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02 Mar 2024
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A note on predator-prey dynamics in radiocarbon datasets

A new approach to Predator-prey dynamics

Recommended by ORCID_LOGO based on reviews by Jesús Rodríguez, Miriam Belmaker and 1 anonymous reviewer

Various biological systems have been subjected to mathematical modelling to enhance our understanding of the intricate interactions among different species. Among these models, the predator-prey model holds a significant position. Its relevance stems not only from its application in biology, where it largely governs the coexistence of diverse species in open ecosystems, but also from its utility in other domains. 

Predator-prey dynamics have long been a focal point in population ecology, yet access to real-world data is confined to relatively brief periods, typically less than a century. Studying predator-prey dynamics over extended periods presents challenges due to the limited availability of population data spanning more than a century. The most extensive dataset is the hare-lynx records from the Hudson Bay Company, documenting a century of fur trade [1]. However, other records are considerably shorter, usually spanning decades [2,3]. This constraint hampers our capacity to investigate predator-prey interactions over centennial or millennial scales. 

Marom and Wolkowski [4] propose here that leveraging regional radiocarbon databases offers a solution to this challenge, enabling the reconstruction of predator-prey population dynamics over extensive timeframes. To substantiate this proposition, they draw upon examples from Pleistocene Beringia and the Holocene Judean Desert. This approach is highly relevant and might provide insight into ecological processes occurring at a time scale beyond the limits of current ecological datasets. 

The methodological approach employed in this article proposes that the summed probability distribution (SPD) of predator radiocarbon dates, which reflects changes in population size, will demonstrate either more or less variation than anticipated from random sampling in a homogeneous distribution spanning the same timeframe. A deviation from randomness would imply a covariation between predator and prey populations. This basic hypothesis makes no assumptions about the frequency, mechanism, or cause of predator-prey interactions, as it is assumed that such aspects cannot be adequately tested with the available data. If validated, this hypothesis would offer initial support for the idea that long-term regional radiocarbon data contain signals of predator-prey interactions. This approach could justify the construction of larger datasets to facilitate a more comprehensive exploration of these signal structures.

 

References

[1] Elton, C. and Nicholson, M., 1942. The Ten-Year Cycle in Numbers of the Lynx in Canada. J. Anim. Ecol. 11, 215–244.

[2] Gilg, O., Sittler, B. and Hanski, I., 2009. Climate change and cyclic predator-prey population dynamics in the high Arctic. Glob. Chang. Biol. 15, 2634–2652. https://doi.org/10.1111/j.1365-2486.2009.01927.x

[3] Vucetich, J.A., Hebblewhite, M., Smith, D.W. and Peterson, R.O., 2011. Predicting prey population dynamics from kill rate, predation rate and predator-prey ratios in three wolf-ungulate systems. J. Anim. Ecol. 80, 1236–1245. https://doi.org/10.1111/j.1365-2656.2011.01855.x

[4] Marom, N. and Wolkowski, U. (2024). A note on predator-prey dynamics in radiocarbon datasets, BioRxiv, 566733, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.1101/2023.11.12.566733

A note on predator-prey dynamics in radiocarbon datasetsNimrod Marom, Uri Wolkowski<p>Predator-prey interactions have been a central theme in population ecology for the past century, but real-world data sets only exist for recent, relatively short (&lt;100 years) time spans. This limits our ability to study centennial/millennial...Bioarchaeology, Environmental archaeology, Palaeontology, Paleoenvironment, ZooarchaeologyRuth Blasco2023-12-12 14:37:22 View
19 Jun 2020
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Platforms of Palaeolithic knappers reveal complex linguistic abilities

The means of complexity in a lithic reduction sequence

Recommended by ORCID_LOGO based on reviews by Antony Borel and 1 anonymous reviewer

The paper entitled “Platforms of Palaeolithic knappers reveal complex linguistic abilities” [1] submitted by C. Gaucherel and C. Noûs represents an interesting reflection about the possibilities to detect the human cognitive abilities in relation to the lithic production.

The definition and the study of human cognitive abilities during the Lower Palaeolithic it has always been a complex field of investigation. The relation between the technical skills (lithic production) and the emergence of the linguistic abilities is not easy to investigate due to the difficulty of finding objective data to refer to. The proposition, made by C. Gaucherel and C. Noûs, of a formal grammar of knapping as a method to study the syntactical organisation of the reduction sequences, constitute a new and theoretical useful approach.

In order to effectively and precisely define the gestures linked to a specific reduction sequence, for example that of the handaxes shaping, a very large number of variables should be taken into consideration (morphology and quality of the raw material, experience of the knapper, context, percussion technique, forecast of use of the handaxe, etc.). But since a simplification, that brings more elements than the classic one [2,3] is needed, the “action grammar approach” can be a good instrument to detect the common element in a shaping reduction sequence. Furthermore, one of the advantages of the proposed methodology lies in the fact that the definition of the different STs (Stone Technology) can be done according to the technological specific characteristics to be studied and to the type of instrument produced.

The deconstruction of knapping sequences could help to detect the degree of complexity of the different steps of the reduction sequences also thanks to the identification of the sub-actions types. The increasing/decreasing of complexity is a very complicate concept in lithic technology. Since at the base of the lithic production there are two basic concepts (angle between the striking platform and the debitage surface - convexity of the debitage/façonnage surface) which are simply declined in an increasingly complex way, it is not easy to define uniquely in what exactly consists the increase in complexity. The approach proposed in the paper “Platforms of Palaeolithic knappers reveal complex linguistic abilities” can help to have new evidences, according to the identification of the required cognitive abilities.

The proposed example of formal grammar still needs to be confirmed on archaeological collections, but it is probable that a practical application will allow to further develop the methodology and possibly to highlight additional possibilities of the approach.

Bibliography

[1] Gaucherel, C. and Noûs C. (2020). Platforms of Palaeolithic knappers reveal complex linguistic abilities. Paleorxiv, wn5za, ver. 6 peer-reviewed and recommended by PCI Archaeology. doi: 10.31233/osf.io/wn5za
[2] Inizian, M. L., Reduron, M., Roche, H. and Tixier, J. (1995). Technologie de la pierre taillée. Préhistoire de la Pierre Taillée 4, Cercle de Recherches et d'Etudes Préhistoriques d'Antibes, Meudon.
[3] Tixier, J., Inizian, M. L. and Roche, H. (1980). Terminologie et technologie. Préhistoire de la pierre taillée 1, Cercle de Recherches et d'Etudes Préhistoriques d'Antibes, Meudon.

Platforms of Palaeolithic knappers reveal complex linguistic abilitiesCédric Gaucherel and Camille Noûs<p>Recent studies in cognitive neurosciences have postulated a possible link between manual praxis such as tool-making and human languages. If confirmed, such a link opens significant avenues towards the study of the evolution of natural languages...Africa, Ancient Palaeolithic, Lithic technology, Theoretical archaeologyMarta Arzarello2020-04-30 14:18:26 View
24 Jun 2021
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The strength of parthood ties. Modelling spatial units and fragmented objects with the TSAR method – Topological Study of Archaeological Refitting

A practical computational approach to stratigraphic analysis using conjoinable material culture.

Recommended by based on reviews by Robert Bischoff, Matthew Peeples and 1 anonymous reviewer

The paper by Plutniak [1] presents a new method that uses refitting to help interpret stratigraphy using the topological distribution of conjoinable material culture. This new method opens up new avenues to the archaeological use of network analysis but also to assess the integrity of interpreted excavation layers. Beyond its evident applicability to standard excavation practice, the paper presents a series of characteristics that exemplify archaeological publication best practices and, as someone more versed in computational than in refitting studies I would like to comment upon.

It was no easy task to find adequate reviewers for this paper as it combines techniques and expertise that are not commonly found together in individual researchers. However, Plutniak, with help from three reviewers, particularly M. Peeples, a leading figure in archaeological applications of network science, makes a considerable effort to be accessible to non-specialist archaeologists. The core Topological Study of Archaeological Refitting (TSAR) method is freely accessible as the R package archeofrag, which is available at the Comprehensive R Archive Network (https://CRAN.R-project.org/package=archeofrag) that can be applied without the need to understand all its mathematical, graph theory and coding aspects. Beside these, an online interface including test data has been provided (https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/), which aims to ease access to the method to those archaeologists inexperienced with R. Finally, supplementary material showing how to use the package and evaluating its potential through excellent examples is provided as both pdf and Rmw (Sweave) files. This is an important companion for the paper as it allows a better understanding of the methods presented in the paper and its practical application.

The author shows particular care in testing the potential and capabilities of the method. For example, a function is provided “frag.observer.failure” to test the robustness of the edge count method against the TSAR method, which is able to prove that TSAR can deal well with incomplete information. As a further step in this direction both simulated and real field-acquired data are used to test the method which further proves that archeofrag is not only able to quantitatively assess the mixture of excavated layers but to propose meaningful alternatives, which no doubt will add an increased methodological consistency and thoroughness to previous quantitative approaches to material refitting work, even when dealing with very complex stratigraphies.

All in all, this paper makes an important contribution to core archaeological practice through the use of innovative, reproducible and accessible computational methods. I fully endorse it for the conscious and solid methods it presents but also for its adherence to open publication practices. I hope that it can become of standard use in the reconstruction of excavated stratigraphical layers through conjoinable material culture.

 

[1] Plutniak, S. 2021. The Strength of Parthood Ties. Modelling Spatial Units and Fragmented Objects with the TSAR Method – Topological Study of Archaeological Refitting. OSF Preprints, q2e69, ver. 3 Peer-reviewed and recommended by PCI Archaeology. https://doi.org/10.31219/osf.io/q2e69.

The strength of parthood ties. Modelling spatial units and fragmented objects with the TSAR method – Topological Study of Archaeological RefittingSébastien Plutniak<p>Refitting and conjoinable pieces have long been used in archaeology to assess the consistency of discrete spatial units, such as layers, and to evaluate disturbance and post-depositional processes. The majority of current methods, despite their...Computational archaeology, TaphonomyHector A. Orengo2021-01-14 18:31:01 View
21 Nov 2022
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Removing Barriers to Reproducible Research in Archaeology

Three levels of reproducible workflow remove barriers for archaeologists and increase accessibility

Recommended by ORCID_LOGO based on reviews by Sam Leggett, Cyler Conrad, Cheng Liu and Lisa Lodwick

Over the last decade, a small but growing community of archaeologists, from a diversity of intellectual and demographic backgrounds, have been striving for computational reproducibility in their published research. In their survey of the accomplishments of this thriving community, Emma Karoune and Esther Plomp (2022) analyzed the wide variety of approaches researchers have taken to enhance the reproducibility of their research. A key contribution of this paper is their excellent synthesis of diverse approaches into three levels of increasing complexity. This is helpful because it provides multiple entry points for researchers new to the challenge of fortifying their research. Many researchers assume that computational reproducibility is only achievable if they have a high degree of technical skill with computers, or is only necessary if their work is very computationally intensive. Karoune and Plomp give three compelling reasons why reproducibility is important for all archaeological research, and through their three levels they demonstrate that how these levels can be accomplished with basic, non-specialized computer skills and widely used free software. They showcase exemplary work from a variety of archaeologists to show how practical and achievable reproducible research is for all archaeologists. They advocate for archaeologists to use the most widely used and supported tools and services to support their reproducible research, such as the R and Python programming languages for data analysis, and Git and GitHub for collaboration. 

This paper, with its extensive appendix including thoughtful responses to frequently asked questions about reproducible research in archaeology, is likely to have a wide reach and influence, beyond previous works on this topic that have largely focused on technical details. Karoune and Plomp have provided the on-ramp for a generation of archaeologists who will find their questions about reproducible research answered here. They will also find an agreeable entry point to reproducible research in one of the three levels described by the authors. Will every archaeologist embrace this way of working? Should they? The work of Leonelli (2018) can help us anticipate the answers to these questions. Leonelli asks where are the limits to reproducibility, and how do the characteristics of different ways of knowing affect the desirability of reproducibility? Leonelli's work invites us to consider that there will be archaeologists coming from different epistemic cultures for whom the motivations presented by Karoune and Plomp will not resonate. For example, archaeologists engaged in mostly hermeneutical social science and humanities research, who do little or no quantitative analysis and statistics, are unlikely to see reproducibility as meaningful or desirable for their work. We can describe these researchers as working in interpretative or constructivist epistemic cultures. In these cultures, the particulars of how an individual researcher engages with their subject are exclusive and unique, and they would argue it cannot be fully captured or shared in an meaningful way (Elman and Kapiszewski 2017). Here, knowledge is situational, emerging from a specific, once-off combination of people and circumstances. One example in archaeology is the chaîne opératoire approach of stone artefact analysis, which Monnier and Missal (2014:61) describe as "based upon the analyst's experience and intuition, and it is not replicable, nor quantifiable". To make sense of this example we can draw on Galison's (1997) concept of 'image traditions' and 'logic traditions'. An image tradition is a way of knowing that is qualitative, based on composing narratives from drawings and photographs. A logic tradition is based on the use of instruments and statistical methods to collect standardised quantitative data. Chaîne opératoire approaches fall into the image tradition, along with many other ways of working in archaeology that do not generate numbers or use them to support claims about the past. Archaeologists working in a logic tradition will find reproducible research to be more meaningful than those working in an image tradition.

We should be mindful not to claim that one epistemic culture is superior to another because reproducibility is not meaningful or attainable for researchers in one culture. Such a claim would threaten the plurality that is essential for the reliability of scientific knowledge (Massimi 2022). Instead we should identify those communities in archaeology where reproducible research is both meaningful and attainable, but has not yet been widely embraced. That is the where the most beneficial effects can be expected. According to Leonelli's (2018) framework, we can recognise these communities by a few basic characteristics. For example: they are doing computationally intensive archaeology, such as using or writing software to collect, simulate, analyse or visualise data; they are doing experimental archaeology; or they are making knowledge claims that are supported by tables of numeric data and data visualisations. Archaeologists whose work shares one or more of these characteristics will find the guidance provided here by Karoune and Plomp to be highly instructive and relevant, and stand the most to benefit from it.  ​​

But it is not only individual archaeological scientists that have potential to benefit from how Karoune and Plomp have lowered the barriers to reproducible research. An especially important implication of this paper is that by lowering the barriers to reproducible research, Karoune and Plomp help us all to lower barriers to participation in archaeology in general. Documenting our research transparently, and sharing our materials (such as data and code and so on) openly, can profoundly change how others can participate in archaeology. By doing this, we are enabling students and researchers elsewhere, for example in low and middle income locations, to use our materials in their teaching and learning. Other researchers and students can apply our methods to their data, and combine their data with ours to achieve syntheses beyond what a single project can do. Similarly, for archaeologists working with local, descendant or marginalized communities, the tools of reproducible research are vital for enabling community members to have full access to the archaeological process, and thus reproducibility may be considered a necessity for decolonising the discipline. Karoune and Plomp present the CARE principles (Carroll et al. 2020) to guide archaeologists in ensuring community control of data so that reproducibility can be ethically accomplished with community safety and well-being as a priority. This may have a profoundly positive impact on the demographics of archaeology, as it lowers the barriers of meaningful participation by people far beyond our immediate groups of collaborators. 

Making archaeology more accessible is of critical importance in stemming the negative social impacts of pseudoarchaeologists, who often claim that archaeologists actively suppress the truth of the archaeological record through secrecy, elitism, and exclusiveness. The harm in this is twofold. First, that pseudoarchaeology typically erases Indigenous heritage by claiming that their past achievements were due to an ancient, extinct advanced civilization, not Indigenous people. These claims are often adopted by white supremacists to support racist and antisemitic conspiracy theories (Turner and Turner 2021), which sometimes leads to prejudice, physical violence, radicalization and extremism. A second type of harm that can come from claims of secrecy and elitism is it drains public trust in experts, leading to science denial. Not only trust in archaeologists, but trust in many kinds of experts, including those working on urgent contemporary issues such as public health and climate change. Karoune and Plomp's work is important here because it provides a practical and affordable pathway for archaeologists to fight claims of secrecy and elitism by sharing their work in ways that make it possible for non-academics to inspect the analyses and logic in detail. Claims of secrecy and elitism can be easily countered by openness, transparently and reproducibility by archaeologists. This is not only useful for tackling pseudoarchaeologists, but also in enacting an ethic of care, framing members of the public as people that not only care about archaeology as part of humanity's shared heritage, but also care for the construction of reliable interpretations of the archaeological record to provide secure and authentic foundations for their social identities and relationships (Wylie et al 2018; de la Bellacasa 2011). By striving for reproducible research in the way described by Karoune and Plomp, we are practicing a kind of reciprocal care among ourselves as archaeologists, and between archaeologists and members of the public as two communities who care about the human past. 

 

References

Karoune, E., and Plomp, E. (2022). Removing Barriers to Reproducible Research in Archaeology. Zenodo, 7320029, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7320029

de la Bellacasa, M. P. (2011). Matters of care in technoscience: Assembling neglected things. Social Studies of Science, 41(1), 85–106. https://doi.org/10.1177/0306312710380301

Carroll, S. R., Garba, I., Figueroa-Rodríguez, O. L., Holbrook, J., Lovett, R., Materechera, S., Parsons, M., Raseroka, K., Rodriguez-Lonebear, D., Rowe, R., Sara, R., Walker, J. D., Anderson, J., and Hudson, M. (2020). The CARE Principles for Indigenous Data Governance. Data Science Journal, 19(1), Article 1. https://doi.org/10.5334/dsj-2020-043​

Elman, C., and Kapiszewski, D. (2017). Benefits and Challenges of Making Qualitative Research More Transparent. Inside Higher Ed 2017,  http://web.archive.org/web/20220407064134/https://www.insidehighered.com/blogs/rethinking-research/benefits-and-challenges-making-qualitative-research-more-transparent (accessed 21 Oct, 2022). 

Galison, P. (1997). Image and logic: a material culture of microphysics. Chicago (IL): University of Chicago Press.

Leonelli, S. (2018). Re-Thinking Reproducibility as a Criterion for Research Quality [preprint]. Available online: http://philsci-archive.pitt.edu/id/eprint/14352 (Accessed 21 Oct 2022).

Massimi, M. (2022). Perspectival realism. Oxford University Press.

Monnier, G. F., and Kele M.. "Another Mousterian debate? Bordian facies, chaîne opératoire technocomplexes, and patterns of lithic variability in the western European Middle and Upper Pleistocene." Quaternary International 350 (2014): 59-83. https://doi.org/10.1016/j.quaint.2014.06.053

Turner, D. D., and Turner, M. I. (2021). “I’m Not Saying It Was Aliens”: An Archaeological and Philosophical Analysis of a Conspiracy Theory. In A. Killin and S. Allen-Hermanson (Eds.), Explorations in Archaeology and Philosophy (pp. 7–24). Springer International Publishing. https://doi.org/10.1007/978-3-030-61052-4_2

​Wylie, C., Neeley, K., and Ferguson, S. (2018). Beyond Technological Literacy: Open Data as Active Democratic Engagement? Digital Culture & Society, 4(2), 157–182. https://doi.org/10.14361/dcs-2018-0209​​​

 

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Removing Barriers to Reproducible Research in ArchaeologyEmma Karoune and Esther Plomp<p>Reproducible research is being implemented at different speeds in different disciplines, and Archaeology is at the start of this journey. Reproducibility is the practice of reanalysing data by taking the same steps and producing the same or sim...Computational archaeologyBen Marwick2022-06-07 10:02:46 View
02 May 2023
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Transmission of lithic and ceramic technical know-how in the Early Neolithic of central-western Europe: Shedding Light on the Social Mechanisms underlying Cultural Transition

A Thought Provoking Consideration of Craft in the Neolithic

Recommended by based on reviews by Bogdana Milić and 1 anonymous reviewer

The pioneering work of Leroi-Gourhan introduced archaeologists to the concept of the chaîne opératoire[1], whereby, like his supervisor Mauss[2], Leroi-Gourhan proposed direct links between bodily actions and aspects of cultural identity. The chaîne opératoire offers a powerful conceptual tool with which to reconstruct and describe the technological practices undertaken by craftspeople, linking material objects to the cultural context in which crafts are learnt. Although initially applied to lithics, the concept today is well known in ceramic studies, as well as, other material crafts, in order to identify aspects of tradition and identity through ideas linked to technological style[3,4] and communities of practice[5].

Utilizing this approach, Denis et al.[6] use the chaîne opératoire to look at both lithics and ceramics together from a diachronic viewpoint, to examine technical systems present over the transition between Linearbandkeramic (LBK) and post LBK Blicquy/Villeneuve-Saint German (BQY/VSG) timeframes. This much needed comparative and diachronic perspective, focuses on material from the sites of Vaux-et-Borset and Verlaine in Belgium, and has enabled the authors to consider the impact of changing social dynamics on these two crafts simultaneously.

The authors examine the ceramic and lithic assemblages from a macroscopic and morphological perspective in order to identify techniques of production. The data gathered testifies to the dominance of one production technique for each craft within the LBK. There is particularly striking homogeneity noted for the lithics that suggests the transmission of a single tradition over the Hesbaye area, whilst the ceramics display greater regional diversity. The picture alters somewhat for the BQY/VSG material where it seems there is an increase in the diversity of production techniques, with both the introduction of new techniques, as well as a degree of hybridization of earlier techniques to form new BQY/VSG chaînes opératoires that have LBK roots. The BQY/VSG diversity noted for the lithics is especially interesting, with the introduction of techniques that attest to increased expertise which the authors attest to the migration of an external group.

The results of this work have allowed Denis et al. to discuss multiple influences on the technical systems they identify. Rather than trying to fit the data within a single model, the authors demonstrate the need for nuance, considering the social changes associated with Neolithic migration and interactions, as multifaced and dynamic. As such, they are able to show not only the influence of contact with other groups, but that the apparent migration of external groups does not simply lead to the replacement of the crafting heritage already established at the sites they have examined.

In concluding the authors acknowledge, that as scholars push the existing state of knowledge (in this respect analysis of raw materials would make an especially important contribution), the picture presented in the paper may alter. Future work will hopefully fill in current gaps, particularly in terms of how far the trends identified extend, and the extent to which the lithic and ceramic pictures diversify on a broader geographical scale. It is certain that based on such results, future work should adopt the comparative approach presented by the authors, who have demonstrated its explanatory potential for understanding the technical and cultural groups we all study.

 
[1] Leroi-Gourhan, A. 1971. Evolution et techniques I- L'Homme et la matière, 2nd Edition. Albin Michel: Paris, Leroi-Gourhan, A. 1973. Evolution et techniques II- Milieu et techniques 2nd Edition. Paris: Albin Michel.

[2] Mauss, M. 2009 [1934]. Techniques, Technology and Civilisation. Edited and introduced by N. Schlanger. New York/Oxford: Durkheim Press/Berghahn Books.

[3] Lechtman, H. 1977. Style in Technology: some early thoughts. In H. Lechtman and R.S. Merrill (eds.) Material Culture: styles, organization and dynamics of technology. Proceedings of the American Ethnological Society 1975, St. Paul, 3-20.

[4] Gosselain, O. 1992. Technology and Style: Potters and Pottery Among Bafia of Cameroon. Man 27(3) 559- 586. htpps://doi.org/10.2307/2803929.

[5] Wenger, E. 1998. Communities of practice: Learning, meaning, and identity. Cambridge: Cambridge University Press.

[6] Denis, S., Gomart, L., Burnez-Lanotte, L. and Allard, P. (2023). Transmission of lithic and ceramic technical know-how in the Early Neolithic of central-western Europe: Shedding Light on the Social Mechanisms underlying Cultural Transition. OSF Preprints, gqnht, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.31219/osf.io/gqnht


 
 

Transmission of lithic and ceramic technical know-how in the Early Neolithic of central-western Europe: Shedding Light on the Social Mechanisms underlying Cultural Transition Solène Denis, Louise Gomart, Laurence Burnez-Lanotte, Pierre Allard<p>Research on the European Neolithisation agrees that a process of colonisation throughout the sixth millennium BC underlies the spread of agricultural ways of life on the continent. From central to central-western Europe, this colonisation path ...Ceramics, Europe, Lithic technology, NeolithicClare Burke2022-11-18 12:03:55 View
05 Jul 2023
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Tool types and the establishment of the Late Palaeolithic (Later Stone Age) cultural taxonomic system in the Nile Valley

Cultural taxonomic systems and the Late Palaeolithic/Later Stone Age prehistory of the Nile Valley – a critical review

Recommended by , ORCID_LOGO and ORCID_LOGO based on reviews by Giuseppina Mutri and 1 anonymous reviewer

The paper entitled “Tool types and the establishment of the Late Palaeolithic (Later Stone Age) cultural taxonomic system in the Nile Valley”  submitted by A. Leplongeon offers a review of the many cultural taxonomic in use for the prehistory – especially the Late Palaeolithic/Late Stone Age – of the Nile Valley (Leplongeon 2023). This paper was first developed for a special conference session convened at the EAA annual meeting in 2021 and is intended for an edited volume on the topic of typology and taxonomy in archaeology.

Issues of cultural taxonomy have recently risen to the forefront of archaeological debate (Reynolds and Riede 2019; Ivanovaitė et al. 2020; Lyman 2021). Archaeological systematics, most notably typology, have roots in the research history of a particular region and period (e.g. Plutniak 2022); commonly, different scholars employ different and at times incommensurable systems, often leading to a lack of clarity and inter-regional interoperability. African prehistory is not exempt from this debate (e.g. Wilkins 2020) and, in fact, such a situation is perhaps nowhere more apparent than in the iconic Nile Valley. The Nile Valley is marked by a complex colonial history and long-standing archaeological interest from a range of national and international actors. It is also a vital corridor for understanding human dispersals out of and into Africa, and along the North African coastal zone. As Leplongeon usefully reviews, early researchers have, as elsewhere, proposed a variety of archaeological cultures, the legacies of which still weigh in on contemporary discussions. In the Nile Valley, these are the Kubbaniyan (23.5-19.3 ka cal. BP), the Halfan (24-19 ka cal. BP), the Qadan (20.2-12 ka cal BP), the Afian (16.8-14 ka cal. BP) and the Isnan (16.6-13.2 ka cal. BP) but their temporal and spatial signatures remain in part poorly constrained, or their epistemic status debated. Leplongeon’s critical and timely chronicle of this debate highlights in particular the vital contributions of the many female prehistorians who have worked in the region – Angela Close (e.g. 1978; 1977) and Maxine Kleindienst (e.g. 2006) to name just a few of the more recent ones – and whose earlier work had already addressed, if not even solved many of the pressing cultural taxonomic issues that beleaguer the Late Palaeolithic/Later Stone Age record of this region. 

Leplongeon and colleagues (Leplongeon et al. 2020; Mesfin et al. 2020) have contributed themselves substantially to new cultural taxonomic research in the wider region, showing how novel quantitative methods coupled with research-historical acumen can flag up and overcome the shortcomings of previous systematics. Yet, as Leplongeon also notes, the cultural taxonomic framework for the Nile Valley specifically has proven rather robust and does seem to serve its purpose as a broad chronological shorthand well. By the same token, she urges due caution when it comes to interpreting these lithic-based taxonomic units in terms of past social groups. Cultural systematics are essential for such interpretations, but age-old frameworks are often not fit for this purpose. New work by Leplongeon is likely to not only continue the long tradition of female prehistorians working in the Nile Valley but also provides an epistemologically and empirically more robust platform for understanding the social and ecological dynamics of Late Palaeolithic/Later Stone Age communities there.

 

Bibliography 

Close, Angela E. 1977. The Identification of Style in Lithic Artefacts from North East Africa. Mémoires de l’Institut d’Égypte 61. Cairo: Geological Survey of Egypt.

Close, Angela E. 1978. “The Identification of Style in Lithic Artefacts.” World Archaeology 10 (2): 223–37. https://doi.org/10.1080/00438243.1978.9979732

Ivanovaitė, Livija, Serwatka, Kamil, Steven Hoggard, Christian, Sauer, Florian and Riede, Felix. 2020. “All These Fantastic Cultures? Research History and Regionalization in the Late Palaeolithic Tanged Point Cultures of Eastern Europe.” European Journal of Archaeology 23 (2): 162–85. https://doi.org/10.1017/eaa.2019.59

Kleindienst, M. R. 2006. “On Naming Things: Behavioral Changes in the Later Middle to Earlier Late Pleistocene, Viewed from the Eastern Sahara.” In Transitions Before the Transition. Evolution and Stability in the Middle Paleolithic and Middle Stone Age, edited by E. Hovers and Steven L. Kuhn, 13–28. New York, NY: Springer.

Leplongeon, Alice. 2023. “Tool Types and the Establishment of the Late Palaeolithic (Later Stone Age) Cultural Taxonomic System in the Nile Valley.” https://doi.org/10.5281/zenodo.8115202

Leplongeon, Alice, Ménard, Clément, Bonhomme, Vincent and Bortolini, Eugenio. 2020. “Backed Pieces and Their Variability in the Later Stone Age of the Horn of Africa.” African Archaeological Review 37 (3): 437–68. https://doi.org/10.1007/s10437-020-09401-x

Lyman, R. Lee. 2021. “On the Importance of Systematics to Archaeological Research: The Covariation of Typological Diversity and Morphological Disparity.” Journal of Paleolithic Archaeology 4 (1): 3. https://doi.org/10.1007/s41982-021-00077-6

Mesfin, Isis, Leplongeon, Alice, Pleurdeau, David, and Borel, Antony. 2020. “Using Morphometrics to Reappraise Old Collections: The Study Case of the Congo Basin Middle Stone Age Bifacial Industry.” Journal of Lithic Studies 7 (1): 1–38. https://doi.org/10.2218/jls.4329

Plutniak, Sébastien. 2022. “What Makes the Identity of a Scientific Method? A History of the ‘Structural and Analytical Typology’ in the Growth of Evolutionary and Digital Archaeology in Southwestern Europe (1950s–2000s).” Journal of Paleolithic Archaeology 5 (1): 10. https://doi.org/10.1007/s41982-022-00119-7

Reynolds, Natasha, and Riede, Felix. 2019. “House of Cards: Cultural Taxonomy and the Study of the European Upper Palaeolithic.” Antiquity 93 (371): 1350–58. https://doi.org/10.15184/aqy.2019.49

Wilkins, Jayne. 2020. “Is It Time to Retire NASTIES in Southern Africa? Moving Beyond the Culture-Historical Framework for Middle Stone Age Lithic Assemblage Variability.” Lithic Technology 45 (4): 295–307. https://doi.org/10.1080/01977261.2020.1802848

Tool types and the establishment of the Late Palaeolithic (Later Stone Age) cultural taxonomic system in the Nile ValleyAlice Leplongeon<p>Research on the prehistory of the Nile Valley has a long history dating back to the late 19th century. But it is only between the 1960s and 1980s, that numerous cultural entities were defined based on tool and core typologies; this habit stoppe...Africa, Lithic technology, Upper PalaeolithicFelix Riede2023-03-08 19:25:28 View
02 Apr 2024
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Similarity Network Fusion: Understanding Patterns and their Spatial Significance in Archaeological Datasets

A different approach to similarity networks in Archaeology - Similarity Network Fusion

Recommended by based on reviews by Matthew Peeples and 1 anonymous reviewer

This is a fascinating paper for anyone interested in network analysis or the chronology and cultures of the case study, namely the Late prehistoric burial sites in Dorset, for which the author’s approach allowed a new perspective over an already deeply studied area [1]. This paper's implementation of Similarity Network Fusion (SNF) is noteworthy. This method is typically utilized within genetic research but has yet to be employed in Archaeology. SNF has the potential to benefit Archaeology due to its unique capabilities and approach significantly. 

The author exhibits a deep and thorough understanding of previous investigations concerning material and similarity networks while emphasizing the innovative nature of this particular study. The SNF approach intends to improve a lack of the most used (in Archaeology) similarity coefficient, the Brainerd-Robinson, in certain situations, mainly in heterogenous and noisy datasets containing a small number of samples but a large number of measurements, scale differences, and collection biases, among other things. The SNF technique, demonstrated in the case study, effectively incorporates various similarity networks derived from different datatypes into one network. 

As shown during the Dorset case study, the SNF application has a great application in archaeology, even in already available data, allowing us to go further and bring new visions to the existing interpretations. As stated by the author, SNF shows its potential for other applications and fields in archaeology coping with similar datasets, such as archaeobotany or archaeozoology, and seems to complement different multivariate statistical approaches, such as correspondence or cluster analysis.

This paper has been subject to two excellent revisions, which the author mostly accepted. One of the revisions was more technical, improving the article in the metadata part, data availability and clarification, etc. Although the second revision was more conceptual and gave some excellent technical inputs, it focused more on complementary aspects that will allow the paper to reach a wider audience. I vividly recommend its publication.

References

[1] Geitlinger, T. (2024). Similarity Network Fusion: Understanding Patterns and their Spatial Significance in Archaeological Datasets. Zenodo, 7998239, ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7998239

 

Similarity Network Fusion: Understanding Patterns and their Spatial Significance in Archaeological DatasetsTimo Geitlinger<p>Since its earliest application in the 1970s, network analysis has become increasingly popular in both theoretical and GIS-based archaeology. Yet, applications of material networks remained relatively restricted. This paper describes a specific ...Computational archaeology, ProtohistoryJoel Santos2023-06-02 16:51:19 View
30 Sep 2022
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Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data

Assessing glutamine deamination in ancient parchment samples

Recommended by based on reviews by Maria Codlin and 3 anonymous reviewers

Data authenticity and approaches to data authentication are crucial issues in ancient protein research. The advent of modern mass spectrometry has enabled the detection of traces of ancient biomolecules contained in fossils, including protein sequences. However, detecting proteins in ancient samples does not equate to demonstrating their endogenous nature: instead, if the mechanisms that drive protein preservation and degradation are understood, then the extent of protein diagenesis can be used for evaluating preservational quality, which in turn may be related to the authenticity of the protein data. 

The post-mortem deamidation of asparaginyl and glutamyl residues is a key degradation reaction, which can be assessed effectively on the basis of mass spectrometry data, and which has accrued a long history of research, both in terms of describing the mechanisms governing the reactions and with regard to the best strategies for assessing and quantifying the extent of glutamine (Gln) and asparagine (Asn) deamidation in ancient samples (Pal Chowdhury et al., 2019; Ramsøe et al., 2021, 2020; Schroeter and Cleland, 2016; Simpson et al., 2016; Solazzo et al., 2014; Welker et al., 2016; Wilson et al., 2012). 

In their paper, Nair and colleagues (2022) build on this wealth of knowledge and present a tool for quantifying the extent of Gln deamidation in parchment. Parchment is a collagen-based material which can yield extraordinary insights into manuscript manufacturing practices in the past, as well as on the daily lives of the people who assembled and used them (“biocodicology”) (Fiddyment et al., 2021, 2019, 2015; Teasdale et al., 2017). Importantly, the extent of deamidation can be directly related to the quality of the parchment produced: rapid direct deamidation of Gln is induced by the liming process, therefore high extents of deamidation are linked to prolonged exposure to the high pH conditions which are typical of liming, thus implying lower-quality parchment.

Nair et al.’s approach focuses on collagen peptides which are typically detected during MALDI-TOF mass spectrometry analyses of parchment and build a simple three-step workflow able to yield an overall index of deamidation for a sample (the parchment glutamine index - PQI) 一 taking into account that different Gln residues degrade at different rates according to their micro-chemical environment. The first step involves pre-processing the MALDI spectra, since Nair et al. are specifically interested in maximising information which can be obtained by low-quality data. The second step builds on well-established methods for quantifying Q → E from MALDI-TOF data by modelling the convoluted isotope distributions (Wilson et al., 2012). Once relative rates of deamidation in selected peptides within a given sample are calculated, the third step uses a mixed effects model to combine the individual deamidation estimates and to obtain an overall estimate of the deamidation for a parchment sample (PQI). 

The PQI can be used effectively for assessing parchment quality, as the authors show for the dataset from Orval Abbey. However, PQI could also have wider applications to the study of processed collagen, which is widely used in the food and pharmaceutical industries. In general, the study by Nair et al. is a welcome addition to a growing body of research on protein diagenesis, which will ultimately improve models for the assessment of the authenticity of biomolecular data in archaeology. 

References

Chowdhury, P.M., Wogelius, R., Manning, P.L., Metz, L., Slimak, L., and Buckley, M. 2019. Collagen deamidation in archaeological bone as an assessment for relative decay rates. Archaeometry 61:1382–1398. https://doi.org/10.1111/arcm.12492

Fiddyment, S., Goodison, N.J., Brenner, E., Signorello, S., Price, K., and Collins, M.J.. 2021. Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis. bioRxiv. https://doi.org/10.1098/rsos.202055

Fiddyment,S., Holsinger, B., Ruzzier, C., Devine, A., Binois, A., Albarella, U., Fischer, R., Nichols, E., Curtis, A., Cheese, E., Teasdale, M.D., Checkley-Scott, C., Milner, S.J., Rudy, K.M., Johnson, E.J., Vnouček, J., Garrison, M., McGrory, S., Bradley, D.G., and Collins, M.J. 2015. Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proc Natl Acad Sci U S A 112:15066–15071. https://doi.org/10.1073/pnas.1512264112

Fiddyment, S., Teasdale, M.D., Vnouček, J., Lévêque, É., Binois, A., and Collins, M.J. 2019. So you want to do biocodicology? A field guide to the biological analysis of parchment. Heritage Science 7:35. https://doi.org/10.1186/s40494-019-0278-6

Nair, B., Rodríguez Palomo, I., Markussen, B., Wiuf, C., Fiddyment, S., and Collins, M. Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data. BiorRxiv, 2022.03.13.483627, ver. 6 peer-reviewed and recommended by Peer community in Archaeology. https://doi.org/10.1101/2022.03.13.483627 

Ramsøe, A., Crispin, M., Mackie, M., McGrath, K., Fischer, R., Demarchi, B., Collins, M.J., Hendy, J., and Speller, C. 2021. Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. Sci Rep 11:7795. https://doi.org/10.1038/s41598-021-87125-x

Ramsøe, A., van Heekeren, V., Ponce, P., Fischer, R., Barnes, I., Speller, C., and Collins, M.J. 2020. DeamiDATE 1.0: Site-specific deamidation as a tool to assess authenticity of members of ancient proteomes. J Archaeol Sci 115:105080. https://doi.org/10.1016/j.jas.2020.105080

Schroeter, E.R., and Cleland, T.P. 2016. Glutamine deamidation: an indicator of antiquity, or preservational quality? Rapid Commun Mass Spectrom 30:251–255. https://doi.org/10.1002/rcm.7445

Simpson, J.P., Penkman, K.E.H., and Demarchi, B. 2016. The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone. J Archaeol Sci 69: 29-38. https://doi.org/10.1016/j.jas.2016.02.002

Solazzo, C., Wilson, J., Dyer, J.M., Clerens, S., Plowman, J.E., von Holstein, I., Walton Rogers, P., Peacock, E.E., and Collins, M.J. 2014. Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles. Anal Chem 86:567–575. https://doi.org/10.1021/ac4026362

Teasdale, M.D., Fiddyment, S., Vnouček, J., Mattiangeli, V., Speller, C., Binois, A., Carver, M., Dand, C., Newfield, T.P., Webb, C.C., Bradley, D.G., and Collins M.J. 2017. The York Gospels: a 1000-year biological palimpsest. R Soc Open Sci 4:170988. https://doi.org/10.1098/rsos.170988

Welker, F., Soressi, M.A., Roussel, M., van Riemsdijk, I., Hublin, J.-J., and Collins, M.J. 2016. Variations in glutamine deamidation for a Châtelperronian bone assemblage as measured by peptide mass fingerprinting of collagen. STAR: Science & Technology of Archaeological Research 3:15–27. https://doi.org/10.1080/20548923.2016.1258825

Wilson, J., van Doorn, N.L., and Collins, M.J. 2012. Assessing the extent of bone degradation using glutamine deamidation in collagen. Anal Chem 84:9041–9048. https://doi.org/10.1021/ac301333t

Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF dataBharath Nair, Ismael Rodríguez Palomo, Bo Markussen, Carsten Wiuf, Sarah Fiddyment and Matthew Collins<p style="text-align: justify;">Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)<span class="math-tex">\( _2 \)</span>. During liming, collagen peptides containing Glutamine (Q)...Bioarchaeology, Europe, Medieval, ZooarchaeologyBeatrice Demarchi2022-03-22 12:54:10 View
26 Oct 2022
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Technological analysis and experimental reproduction of the techniques of perforation of quartz beads from the Ceramic period in the Antilles

Using Cactus Thorns to Drill Quartz: A Proof of Concept

Recommended by and ORCID_LOGO based on reviews by Viola Stefano, ? and 1 anonymous reviewer

Quartz adornments (beads, pendants, etc.) are frequent artifacts found in the Caribbean, particularly from Early Ceramic Age contexts (~500 BC-AD 700). As a form of specialization, these are sometimes seen as indicative of greater social complexity and craftsmanship during this time. Indeed, ethnographic analogy has purported that such stone adornments require enormous inputs of time and labor, as well as some technological sophistication with tools hard-enough to create the holes (e.g., metal or diamonds). However, given these limitations, one would expect unfinished beads to be a common artifact in the archaeological record. Yet, whereas unworked/raw materials are often found, beads with partial/unfinished perforations are not.
 
Could the perforations of stone beads be made using more accessible materials? Some ethnographic sources from Central America suggest certain plant materials could work. Thus, Raymond et al. (2022) endeavored to test the manufacturing process of stone beads by experimenting with several underrated (yet readily available) materials from the Caribbean: various species of wood, bone, thorns, and chert. As it turns out, thorns from an endemic cactus (Melocactus intortus) worked best and were actually harder than many of the other materials attempted. Even the chert drills were too large and fragile to be effective (neither are they found archaeologically). Using debitage powder from the rock itself, some water, and a basic bow drill mounted with a cactus thorn, the team successfully created perforations on unworked samples of quartz that were similar to those found archaeologically. This was corroborated by analyzing the results at different levels of magnification, including X-ray microtomography and SEM, and then comparing that to similar studies on ancient beads.
 
The results of this study offer useful parameters for the feasibility of bead craftsmanship in the ancient Caribbean. For one, all of the materials used are fairly common in the region, including quartz (although the source of amethyst in the Caribbean is believed to be Guyana (Cody 1990)). Additionally, the practice does not require much skill, as the authors (neophyte craftspeople) were able to replicate the holes. Presumably, a child could do this (an intriguing prospect). The study therefore offers practical data for the once mysterious production of precolumbian personal adornments. Indeed, the article indirectly offers arguments for the presence of bead crafting specialists in other areas of the world as well, where production of ornaments entails similar time investments and complexity. For example, similar quartz materials, like carnelian or agate, shaped into long barrels or cylindrical beads forming beautiful parures, are common to pre-metallic contexts of agro-pastoral societies of Europe and North Africa in the VI and V millennium BC.
 
That said, the huge time commitment (over 200 hours per bead), although far less than the years (or lifetimes) some researchers had previously estimated, socially translates into a distraction from subsistence activities, which may indicate the presence of individuals devoted (at least part-time) to producing non-utilitarian adornments (see also Kenoyer et al. 1991 on this topic). 
 
Focusing on the specific aspect of finding the most appropriate substitute to metal piercing devices and the related aspects of the overall chaîne opératoire, the document invites further research, for example on the bead locking system during the piercing phase, in the management of the force exerted during the process, and in the number of failures (and on their potential uses).
 

References:
Raymond, M., Fouéré, P., Ledevin, R., Lefrais, Y., and Queffelec, A. (2022) Technological analysis and experimental reproduction of the techniques of perforation of quartz beads from the Ceramic period in the Antilles. SocArXiv, a5tgp, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://osf.io/preprints/socarxiv/a5tgp


Cody, A.K. (1990) Prehistoric patterns of exchange in the Lesser Antilles: materials, models, and preliminary observations. PhD thesis, San Diego State University.


Kenoyer, J.M., Vidale, M. and Bhan, K.K. (1991) Contemporary stone bead-making in Khambhat, India: Patterns of craft specialization and organization of production as reflected in the archaeological record. World Archaeology 23 (1), 44-63. https://doi.org/10.1080/00438243.1991.9980158

Technological analysis and experimental reproduction of the techniques of perforation of quartz beads from the Ceramic period in the AntillesMadeleine Raymond, Pierrick Fouéré, Ronan Ledevin, Yannick Lefrais and Alain Queffelec<p style="text-align: justify;">Personal ornaments are a very specific kind of material production in human societies and are particularly valuable artifacts for the archaeologist seeking to understand past societies. In the Caribbean, Early Ceram...Lithic technology, Neolithic, South America, Symbolic behaviours, TraceologyDonatella Usai2022-09-06 14:01:51 View
12 Dec 2022
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Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?

Mobility in pigs: A microanatomical perspective

Recommended by ORCID_LOGO based on reviews by Max Price and Ignacio A. Lazagabaster

Pig domestication and husbandry involved complex processes of introduction, introgression, and feralization that challenge our understanding of human/suid interactions in ancient times. This challenge is a constant stimulus for the development of novel methods and techniques to illuminate aspects of early pig husbandry, such as human-induced changes in mobility. Using geometric morphometrics, Harbers et al. (2020) have shown that the calcaneus records a plastic response to reduced mobility and hence to human management. In the present study, Cottereau et al. (2022) explore the possibility that a similar plastic response to different mobility regimes can be observed in the microanatomy of the calcaneus using CT scans. Their research utilizes a sample of calcanei obtained from Mesolithic specimens, and also from recent suids kept in natural habitat, large pen, and stall. Their results suggest that bone microanatomy is more affected by population differences than by mobility patterns, as illustrated by the similarity between Mesolitic boar calcanei and their difference from recent, free wild boar. 


This is an important negative result, and, as Max Price has remarked in his review, such results are biased against in the scientific literature. Beyond the merit of its careful planning and execution, I find the study thought-provoking, as it marks a scale threshold below which the plastic signal of mobility is lost. At the same breath, the close similarity between Mesolithic boars in the microanatomical scale opens a door to the investigation of inter-population anatomical differences beyond that threshold. 

 

References

Cottereau R, Ortiz K, Locatelli Y, Houssaye A, Cucchi T (2022), bioRxiv, 504790, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.1101/2022.08.22.504790

Harbers H, Neaux D, Ortiz K, Blanc B, Laurens F, Baly I, Callou C, Schafberg R, Haruda A, Lecompte F, Casabianca F, Studer J, Renaud S, Cornette R, Locatelli Y, Vigne J-D, Herrel A, Cucchi T (2020) The mark of captivity: plastic responses in the ankle bone of a wild ungulate (Sus scrofa). Royal Society Open Science, 7, 192039. https://doi.org/10.1098/rsos.192039

 

Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?Romain Cottereau, Katia Ortiz, Yann Locatelli, Alexandra Houssaye*, Thomas Cucchi*<p style="text-align: justify;">Reduced mobility associated with captivity induce changes in biomechanical stress on the skeleton of domesticated animals. Due to bone plasticity, the morphology and the internal structure of the bones can respond t...Neolithic, ZooarchaeologyNimrod Marom2022-08-26 20:29:01 View