Structural differences in archaeologically relevant calcite

We show that two different sources of calcite (geogenic flowstones and anthropogenic lime plaster) have complex, yet distinctive, structural disorder signatures. It is effective to identify these differences by pairing a rapid, fieldwork-compatible technique (Fourier transform infrared (FTIR) spectroscopy) with a robust laboratory-based technique (X-ray diffraction (XRD) peak width analyses). We demonstrate that crystalline domain size, microstrain fluctuations, and lattice strain each affect the FTIR spectra of calcite. To focus on each variable separately, XRD data and FTIR absorption spectra are compared among calcite samples formed by different processes. Small crystalline domain sizes cause changes to FTIR peak intensity ratios (grinding curves). However, larger microstrain fluctuations or larger lattice strain also produce similar changes. Thus, inferring structural differences from calcite FTIR spectra alone is not advisable. Instead, we advocate using FTIR grinding curves in conjunction with analyses of angle-dependent XRD peak widths using the Williamson–Hall relation. Thus, combining these two analysis techniques is more powerful and informative than using either one alone. These findings are relevant for heritage science, including archaeology

Inferring causal molecular networks: empirical assessment through a community-based effort

Inferring molecular networks is a central challenge in computational biology. However, it has remained unclear whether causal, rather than merely correlational, relationships can be effectively inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge that focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results constitute the most comprehensive assessment of causal network inference in a mammalian setting carried out to date and suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess the causal validity of inferred molecular networks

Inferring causal molecular networks: empirical assessment through a community-based effort

It remains unclear whether causal, rather than merely correlational, relationships in molecular networks can be inferred in complex biological settings. Here we describe the HPN-DREAM network inference challenge, which focused on learning causal influences in signaling networks. We used phosphoprotein data from cancer cell lines as well as in silico data from a nonlinear dynamical model. Using the phosphoprotein data, we scored more than 2,000 networks submitted by challenge participants. The networks spanned 32 biological contexts and were scored in terms of causal validity with respect to unseen interventional data. A number of approaches were effective, and incorporating known biology was generally advantageous. Additional sub-challenges considered time-course prediction and visualization. Our results suggest that learning causal relationships may be feasible in complex settings such as disease states. Furthermore, our scoring approach provides a practical way to empirically assess inferred molecular networks in a causal sense

Radiocarbon Dating of Anthropogenic Carbonates: What Is the Benchmark for Sample Selection?

Anthropogenic carbonates are pyrotechnological products composed of calcium carbonate, and include wood ash, lime plaster/mortar, and hydraulic mortar. These synthetic materials are among the first produced by humans, and greatly influenced their biological and cultural evolution. Therefore, they are an important component of the archeological record that can provide invaluable information about past lifeways. One major aspect that has been long investigated is the possibility of obtaining accurate radiocarbon dates from the pyrogenic calcium carbonate that makes up most of these materials. This is based on the fact that anthropogenic carbonates incorporate atmospheric carbon dioxide upon the carbonation of hydrated lime, and thus bear the radiocarbon signature of the atmosphere at a given point in time. Since plaster, mortar, and ash are highly heterogeneous materials comprising several carbon contaminants, and considering that calcium carbonate is prone to dissolution and recrystallization, accurate dating depends on the effectiveness of protocols aimed at removing contaminants and on the ability to correctly identify a mineral fraction that survived unaltered through time. This article reviews the formation and dissolution processes of pyrogenic calcium carbonate, and mineralogical approaches to the definition of a ‘dateable fraction’ based on its structural properties

Crystallinity assessment of anthropogenic calcites using Raman micro-spectroscopy

Abstract Anthropogenic calcite is a form of calcium carbonate produced through pyrotechnological activities, and it is the main component of materials such as lime binders and wood ash. This type of calcite is characterized by a significantly lower degree of crystallinity compared with its geogenic counterparts, as a result of different formation processes. The crystallinity of calcite can be determined using infrared spectroscopy in transmission mode, which allows decoupling particle size effect from atomic order and thus effectively distinguish anthropogenic and geogenic calcites. On the contrary, Raman micro-spectroscopy is still in the process of developing a reference framework for the assessment of crystallinity in calcite. Band broadening has been identified as one of the proxies for crystallinity in the Raman spectra of geogenic and anthropogenic calcites. Here we analyze the full width at half maximum of calcite bands in various geogenic and anthropogenic materials, backed against an independent crystallinity reference based on infrared spectroscopy. Results are then used to assess the crystallinity of anthropogenic calcite in archaeological lime binders characterized by different states of preservation, including samples affected by the formation of secondary calcite, and tested on micromorphology thin sections in which lime binders are embedded in sediments

FTIR-Based Crystallinity Assessment of Aragonite–Calcite Mixtures in Archaeological Lime Binders Altered by Diagenesis

Lime plaster and mortar are pyrotechnological materials that have been employed in constructions since prehistoric times. They may nucleate as calcite and/or aragonite under different environmental settings. In nature, aragonite and calcite form through biogenic and geogenic processes that lead to different degrees of atomic order. The latter is a result of defects in the crystal lattice, which affect the properties of crystals, including their interaction with infrared light. Using Fourier transform infrared spectrometry (FTIR) with the KBr pellet method, it is possible to exploit these differences and assess the degree of atomic order of aragonite and calcite crystals and thus their mechanisms of formation. Here we use FTIR to characterize the degree of short-range atomic order of a pyrogenic form of aragonite recently observed in experimental and archaeological lime binders. We show that pyrogenic aragonite has a unique signature that allows its identification in archaeological sediments and lime binders of unknown origin. Based on these results, we developed a new FTIR-based method to assess the integrity and degree of preservation of aragonite and calcite when they occur together in the same material. This method allowed a better assessment of the diagenetic history of an archaeological plaster and finds application in the characterization of present-day conservation materials, such as lime plaster and mortar, where different polymorphs may nucleate and undergo recrystallization processes that can alter the mechanical properties of binders

Human occupation of the semi-arid grasslands of South Africa during MIS 4: New archaeological and paleoecological evidence from Lovedale, Free State

International audienceMarine Isotope Stage (MIS) 5 and 4 are periods of major cultural innovations in the Middle Stone Age (MSA) of southern Africa. While extensive data is available for the coast, far less is known about the interior, in particular its central plateau. This is likely due to the large geographic extent of this area and a general paucity of caves and rock shelters that can provide long stratigraphic sequences and environmental records. The lack of information and systematic research has hindered our understanding of regional variation and patterns of human dispersal within the subcontinent. Our research at the open-air MSA site of Lovedale situated on the Modder River addresses this issue. Using sediment micromorphology, infrared spectroscopy of bones and sediments, phytolith and faunal analyses, as well as luminescence dating, we have reconstructed the evolution of paleoenvironments in this region at specific points over the last ~80,000 years. Our results help contextualize human occupation and hunting strategies associated with a pre-Howiesons Poort technology that occurred in a wetland environment during a short-lived warm, dry period dated to ~70 ka. These results show that humans settled the grasslands of the central interior at the onset of MIS 4 and confirm the importance of wetlands in human subsistence strategies, especially in times of climatic stress