Eos has an article about NSF funding strategies for ocean sciences: “A Transformational Path Forward for the Ocean Sciences Community”. Ocean research requires some expensive investments in infrastructure projects, including a fleet of research ships, offshore drilling projects, and research centers. The costs of maintaining this vast infrastructure have increased during the last 10 years, so that more NSF funding is going to support infrastructure than basic research grants to institutions and researchers. In broad terms, NSF is helping to maintain a fleet of research vessels but is thereby unable to fund research grants to put those ships to their best use. So a new funding strategy would reduce the infrastructure and reallocate funding into research by investigators.
The investment in ocean sciences must balance the interests of independent research with shared facilities. From the article:
The second major revelation is the recommendation to immediately reduce infrastructure expenses by 10% and implement a further 10%–20% reduction within 5 years, with the savings invested back in the core science programs. This rebalancing will eventually return the portfolio to a ratio nearing 60% science and 40% facilities.
I’m linking to this article because it made me think about how NSF has approached paleoanthropology over the last 20 years. We do not have the kind of shared infrastructure that ocean sciences require, but we do have a great need for large projects to generate shared datasets that can be used by other scientists. In my opinion, NSF should allocate its funds in ways that will create the greatest net benefit for the science. It is obvious that the science goes more slowly when funds are invested in peripheral subjects that do not generate data useful to the broader scientific community.
Independent research projects during the last 20 years have been required to outline strategies to share their data, but I have never seen any assessment of the effects of those requirements or rates of compliance by investigators. I have been browsing through funded NSF grants over the last 20 years, and have found a number referencing the creation of datasets or databases that do not presently exist in any web-accessible form. I found one large grant to build a web resource that I cannot presently find online.
Meanwhile, NSF has invested a large amount of money in a small number of graduate training programs devoted to paleoanthropology during the last 20 years, but I cannot find any assessment of the impact of those programs upon the field—such as success of underrepresented minorities in faculty positions, or representatation of the graduates of such programs in fieldwork projects. NSF funds these programs as a way of prompting institutions to change their administrative structure in a question-focused way (e.g., the interdisciplinary focus of the IGERT program), and so they bring money from outside the traditional Biological Anthropology and Archaeology funding programs. Seems like a good thing, at least on the surface. But how exactly do such programs compare to traditional graduate programs, when controlled for the funding they provide? Should we be redirecting the effort of graduate students away from mainstream questions—especially the I suspect that providing the same amount of money across paleoanthropology to support student fieldwork would have a massively greater effect on the science, and would spread funding to a much larger cross-section of early researchers.
I wanted to share a quote from the interview about Stephen Jay Gould, which is insightful about Gould’s role in evolutionary biology. The interview begins with Lewontin’s recollection of the famous paper, “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme”, which he wrote with Stephen Jay Gould in 1979. That paper evocatively presented a critique of the study of adaptation, arguing that biologists should devote more attention to nonadaptive factors such as genetic drift, structural and developmental constraint.
The paper is remembered (and assigned to students today) for its style of argument. In the interview, Lewontin reflects on how Gould approached these issues:
Now I should warn you about my prejudices. Steve and I taught evolution together for years and in a sense we struggled in class constantly because Steve, in my view, was preoccupied with the desire to be considered a very original and great evolutionary theorist. So he would exaggerate and even caricature certain features, which are true but not the way you want to present them. For example, punctuated equilibrium, one of his favorites. He would go to the blackboard and show a trait rising gradually and then becoming completely flat for a while with no change at all, and then rising quickly and then completely flat, etc. which is a kind of caricature of the fact that there is variability in the evolution of traits, sometimes faster and sometimes slower, but which he made into punctuated equilibrium literally. Then I would have to get up in class and say “Don’t take this caricature too seriously. It really looks like this…” and I would make some more gradual variable rates. Steve and I had that kind of struggle constantly. He would fasten on a particular interesting aspect of the evolutionary process and then make it into a kind of rigid, almost vacuous rule, because—now I have to say that this is my view—I have no demonstration of it—that Steve was really preoccupied by becoming a famous evolutionist.
There is a role for provocative argument in science. Without a clear statement of an idea, other scientists cannot evaluate it. Extreme descriptions can be very helpful, and often surprisingly hard to reject. When we cannot reject the extreme version of an idea, that should tell us something important about the (poor) quality of the evidence.
I also think that scientists should be advocates for their ideas. That doesn’t mean I think that we should cling to ideas that have been proven wrong. But usually it is not so easy to say that an idea is wrong: New evidence may weigh against the extreme version of a hypothesis, but a slight change to the hypothesis may save it. It is worth exploring those changes fully, especially if the hypothesis seems to be supported by other sources of data, because nature often isn’t simple. Debate helps us to draw out the consequences of models that we might not think about without such a challenge. To test an idea seriously requires exploring its implications for some time, really becoming an expert on its intricacies and the strengths and weaknesses of evidence. Good scientists will take their time to do that, and by systematizing the variations on an idea, they serve the cause of science—even if the idea turns out to be incomplete or wrong.
There’s no question that Gould was a provocateur, and many would argue that he went too far toward advocating ideas that were extreme. But in general I think that provocateurs play an important role in science, and should be recognized for it.
Still, I was never really a fan of Gould. I discovered his writing not long before I entered paleoanthropology, and I found that he was consistently wrong about human evolution. Although he mainly addressed the issue superficially in a few of his Natural History columns and book reviews, his writing had a broad influence among the public at a time when few anthropologists had such prominent venues for publishing their ideas. I don’t fault him for writing about the field in provocative terms, but I’m glad that today people have so many more places to read about human evolution, from actual experts in the field.
Regardless, these results throw up some interesting questions. Is the higher diversity of the hunter-gatherer microbiome down to the wider diets of their owners, or to a wider range of parasites? After all, Morton found that if the Cameroonians had a triple-bill of parasites, including a roundworm and a whipworm along with Entamoeba, their microbiomes were even more diverse. Diversity is generally seen as a good thing. Is it?
A naive prediction from community ecology would be that a harmful element disrupting the microbiome should restrict its diversity, not increase it. But from the view of the microbes, the parasites add nutrients to the gut system by extracting more energy from the host, creating opportunities for microbial niches that may not be there in a healthy gut. Your microbiome is not all about you, after all.
Yong also includes a nice discussion of the misconception of “ancestral” or “more ancient” as applied to microbial diversity:
Hold on, though. The Hadza and the Matses are not ancient people, and their microbes are not “ancient bacteria”, as one headline stated. They are modern people, carrying modern microbes, living in today’s world, and practicing traditional lifestyles. It would be misleading to romanticise them and to automatically assume that their microbiomes are healthier ones.
The entire post is a great warning against the oversimplification of microbiomes, diet, and health.
Notable paper: Solodenko N, Zupancich A, Cesaro SN, Marder O, Lemorini C, et al. (2015) Fat Residue and Use-Wear Found on Acheulian Biface and Scraper Associated with Butchered Elephant Remains at the Site of Revadim, Israel. PLoS ONE 10(3): e0118572. doi:10.1371/journal.pone.0118572
Synopsis: Natalya Solodenko and colleagues examined a set of stone tools from a Late Acheulean context, where the tools were found in association with elephant bones bearing cutmarks. They looked at the microscopic wear on the cutting surfaces of the tools to assess how they had been used, finding that a biface was probably used for scraping hides and a scraper was used for processing flesh or hides and also for wood. They also examined the tools using a Fourier Transform Infrared reflectance methodology, finding evidence for both bone residue (likely from bone particles in the deposit rather than use of the tools) and adipocere, a residue of ancient fat from the use of the tools on animal flesh.
Interesting because: As the authors note, there have been few previous instances where both usewear and residue analysis have been applied to tools from the Lower Paleolithic. Yet it seems a promising area:
Herrygers (2002) was able to detect wood residue on Oldowan tools from Koobi Fora, this results support the conclusion drawn from use-wear analysis carried out by Keeley and Toth (1981) [57, 68]. Another example is given by Dominguez-Rodrigo et al (2001) who identified phytoliths on several handaxes from the Acheulian site of Peninj . Hardy and Moncel (2011) identified several plant and animal residues on stone tools related to the Neanderthal Middle Palaeolithic occupation excavated at the site of Payre (France) . Only few works (e.g. [58, 60, 61, 69, 70]) included a combination of both use-wear and residues analyses.
Where is this going? We’re not so long past the days when archaeological projects routinely washed every artifact, eliminating most chances of finding small traces of organic material that might adhere to their surfaces from use. We shouldn’t get carried away with the idea of forensic examination of every flake, as this is incredibly work-intensive and would in many cases impede the recovery of other information from a site. But excavation strategies should include a clear strategy for sampling usewear and residues on artifacts. The field really needs a more coherent infrastructure for carrying out such analyses integrated with the traditional processes of excavation and lithic analysis. This would ideally include blinded study and replication across multiple labs, to regularize the interpretation of both non-destructive methods like FTIR and destructive sampling of residues and sediments.
Science word of the day:Adipocere, often known as “corpse wax”, is a chemical outcome of decay of fat into a soaplike substance.
The transition to Jekyll last year markedly improved many behind-the-scenes aspects of the weblog, and also adds a lot of flexibility to the way archived content is made available. I’ll be experimenting with some new approaches to keep some of the archived essays vital as the science continues to change. Many of these will be related to an upcoming project that will roll out over the next few months. More to come!
Smithsonian Magazine sent Joshua Hammer to tour the new facsimile recreation of Chauvet Cave, which is called Caverne du Pont d’Arc: “Finally, the Beauty of France’s Chauvet Cave Makes its Grand Public Debut”. The result is a great article describing the interior of the cave from a tourist’s point of view and the behind-the-scenes story of how a large team worked to create the facsimile:
Five hundred people—including artists and engineers, architects and special-effects designers—collaborated on the project, using 3-D computer mapping, high-resolution scans and photographs to recreate the textures and colors of the cave. “This is the biggest project of its kind in the world,” declares Pascal Terrasse, the president of the Caverne du Pont d’Arc project and a deputy to the National Assembly from Ardèche. “We made this ambitious choice... so that everybody can admire these exceptional, but forever inaccessible treasures.”
The article briefly recounts the problems that emerged after the discovery of Lascaux Cave, which prompted the creation of the facsimile Lascaux II, and led ultimately to the restriction on visits to Chauvet from the time of its discovery in 1994. More interesting, Hammer tells some of the story of the cave’s discovery, including feuds among spelunkers to be credited for different aspects of the find. Much of this drama has been publicly aired in French news magazines, but will be unfamiliar to English language readers.
I find the story discouraging yet foreign to my experience. I have worked for the last two years with an exceptional community of cavers in South Africa, who very much operate on a collaborative and team-oriented approach. So it is sad to see French cavers vying with such vitriol over these issues.
Clottes’ role in the discovery is likewise very interesting, and the article describes how bitter archaeologists and prehistorians can be about interpretation of cave art:
Clottes’ original interpretation of Paleolithic art was at once embraced and ridiculed by fellow scholars. One dismissed it as “psychedelic ravings.” Another titled his review of the Clottes-Lewis-Williams book, “Membrane and Numb Brain: A Close Look at a Recent Claim for Shamanism in Paleolithic Art.” One colleague berated him for “encouraging the use of drugs” by writing lyrically about the trancelike states of the Paleo shamans. “We were accused of all sorts of things, even of immorality,” Clottes tells me. “But altered states of consciousness are a fundamental part of us. It is a fact.”
It is an interesting aspect of the history of science that the study of prehistoric art was initiated outside of a scientific framework. Science has over the years been retrofitted into the process of investigating these finds, and has made a great deal of progress understanding not only the chronology but also the composition of groups who participated in creating them. Yet there is so much information latent in the paintings themselves that is resistant to scientific investigation. The symbolic and traditional aspects of such artistic creations only be approached from a humanistic perspective.
Cave art speaks to us across the years with a distinctively human voice. The dense symbolic and iconic information in artistic creations of the Upper Paleolithic has often caused us to miss the whispers of earlier human artifacts, which present only snippets of information about ancient social and cultural systems. But by understanding the repeated cultural circumstances that led different ancient peoples to mark their worlds in this artistic way, we may find new insights about the smaller-scale creation of objects like the Trinil incised shell, the Krapina eagle talons, or the Blombos ochre engravings.
Kristina Killgrove describes a great exercise in which she has her students prepare a whole dinner using only stone tools: “Hominin Iron Chef”.
I was there. I know who did the actual work in the labs in my fields of interest. I know the way a finding or paper or model resulted in the lab head having copious funding for a decade and a half, verging on two decades now. I know which of those scientists of my generation failed to make it big. There are a lot of them that will never achieve their promise. A lot who had to bail entirely on the career after what would have been a career-making paper as a trainee, if they were just a generation older. I can point to very few of the Gen X people in my fields of closest interest who have hit mid career with anything like the funding, verve and accomplishment of even some of the more, shall we say, pedestrian members of the generation just prior to mine. Actually, come to think of it, I am hard pressed to point to a single one.
There are two key observations:
(1) Increases in the cost of scientific research have not been matched historically by increases in NIH funding, so that fewer projects are being funded, and new principal investigators are being funded at older and older ages. Presently, the average age of a first-time grantee for the R01 mechanism is more than 42. For many years, “New Investigator” status was going to Baby Boomers who were even older than this.
(2) The training time for PhD and postdocs has radically increased, to the point where many people are spending 6+ years in graduate school and going through multiple rounds of 3-5 year postdocs.
I think he has a valuable perspective on the problems of building a scientific career. Federal grant funding may once have been well-suited to career building, but those days are mostly past. Sure there are exceptions, individual scientists who are early grant successes and can leverage early discoveries into a stable funding pattern across multiple cycles. But most working scientists will not start their careers as independent researchers in this way. Depending upon federal grant programs as a career development mechanism is not a viable strategy.
Notable paper: Cofran, Z. and DeSilva, J. 2015. A neonatal perspective on Homo erectus brain growth. Journal of Human Evolution (in press) doi:10.1016/j.jhevol.2015.02.011
Synopsis: Cofran and DeSilva consider the Mojokerto skull, an immature Homo erectus calvaria from as early as 1.8 million years ago, but possibly more recent. The size of the brain at the time of the individual’s death is very clear, around 630 cubic centimeters. But the age of the individual at the time of death is a matter of debate—some have argued that it was less than a year old, others that it was as old as 6–8 years old. A younger age at death would tend to suggest a higher rate of brain growth during the first year of life, and therefore a more humanlike developmental pattern. Cofran and DeSilva compare the rate of proportional size change in living chimpanzees, gorillas and humans, arriving at the conclusion that the Mojokerto skull must have resulted from a proportionally higher rate of brain growth than in living great apes.
Interesting because: Logically there are two ways that a species can change its developmental trajectory to result in a larger adult brain size. The species can maintain a fast rate of growth for a short time, or can extend a slower rate of growth for a long time. Humans maintain a high rate of growth of the brain during the first year of life, but a slow rate of growth of the body during an extended childhood. Cofran and DeSilva’s argument suggests that the commitment to a period of fast postnatal brain growth occurred in early Homo.
But… Cofran and DeSilva apply a model for neonatal brain size based on the sizes of adult crania of Javan Homo erectus, which average over 800 cubic centimeters. But at Dmanisi, we know that earlier crania attributed to Homo erectus have much smaller adult brain sizes, between 550 and 650 cc. The Mojokerto skull may be a one-year-old in a population of Javan Homo erectus, but its brain size is larger than many adults in the Dmanisi sample. Perhaps the developmental trajectory of these different kinds of “Homo erectus” were substantially different from each other.
Davorka Radovčić and colleagues have published a new analysis of eagle talons from the faunal assemblage excavated from the rock shelter at Krapina, Croatia (“Evidence for Neandertal Jewelry: Modified White-Tailed Eagle Claws at Krapina”). This assemblage was first recovered by Dragutin Gorjanović-Kramberger beginning in 1899 and the eagle talons were rapidly identified. But the first scientists to examine them all missed the evidence for cutmarks upon the eagle talons. And nobody thought it strange that the Krapina faunal assemblage includes eight of them:
Eagle talons are rare at other Neandertal localities and no sites have yielded eight talons from white-tailed eagles or any other raptor. Since three-four different eagles are represented, they must have been acquired in separate events and were preserved as a unit before they were lost in the sediments. Others have noted [6–7, 27, 41–43] that raptor bones found in late Pleistocene sites signal some kind of symbolic activity. At Krapina, cut marks on the pedal phalanx and talons are not related to feather removal or subsistence, so these must be the result of severing tendons for talon acquisition. Further evidence for combining these in jewelry is edge smoothing of the cut marks, the small polished facets, medial/lateral sheen and nicks on some specimens. All are a likely manifestation of the separating the bones from the foot and the attachment of the talons to a string or sinew. Cut marks on many aspects, but not the plantar surfaces, illustrate the numerous approaches the Neandertals had for severing the bones and mounting them into a piece of jewelry.
Radovčić and colleagues observe that some of the cutmarks have evidence of smoothing, and there are polished facets on the talons that suggest they had been tied together and worn against a surface, as would naturally occur if they were part of a necklace or bracelet. The Krapina archaeological layers date to around the time of the last interglacial, as early as 130,000 years ago. The antiquity of the talons removes any possibility that the behavior was a consequence of stimulus diffusion or direct copying from modern humans.
The University of Kansas has done a nice interview with David Frayer, one of the authors of the study, explaining the significance and context of the cutmarks:
Again, more discoveries to be made in museum collections by looking carefully for evidence that earlier (and often overworked) analysts may have missed…
Radovčić D, Sršen AO, Radovčić J, Frayer DW (2015) Evidence for Neandertal Jewelry: Modified White-Tailed Eagle Claws at Krapina. PLoS ONE 10(3): e0119802. doi:10.1371/journal.pone.0119802
A new paper in Molecular Biology and Evolution provides an interesting new example of recent adaptation in a human population. Carina Schlebusch and colleagues examined the genetics of a group living in the Andes of northern Argentina, with a high load of arsenic in their environment. They surveyed more than 4 million single nucleotide polymorphisms (SNPs) across the genome and found that SNPs around the gene AS3MT explain a good deal of the variance in arsenic metabolites in urine. What’s more, these SNPs are highly differentiated between the arsenic-exposed population and other nearby peoples who do not have the same environmental exposure to arsenic.
Since AS3MT stands for “arsenic [+3 oxidation state] methyltransferase”, that seems like a clue that something is going on with arsenic metabolism in this population. And indeed, it seems that these people tend to have greater excretion of a dimethylated arsenic, which has lower toxicity. As the study makes clear, this is not a total resistance to arsenic poisoning, it merely reduces the impact of arsenic.
This is a neat study because it combines functional data on arsenic metabolism within the target population and the analysis of genetic differences between this population and nearby relatives. That combination of function and population genetic measures is rare in the study of recent natural selection. This is a somewhat similar approach to the study of adaptation to high altitude hypoxia in Tibetan populations.
In both this case of arsenic adaptation and the Tibetan high altitude adaptation, the key selected variants do not show up as significant in genome-wide scans for recent selection. Both are consistent with selection upon standing genetic variation, at least in the broad sense. The Tibetan altitude case includes one allele that has come from a Denisovan-like population, so it clearly was in the population for tens of thousands of years, but the time when it became important to a high-altitude population is not yet known. The SNPs of AS3MT that are associated with arsenic metabolism in this case are present in worldwide populations in a similar haplotype background, so this seems to be the enrichment in one population of a functional allele that occurs in many populations around the world. The study suggests that the key functional variants in this case are likely regulatory, because the highest SNP association scores occur upstream of the AS3MT coding region itself.
Interestingly, it doesn’t take much selection to yield the observed frequency of this inferred variant:
We estimated the selection coefficient to range between 0.003 and 0.005, which is smaller than the estimated selection coefficients associated with lactase persistence (Tishkoff et al. 2007), and resistance to malaria (Chen and Slatkin 2013), two previously well-established examples of strong positive selection leading to adaptation in humans.
This may indicate that the pattern of methylation of arsenic caused by the protective allele doesn’t have much of a protective effect. Even a slight effect might have an advantage in survival or reproduction, but the correlation between reproduction and this allele need not be very high. Three tenths of a percent per generation is pretty small.
Schlebusch, C. et al. 2015. Human Adaptation to Arsenic-Rich Environments. Molecular Biology and Evolution (in press) doi:10.1093/molbev/msv046
The two recombination-based methods presented agreed that μ≈1.65×10−8. However, many pedigree and trio based studies seem to converge on μ=1.2×10−8. Most people seemed to think that the pedigree studies are undercalling mutations, but there was no clear explanation or evidence for that. On the other hand, calibration using ancient DNA from the directly dated Ust’-Ishim sample presented by Qiaomei Fu suggested a lower rate of around ν=0.4×10−9, consistent with the pedigree estimates. This leaves us with something like a 25% discrepancy which needs to be explained.
This is a topic of long-term interest here (“What is the human mutation rate?”). I don’t have time to write up any extensive thoughts about the mutation rate now (or to fix the references in the older posts) but it’s interesting to see people talking seriously about a mutation rate slowdown in the African apes.
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.
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.