A modified sampler for uncontaminated DNA cores from soft sediments

A piston-type mud sampler is described. It is a development of the Livingstone corer and was designed to extract cores for DNA analysis of sediments. Prevention of contamination was paramount. As the entire system is self-contained and the sample is retained in the corer, it was found ideal for extracting very soft sediments which could not be captured by existing corers.     

Disturbing geography: obsessive‐compulsive disorder as spatial practice

This paper explores the spatial practices of obsessive‐compulsive disorder (OCD). It begins by introducing the key elements of the disorder: obsessions and compulsions. It then concentrates on obsessions and compulsions relating to fears of bodily contamination. Such fears necessitate the formation of psycho‐social boundaries in ways that are similar to agoraphobia and other mental‐health problems. Avoiding bodily contamination also involves complex spatial orderings to prevent the illicit movement of contaminants. The vital importance, yet fragile nature, of these spatial formations means that negotiating social space and interactions can be immensely fearful, and the OCD sufferer may retreat to the relative safety of home. However, the domestic is a space of ambivalent safety. Everyday objects become saturated with fear, transforming the experience of ‘home’. Boundaries and spatial orderings are transgressed in the movement of people and objects. Thus, the OCD sufferer is driven to (re)order space constantly, and in doing so often uses everyday materials in inventive ways. We critique the depiction of OCD as irrational and excessive, and set the creative practices of OCD in relation to the ‘slippage’ of Michel de Certeau's distinction between spatial strategies of domination and the art of tactical living.     

A geography of residents' worry about the disruptive effects of contaminated sites

While the links between contaminated sites and adverse effects on human health and well‐being are being increasingly recognised, some argue that the magnitude of the health problem is inadequately addressed because it is largely invisible. Health geographies literature has sought to highlight this invisibility by focusing on the link between contaminated sites and health. This study adds to health geographies by presenting unique insights into the geography of residents' worry about the disruptive effect of environmental contamination on health and well‐being. It analyses a sample of residents (n = 485) living near 13 contaminated sites across Australia. Ordinal logistic regression analysis of closed‐format survey questions was combined with coding of open‐ended survey questions to reveal the geography of residents' worry about contamination from nearby sites. First, the study explores some of the main relationships between residents, their environs, and contaminants from nearby source sites, which determines their levels of worry: residents' demographics, residents' proximity to sites, contaminant boundaries and borders, and type of contaminant. Second, the study investigates how worry affects residents' health and well‐being, ranging from effects on their personal functioning through to their sense of ontological security, which depends in part upon their perceptions of contaminants' impacts. Despite having identified a range of diverse and negative effects of worry about contamination on residents, we found that worry for contamination can also prompt coping strategies and problem‐solving, reinforcing the need for more research on this subject.     

RADIOCARBON DATING OF KILL SITES

Age determinations of kill sites, where charcoal is generally absent, has usually depended on radiocarbon analyses of bone material. However, it has been seen with known-age samples that these dates are often in error due to contamination by plant products or ground water carbonates. The use of soil samples from strata both above and below, as well as the level containing the artifacts, offers important advantages. The soil profiles present sequences of dates, whereas the bones are only individual samples. The distribution of the soil date values can indicate upper and lower limits for the age of the kill site. The Taima-taima paleo-indian site in the state of Falcón, Venezuela is presented as an illustration of the application of radiocarbon dating of soil to archaeological problems. A total of 22 samples were processed. It is seen that soils from two profiles indicate a dating of 13 000 years for the kill. Taking into account reasonable extents of error, uncertainties of ± 2000 years can be estimated. The non-carbonate fraction dates are in agreement with the earth samples, but this is probably due to the organic matter extracted from these materials being mostly soil contamination in the porous bone matrix. Fluorine measurements on the bones confirm the Pleistocene origin.     

EXPERIMENTAL EVALUATION OF SAMPLE‐EXTRACTION METHODS AND THE POTENTIAL FOR CONTAMINATION IN CERAMIC SPECIMENS*

Contamination of ceramic specimens resulting from sample‐preparation techniques has the ability to confound efforts of chemical characterization. Primary contamination, identified by significant concentrations of one or more elements, is easily identified. Secondary contamination, resulting from undetected elements influencing detected elements, is more difficult to identify. Evaluation of six powder‐extraction techniques identifies variable effects of contamination. Extraction by drilling carries the highest risk of contamination. The grinding of specimens with silicon‐carbide wheels may artificially deplete abundances by introducing Si and C. Grinding specimens in an agate mortar and pestle is found to be the technique least likely to result in contamination effects.     

Toxic torts as compensation: Legal geographies of environmental contamination litigation

Residents living in close proximity to contaminated sites may experience adverse effects from financial losses and property devaluation, leading to poor mental health and physical illnesses—effects that may require compensation. The most common legal process of seeking compensation is the toxic tort—litigation pressed on the basis that contamination has harmed the victims. Several recent toxic tort class actions in Australia brought by residents living in areas affected by contamination from per- and poly-fluoroalkyl substances (PFAS) exemplify that process. Two such actions, those at Williamtown and Richmond, provide an opportunity to explore how toxic torts currently function as a means to secure compensation, whether they mitigate the harms of the contamination and considering how spatio-legal manoeuvres may shape the litigation. In this article, we use a legal geography approach to analyse how plaintiffs’ bodies, litigants’ properties, and the state are constructed and represented by parties involved in these toxic torts. Legal geographers contend that examining the spatio-legal manoeuvres made via litigation can make visible the effects of legal action on those involved and draw out how the law and its instruments may shape places and communities. Toxic tort class actions have allowed those affected by the contamination to be heard and receive some compensation. However, we argue that they do little to alleviate plaintiffs’ concerns about the effects of contamination on their health, properties, and the environment. The findings have significance given that torts will likely play an increasingly prominent role in dealing with such challenges.     

‘Not All That Is White Is Lime’—White Substances from Archaeological Burial Contexts: Analyses and Interpretations

Archaeological burial contexts may include a variety of white substances, but few analyses have been published. This study reports on the physico‐chemical characterization of such residues from seven archaeological sites. It is often assumed that white materials from burial contexts are lime. Our findings demonstrate that they can be gypsum, calcite (chalk), aragonite, brushite, degraded metal, natural (gum) resins or synthetic polymer–based products. These may be present as the result of diagenetic processes, funerary practices or modern contamination. This paper provides an analytical approach for the holistic investigation of white materials encountered in burial contexts.     

LEAD POLLUTION OF THE ENVIRONMENT FROM AUTOMOTIVE EXHAUST GASES

The impact of lead contamination of soils and plants along highways of Novgorod Oblast (between Moscow and Leningrad) is investigated. Lead content in roadside soils and crops is compared with control plots situated at a greater distance from highways. Lead content in soils up to 100 meters from roadways is found to be up to 15 times higher than in control plots; lead content in roadside crops, up to 10 meters from roadways, is found to be up to six times higher than in control plots. It is recommended that dwellings and garden plots be moved back from highways beyond the harmful zone. In the case of Novgorod Oblast such a protective roadside zone should be 100 meters wide.     

Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera,Italy

The majority of ancient DNA studies on human specimens have utilised teeth and bone as a source of genetic material. In this study the levels of endogenous contamination (i.e. present within the sample prior to sampling for the DNA analysis) are assessed within human bone and teeth specimens sampled from the cemetery of Santa Lucia alle Malve, Matera, Italy. This site is of exceptional interest, because the samples have been assayed for 18 measures of biochemical and physical preservation, and it is the only one identified in a study of more than 107 animal and 154 human bones from 43 sites across Europe, where a significant number of human bones was well preserved. The findings demonstrate several important issues: (a) although teeth are more resilient to contamination than bone, both are readily contaminated (presumably through handling or washing), and (b) once contaminated in this way, both are difficult (if not impossible) to decontaminate. Furthermore, although assessed on bone samples, several of the specific biochemical and physical characteristics that describe overall sample preservation, levels of microbial attack and related increases in sample porosity directly correlate with the presence of observable contamination in both bone and teeth samples from individual samples. While we can only speculate on the cause of this relationship, we posit that they provide useful guides for the assessment of whether samples are likely to be contaminated or not.     

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Accurate identification of the biological sex of ancient remains is vital for critically testing hypotheses about social structure in prehistoric societies. However, morphological methods are imprecise for juvenile individuals and fragmentary remains, and molecular methods that rely on particular sex-specific marker loci such as the amelogenin gene suffer from allelic dropout and sensitivity to modern contamination. Analyzing shotgun sequencing data from 14 present-day humans of known biological sex and 16 ancient individuals from a time span of 100 to ∼70,000 years ago, we show that even relatively sparse shotgun sequencing (about 100,000 human sequences) can be used to reliably identify chromosomal sex simply by considering the ratio of sequences aligning to the X and Y chromosomes, and highlight two examples where the genetic assignments indicate morphological misassignment. Furthermore, we show that accurate sex identification of highly degraded remains can be performed in the presence of substantial amounts of present-day contamination by utilizing the signature of cytosine deamination, a characteristic feature of ancient DNA.     

An assessment of the effect of gravity waves on the width of radar Doppler spectra

Radars can be used to obtain turbulence parameters by measuring the width of the Doppler spectrum of returned power. Other effects can contribute to the Doppler-spectrum width, including short-period gravity waves, making turbulence parameter measurements more difficult. In this paper, an experimental study of the effect of gravity waves on the width of the Doppler spectrum is presented. The data were obtained using the Poker Flat 50 MHz VHP radar. A parameter Y_i is used to describe the discrepancy between the width of spectra sampled over a long period of time and that taken over a shorter time. If Y_i is not significantly different from 1.0, no contamination is present. The experimental data considered were of a time resolution that allowed the period and amplitude of the contaminating gravity wave to be determined. A theoretical expression for gravity wave contamination proposed by Hocking [(1988) J. geophys. Res.93, 2475–2491] was tested and found to agree with measurements. It was also found that non-unity values of Y_i occurred in some cases. This suggests that, at commonly used sampling times, short-period gravity waves can contaminate spectral width estimates.     

A SAMPLING STYLUS FOR USE WITH THE ELECTRON PROBE

A simple device is described which enables inconspicuous samples of entire objects to be taken for electron microprobe analysis without introducing background contamination. Transport of artefacts and their exposure to vacuum are thereby obviated.     

Alterations of Na,K and Rb concentrations in Mycenaean pottery and a proposed explanation using X‐ray diffraction

One of the most important reference groups for Mycenaean pottery is the Mycenae/Berbati (MB). In several studies, a second group has been identified (MBKR). The chemical compositions were similar to MB, but with important differences in the Na, K and Rb contents. The present study suggests that these differences are due to selective alteration and contamination processes that are indirectly determined by the original firing temperature. Therefore, groups MB and MBKR should be considered as a single reference group.     

AMALGAM TINNING OF CHINESE BRONZE ANTIQUITIES*

This paper investigates the question whether or not amalgam tinning was used for the plating of bronze objects in pre‐Han and Han dynasty China. The relevant literary sources are reviewed and amalgam tinning is characterized experimentally with regard to its micro‐structure and residual mercury content using metallography and electron microprobe analysis. Examination of a tinning sample from a Warring States dagger previously assumed to be amalgam tinned demonstrates that this was probably not the case, but that a trace of mercury found in the plating is likely to be the result of contamination.     

Evaluating effects of chemical weathering and surface contamination on the in situ provenance analysis of building stones in the Cuzco region of Peru with portable XRF

As the only type of instrument capable of determining artifact geochemistry in a wide variety of settings, portable X-Ray Fluorescence (PXRF) may be frequently utilized as probably the best option for collecting data when removal of objects in part or in whole is unfeasible. However, using PXRF in circumstances where sample selection and preparation diverge from standards developed for lab-based instrumentation requires assessing the impact of new and potentially limiting factors to establish the validity of the method in these new contexts. Here we examine the effects of surface contamination and chemical weathering on the ability to assess provenance of igneous building stones used in the Cuzco region of Peru. Surface contamination was assessed through comparing low-impact cleaning methods on diorite and andesite blocks, and weathering was examined by comparing weathered vs. fresh surfaces of samples from two andesite quarries. In general, the lightest elements were most impacted by contamination and weathering while measurements of many of the heavier elements commonly used in provenance studies were relatively unaffected. Concentrations of Pb and Zn were problematic in the urban context of Cuzco because of pollution. Ability to determine provenance of building stones within those limitations (i.e., the validity of this application of PXRF) was demonstrated in a preliminary study by comparing measurements from uncleaned, exposed building stones in the region to fresh quarry samples.     

Paper 3: Impact of the Indoor Climate on the Performance of Building Materials Contaminated with Salt Mixtures

Abstract

Archaeological sites are essentially submitted to decay phenomena inherent on their history as well as the environment to which they are exposed after excavation. The history of such archaeological sites is particularly related to their long-term underground conservation conditions during which they were subject to salt migration into the architectural remains.

It is well known that soluble salts present in building materials can cause damage, mainly by producing stresses in the substrate. A lot of research has been done in the past concerning the behaviour of salts in built constructions. However, most studies include single salts, of which the deliquescence points are well documented, while in situ one mostly finds complex salt mixtures, which makes the conservation strategy much more intricate.

The environmental conditions to minimize damage of salt-laden porous building materials can be modelled using a computer program ECOS capable of predicting the crystallization behaviour of salt mixtures. To use the model data of quantitative salt analyses are required as input. The program is then able to predict from a thermodynamic point of view which minerals will exist in the solid state under specified climatic conditions.

This paper deals with the results of a systematic investigation of the salt contamination of the building materials of the Coudenberg site and a prediction of the behaviour of the salt mixture related to the actual climate, as part of the environmental assessment.     

Contamination controls when preparing archaeological remains for ancient DNA analysis

Contamination is of utmost concern when working with ancient DNA as it easily leads to false positive results. The best way to prevent or minimize contamination is to start precautionary measures as early as possible, ideally commencing with sample collection and preparation by field archaeologists. This paper discusses the nature of contamination in ancient DNA studies and offers some practical guidelines as to how archaeologists in the field can “clean-collect” samples for ancient DNA analysis. Methods for preparing contaminated samples from museum collections for ancient DNA analysis are also discussed.     

Dating European Palaeolithic Cave Art: Progress,Prospects, Problems

Over the last decade several dozen direct dates on cave art pigments or associated materials have supplemented more traditional style-based attempts to establish a chronological (and developmental) scheme for cave art. In the “post-stylistic” era an holistic integration of pigment “recipe” analysis, formal stylistic analysis and direct chronometric dating have been applied to a handful of dates. Here, we examine the state-of-the-art of Palaeolithic cave art dating, with particular emphasis on certain radiocarbon and Uranium-series projects. We examine the relative successes and weaknesses of this cutting edge science. We conclude that there are several weaknesses in current applications that are in serious need of addressing. Issues of sample contamination and of the heuristic relationship between materials dated and the production of the art are particularly problematic. It follows that one should at present be very cautious about straightforward interpretations of apparent “dates” of cave art.     

Clues to Stone Tool Function Re-examined: Comparing Starch Grain Frequencies on Used and Unused Obsidian Artefacts

The identification of plant residues observed on prehistoric stone artefacts has often been used to inform on tool function without adequate consideration of potential contamination due to post-depositional processes. The paper redresses this balance by proposing a methodology which combines use-wear and residue analyses with systematic testing of depositional context to distinguish residues formed during tool use from accidental contamination. A case study involving obsidian artefacts from an open site in Papua New Guinea is used to illustrate the new approach. Starch grains, a class of residue which has had little attention outside Australia, were chosen as the focus of study because of their abundance at this site. The frequency of starch grains extracted from residues on stone artefacts was compared with those in sediments adhering to and adjacent to the artefact. A use-wear study conducted as a blind test provided an independent measure of whether the artefacts had been used. The frequency of starch grains was shown to be significantly correlated with used artefacts and not correlated with unused artefacts or the sediments. The case study demonstrates the importance of testing for contamination and also illustrates the benefit of studying starch grains as a class of plant residue.