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paleoanthropology, genetics and evolution

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

Many people know the story that Carl Sagan was rejected for membership in the National Academy of Sciences of the United States. The story has given rise to the idea of the “Sagan Effect”, whereby scientists who are active in popularizing and explaining science to the public are perceived by other scientists as being somehow less serious about their research.

Someone asked me about this today and I ran across a quote from the journalist Joel Achenbach, who had profiled Sagan in 1996, in an article reprinted in the book, Conversations with Carl Sagan (Carl Sagan and Tom Head, editors, 2006). This excerpt is from page 158:

In 1992, Sagan's name was one of sixty nominated for membership in the National Academy of Sciences. The other fifty nine made it without a hitch. But someone objected to Sagan.
Sagan's case was argued by Stanley Miller, a chemist who did pioneering work on the origin of life. He believes Sagan's scientific work, such as his research on the atmosphere of Venus, is often overlooked. The anti-Sagan faction countered that if the fluffy stuff of Sagan's career were swept away, there wouldn't be enough hard science underneath.
One member who was present says, "If he had not done television, he probably would be in the academy."

Theodosius Dobzhansky, “Man and Natural Selection” (American Scientist 49:285, 1961):

By changing what man knows about the world, he changes the world he knows; and by changing the world in which he lives, he changes himself. Herein lies a danger and a hope; a danger because random changes of the biological nature are likely to produce deterioration rather than improvement; a hope because changes resulting from knowledge can also be directed by knowledge.

Ars Technica has a long article in honor of the anniversary of the Apollo 13 by writer Lee Hutchinson, giving background to the famous accident that the movie (and books that I’ve read about the space program) omitted: “45 years after Apollo 13: Ars looks at what went wrong and why. I’ve never read such a clear account of why the oxygen tank exploded.

And the real moral of the story:

For Apollo 13, keeping calm and working the problems as they appeared allowed three astronauts to escape unharmed from a complex failure. The NASA mindset of simulate, simulate, simulate meant that when things did go wrong, even something of the magnitude of the Apollo 13 explosion, there was always some kind of contingency plan worked out in advance. Controllers had a good gut-level feel for the limits of the spacecraft’s systems when trying to work through emergency problems.

Esther Ingliss-Arkell has an interesting short description of “What Happens When You Get The Wrong Blood Type?” on io9.

The first sign of a transfusion gone wrong is "a feeling of impending doom." This is a legitimate medical symptom, and doctors who regularly work with blood transfusions are told to look for it. Other sign of a mismatched blood type is the usual immune system warning flags — flu-like fever, ache, and chill, as well as a burning sensation at the injection site.

I teach the ABO system as part of my usual human genetics lectures, and I’ve never read a great description of the range of transfusion reactions—I was really only aware of the most catastrophic type. So this can be an interesting piece for those teaching ABO as well as those who’ve just always wondered.

Stone tools now 3.3 million years old

Sonia Harmand presented a talk at the Paleoanthropology Society meeting this week describing her team’s discovery of stone tools in a 3.3-million-year-old context at Lomekwi, on the west side of Lake Turkana. Michael Balter reported on the talk in a story in Science: “World’s oldest stone tools discovered in Kenya”:

In 2011, Harmand’s team was seeking the site where a controversial human relative called Kenyanthropus platyops had been discovered in 1998. They took a wrong turn and stumbled upon another part of the area, called Lomekwi, near where Kenyanthropus had been found. The researchers spotted what Harmand called unmistakable stone tools on the surface of the sandy landscape and immediately launched a small excavation.

The story discusses the contents of the talk, that the tools have been found both from surface and excavation contexts. According to the article, the artifacts show quantitative differences from known Oldowan assemblages, all of which are at least 700,000 years more recent. These differences led Harmand and colleagues to name a new tradition, which they are calling the “Lomekwian”.

I can’t really comment more informatively about this until the work is published so that I can evaluate it. The obvious implication is that stone tools were invented and used by multiple lineages of early hominins. Just as there were different styles of body shape and bipedal mechanics among early hominins, there were likely different styles of technical traditions. A few of these were stone, but almost certainly there were perishable tool traditions among most populations of early hominins. Just taking what we know from living chimpanzee populations, with different traditions of tool use, complex tool sets made from perishable materials, and occasional use of durable objects made from stone. All hominins added initially was the deliberate flaking of stone to make objects recognizable in the archaeological record.

That is to say, humans have elaborated upon a technical ability that is latent among all the apes. This technical ability rests upon social learning skills that are necessary in chimpanzee societies, and early hominin societies inherited those skills from the common ancestors of humans and chimpanzees. After millions of years of exploring this technical space, some experiments led to the manufacture of stone flakes and choppers. Possibly one or more experiments led to the manufacture of bone points or piercers, as evidenced at Swartkrans and Kromdraai, and often attributed to robust australopithecines.

Such traditions may or may not have been shared across different hominin populations. In chimpanzees, technical traditions are not widely shared, yet we know that they may last locally for at least a few thousand years. If a chimpanzee-like model applied across the Pliocene, traditions that lasted a few thousand years across local areas would occasionally be visible to archaeologists, if they were looking for them.

Now they are.

Boston University’s research office has a nice article about Kristi Lewton’s research on pelvic biomechanics: “In defense of wide hips”. The piece refers to Lewton’s investigation of the “obstetrical dilemma”, the hypothesis that the demands of bipedalism for a shortened pelvis may have sharpened the constraint on gestation time in hominins because of the demands of birthing infants.

If the basic assumptions of the obstetric dilemma are right, says Lewton, participants with wider hips should run and walk less efficiently than those with narrow ones. But that wasn’t what Lewton and her team found. Instead, they found no connection at all between hip width and efficiency: wide-hipped runners moved just as well as their narrow-hipped peers. Lewton and her colleagues published their results in March 2015 in the online journal PLOS ONE. The work was supported by grants from the National Science Foundation and The Leakey Foundation.
“This ‘trade-off’ between hips wide enough for a big baby and small enough for efficient locomotion does not seem to occur,” says Lewton. “That means that we have to rewrite all of the anthropology textbooks! Even outside of textbooks, the general public thinks that if your hips are wide, you’re a bad biped, and that does not seem to be the case.”

The research paper discussed in the article is the recent one by Anna Warrener and colleagues, “A Wider Pelvis Does Not Increase Locomotor Cost in Humans, with Implications for the Evolution of Childbirth”.


Warrener AG, Lewton KL, Pontzer H, Lieberman DE (2015) A Wider Pelvis Does Not Increase Locomotor Cost in Humans, with Implications for the Evolution of Childbirth. PLoS ONE 10(3): e0118903. doi:10.1371/journal.pone.0118903

James Gorman of the New York Times has an article today about the long-term field research on hunting by the chimpanzees at Fongoli, Senegal.

The Fongoli chimps find the bush babies in their dens in trees. Chimps will stab and poke one of the small animals, sometimes wounding but not impaling it, until it comes out of its hiding place. The chimps will grab it, Dr. Pruetz said, and immediately “bite the head off.”
Females, even those with infants, and juvenile chimps can do this kind of hunting. The process does not put a premium on speed and strength as the chase does, so big males do not have an advantage. But there is more than technique and technology involved. There is social change.

Last year for my MOOC, I interviewed Jill Pruetz about her work at Fongoli. There are many interviews with her online, but this one really digs into the details of female hunting, the unique savanna setting of the Fongoli group, and the ways that chimpanzees use water in this seasonal environment.

It is a great interview, and like many of my other videos available on my YouTube channel.

Me: “So apparently today is the tenth anniversary of the first Eccleston episode.”

Gretchen: “Yeah, no, that was like two weeks ago.”

Sophie: “Don’t try to out-nerd us on this, Dad.”

Me: “I just saw it on somebody’s Facebook feed.”

Gretchen: “Um, hon, I follow Doctor Who on Facebook.”

Sophie: “Geez, Dad.”

Notable paper: Rangan H, Bell KL, Baum DA, Fowler R, McConvell P, et al. (2015) New Genetic and Linguistic Analyses Show Ancient Human Influence on Baobab Evolution and Distribution in Australia. PLoS ONE 10(4): e0119758. doi:10.1371/journal.pone.0119758

Synopsis: Rangan and colleagues investigate whether ancient Aboriginal Australian people were responsible for dispersing the boab tree (Adansonia gregorii) across its current geographic range in northwestern Australia. Although tree was not formally cultivated, its fruit has long been consumed by local people. The authors studied the pattern of gene flow in the tree’s phylogeography, finding it to be very similar to the pattern of loan words for the tree among Australian languages, suggesting that the practices of ancient people were responsible for the tree’s current distribution sometime after the Last Glacial Maximum.

Interesting because: Baobab species have been used by humans in Africa, Madagascar and Australia. Previous work has shown that African baobab distributions have been influenced by human agency, but people have assumed that ancient people weren’t involved in dispersal of the Australian species. The new result shows the extent that hunter-gatherers may have been intentionally dispersing useful plant species in Australia.

Link: The girl with baboon in her spine

New Scientist reports on a presentation at the Paleoanthropology Society meeting, in which Marc Meyer and Scott Williams describe one of the vertebral elements attributed to A.L. 288-1, the famous “Lucy” skeleton, as the vertebra of a gelada: “Baboon bone found in famous Lucy skeleton”.

One possible explanation was that the vertebra fragment came from a second, juvenile member of Lucy's species. So Williams and Meyer did a comparative study that included vertebrae from other Australopithecus fossils. To satisfy a personal hunch, Williams also added vertebrae from other animals known to have lived in the Hadar region 3.2 million years ago, such as porcupines and pigs. The results showed, surprisingly, that the fragment may not have belonged to Australopithecus at all.
"Baboons were a close match, both in shape and size," says Williams. "So we think we've solved this mystery. It seems that a fossil gelada baboon thoracic vertebra washed or was otherwise transported in the mix of Lucy's remains."

Mistakes in field identification of fossil remains are inevitable. It is rare for such misidentifications to persist for long under laboratory analysis, although it has happened with fossil hominins before. Most notably, the initial publications of the OH 7 type specimen of Homo habilis included a few bones amid the hominin hand remains, which were later identified as belonging to a large fossil monkey. Subtle anatomical mismatches, like a vertebra that is slightly wrong, require some detailed analysis to discover.

One thing that helps is greater access: As more and more specialists come to study fossil hominins, they bring a breadth of experience with different species and anatomical elements that no single expert can match.

Link: Selection for tall Dutch men

Carl Zimmer comments on a new paper that shows that the exceptionally tall average stature of today’s Netherlands population has been augmented by natural selection during the last fifty years: “Natural Selection May Help Account for Dutch Height Advantage”.

Among those born in the early 1950s, for example, men who were 5 feet 6 inches had on average 2.15 children. Men who were 6 feet 1 inch had 2.39 children. The scientists found that the trend toward taller men having more children persisted for more than 35 years.
Among women, the pattern was more complex. Over all, Dutch women of average height had the most children. But that was because taller women tended to take longer to become mothers. Once they entered their childbearing years, taller mothers had children at a faster rate than shorter women.

Zimmer makes a brief reference at the end of the article to a population in Massachusetts where the evidence goes in the opposite direction. This is the long-term Framingham Heart Study, in which shorter women have consistently shown larger family sizes than taller women. It does seem remarkable that different industrialized nations actually have experienced selection in opposite directions during the last fifty years.

The levels of selection are not small: the difference in lifetime fitness between tall and short Dutch men is more than 10 percent. The change per generation will be lower, because (1) women do not show the same fitness difference, (2) the heritability of stature is around 0.8 or so, and (3) it depends on the distribution of fitness across the population, not just the difference between tall and short classes. But still, 2 or 3 percent of stature per generation is strong selection. Over many generations, that kind of difference would result in a large and rapid change. Of course, without knowing the cause of selection—social dynamics? sexual selection? correlation with some other selected trait?—we can’t predict whether the selection will be maintained in the future.

Notable paper: Saladié P, Cáceres I, Huguet R, Rodríguez-Hidalgo A, Santander B, et al. (2015) Experimental Butchering of a Chimpanzee Carcass for Archaeological Purposes. PLoS ONE 10(3): e0121208. doi:10.1371/journal.pone.0121208

Synopsis: Palmira Saladié and colleagues butchered a dead chimpanzee to study the traces of cutmarks and marrow removal that might characterize cannibalism on Paleolithic human remains. They found that the resulting bone traces were similar to those found in the hominin remains from Gran Dolina, Spain—an early Middle Pleistocene site at which cannibalism has been suggested. And only a minority of the bone fragments from the butchered chimp bore the distinctive traces of human modification.

Interesting because: They butchered a chimpanzee carcass with stone tools!

But… As far as experimental archaeology goes, a single specimen is not really a sufficient sample for comparison with ancient remains. But it is a rare opportunity to treat the remains of a hominoid in this way, and I’m glad they described the results. Maybe further work with human cadavers will become possible to replicate these patterns with larger samples.

Notable paper: Kay, G. L. et al. (2015) Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat. Commun. 6:6717 doi:10.1038/ncomms7717.

Synopsis: Gemma Kay and colleagues used a metagenomic approach to investigate the tuberculosis infections of eight natural mummified bodies from seventeenth-century Hungary. They found that five of the individuals carried multiple strains of tuberculosis, and that all the strains in these bodies are of types still present in Europe today.

Interesting because: Our understanding of the past epidemiology of tuberculosis has rapidly grown, mostly due to ancient DNA techniques. Last year, research on ancient remains from Peru showed that ancient people may have obtained tuberculosis from seals, only to be replaced by Old World human tuberculosis lineages in post-Columbian times. Research on historic remains from Europe, Asia and Africa will help to understand the dynamics of tuberculosis in those populations.

My UW-Madison mathematics colleague Jordan Ellenberg has an interesting feature in Nautilus that describes a simple model capable of generating very complex behavior: “The Amazing, Autotuning Sandpile”. The dynamics of sand tumbling down when it reaches a critical point may help to inform us about the dynamics of social forces in the real world.

Real-world political phase transitions tend to happen not in neat sequences, but in sudden coordinated fits, like the Arab Spring, or the collapse of the Eastern Bloc. These reflect quiet periods punctuated by crises—like a sandpile. You can add grains of sand to the top of a sandpile for a while, to no apparent effect. Then, all at once, an avalanche sweeps sand down from the top in an irregular pattern, possibly setting off little sub-avalanches as it goes.
This analogy doesn’t necessarily get us anywhere. After all, real sand is hard to analyze, just like real politics. But here’s the miracle. A kind of abstraction of a sandheap, known as the “abelian sandpile model,” created by physicists Per Bak, Chao Tang, and Kurt Wiesenfeld in 1987, seems to capture some of the rich, chaotic features of real sandpiles, not to mention other complex systems from biology, physics, and social science—while remaining simple enough to study mathematically.

I think about sandpile models quite a lot. While Ellenberg focuses in this article upon the intricate fractal patterns that simple rules can generate, I find other issues more relevant, including the interaction of randomness with critical thresholds.

Notable paper: Heyer, E., Brandenburg, J.-T., Leonardi, M., Toupance, B., Balaresque, P., Hegay, T., Aldashev, A. and Austerlitz, F. (2015), Patrilineal populations show more male transmission of reproductive success than cognatic populations in Central Asia, which reduces their genetic diversity. American Journal of Physical Anthropology. doi:10.1002/ajpa.22739

Synopsis: Heyer and colleagues examined Y chromosome and mtDNA from several populations in Central Asia, including patrilineal populations (where inheritance is determined by the father’s line) and cognatic populations (where inheritance is determined by both parents’ lines). They found that gene genealogies indicate a substantial inheritance of reproductive success in most of the societies they examined, and in the patrilineal populations that inheritance of reproductive success especially determined a low variation of the Y chromosome relative to mtDNA and the autosomes.

Interesting because: Human populations are relatively inbred. One way that inbreeding can happen in a large population is if fitness is inherited: that is, most people tend to come from a few large families, and these tend to propagate through time. That’s exactly what Heyer and colleagues document in many of these Central Asian populations.

Sheds light upon… Recently, another study reported that Y chromosome diversity shows a bottleneck in early farmers. The press around that study concentrated upon a literal bottleneck, with a reduction in the number of males. In reality, an inheritance of reproductive success by males can explain the proliferation of a few patrilines in ancient people. That is, some measures of genetic variation can decrease even as population size is rapidly increasing, as long as some patrilines are increasing disproportionately.