Alice Dreger discusses her new book, Galileo’s Middle Finger: Heretics, Activists, and the Search for Justice in Science in The Scientist: “Stirring the Pot”.
Three important insights I’ve gained from studying what has happened to scientists whose research has ticked off activists working within social justice movements: (1) If you want to get in trouble, study sex. (2) Anybody who tells you “all publicity is good publicity” has never been accused of genocide. (3) Death threats are rarely grammatically correct. I illustrate each of these lessons in my new book, Galileo’s Middle Finger: Heretics, Activists, and the Search for Justice in Science.
Among other recent cases of “hereticism”, the book discusses her reporting on Napoleon Chagnon and James Neel.
I am back in Johannesburg this week and next, working with the fossil collection at the University of the Witwatersrand.
Meanwhile, “The Long-Term Evolution Experiment (LTEE) turns 27”. Directed by Richard Lenski at Michigan State University, the LTEE maintains multiple colonies of E. coli in a constant, stable environment. Begun to answer questions about the rate of adaptation over time, the experiment has generated important new insights about the limits and patterns of evolution. In some experiments, frozen samples of past generations have been used to “rewind the tape” of evolution, ultimately showing the role of chance in adaptation as new mutations occur differently. It’s a great example of the importance of long-term support, since this relatively simple research effort has gained more and more importance over the years.
Lenski has lots of stuff worth exploring on his blog. One recent post, “Science Communication: Where Does the Problem Lie?” asks a painful question and attracts some interesting comments.
Notable paper: Smith TM, Tafforeau P, Le Cabec A, Bonnin A, Houssaye A, et al. (2015) Dental Ontogeny in Pliocene and Early Pleistocene Hominins. PLoS ONE 10(2): e0118118. doi:10.1371/journal.pone.0118118
Synopsis: Tanya Smith and colleagues report on the largest-ever study based on synchotron scanning of juvenile teeth from early hominin species. They examined 25 specimens that represent Australopithecus anamensis (from Kanapoi, Kenya), Au. africanus (from Sterkfontein and Makapansgat, South Africa), Paranthropus robustus (from Swarkrans and Drimolen, South Africa), and early Homo (species unidentified, from Drimolen, South Africa). They examined the growth increments of the teeth, showing that these early hominin samples have a substantial variation in the periodicity and formation time of their molar crowns.
Interesting because: We would like to know more about the growth and development of fossil hominins. The formation of enamel in teeth happens at a characteristic rate, leaving growth increments that can be examined microscopically. The synchotron scans allow this enamel formation to be studied non-destructively. Up to now, conclusions about the growth rate of early hominin teeth have been based on very small samples. Looking at the larger sample has yielded a broader picture of variation, while supporting differences among species (like the apparently faster development of P. robustus teeth.
More: The teeth in this study all come from juvenile specimens, and yield a more precise estimate of age at time of death for them. Some of them were surprisingly older than originally thought, some younger. Again, the better data yield a picture of variability. It’s great that the authors put this into the open access PLoS ONE so that it can be widely read, because it’s a good empirical paper.
I’ll be appearing in La Crosse on Thursday evening to lecture at UW-La Crosse. The topic will be the origin of modern humans, with the event sponsored by the Mississippi Valley Archaeology Center.
Booting Up Humanity
The origin of our species was surprisingly complex. We have within us the genes of ancient Africans, Neandertals, and a mysterious population known as the Denisovans. Only a relative handful of genetic changes mark humans today as different from these ancient people. So how did the characteristics of modern humans, including complex social systems, symbolic thought, and language, evolve? New discoveries point in a surprising direction: Modern humans used a diversity of genes in a common social environment to bootstrap themselves to humanity. With the origin of modern human behavior, cultural evolution began to direct our genetic evolution, with rapid and unprecedented results.
I know I have some readers in that area, so here are the details, courtesy of the UW-L Campus News:
- Who: John Hawks, professor of Anthropology, UW-Madison
- What: Presentation on human evolution, genetics
- Where: Valhalla, Cartwright Center-Gunning Addition
- When: 7 p.m. Thursday, Feb. 19
- Admission: Free
UPDATE (2015-02-23): The evening lecture was a wonderful success, with a huge crowd in attendance. I had a great time visiting with colleagues at the Mississippi Valley Archaeology Center and hearing about the great work they’ve been doing during the last couple of years. The archaeology program at La Crosse is such a valuable resource to the community and the state. Meanwhile, I got to tell around a hundred undergraduate students about the excavation at the Rising Star site, always a fun talk for me.
It happens that I have a book chapter in press that examines Neandertals as a humanistic perspective. This seems to fit the zeitgeist.
A couple of news articles this week look at the emerging humanist perspective on Neandertals. From the New Yorker by Elizabeth Kolbert, “Our Neanderthals, ourselves”. Kolbert reflects on a series of recent papers, concluding:
It had been comforting to think that the Neanderthals were inferior to modern humans—less clever or dexterous or communicative—and that that’s why they’re no longer around. It turns out, though, that the depiction of Neanderthals as hairy, club-wielding brutes—popular ever since the first Neanderthal bones were discovered, in the eighteen-fifties—says more about us than it does about them. With each new discovery, the distance between them and us seems to narrow. Probably they are no longer here precisely because we are. And that only makes the likeness more disquieting.
Does she mean that all those anthropologists who have made up stories about Neandertals were really being self-centered?
From the Boston Globe by Ruth Graham: “Our lost cousins, the Neanderthals”. This story quotes Steven Churchill and Paola Villa, but exerts most of its attention on Pat Shipman’s upcoming book, The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction. Shipman argues that the domestication of dogs converted modern human groups into a deadly horde.
Framing humans as “invasive predators” in longtime Neanderthal territories, she describes how harnessing canines’ speed, their ability to track by scent, and propensity to surround and harass prey would put humans at a huge competitive advantage. “That would be the kiss of death,” she said. “A wolf-dog and a human in that ecosystem with those weapons and those prey species would have been just about unstoppable.”
My first reaction: this is a bit like the most recent Hobbit movies, where the warg-riding orcs are deadly and fearsome out of all proportion to Tolkien’s book. Wolf-dog-empowered humans might indeed have been fearsome, but the idea strikes me as yet one more in a long list of single-factor explanations for the Neandertal endgame. So my initial reaction is one of skepticism. Still, I will be interested to read Shipman’s take on this idea.
I’d like to take note of this post by Sabine Hossenfelder, “Open peer review and its discontents”. She reflects on a growing cultural divide in science between those who see science as an open conversation and those who see it as a curated hierarchy.
[Science journalist Philipp] Hummel wrote by email he found my blogpost very useful and that he had also contacted the author asking for a comment on my criticism. The author’s reply can be found in Hummel’s article. It says that he hadn’t read my blogpost, wouldn’t read it, and wouldn’t comment on it either because he doesn’t consider this proper ‘scientific means’ to argue with colleagues. The proper way for me to talk to him, he let the journalist know, is to either contact him or publish a reply on the arxiv. Hummel then asked me what I think about this.
To begin with I find this depressing. Here’s a young researcher who explicitly refuses to address criticism on his work, and moreover thinks this is proper scientific behavior. I could understand that he doesn’t want to talk to me, evil aggressive blogger that I am, but that he refuses to explain his research to a third party isn’t only bad science communication, it’s actively damaging the image of science.
I get concerned when I hear of early career scientists behaving this way. Obviously I’m not a physicist but the same dynamic can occur in biological anthropology. Some scientists are markedly open and see the public discussion of their ideas as helpful, others react defensively.
I can handle senior scientists having this reaction. I have heard from a number of them that open discussion of their research, sharing of data and public engagement is “not the proper way to conduct science”. That’s OK, these old fogies will be gone before too long. What worries me is that they may be replaced by like-minded mid-career people who have long been waiting for “their turn” to reap the benefits of status.
I’m not talking about revealing ideas before they are fully developed. Every scientific idea undergoes a birth process. The birth canal, to strain an analogy, is tortuous and the idea must deform and shift as it passes through. The idea shouldn’t be reviewed until a researcher reaches a stage where review will be productive and helpful. So much research today is developed by teams of researchers, and engineering a collaborative paper requires trust between people who may not have worked together before. This trust can only build in a confidential environment where frank discussion of ideas is possible.
Many scientists now publish pre-prints at the time they are ready to receive such commentary. Others submit papers for confidential pre-publication review and discuss them only after they are published. But in either case, once a scientist is ready to present ideas, he would be a fool not to listen to critique and commentary in every form available.
Returning to Hossenfelder’s post, the issue of open review has two sides. A researcher should be willing to hear commentary on her work, adjusting it where appropriate. But outside experts should be equally willing to offer frank commentary. As it stands, few ideas are subject to robust review:
[M]ost of my colleagues in theoretical physics entirely ignore papers that they think are wrong. They are convinced that in the end only truth will prevail and thus practice live-and-let-live. I used to do this too. But look at the evidence: it doesn’t work. The arxiv now is full with paid research so thin a sneeze could wipe it out. We seem to have forgotten that criticism is an integral part of science, it is essential for progress, and for cohesion. Physics leaves me wanting more every year. It is over-specialized into incredibly narrow niches, getting worse by the day.
We get more of what we reward, and less of what we punish. As science stands today, there is no reward for good review of work, either pre-publication or post-publication. The scientists who carry out review for journals, on blogs, preprint servers, or elsewhere, are performing a charitable service. It is foolish to expect more and better review, whether open or not. So authors should be eager to take what they can get.
Louis Leakey, writing in Nature in 1966 as part of a defense of the Homo habilis definition:
Even though H. erectus and the australopithecines share a number of cranial characters in their occipital bones, and in having a maximum width at the base of the skull, I have never been able to accept the view that Australopithecus represented a distinct ancestral stage leading to H. erectus, and I disagree even more strongly with the present suggestion of placing H. habilis between them. It places a hominid type which has a wholly distinct cranial morphology and one recalling the H. sapiens type between these two. It is possible that H. habilis may prove to be the direct ancestor of H. sapiens, but this can be no more than a theory at present. If true, it would mean that there had been two distinct species of the genus Homo at a very early stage—one leading to H. erectus and subsequent extinction and the other to H. sapiens.
John Robinson had in 1965 published an attack on H. habilis, claiming that the remains could not be distinguished from Australopithecus on the one hand, and that the H. habilis remains provided a possible intermediate toward H. erectus on the other hand. In his view, the situation was best handled by recognizing the gradual transformation of Australopithecus into Homo erectus, and not by erecting a new species between them. Phillip Tobias had responded to Robinson’s attack, but did not disagree with Robinson’s central point that H. habilis was a logical intermediate between Australopithecus africanus and Homo erectus.
Leakey demurred from this point of view, and chose to write his own response to Robinson, in which he pointedly marked his disagreement with Tobias. Leakey could not see H. habilis as an intermediate between Australopithecus and H. erectus. His main argument was that the cranial form of H. habilis shared some derived features with Homo sapiens, whereas H. erectus was much more like Australopithecus in these same respects.
Leakey today is often associated with the concept of a very deep phylogenetic split between humans and the australopithecines. This short article is a very nice illustration of the morphological evidence that drove him toward that hypothesis.
California Sunday Magazine has a feature profiling farmers losing their water to nut growers in California’s San Joaquin Valley: “Dry”. It’s a story of wells going deeper and deeper in search of a shrinking aquifer, and the change from small landowner-run operations to huge orchards owned by overseas investors. I thought this paragraph was worth sharing:
The math is simple: Each acre of nuts produces 3,000 pounds of crop. Each pound sells for more than $3. It takes only 100 acres to make a million-dollar harvest every year. So farmers have pulled out cotton and stone fruit and grapes to plant nuts. They’ve bought hog wallows and coached up the ground to plant nuts. They’ve gone into the hillsides, mostly because drip irrigation lines can take them there, to plant nuts. It’s as if middle California has undergone a change of civilizations.
That kind of major change in land use, and the resulting social and ecological shifts, is exactly what archaeologists look for when they examine the changes between ancient civilizations.
A new study of more than 50,000 people has identified some of the genetic variations that underlie cognitive variation among middle-aged and older adults (Davies et al. 2015). This cohort was developed by combining several different large cohort studies to look for the factors that underlie cognitive decline and heart disease.
To date, behavior genetic research—using twin, adoption and family designs—shows that general cognitive ability is substantially heritable across the life course, from late childhood to old age. The heritability of general cognitive functioning in old age might decrease slightly from its levels in young and middle adulthood. Candidate gene studies have found that variation in APOE genotype is the only reliable individual genetic associate of cognitive function in older age, but that might apply especially to cognitive change rather than cognitive level in old age. Using the genome-wide complex trait analysis procedure (GCTA), genome-wide association studies (GWAS) found that ~51% (the s.e. was large, at 11%) of the variation in general fluid cognitive function in late middle age and older age could be accounted for by genetic variation that is tagged by single-nucleotide polymorphisms (SNPs) on the Illumina610-Quadv1 chip. That study was conducted in a total discovery sample of 3511 individuals, with replication in 670 independent individuals. It found no genome-wide significant single SNP associations. From other GWAS studies of complex traits, we now know that this sample size is likely to be too small, by an order of magnitude, to detect genome-wide significant SNPs.
Twin studies have shown that on the order of half the variance in cognitive performance is additive. Until the last couple of years, no one had any real success discovering which genes might explain this additive variance. Many other complex traits were similar stories: From stature to schizophrenia, these traits are affected by many genes, with no single common allele having a very large effect on the phenotype. A sample of a thousand individuals may sound large, but is actually very small for this kind of investigation, capable of demonstrating large effects of common alleles, but not small effects or effects of rare alleles. By looking at 50,000 people, this cohort study made it possible to test smaller effect sizes on common alleles. Several genes stuck out as having significant effects in this large sample, and across the whole genome the genotypes explain 29% of the phenotypic variance in the study’s measures of cognitive function. That’s a very high proportion of the additive variance, although the genes that explain the variance in this particular sample may not replicate in other populations.
I mentioned last month the move in Congress toward funding research into personalized medicine (“Link: Personalized medicine going to Congress”). That effort is centered around the development of a super large cohort, with genotyping or sequencing of a million individuals, including many who are parts of existing cohort studies with phenotype data. Massive cohorts may or may not help to find effective treatments for complex disorders. But with good phenotype data, massive cohorts will certainly help to uncover the small-effect genes that underlie normal human variation.
Davies, G. and lots of others. (2015). Genetic contributions to variation in general cognitive function: a meta-analysis of genome-wide association studies in the CHARGE consortium (N=53 949). Molecular Psychiatry (online) doi:10.1038/mp.2014.188
Carl Zimmer reported this week in the New York Times on research into the natural history of bedbugs in Europe: “In Bedbugs, Scientists See a Model of Evolution”. Zimmer describes a new paper by Warren Booth and colleagues that examined European bedbugs, focusing on the differences between the bedbugs that infest human hosts and those that infest bats living across the same region, often sharing human structures like attics and eaves. Both the bat-infesting and human-infesting bedbug populations are classified within the same species (Cimex lenticularis) but their evolution has taken them in different directions. The case is interesting from the point of view of evolutionary theory because the differentiation may have taken place across a single geographic region—it is a case of sympatric speciation in action, where the mode of isolation is adaptation to different host populations.
The bat-infesting bedbugs exhibit greater genetic diversity than the ones that infest humans. Greater genetic diversity can result from an older origin for the bat-infesting population, or greater gene flow across the population’s range (so that founder events are less important to dispersal). Or a low genetic diversity in the human-infesting population may reflect the long history of humans attempting to eradicate the pests, with today’s local populations having been recolonized at long distance from a small number of source populations.
Most of the human-associated bedbug populations are highly inbred, which reflects their dispersal pattern in which homes may be initially colonized by a single male-female pair or egg-laying female. This contrasts with the pattern in the bat-associated populations. From Booth and colleagues’ paper:
The genetically depauperate nature of the human-associated populations may also provide insight into the stability of bed bug populations. Population establishment, high population turnover, and extinction events are expected to be common with little opportunity for population admixture, likely due to human-mediated movement and frequent interventions through pest control. Thus, human-associated bed bugs appear to live in highly structured metapopulations. In contrast, C. lectularius populations within bat roosts may be expected to be more stable, albeit with temporal fluctuations due to weather events, bug mortality and host dispersal, with multiple introduction events resulting from the latter.
We still have a lot to learn about the origins of the bedbugs that are obligate parasites of humans. The great extent of divergence does tend to suggest that bedbugs started their association with ancient humans sometime long before people began living in sedentary villages. However, such great divergence between the human and bat-infesting forms in Europe might not be reflected in other parts of the world. Broader comparisons would tell us more about the early phase of host-parasite association.
My intuition is that Pleistocene humans did not inhabit any caves with the kind of regularity that would allow a stable human-infesting bedbug population. Adult bedbugs can go for several weeks without a blood meal, but young bedbugs need to feed at least every few days, which I would have thought requires a human occupation more intense than most caves show. My intuition could be wrong, and some caves in the Near East do show evidence of substantial amounts of plant material carried in for bedding over some period of time—just the kind of place where bedbugs might have sheltered. And perhaps we should consider whether the transition to humans might have been facilitated by reliance on other animal hosts, like hibernating cave bears.
Booth, William, Ondřej Balvín, Edward L. Vargo, Jitka Vilímová and Coby Schal. (2015) Host Association Drives Genetic Divergence in the Bed Bug, Cimex lectularius. Molecular Ecology (in press) doi:10.1111/mec.13086
Louis Leakey, in a letter to Wilfrid Le Gros Clark (cited in Morrell, V., Ancestral Passions, p. 209), just after his and Mary’s discoveries of Zinjanthropus, Homo habilis, and Olduvai Homo erectus fossils in 1959 and 1960:
You may be wondering, as others have done, why we are finding so much hominid material now.... The answer is simple. We have been working continuously now since February with adequate funds and a huge labour staff, and have already put in some 72,000 man hours this year. Had we been able to do this sort of thing before, we would have had the results before.
Carl Zimmer has a nice post today discussing the evolution of endogenous retroviruses in primates: “Our Inner Viruses: Forty Million Years In the Making”. Fragments of viruses make up more than five percent of our genome. Most of them are legacies of ancient primate evolution, but a few have been active during the last few million years. Zimmer describes a new study by Gkikas Magiorkinis and colleagues that estimates the times of activity of the major ERV types:
In the Old World monkeys–represented in the new study by baboons and macaques–the rate of new virus copies pretty much stayed the same over the past 30 million years. But the apes tell a different story. The rate dropped in every ape branch. The same shift occurred in parallel in the ancestors of humans, chimpanzees, gorillas, orangutans, and gibbons.
Zimmer discusses some reasons that may explain this slowdown, including larger body size and reduced transmission between individuals, but with no clear answers.
BBC Earth is running a story by Colin Barras looking at the origins of music in ancient humans and possible perceptual preadaptation to music in other primates, with the awkward headline: “Did early humans, or even animals, invent music?” The piece is really a linkfest that includes a sentence or two on a broad range of recent studies, from Atapuerca hyoid bones to Upper Paleolithic flutes and monkey rhythm:
Why would the monkeys have this ability when they don’t seem to use it in the wild? “I don’t have an easy answer for that,” says Ravignani. He is now studying the musical talents of other primates, beginning by giving captive chimps access to a custom-built electronic drum machine. “I want to investigate to what extent their natural drumming resembles ours, and see what kind of musical patterns chimpanzees can imitate.”
This line of research has been active for a long time. I wrote about it in 2006: “Monkey music mixmasters”
So maybe studying these reactions in monkeys is question-begging. The real question is what about the human mind makes music compelling or attractive for people? We can say that whatever that is, these primates either don't have it or differ from humans sufficiently to make them not react the same way as humans to human music. But then, humans react quite differently to different brands of human music, in a way that is clearly culturally influenced if not completely culturally determined (and the balance between these alternatives is indeterminate).
Music has emerged in every human culture in one way or another, with musical instruments, rhythms, and tone sequences independently invented again and again. We do have a musical urge, as a species.
Those different musical traditions reflect an evolutionary heritage. Maybe that musical ability is a fortuitous side effect of other traits (such as language). Some anthropologists argue that music would have been an advantage to ancient humans by helping cement social relationships, or by serving as a mode of competition for mates. But like other kinds of cultural sophistication, what we make of music today can be far more elaborate than the forms that may have existed in our distant ancestors. That makes it very difficult to test hypotheses about musical origins.
Notable paper: Zaman L, Meyer JR, Devangam S, Bryson DM, Lenski RE, et al. (2014) Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability. PLoS Biol 12(12): e1002023. doi:10.1371/journal.pbio.1002023
Synopsis: Zaman and colleagues use a digital model of the evolutionary process to assess the way that parasites may affect the evolution of complexity in their hosts. The presence of a parasitic form within a host population tended to select for a more complex instruction set in the hosts, full of old and emerging resistance strategies. The two forms together drove an increase in complexity relative to a single population on its own.
Interesting because: The initial evolution of complexity among simple organisms may reflect just such a scenario, in which the accumulation of complexity in some emerging species depends on parasitism from below. A more complex instruction set will include many more “features” that can change in the presence of new conditions, in other words increasing “evolvability”. At the same time, complexity is one cost of competition with different forms.
Unexpected connections: One of the most interesting parts of the paper involved removing the parasite from the population, after which the host complexity began to decrease. It’s similar to classic selection experiments, in which the selection condition is removed or reversed partway through.
Aeon has a long article by Jill Neumark, titled “The retraction war”, which asks: “Is science broken?” The article goes through several ways of counting scientific retractions, and notes that a major problem is that many scientists continue to cite retracted papers without noting that they have been retracted.
Retraction matters so much to so many because the scientific enterprise is key to our survival, and so that enterprise must be sound.
Honesty and openness both make the scientific process work more smoothly, enabling more independent people to examine and understand results and their importance. This helps to direct resources and interest to questions and methods that lead to new discoveries and knowledge.
Still, science is hard to break. Its method is resilient because it doesn’t depend on trust, it depends on replication. Neumark’s article also covers how replication studies have a lack of perceived value. A culture of non-replication is much more dangerous to science than retractions.