:

The scientific community should rethink how manuscripts are reviewed. Referees should be instructed to assess the work in front of them, not what they think should be the next phase of the project. They should provide unimpeachable arguments that, where appropriate, demonstrate the study's lack of novelty or probable impact, or that lay bare flawed logic or unwarranted conclusions. They should abandon the attitude that screams: "look, I've read it, I can be as critical as the next dude and ask for something that's not yet in the manuscript", a reflexive approach to reviewing that has unfortunately become more or less standard. Many reviewers are also, of course, authors, who will receive such unreasonable demands in their turn, so why does the practice persist? Perhaps there is a sense of 'what goes around comes around', and scientists relish the chance to inflict their experiences on others.

Shorter version: Peer review as practiced today is a form of hazing.

Reference

Ploegh, H. (2011). End the wasteful tyranny of reviewer experiments. Nature 472, 391. doi:10.1038/472391a

Link: Carl Safina on animal grief

An evocative excerpt from the new book by Carl Safina, Beyond Words: What Animals Think and Feel:

A researcher once played a recording of an elephant who had died. The sound was coming from a speaker hidden in a thicket. The family went wild calling, looking all around. The dead elephant’s daughter called for days afterward. The researchers never again did such a thing.

Also, this on elephant burial:

Elephants sometimes cover dead elephants with soil and vegetation, making them, as far as I’m aware, the only other animals who sometimes perform simple burials. Elephants have done the same when humans are involved on several recorded occasions. When sport hunters shot a large male elephant his companions surrounded his carcass. The hunters returned hours later to find that the others had not only covered their dead comrade with soil and leaves—they had covered his large head-wound with mud.

If I can editorialize for a moment, sometimes I cannot believe that archaeologists argue about whether Neandertals could conceive of death, or whether they ever really buried the dead. Burial is not universal among historic human groups, but all cultures have some kind of special treatment of dead bodies. We do not know how deep in our family tree these kinds of cultural behaviors may go, but the evidence from chimpanzees (also discussed by Safina) suggests that whatever cognitive resources are employed in recognizing death and grieving were well in place long before the origin of the hominins. I think that such behaviors are emergent qualities of long-lived social beings.

We don’t yet fully understand the scope of these kinds of behaviors in other animals, like elephants. It seems far-fetched to think that we will ever find paleontological traces of elephant mortuary behaviors in the past. Why not mammoths, mastodons, gomphotheres? In elephants, in primates, in cetaceans, these behaviors may have originated before the Miocene.

What sequences deserve a peer-reviewed publication?

David Roy Smith asks whether sequencing mitochondrial DNA is still worth a scientific paper: “Opinion: Too Many Mitochondrial Genome Papers”.

Few would question the utility of mitochondrial DNA (mtDNA) as a genetic marker. But it is increasingly clear that sequencing mtDNA has become an easy route to peer-reviewed publications; at times, the pursuit of these publications is encumbering journal editors, referees, and the research infrastructure as a whole. Is publishing papers on mitochondrial genomes a relic of the “publish or perish” academic landscape? Should mtDNA sequences go directly into GenBank? Are we still gaining new and significant insights from mitochondrial genome data?

The question here is about “new” mitochondrial genomes obtained for species that have not yet been sampled in that way. Smith contrasts the publication of a mere sequence with “fundamental questions”, although he doesn’t specify which questions those include:

With state-of-the-art methods for generating complete mtDNA sequences there came a deluge of publications describing these sequences. The scientific literature is saturated with mitochondrial genome papers. Some of these papers address fundamental questions, but others, unfortunately, add little in terms of new knowledge, and reflect more on some researchers’ desires to accumulate peer-reviewed papers in place of achieving scientific progress. Many journals have become dumping grounds for mtDNA papers of varying quality. All of this is tying up editors, reviewers, and the authors themselves, and potentially distracting them from more valuable tasks.

Sometime around 1996, human genetics passed the point where a single mtDNA partial sequence reported from a previously unsampled human population was worth a peer-reviewed publication. Sometime around 2000, the same was true of whole mitochondrial genomes. A single mitochondrial genome from any previously unsampled ancient hominin population is still of the greatest scientific interest, and even single mtDNA sequences from Neandertals are worth publishing rather than merely depositing them into Genbank. This is because these ancient sequences add substantively to our knowledge of human evolution and variation, while a single sequence from any living human today almost certainly does not do so—unless we find a living human who has the mtDNA sequence of a Neandertal, for example.

So what Smith is saying is that most of the current surge of mtDNA genome sequencing is adding incrementally rather than substantively to our understanding of variation on the tree of life. He further emphasizes that most effort has been allocated to metazoans, and very little to microbial eukaryotes where fundamental questions remain unanswered.

It seems to me that funders should enable this kind of work to become part of training programs for undergraduates, or even high school students. These genomes should all be published, but in journals that emphasize training with the potential that new genomes may be effectively replication studies for hypotheses already tested at other points in the phylogenetic tree. With some central coordination, such work can fill in the tree of life, allowing tests of hypotheses that no single lab could have accomplished.

How long until paleoanthropologists must deposit data upon submission?

Genetics journals have for years routinely required sequence data to be deposited in a public database at the time that an article is published. Increasingly, these journals have broadened to require such deposits for other types of data, such as gene expression, methylation, or genotype-phenotype association data. Some journals have begun to expect data to be deposited at the time of article submission, instead of publication. In principle such a policy enables referees to examine the data in addition to the analytical methods and results reported in a paper. In practice it gives editors more leverage to ensure that the data actually end up being deposited, since when they have made the decision to publish, the ultimate submission of the datasets can fall through the cracks.

Nature Genetics in a recent issue published an editorial commentary, “No impact without data access”. The editorial accompanies an article reviewing the major features of the European Genome/Phenome Archive. Researchers who are investigating the role of genes in disease or other phenotypes can deposit their data in this archive for long-term access control. The editorial raises several issues that made me consider how paleoanthropological data access may be destined to change during the next decade.

Openness and biomedical data

Biomedical research poses an inevitable tension between open data access and the need for the privacy of research subjects, many of whom are patients undergoing treatment for disease. Patient rights provide a clear reason why public access to data should not be allowed against widespread distribution of data.

At the same time, the genetics community has long recognized both practical and moral reasons why data sharing is imperative. On the practical side, open access to data enables replication studies and the extension of results from one patient group or national population into other populations. Maybe most significantly, small trials are inevitably underpowered to find significant correlations, but if the data is archived and open to other researchers, they can be combined into larger-scale metaanalyses that can test for smaller effect sizes.

The moral argument for data sharing recognizes the huge gift that patients give by allowing their data to be used for research. Further, government and private funder resources are invested into research. Scientists should be responsible stewards of both by making the maximum scientific impact that they can. The reuse and broader dissemination of data are good scientific practice.

The generosity of research subjects is not unlimited: Most patients who participate in scientific research do not give consent for public release of their medical, DNA, or epigenetic data. Some people will participate in research even if their data are made totally open to the public, as demonstrated by the Personal Genome Project. But most prefer that their data be kept private. Scientists are expected to maintain patient privacy, which can make it difficult to share data. Although de-identification of data is possible, a number of studies have shown the ease of using supposedly de-identified, anonymous data to obtain personal details of research participants. From the Nature Genetics editorial:

In addition to public variants, individual-level genetic and phenotypic data or summary statistics from the research projects are often required for replication, meta-analysis and many other secondary uses, such as methods development or use as control samples. However, these data must be processed, archived and transferred in a manner that respects the consent agreements signed by the study subjects. This often means that data can only be provided to bona fide researchers and used for specific research aims.

Research communities have implemented a number of solutions to enable sharing data while maintaining privacy. A well-known instance is the dbGaP (database of Genotypes and Phenotypes) administered by the National Institutes of Health, for example, requires investigators to apply for access and agree to a code of conduct. When judged in light of data security, the provisions of dbGaP are in reality very weak, because they depend upon researchers and institutions complying with agreements, rather than enforcing strong protection through cryptography and segmented access. But the guidelines do comport with the general U.S. regulatory approach to medical records.

The European Genome/Phenome archive is basically similar in function but addresses a different regulatory framework than dbGaP. As in the U.S., there is a tension between data access and patient privacy, but complicating matters is the variety of national regulations on biomedical research and data among European countries. Since many European biomedical research projects are international in scope, there is a huge array of bureaucratic variation governing the conditions under which any particular dataset can be shared.

What’s interesting about the Nature Genetics editorial is a passage in which the journal extends beyond the U.S. and Europe-centric databases to consider the regulatory burden upon local research enterprises elsewhere in the world.

Although we recognize that these US and European databases are suitable for most research in the field, national laws may require local databases and access protocols to be developed for different communities. The most positive benefit that could be accrued by local data stewardship would be capacity building through using data access to recruit qualified international experts to collaborate or work locally on the data. But, given the global reach of the internet and cloud, capacity could be built electronically as well as in person, so we urge forward-looking strategists and legislators to anticipate these benefits rather than to be unnecessarily restrictive.

Some thoughts: I don’t agree that recruiting international experts to work locally on data is “the most positive benefit” that could result from local databases. Most nations will want to develop local scientific capacity through training and increased publication by local scholars. Countries are wise to develop local areas of strategic advantage in which they can lead rather than follow international collaborations. The variation of human biology across populations is one area where nearly every country has both local scientific interest and global importance.

Paleoanthropology and data access

Paleoanthropology holds in common with human genetics that many of our most important research subjects are outside of Europe and the U.S. The research objects of paleoanthropology are not only essential parts of world heritage, but also the national heritage of many countries around the world. Institutions charged with responsibility for protecting heritage are rightly concerned that international collaboration not place them at a disadvantage. The fossil record of human evolution can be a strategic asset for local development, just as the biological heritage of human populations can be a strategic asset for development of local biomedical research expertise.

Reading this Nature Genetics editorial, I wonder how long before a similar editorial could be written about fossil hominins. This passage strikes me as especially freighted with implications (I added the emphases):

We regard a data descriptor and a live accession code to a permanent data set in a supported repository as the minimum acceptable data access provision compatible with publication in a high-impact, journal and therefore hold the view that restrictive legislation with regard to access to data will inevitably place local researchers at an international disadvantage with respect to reputation, publication and collaboration. Without specific access provisions for qualified applicants to use data for purposes for which they were originally consented, such costive data management will also undermine trust in the research.

Paleoanthropologists should be familiar with having their research results questioned on the basis of whether their data can be trusted. Some large communities of people organize their beliefs around skepticism of the basic fossil data that underlies our knowledge of human evolution. Although we can do little to change the minds of those who will not look at the evidence, we can do much to make the evidence much more widely available to those who would. Of course there is no “informed consent” for paleaonthropological data, but there are considerations of heritage protection and public education, both of which argue for much wider distribution of original data.

Few paleoanthropologists or institutions have adopted the tools of open data accessibility to enhance trust in their research. This is a strategic failure. Replicability, transparency of methods and results, and access to primary materials are essential foundations of scientific practice. Paleoanthropology has nothing to gain from resisting a full integration with mainstream science; indeed such integration is essential to the future of our increasingly interdisciplinary field.

Logically, the “high impact” journals may prefer to lead the way in requiring data access—not because of an altruistic notion of quality science, but because data accessibility is one defense against the growing flood of retracted and non-replicated papers in biomedical fields. Faced with disputed findings, the journal can point to the availability of data and encourage replication and independent examination; ideally this will happen more and more commonly before publication instead of afterward.

Paleoanthropology so far has been an exception to this trend. For a long time it has been clear that the major “high impact” journals publish more questionable and sensationalized results than field-specific or open access journals. Still, we have seen very few retractions or corrections even in cases where a paper’s results were overturned by replication studies. Of course, when data are not available for a fossil sample, and when independent investigators are unable to examine the fossils, then no replication is possible. Hence, journals have been free to pursue studies that will attract media hype without facing real scrutiny.

I have undergone the review process at high impact journals (Science, Nature, and PNAS) many times in my career, including several published papers and several that were ultimately rejected. When I have published on genetics, reviewers have regularly included comments that request some assurance that data will be accessible upon publication. I have never had a reviewer of a paleoanthropology submission to these journals request any data accessibility whatsoever. That’s not a problem with the field in general: for example, when I have edited and reviewed papers, I consistently require (as an editor) or request data to be provided. But apparently neither I nor anyone like me reviews papers for Nature or Science.

This situation is not sustainable for exactly the reasons that the Nature Genetics editorial notes for biomedical data, namely:

restrictive legislation with regard to access to data will inevitably place local researchers at an international disadvantage with respect to reputation, publication and collaboration.

Restricting access to fossil data may provide advantages for a small coterie of Western investigators, but it harms the local institutions that are custodians of fossil remains. Forward-thinking institutions are building collaborations with a broad range of international investigators on questions of mutual interest, building the scientific significance of their fossil heritage.


This is a footnote in Theodosius Dobzhansky’s notable 1944 paper, “On species and races of living and fossil man”:

In his 1940 paper, Weidenreich denotes Java man and Peking man as Homo erectus javanensis and Homo erectus pekinensis respectively (the name Homo erectus erectus would be the correct one for the former). But in 1943 this author relapses into the use of the misleading names Pithecanthropus erectus and Sinanthropus pekinensis, continuing to admit that they represent only races and not separate species or genera, and arguing that these are “just names without any ‘generic’ or ‘specific’ meaning.” Unfortunately, these names do connote a generic and a specific, rather than a racial, difference to anyone familiar with the biological nomenclature. The abuse of generic and specific names by students of the hominid evolution is notorious; it is making this fascinating field rather bewildering to other biologists.

Reference

Dobzhansky, T. (1944). On species and races of living and fossil man. American Journal of Physical Anthropology, 2(3), 251-265.


I was surprised to find this quote from George Bartholomew, Jr. and Joseph Birdsell (1953:495), explicitly mentioning the possibility that the spread of hominin populations was accomplished with introgressive hybridization of previous populations:

The replacement of the australopithecines by somewhat more advanced but related hominids may have followed the usual mammalian pattern of the gradual expansion of the more efficient form, and the slow reduction of the numbers of the less efficient. In many instances, however, population change must have resulted from gradual genetic penetration, and much of human evolution in the Pleistocene could easily have been powerfully affected by introgressive hybridization. In this regard it should be remembered that anatomical differences do not necessarily indicate genetic incompatability between groups, and that there is no evidence of reluctance to hybridize even between widely different human types. If rapid and dramatic group replacement did occur it must have been a rare event occurring in special circumstances.

The final sentiment, that “rapid and dramatic group replacement” must have been a rare event, is unfortunately worded—they clearly were thinking about introgressive hybridization as a slow event, “gradual genetic penetration”. On a geological scale, such episodes may often be indistinguishable in their speed from total replacement.

Reference

Bartholomew, G. A., & Birdsell, J. B. (1953). Ecology and the Protohominids. American Anthropologist, 55(4), 481-498.


Stanley Garn, writing in “Culture and the direction of human evolution” (1963: 222):

But to speak of higher things, when we turn to the size of the brain there is no doubt of an increase from the African and Asiatic megadonts through the Javanese and Chinese fossils and on through to the forms we accept as cospecific with us today. Some of this increase in brain size is necessarily allometric, the simple growth-associated relationship between bigger frames and bigger brains. Some of this brain increase, perhaps the largest portion, is a true increase in the volume of the brain; and here we must rack our brains to explain our brains. It is no longer enough to attribute even the first increase of hominid brain size to the mere rudiments of technology, and certainly not the second increase that followed Pithecanthropus. Surely man did not double and nearly redouble his cerebral volume merely to pick up sticks.

Reference

Garn SM (1963) Culture and the direction of human evolution. Human Biology 35:221-236.

First Peoples: Asia, and Australia

First Peoples continues tonight on PBS, with two episodes that focus on the dispersal of modern humans into Asia and Australia.

The Asia episode includes archaeological work at Tam Pa Ling, Laos, and goes to the Arabian peninsula with Jeff Rose to track the earliest archaeological evidence of African contacts there. The episode introduces the mysterious Denisovans and talks about the importance of this population mixture to present-day populations.

The Australia episode begins with the Lake Mungo skeletal remains, which similar to the Kennewick skeleton in the U.S. were the subject of conflict between government and indigenous groups. The film visits several sites of heritage significance in Australia, guided by the aboriginal caretakers. And the narrative focuses on the long habitation of the Australian continent through periods of climate change, and the cultural innovations that made it possible to maintain populations within the harsh conditions of the Australian interior.

Coming: 'First Peoples' on PBS

This month, PBS in the United States will be premiering a new five-part series on the origins and spread of modern humans around the world, called First Peoples. The first two episodes, featuring the spread of people into the Americas and the initial origin of modern humans in Africa, will be shown on most PBS stations on the evening of Wednesday, June 24. Later episodes cover the entry of modern humans into Asia and Europe, where they mixed with Neandertals and Denisovans, and the appearance of ancient peoples in Australia.

I’m very proud to appear in all five episodes, where I help to provide a common thread discussing the success of modern humans and the importance of population mixture in our origins. I’m also very pleased with the overall balance of the series. Each episode covers new archaeological discoveries, often from sites that have only been known for a few years, and in several cases discussing unpublished work. Going into the field to cover these archaeological sites adds a real beauty to the series. Meanwhile in each episode new genetic findings come into the story, especially those from ancient DNA that have added so much to our understanding of the interaction of ancient people.

PBS has set up a great website for the series, with background information and clips. Here’s a link to a clip where I describe the importance of population connections across Africa during the early MSA: “The Secret to Our Success - Connectivity”.

I’ll be following up with more information about each of the episodes as the air date approaches.


From Plagues and Peoples by William H. McNeill, a passage synthesizing the role of endemic parasites in weakening entire populations:

Whatever the ancient distribution of schistosomiasis and similar infections may have been, one can be sure that wherever they became widespread they tended to create a listless and debilitated peasantry, handicapped both for sustained work in the fields and digging irrigation channels, and for the no less muscularly demanding task of resisting military attack or throwing off alien political domination and economic exploitation. Lassitude and chronic malaise, in other words, of the kind induced by blood fluke and similar parasitic infections, conduces to successful invasion by the only kind of large- bodied predators human beings have to fear: their own kind, armed and organized for war and conquest. Although historians are unaccustomed to thinking of state building, tax collection, and booty raids in such a context, this sort of mutual support between micro- and macroparasitism is, assuredly, a normal ecological phenomenon.

Alex Tabarrok writes at Marginal Revolution: “Should we care if the human race goes extinct?”

Why should we be worried about the end of the human race? Oh sure, there are some Terminator like scenarios in which many future-people die in horrible ways and I’d feel good if we avoided those scenarios. The more likely scenario, however, is a glide path to extinction in which most people adopt a variety of bionic and germ-line modifications that over-time evolve them into post-human cyborgs. A few holdouts to the old ways would remain but birth rates would be low and the non-adapted would be regarded as quaint, as we regard the Amish today. Eventually the last humans would go extinct and 46andMe customers would kid each other over how much of their DNA was of the primitive kind while holo-commercials advertised products “so easy a homo sapiens could do it”. I see nothing objectionable in this scenario.

Regarding others as quaint is a cultural armament of a particular local median. The Amish population in the U.S. has a doubling time on the order of 22 years and in recent years around 85% of those born into Amish communities have remained in those communities as adults. Cultural forces are strongest at the local median, and in 21st century nation-states, the difference between local and global is defined by religious and ethnic boundaries.

Why do male bonobos have such low body fat?

I can’t be the only one surprised at how little body fat male bonobos have. A study of bonobo dissections by Adrienne Zihlman and Debra Bolter (2015) included data from six female and seven male bonobos collected over many years. The females had very low body fat percentages, with the highest value only 8.6% and three of the six females under 1.2%. But the males were the interesting story, with no male among the seven measured as high as 0.01% body fat.

As Zihlman and Bolter explain, these are minimum estimates, since the necropsied bonobos did not necessarily include fat included in the viscera or near internal organs, and fat that could not be dissected as separate chunks was not weighed separately. But subcutaneous fat and other small adipose areas are included in this estimate, and comparable values for male humans are upward of 20%. They comment on the surprising finding:

The negligible measurable fat in all seven P. paniscus males was unexpected, overriding captivity, age, and body mass. Among wild chimpanzees, there is little indication of an ability to mobilize fat stores during times of caloric restriction, a key adaptive feature found in orangutans and possibly to a lesser degree in gorillas (24, 52, 53). Without selection pressure for storage fat, and with over half of body mass in muscle, the male P. paniscus does not easily accumulate body fat, even under optimal circumstances of captivity. Remarkably, none of the males and females manifested detrimental health as a consequence of having little fat, in stark contrast to H. sapiens.

I was interested in whether this is a bonobo-specific phenomenon. Zihlman and McFarland (2000) dissected four captive gorillas and found both males and females to have substantial body fat percentages, ranging from 19.4% to 44%. Wolfgang Dittus (2013) reported on the body fat distribution of wild toque macaques, finding that they had approximately 2.1% body fat, more than 80% carried within the viscera and other intra-abdominal areas and only a small amount subcutaneously. Males and females did not differ on average.

Interestingly, a study of zoo chimpanzees by Elaine Videan and colleagues (2007) found that no male chimpanzees could be categorized as overweight, and that they differed from females in skinfold and triglyceride levels. From that paper:

The range of serum triglyceride and glucose levels for male chimpanzees was considerably smaller than that of female chimpanzees (Figs. 2, 3). In fact, none of the male chimpanzees in this study had serum triglyceride levels above 150mg/dl (< 150 mg/dl 5 normal human reference range) despite having BMIs that ranged as high as 149.5. In addition, most of the mean skinfold measurements for male chimpanzees were half that of the female values (Table 1). We hypothesize that the high BMIs observed in many of the male chimpanzees in this study reflects high lean body mass (i.e., muscle mass) rather than high body fat.

So there does seem to be something about male chimpanzees and bonobos.

Lest you think that human body fat is just a post-agricultural phenomenon, Herman Pontzer and colleagues (2012) reported on body composition in the Hadza population of Tanzania, who live a hunter-gatherer lifestyle. In that population, women range from 12.4 to 27.7 percent body fat, and men range from 7.4 to 23.1 percent body fat. This is much less than in Westernized societies and is also less than in subsistence farmers, although the difference there is not so great as most might assume. There is a story of body fat in human evolution, and certainly the high body fat composition of humans—even human foragers—contrasts with most wild primate populations. It may be that bonobos and chimpanzees are not the appropriate comparison because of their own distinctive evolutionary trajectories.

References

Pontzer H, Raichlen DA, Wood BM, Mabulla AZP, Racette SB, Marlowe FW (2012) Hunter-Gatherer Energetics and Human Obesity. PLoS ONE 7(7): e40503. doi:10.1371/journal.pone.0040503

Dittus WP (2013). Arboreal adaptations of body fat in wild toque macaques (Macaca sinica) and the evolution of adiposity in primates. American journal of physical anthropology, 152(3), 333-344. doi:10.1002/ajpa.22351

Videan, E. N., Fritz, J., & Murphy, J. (2007). Development of guidelines for assessing obesity in captive chimpanzees (Pan troglodytes). Zoo biology, 26(2), 93-104.

Zihlman AL, Bolter DR (2015). Body composition in Pan paniscus compared with Homo sapiens has implications for changes during human evolution. Proceedings of the National Academy of Sciences, 201505071. doi:10.1073/pnas.1505071112

Zihlman, A. L., & McFarland, R. K. (2000). Body mass in lowland gorillas: a quantitative analysis. American Journal of Physical Anthropology, 113(1), 61-78.

On the importance of saying you're wrong

Lior Pachter writes this week on his blog about the reactions and commentary around a post-publication peer review exercise he conducted on a 11-year-old paper. In the process, he reflects on some of the problems that attend the frank public conversation about weaknesses and strengths of scientific work: “I was wrong”.

Earlier in this post I admitted to being wrong. I have been wrong many times. Even though I’ve admitted some of my mistakes on this blog and elsewhere in talks, I would like to joke that I’m not going to make it easy for you to find other flaws in my work. That would be a terrible mistake. Saying “I was wrong” is important for science and essential for scientists. Without it people lose trust in both.
I have been particularly concerned with a lack of “I was wrong” in genomics. Unfortunately, there is a culture that has developed among “leaders” in the field where the three words admitting error or wrongdoing are taboo.

He discusses recent examples including the snafu induced by the ENCODE Consortium’s insistence that 80% of the human genome is “functional”. He goes on to discuss the importance of public critique of the professional behavior of scientists, with a quote that deserves sharing:

I therefore believe it is not only acceptable but imperative to critique the professional behavior of persons who are scientists. I also think that doing so will help eliminate the problematic devil–saint dichotomy that persists with the current system. Having developed a culture in which personal criticism is outlawed in scientific conversations while only science is fair fodder for public discourse, we now have a situation where scientists are all presumed to be living Gods, or else serious criminals to be outlawed and banished from the scientific community. Acknowledging that there ought to be a grey zone, and developing a healthy culture where critique of all aspects of science and scientists is possible and encouraged would relieve a lot of pressure within the current system. It would also be more fair and just.

The study he describes in the post, and the attendant experiment in examining p-values for certain kinds of genomic questions, are interesting and worth reading. As many have pointed out, it is unfortunate that so few pieces of scientific work can achieve such broad interest in the form of public discussion.

I also think it’s worth sharing an excerpt from a comment at the site from Claudiu Bandea:

“The traditional, closed peer-review system and the conventional ‘civility’ associated with the science enterprise, have allowed, if not encouraged, people to prosper by misrepresenting facts and overhyping their work (at the expense of science and their colleagues), without the *fear* of open and explicit exposure.
And, unfortunately, in order to be able to compete in such a corrupt environment, many of their peers had little choice but to lower their ethical and scientific standards and join this unproductive and reckless competition; and, by doing so, all of them (even the most reckless ones, who often display embarrassing CVs inflated with pompous titles and rewards) have become victims of the system.

When I hear people talk about being unwilling to engage in debate except in the “proper” peer-reviewed forums, this is exactly what I assume they mean.


Recommended: a post by history of science student Paige Madison on the forgotten George Busk: “On Being Remembered: Huxley, Busk, & Scientific Friendships”.

MSA from Karungu, Kenya and the patchy landscape of Late Pleistocene Africa

J. Tyler Faith and colleagues report in the current Journal of Human Evolution on their work understanding the context of the Middle Stone Age archaeological deposits from Karungu, Kenya. Karungu is an area on the eastern shore of Lake Victoria, with many Pleistocene exposures that contian archaeological evidence. Faith and colleagues set out to reinvestigate archaeological sites that were first explored during the 1930s and then later in the 1980s, to hopefully determine where they fit in time and context of other East African MSA occurrences.

The article presents paleoenvironmental data including the faunal list, species abundances of different faunal elements, and some stable isotope data on the fauna, all of which reflect an arid grassland paleoenvironment. That’s a contrast to today’s local environment in the Lake Victoria basin, which is woodier, including a range of bushlands and forests. The team were able to narrow down the timing of the archaeological deposits to some extent, placing them between approximately 92,000 and 45,000 years ago, the later part of the MSA in this part of Africa.

There are two really interesting aspects to Faith and colleagues’ presentation of the data, that together add up to a hypothesis about the movement and contacts of people during late MSA times in eastern Africa. First is a series of observations that suggest that Lake Victoria was much reduced during the time of the Karungu deposits, with lots of herbivores adapted to an arid grassland environment. Second is a statistical link between the archaeological assemblages at Karungu and other sites further to the north. When combined, Faith and colleagues argue that these data suggest north-to-south dispersal of archaeological patterns along with the spread of arid grasslands during the Late Pleistocene. The timing is very interesting: At or shortly after modern humans had established populations in West Asia, some populations of MSA people may have been expanding to the south through East Africa.

Paleoenvironment

The Karungu sites present abundant evidence of now-extinct grassland-adapted species. These include extinct relatives of modern blesbok, impala, wildebeest and oryx. As Faith and colleagues discuss, several of these species were thought to have become extinct more than 400,000 years earlier:

Previous research on late Quaternary fossil assemblages from East Africa indicated that—with a few minor exceptions (Marean and Gifford-Gonzalez, 1991 and Marean, 1992)—an essentially modern faunal community was in place by ∼400 ka (Potts et al., 1988 and Potts and Deino, 1995). However, the emerging evidence from the Lake Victoria Basin reveals the long-term survival of archaic lineages thought to have disappeared >500 ka, including Kolpochoerus, together with the many extinct bovids characterized by large body mass or exceptional hypsodonty, including S. antiquus, Megalotragus, D. hypsodon, R. atopocranion, and Aepyceros sp. nov. ( Faith et al., 2011, Faith et al., 2012, Faith et al., 2014 and Faith, 2014). Of these, only S. antiquus and D. hypsodon are known from other Late Pleistocene faunal assemblages in East Africa ( Marean and Gifford-Gonzalez, 1991, Marean, 1992, Faith et al., 2012 and Rowan et al., 2015).

In addition to these extinct species, the faunal community is further dominated by grassland species that still exist today, including some that have geographic ranges fairly far from the Lake Victoria region. They further note that Mfangano Island has Pleistocene fauna that may date to 80,000 years ago that similarly suggest an open grassland and a connection to the mainland, which would have required at least a 25 m reduction in the lake level. Put together, these pieces of evidence suggest that sometime between 100,000 and 50,000 years ago, the Lake Victoria region was a grassland mecca hosting a mix of species no longer found anywhere in Africa.

This raises a question: Was the Lake Victoria area a refuge for these grassland species into the later Middle and Late Pleistocene? Or have the extinct species been missed at other sites because of small faunal samples? Faith and colleagues do not exclude either of these possibilities. Considering the evidence for substantial fluctuations in African rainfall and lake levels, it seems unlikely to me that the Lake Victoria region was a long-term refugium; those animals must have been living somewhere else during Pleistocene times that rainfall and lake levels were higher.

It is a sobering message that the sampling of African paleoecology during the Middle Pleistocene is so sparse that we have missed many large herbivores in the period following 500,000 years ago. Even more sobering is the implication that previous paleoecologists and archaeologists have promoted the idea of a large-scale faunal turnover which in reality merely marks local environments and sparse sampling.

MSA archaeology

Ancient humans seem to have been effective at dispersing within this arid grassland. Faith and colleagues compared the archaeological assemblage from Karungu with other sites across eastern Africa, keeping track of sites both above 5 degrees North latitude and at the equator and further south. They find that these sites contrast in the pattern of assemblage composition in a way that reflects latitude, with the more northern sites contrasting with southern sites. The Lake Victoria sites, Karungu and Rusinga, are outliers in their similarity to sites further to the north.

Our analysis of the Late Pleistocene MSA record from East Africa reveals previously unrecognized north–south variation in assemblage composition (Fig. 10), paralleling the geographic patterns observed in the genetic records of ungulates (Lorenzen et al., 2012) and other vertebrates (Dehghani et al., 2008 and Miller et al., 2011). We interpret these differences, reflecting to some extent the variable occurrence of bipolar cores, anvils, large bifaces, and Levallois points or point cores (Table 5), as potentially indicating the development of regionally distinct behavioral patterns during past episodes of population fragmentation, for which the equatorial dispersal barrier is a probable driver. In agreement with Cowling et al. (2008), this implies that the potential for north–south human dispersals across East Africa would have been maximized during climate phases that promoted an expansion of grassland cover.
The grassland-associated MSA assemblages from Karungu and nearby Rusinga Island are characterized by a combination of artifact types that is more typical of sites found further north of the equator. This may reflect the southward dispersal of northern behavioral repertoires during a grassy phase that facilitated dispersals, including those dispersals of northern ungulates such as Grevy's zebra and white rhinoceros (Fig. 8).

The “equatorial dispersal barrier” here refers to the forest corridor that expands across the African equatorial region during wetter periods of time. Although this forest serves as a major dispersal corridor for species that depend upon it, including the great apes, it has been conceived as a barrier for grassland-adapted species.

Faith and colleagues help to show that different patterns of material culture existed within an area where they had not previously been noted in this way. In other parts of Africa, long-term cultural differences during the MSA have long been apparent. These are the traces of ancient populations that were to some extent biologically differentiated, but of whom we have very little evidence from physical appearance. We have some evidence from the genetics of living Africans that highly-differentiated populations once coexisted, and later mixed. It is not evident from genetics whether those populations existed over large parts of the continent or whether they were more localized. Nor is it apparent how many such populations there may have been.

It is therefore very significant that Faith and colleagues are able to show long-distance connections across the grassland environment of East Africa. The connections between the Lake Victoria sites and other MSA sites to the north are one piece of evidence for such connections. Another is the presence of exotic obsidian in the archaeological assemblage from Karungu, which they show is most likely to have come from the Rift Valley 250 km to the east. Another suggestion of contacts with the Rift Valley comes from a third outlier in the north-south dichotomy of archaeological pattern, the site of Prolonged Drift, which lies near Lake Nakuru in the Kenyan rift. Humans were able to exploit a changing climate, even as it became more arid. They maintained long-distance trade and exchange of ideas across distances of hundreds of kilometers.

Maybe this population was mixing more with people who had formerly been more isolated and differentiated from each other.

Or maybe this apparent expansion of northern technical patterns merely represents one layer among a series of flows of populations through the region during the Late Pleistocene. I am hesitant to accept the notion of an “equatorial dispersal barrier” as applied to human populations generally. Even as applied to herbivores, the concept has problems, as the interruption in gene flow caused by spreading forests is relatively short compared to the time that grazing species have existed. With humans, the problem is that dispersal is not limited to grasslands. Some human cultures elsewhere seem to have been very effective at dispersing along ecotones, edge habitats between savanna and woodland.

As an example, today’s central African Pygmy peoples descend from ancient populations that had already become established by 50,000 years ago. Many have speculated that the ancestors of today’s Pygmy peoples, established by 50,000 years ago, were forest-adapted people from their earliest times. If so, the habitation of some of the forested parts of central Africa may have been well underway by the time of the Karungu sites. A continuous forest may be a barrier to the dispersal of people with a grassland cultural commitment, but its edges and even its center may have been prime dispersal corridors for other cultural groups.

Culture itself may have been the more formidable barrier to human dispersal. In earlier phases of human evolution, it is possible to imagine that the store of cultural knowledge within any given group would have been fairly low. A population may have expanded to exploit a new habitat without abandoning much of an investment in the old habitat, and the ability of a group to expand or displace other people within a habitat may have relied only in minor ways upon their inherited cultural knowledge. By contrast, the MSA shows signs of greater differences between groups in material culture, suggesting a deeper store of cultural knowledge. Human groups entering new environments without existing human populations would have been able to expand rapidly, but groups entering a previously-occupied habitat niche would face a cultural deficit that would be hard to overcome.

If the dispersal of human populations during the MSA appears to have followed habitat gradients, it may be ultimately for cultural reasons. That scenario is not one in which a mobile grassland population would necessarily have connected other populations that had previously been more isolated. It is a scenario in which an unstable balance of culture areas may have been fluctuating as climate oscillations caused some ecologies to expand and others to contract continent-wide. And again, the sobering reality is the proportion of Africa that does not contribute to our current knowledge of this MSA cultural variability.

Reference

Faith JT et al. (2015) Paleoenvironmental context of the Middle Stone Age record from Karungu, Lake Victoria Basin, Kenya, and its implications for human and faunal dispersals in East Africa. Journal of Human Evolution 83:28-45. doi:10.1016/j.jhevol.2015.03.004