As many readers know, I recently offered a massive open online course (MOOC), titled "Human Evolution: Past and Future". The course included video interviews with more than 25 scientists in paleoanthropology and related fields, because I wanted people to see the field through the perspective of the experts who know it best.
I'm going to be releasing many of these interviews here on the blog. To start the series, I'm posting my interview with Lee Berger.
This interview covers Lee's discoveries at Malapa, South Africa, including the species Australopithecus sediba. He also talks about the importance of an open approach to his team's research, and the importance of field exploration in bringing new evidence to paleoanthropology.
This interview was filmed last summer, long before the Rising Star site was discovered. It's fascinating to watch it today, a reminder that chance favors the prepared mind.
These interviews are great resources for classes, and please feel free to share them widely.
Every semester for the past three years, I have begun my Anthropology 105 course with a "concept inventory" quiz, otherwise known as a pretest. My students are coming in from a broad range of backgrounds, especially with variation in how long ago they had high school biology and what level of biology they attained in previous work. The pretest gives me valuable information about how prepared they are for the course. Because the pretest includes several topics that we will cover in biological anthropology, as opposed to stock high school biology, it gives the students an early appreciation of how the subject matter of my course may differ from their previous training. And comparison with a post-test after the course gives a direct assessment of what they learn during the semester.
Now, Benedict Carey in the New York Times reports on research that shows pretesting before a course begins can improve learning throughout the course: "Why flunking exams is actually a good thing".
This is the idea behind pretesting, one of the most exciting developments in learning-science. Across a variety of experiments, psychologists have found that, in some circumstances, wrong answers on a pretest aren’t merely useless guesses. Rather, the attempts themselves change how we think about and store the information contained in the questions. On some kinds of tests, particularly multiple-choice, we benefit from answering incorrectly by, in effect, priming our brain for what’s coming later.
That is: The (bombed) pretest drives home the information in a way that studying as usual does not. We fail, but we fail forward.
The bottom line is that pretesting can help to frame subsequent learning activities for students, so that they are more aware of they don't know. The pretest also makes them more attentive to how the topics of the course can fit together to solve problems.
I have consistently been surprised by the pretesting I have done in my course. The students really invest energy into their answers, even though in my course they will receive full credit for any attempt, even simply writing "I don't know". They do want to show off their knowledge.
Meanwhile, the results have shown me that many students come in with the stock misconceptions of evolutionary theory that are well known in the education literature. We do our best in the course to remove misconceptions.
The Gauteng Tourism Authority has a nice article about the opening of the protective structure over the paleoanthropological site of Malapa: "Malapa Structure Launch at the Cradle of Humankind".
The structure is a curved dome which is raised off the ground on eight legs giving it the nickname of “the beetle”. Each leg makes contact with the ground by four thin pins, giving it the minimal contact interface with the very sensitive caste system immediately below it. None of the legs is independently load bearing, meaning that any one of them may be removed and repositioned if such action is necessitated by subsequent palaeoanthropological excavations revealing that there is scientifically significant fossil material in close proximity to any one of the legs.
The roof of the dome appears to float above the the structure. It has an organic profile in plan based on the shape of the leaf of the White Stinkwood (Celtis africanus), the dominant tree at the site. The water from the roof is drained off into two excellently concealed tanks, which will supply adequate water for toilets, sanitation and sewage. There is also provision made for sourcing of additional water should it be required on the site.
What is most impressive about the structure is how completely it blends into its surroundings. A mere 200 meters away, it is barely visible. Those "beetle" legs are angled very much like the branches and trunks of the trees. Here's one of my photos:
I've been out to the site many times and it is always a strikingly impressive trip. The Malapa Nature Reserve is a private reserve stocked with local endemic species and subspecies of antelopes, like blue wildebeest. The area is truly beautiful and reachable only with a four-wheel-drive vehicle, so this structure is part of a larger effort to develop a unique tourism capacity there.
Once upon a time, the U.S. had a President who could write articles about human evolution: Theodore Roosevelt!
In 1916, the former president wrote a long illustrated book review of Men of the Old Stone Age, by Henry Fairfield Osborn. Osborn was long-time curator of vertebrate paleontology at the American Museum of Natural History, and his book was the first major American volume devoted to human evolution.
National Geographic commissioned the review from Roosevelt, running it accompanied by illustrations from the book. The review itself is more or less a reprise of the book's major themes, with few flashes of the characteristic Roosevelt "Bully!" personality. But can you imagine any recent president writing this?
Lord Avebury's "Prehistoric Times" was written when it was still necessary to argue with those who disbelieved in the antiquity of man, their reasons being substantially similar to those of the other conservatives who a couple of centuries earlier treated as impious the statement that the earth went round the sun.
The current issue of Scientific American is specially devoted to human evolution. There are great articles by Kate Wong, Ian Tattersall, Frans de Waal, Bernard Wood, and me.
My article, "Still evolving (after all these years)", covers the evidence for recent natural selection in humans during the last 30,000 years. Only a teaser is available online for free, but the magazine is well worthwhile this month.
I'd like to draw some attention to Kate Wong's introduction to the issue, "The new science of human origins". Wong ably describes some of the groundbreaking changes that have swept the world of paleoanthropology during the last ten years, from ancient DNA to, well, the Rising Star Expedition:
Through the Post Box, up the Dragon's Back, down the Chute and over to the Puzzle Box. Last fall the world followed, via tweets, blogs and videos, as scientists negotiated these fancifully named landmarks of the underground system of caves known as Rising Star just outside Johannesburg, South Africa. The tight squeezes and steep drops made for difficult, dangerous work. The researchers, however, had their eyes on the prize: fossilized remains of an extinct member of the human family. Paleoanthropological fieldwork is usually done in secret, but this time the scientists posted thrilling multimedia missives along the way for all to see.
It is a fitting beginning. The excavation at Rising Star shows that many major discoveries are still waiting to be made. The science of the next ten years will increasingly draw upon public participation, and technology makes it possible for us to share the science much faster and more broadly than ever before.
What is evolution?
In its original sense, evolution meant "unrolling", as if a papyrus scroll were being unrolled to reveal its contents. We may talk about the "evolution" of many things, from an individual's lifetime to the evolution of the universe. In the most general sense, evolution means "change".
Biologists are very specific about the kinds of processes that qualify as "evolution" in the biological sense. Biological evolution is genetic change in a population over time. Populations and individuals change in many ways, but only some changes are evolution.
Here's a list of seven things about evolution. It's not comprehensive but it hits on several important issues that help to understand how evolutionary biologists think about the process of evolutionary change.
Evolution is change in a population. Individuals change during their lifetimes, even day to day. Those changes are not biological evolution, although they may be products of evolution in past populations. Likewise, a forest may change over time, as some kinds of trees proliferate and others disappear. Those changes in community structure are not themselves biological evolution, although they may influence the evolution of the populations of trees composing the forest.
Evolution is genetic change. Many kinds of phenotypic changes don't involve evolution. For example, many human populations have markedly increased in lifespan during the last 100 years, mostly as a result of improvements in nutrition and reductions in disease. Those changes are important and highly visible, but they are not biological evolution. Physical characteristics and behaviors can only evolve if they have some genetic contribution to their variation in the population -- that is, if they are heritable.
Many kinds of genetic changes are important to evolution. Mutations happen when a DNA sequence is not replicated perfectly. A sequence may undergo a mutation to a single nucleotide, small sequences of nucleotides can be inserted or deleted, large parts of chromosomes can be duplicated or transposed into other chromosomes. Some plant populations have undergone duplications or triplications of their entire genomes. These patterns of genetic change can have a wide range of effects on the physical form and behavior of organisms, or may have no effects at all. But all of them follow the same mathematical principles as they change in frequency within populations.
Evolution can be non-random. Populations of organisms cannot grow in numbers indefinitely, so that individuals that successfully reproduce will have their genes increase in proportion over time. Among the genes carried by such successful individuals may be some that actually cause them to survive or reproduce, because they fit the environment better. The survival and proliferation of such genes is not a matter of chance; it is a result of their value in the environment. This process is called natural selection, and it is the reason why populations come to have forms and behaviors that are well-suited to their environments.
Evolution can be random, too. Many genetic changes are invisible and make no difference to the organisms. Many changes that do make a noticeable difference to the organisms' form or behavior nevertheless still do not change the chance of reproducing. Even individuals with the best genes still have a strong random component to their reproduction, and in sexual organisms genes assort randomly into sperm and egg cells. As a result, even when an individual has a beneficial gene that increases the chance of reproducing, that valuable gene still is very likely to disappear quickly after it first appears in the population. Genetic drift is strongest when populations are small or genes rare, but it is there all the time. Random chance has a continual role in evolutionary change.
Populations evolve all the time. No population can stay static for long. Reproduction is not uniform, and no organism replicates DNA perfectly. The genome of the simplest bacterium has thousands of nucleotides, ours has billions. Keeping these sequences constant, generation after generation, is a task no population has ever managed to do. Genetic variation is constantly introduced into populations by mutation and immigration, rare genetic variations are constantly disappearing when individuals who carry them don't pass them on, and occasionally rare genes become common -- whether by natural selection or genetic drift. If a population's physical form remains the same for a long time, we have a good reason to suspect that natural selection is working to oppose random changes.
Evolutionary theory has changed a lot since Darwin's day. Charles Darwin recognized several key insights about biological evolution, including the process of natural selection, the tree-like pattern of relationships among species, and the potential for significant changes when processes act through small, incremental steps across geological timescales. But we know a lot more now than Darwin knew. We understand the molecular basis of genetic changes, and many of the ways that the features of organisms can be affected by genetic and environmental change. We have learned much about the limits of evolution, the alternative patterns of change caused by environments, and the importance of randomness. We now know much about the changing pace of evolution, seeing it as a dynamic process that can happen in fits and starts.
Evolution is the most powerful idea in biology, organizing our knowledge about the history and diversity of life. We understand our own origins using the same tools that we use for organisms across the tree of life, from the simplest bacteria to the largest whales.
(this is a repost, originally posted 2014-01-21)
Notable paper: Wilkins J, Schoville BJ, Brown KS (2014) An Experimental Investigation of the Functional Hypothesis and Evolutionary Advantage of Stone-Tipped Spears. PLoS ONE 9(8): e104514. doi:10.1371/journal.pone.0104514
Synopsis: Jayne Wilkins and colleagues made a series of stone-tipped and non-stone-tipped pointed spears and shot them into ballistics gel with a calibrated crossbow. The resulting tracks document the increased wound tracks created by sharp stone points.
Important because: Archaeologists have long suggested that the bloodletting power of a hafted spear would make it a deadlier weapon, yet experimental results have been mixed because pointed sticks have deeper penetration. Wilkins and colleagues are able to show that the hafted spears create a larger wound even though they don't penetrate as far into the flesh.
Waiting for... Ancient humans using Middle Paleolithic-era hunting strategies would sometimes have found themselves in a prolonged and deadly fight with a prey animal. To understand the dynamics of lethal technology, we must go beyond the initial strike to consider the entire encounter. Another aspect of hafted points is that their sharp sides can cause further damage when a prey animal struggles or attempts to run. Or a struggle may break the point within the wound, leaving a shard to damage the prey further but rendering the spear much less useful for repeated strikes. In other words, it's not obvious how the damage at impact may relate to the overall effectiveness of a spear in Middle Paleolithic hunting strategies.
Human hunter-gatherers, despite living in small groups of 20-50 individuals, make social contacts with up to a thousand other individuals in across their lifetimes. That's the conclusion of Kim Hill and colleagues, who incorporated long-term field observations from two hunter-gatherer populations (the Hadza of Tanzania and the Ache of Paraguay) to understand the extent of social contacts that adult males develop in the course of their lives.
This may seem obvious -- after all, people talk to each other and readily tolerate the presence of hundreds of other people around them. But small human groups don't give opportunities to chat with hundreds of people very often. Members of a small-scale band may only see people outside their immediate circle of 20-50 people every few months.
Chimpanzees and bonobos have similar community sizes, ranging up to 50 individuals or so. But chimpanzee groups are famously antagonistic, with many intergroup encounters resulting in violent aggression. Humans do have aggression between groups, even in small-scale societies, but not indiscriminately.
On balance, then, the greater interaction rate of human foragers should lead to more lifetime contacts. Hill and colleagues use their data to quantify the effect of this over an individual's lifetime:
Among the Ache and Hadza, frequent visiting and long lifespans mean that adults typically interact with more than three hundred same-sex adults during their lifetimes. This implies a social universe of about a thousand individuals, when opposite-sex adults and children are included. Recent work on the San Bushmen also suggests a similarly high number of significant interactants . Additionally, close companions often interact with a somewhat different set of individuals, so that the total number of indirect interactants that each individual hears about repeatedly in detailed stories, and could expect to possibly meet some time during their lifetime is clearly more than 1,000. This is a much higher number of individually known social interactants than reported for any other primate, and possibly more than any other species on earth. It is also much greater than the predicted 150 significant social interactants (known as "Dunbar's number") that was extrapolated from primate brain by social group size regressions , . It should not surprise us that humans have more relationships than their brain size alone predicts, as humans alone use language and symbolic devices to store information about potential relationships. The main reason why humans interact with so many more individuals than other apes is because: 1) human lifespans are much longer, and 2) interaction between neighboring and distant residential social units is extensive.
It is notable that the authors approached this work by replicating the results in two very different groups. The replication adds strength to the conclusion about the extent of interaction in human societies compared to other primates.
This is a conceptually simple but very important piece of evidence about the value of human sociality. Our connections with other people give us the opportunity to learn things our intimate group members may not already know. Innovations can spread among groups, even some that are very difficult to produce, because the individuals within a group will have multiple contacts with those outside their own group. High-value inventions in this context will spread disproportionately faster.
The "lifetime interaction probability" is one quantitative focus of the paper:
The relationship between yearly probability of interaction and expected proportion of the population that will interact in a lifetime asymptotes quickly, and even low rates of interpersonal interaction among hunter-gatherers lead to lifetime interactions with most other adults (Figure 4). This is because the human adult lifespan is so much longer than that of chimpanzees. The average expected time that both members of an Ache or Hadza dyad who enter adulthood together will both still be alive is about 27 years while the average expected time that two male chimpanzees from the same community, entering adulthood together, are still both alive is only 6 years.
Lifetime interactions are not necessarily relevant to the issue of innovations spreading, at least not directly. The lifetime interaction probability between adults may be central to the maintenance of reputation. Reputation is one of the most effective controls on social behavior in small-scale human societies. Gossip has real bite, but even moreso when the hearers can be assumed to have interacted with the subject of the gossip at some point in their lives.
Hill KR, Wood BM, Baggio J, Hurtado AM, Boyd RT (2014) Hunter-Gatherer Inter-Band Interaction Rates: Implications for Cumulative Culture. PLoS ONE 9(7): e102806. doi:10.1371/journal.pone.0102806
Carl Zimmer connects Bigfoot with an explanation of the history of "null hypothesis" in a Nautilus essay: "Why we can't rule out Bigfoot". He discusses a recent paper by Bryan Sykes' lab, which systematically tested purported Yeti and Bigfoot samples.
Some skeptics have offered up an alternative explanation for Sykes’ finding. It’s possible that the polar bear-like DNA actually comes from a living mammal—perhaps a brown bear—that happened to pick up a few mutations that created a false resemblance to that ancient polar bear DNA.
What these skeptics have done, in effect, is create a null hypothesis. And there’s a straightforward way to set about disproving it. Scientists would need to find more DNA from these mysterious bears. If other regions of the DNA also matched ancient polar bears, then scientists could reject the null hypothesis.
I think this would be a good essay for undergraduate courses introducing science. Zimmer gives a good account of how R. A. Fisher conceived of frequentist statistical testing and the role of the null hypothesis in it.
Applied to Bigfoot, I think we should be very skeptical about the choice of a null hypothesis. That's in part why I think it would be a good essay for a class discussion. I don't think that Sykes approached his study with the null hypothesis that the samples would all represent other mammals. I think he tested the hypothesis that each sample could represent an unknown primate, and refuted it in each case by showing some other animal (from raccoons to bears) is a close genetic match to the sample.
Notable paper: Blasco, R., Finlayson, C., Rosell, J., Marco, A.S., Finlayson, S., Finlayson, G., Negro, J.J., Pacheco, F. G., Vidal, J. R. (2014) The earliest pigeon fanciers. Scientific Reports 4:5971. doi:10.1038/srep05971
Synopsis: Ruth Blasco and colleagues studied 1724 rock dove bones from Gorham's Cave, finding evidence for human processing, cooking and/or consumption of the birds in 11 out of 19 Neandertal contexts, through at least 40,000 years of Neandertal occupations.
Important because: The work documents that hunting and eating these medium-sized birds was a recurrent part of Neandertal (and later modern human) diets. Once it was common to see "small mammal and bird hunting" in lists of behavioral traits limited to modern humans. Now we know that Neandertals regularly took large birds for feathers and medium to large birds for food. This isn't a single occurrence, it is a sampling of the behavior of people over tens of thousands of years.
Plus, who knew? Rock doves are the wild progenitor species of common pigeons, and they are indistinguishable from fragmentary bone remains.
Jonathan Weiner wrote a well-known book about the long-term field studies of Galapagos finches by Peter and Rosemary Grant, titled The Beak of the Finch: A Story of Evolution in Our Time (Vintage). On the publication of their new book about their continued work, Weiner has written an essay of appreciation in the New York Times: "In Darwin’s Footsteps".
They kept up their watch during years of downpours and years of drought — seasons of feast and famine for the finches. And Darwin’s process unfolded before their eyes in intense episodes that illustrated better than anything in the Origin the struggle for existence, and the ways that life adapts and emerges fitter from the struggle.
Weiner describes the most interesting discovery, the establishment of a new population that behaves like an incipient species, from a single founder.
The Grants' book is titled, 40 Years of Evolution: Darwin's Finches on Daphne Major Island.
A photo from outside the Neandertal Museum, in Mettmann, Germany:
The full-size sculpture was originally in a local biergarten, dating to the 1910's, where it entertained patrons for many years.
Notable paper: Coqueugniot H, Dutour O, Arensburg B, Duday H, Vandermeersch B, Tillier, A-M. (2014) Earliest Cranio-Encephalic Trauma from the Levantine Middle Palaeolithic: 3D Reappraisal of the Qafzeh 11 Skull, Consequences of Pediatric Brain Damage on Individual Life Condition and Social Care. PLoS ONE 9(7): e102822. doi:10.1371/journal.pone.0102822
Synopsis: Hélène Coqueugniot and colleagues look closely at a cranial wound on an early modern human skull from Israel, Qafzeh 11. They show that the injury had profound effects on the right frontal lobe of the brain, and argue that the individual suffered a delay in brain development and psychological or developmental disabilities as a result.
Important because: Qafzeh 11 was deliberately buried with red deer antlers apparently placed over the body. The individual seems to represent a child who was a victim of some horrific trauma, who had severe developmental issues, who was nonetheless integrated into a social group and treated with special care when she or he died. It is a window into the social behavior of Middle Paleolithic people.
But... Despite the fact that it's an undeniably severe injury, we may not be able to infer that much about the life of this individual. His or her brain was small for age, but well within the range of developmentally normal adults today.
Experimental psychology has recently become embroiled in a controversy about whether replication of high-profile findings should be a serious goal of new research. Bioethicist Michelle Meyer and psychologist Christopher Chabris have a weighty essay in Slate about the problem: "Why Psychologists’ Food Fight Matters".
They focus on the complaints that some experimenters have raised, that they feel "persecuted" or "bullied" by other scientists who are attempting to replicate their findings. In some cases, young researchers worry that their job prospects or tenure cases may suffer as other scientists unjustifiably discredit their earlier work, without being given an opportunity to respond in print in a timely way.
My first reaction to this was, "Oh, really? Well, that's science." But there are some real cases of boorish behavior. For example,
Once the journal accepted the paper, Donnellan reported, in a much-tweeted blog post, that his team had failed to replicate Schnall’s results. Although the vast majority of the post consisted of sober academic analysis, he titled it “Go Big or Go Home”—a reference to the need for bigger sample sizes to reduce the chances of accidentally finding positive results—and at one point characterized their study as an “epic fail” to replicate the original findings.
Now, I think that reflects worse on the replicator than on the original researcher. But it's easy to see how it puts a responsible scientist into an impossible position. What we need is a less confrontational attitude toward replication, one that sees replicability as a hallmark of good science and accepts replication studies into journals without needing a "crisis of replication" to make them newsworthy.
Some have legitimate complaints about "failures to replicate" that do not correctly implement the experimental protocol, or change some key aspect that leads to a different outcome. Meyer and Chabris do a good job of presenting the nuances of such concerns, which basically revolve around competence. Are researchers capable of describing what they've done accurately, so that the results can be replicated? Or does every result depend on some "special skill" that the original lab has developed, that somehow cannot be described?
We should remember the cases in experimental psychology where the "special skill" involved falsifying results.
I agree with most of Meyer and Chabris' suggestions, particularly the concept that replication should not depend upon the original researchers' cooperation.
Replicators have no obligation to routinely involve original authors because those authors are not the owners of their methods or results. By publishing their results, original authors state that they have sufficient confidence in them that they should be included in the scientific record. That record belongs to everyone. Anyone should be free to run any experiment, regardless of who ran it first, and to publish the results, whatever they are.
In sciences with unique specimens, cell cultures, or other materials, this principle means that the original materials must be available for examination or use by qualified researchers. Where substantial investment or assistance has been provided by the original researchers to enable replication, obviously they should be included as authors. Many journals now provide a standard format for reporting contributions to a paper, and "provided reagents or samples" is one of the standard entries. There are cases where the contribution does not rise to the level of authorship, but at least such assistance should be acknowledged.
Paleoanthropologists often ignore the fundamental principle of replicability. But providing the full ability to replicate paleoanthropological work really is not very hard. Just make sure that qualified researchers can access the specimens. Many of the observations that paleonthropologists depend upon are simple measurements that could be replicated easily on 3-d models. Heck, in many cases nowadays the original measurements may have been taken on 3-d models.
That means there should never be any question of access to the same models for replication.
Personally, I wonder whether we should make grant funding contingent on first replicating some prior finding. Yes, that would take time that researchers might otherwise devote to new work. But to do effective research most experimentalists already need a pipeline capable of replicating earlier work in the same area of research. And they need to convince a grant panel that they are already prepared to carry out such work. Replication studies are a good way to accomplish both goals, and might sometimes actually lead to rejection of overhyped bad ideas.
Besides, we know that most grant applications that are funded actually describe work that already exists in pilot form. They may as well be doing something for the good of the science. Instead of rehashing their own old results, they could rehash other people's!
Many futurists and not a few science fiction writers hold the idea that computer technology is developing toward a point where artificial intelligence will begin to develop new technology instead of people. At that near-future time, they argue, the progress of technology will no longer be predictable. It is a "singularity", beyond which no laws of technological progress can apply.
This idea has been around for many years and has its merits. I just wanted to point to a comment by the physicist Sabine Hossenfelder, who suggests that word doesn't mean what they think it means: "What is a singularity?".
What one typically means with a singularity is a point where a function behaves badly, so that one or several of its derivatives diverge, that is they go to infinity. The ubiquitous example in school math is the poles of inverse powers of x, which diverge with x to zero.
However, such poles are not malign, you can remove them easily enough by multiplying the function with the respective positive power. Of course this gives you a different function, but this function still carries much of the information of the original function, notably all the coefficients in a series expansion. This procedure of removing poles (or creating poles) is very important in complex analysis where it is necessary to obtain the “residuals” of a function.
Hossenfelder points out that von Neumann first introduced the analogy in reference to technology.