Latest recommendations
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21 Mar 2023
![]() Hafted stone and shell tools in the Asia Pacific RegionChristopher Buckley https://doi.org/10.31234/osf.io/8cwa2From Polished Stone Tools to Population Dynamics: Ethnographic Archives as InsightsRecommended by Solène Denis based on reviews by Adrian L. Burke and 1 anonymous reviewerMost archaeological contexts provide objects without organic materials making them quite silent regarding their hafting techniques and use. This is especially true for the polished stone tools that only thanks to a few discoveries in a wet environment, we can obtain some insights regarding their hafting techniques. Use-wear analysis can also be of some support to get a better picture of these artefacts (e.g. Masclans Latorre 2020), whose typology testifies to an important diversity in European Neolithic contexts that sometimes are well-documented from the chaîne opératoire perspective (see De Labriffe and Thirault dir. 2012). The study offered by Chris Buckley (2023) constitutes an important contribution to animating these tools. His work relies on the Asia Pacific region, where he gathered data and mapped more than 300 ethnographic hafted stone and shell tools. This database is available on a webpage https://www.google.com/maps/d/u/0/viewer?mid=1D_sC7VUtQRuRcCgc9rROVU7ghrdiVAg&ll=-2.458804534247277%2C154.35254980859378&z=6, providing a short description and pictures of some of the items, completed by Supplementary data. Thanks to this important record of entire objects, the author presents the different possibilities regarding hafting styles, blade orientations and attachment techniques. The combination of these different characteristics led the author to the introduction of a dynamic typology based on the concept of ‘morphospace’. Eight types have been so identified for the Asia Pacific region. The geographical distribution of these types is then presented and questioned, bringing also to the forefront some archaeological findings. An emphasis is made on New Guinea island where documentation is important. We can mention the emblematic work of Anne-Marie and Pierre Pétrequin (1993 and 2020) focused on West Papua, providing one of the most consulted books on stone axes by archaeologists. The worthy explanations tested to understand this repartition mobilize archaeological or linguistic data to hypothesise a three waves model of innovations in link with agricultural practices. A discussion on the correlation between material culture and language highlights in the background the need for interdisciplinary to deal finely with these interactions and linkages as has been effectively demonstrated elsewhere (Hermann and Walworth 2020). To conclude, the convergence between European Neolithic and New Guinea polished stone tools is demonstrated here through ‘morphospace’ comparisons. Thanks to this study, the polished stone tools come alive more than any European archaeological context would allow. The population dynamics investigated through these tools are directly relevant to current scientific issues concerning material culture. This example of convergent evolution is therefore an important key to considering this article as a source of inspiration for the archaeological community. References Buckley C. (2023). Hafted Stone and Shell Tools in the Asia Pacific Region, PsyArXiv, v.3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.31234/osf.io/8cwa2 De Labriffe A., Thirault E. dir. (2012). Produire des haches au Néolithique, de la matière première à l’abandon, Paris, Société préhistorique française (Séances de la Société préhistorique française, 1). Hermann A., Walworth M. (2020). Approche interdisciplinaire des échanges interculturels et de l’intégration des communautés polynésiennes dans le centre du Vanuatu, Journal de la Société des Océanistes, 151, 239-262. https://doi-org.docelec.u-bordeaux.fr/10.4000/jso.11963 Masclans Latorre A. (2020). Use-wear Analyses of Polished and Bevelled Stone Artefacts during the Sepulcres de Fossa/Pit Burials Horizon (NE Iberia, c. 4000–3400 cal B.C.), Oxford, BAR Publishing (BAR International Series 2972). Pétrequin P., Pétrequin A.-M. (1993). Écologie d'un outil : la hache de pierre en Irian Jaya (Indonésie), Paris, CNRS Editions. Pétrequin P., Pétrequin A.-M. (2020). Ecology of a Tool: The ground stone axes of Irian Jaya (Indonesia). Oxbow Books. | Hafted stone and shell tools in the Asia Pacific Region | Christopher Buckley | <p>Hafted stone tools fell into disuse in the Pacific region in the 19th and 20th centuries. Before this occurred, examples of tools were collected by early travelers, explorers and tourists. These objects, which now reside in ethnographic collect... | ![]() | Asia, Conservation/Museum studies, Lithic technology, Neolithic, Oceania | Solène Denis | 2022-11-09 18:37:08 | View | |
06 Oct 2023
![]() From paper to byte: An interim report on the digital transformation of two thing editionsAuth. Frederic; Rösler, Katja; Domscheit, Wenke; Hofmann, Kerstin P. https://doi.org/10.5281/zenodo.7304578Revitalising archaeological corpus publications through digitisation – the Corpus der römischen Funde im europäischen Barbaricum and the Conspectus Formarum Terrae Sigillatae Modo Confectae as exemplary casesRecommended by Felix Riede, Sébastien PlutniakThe paper entitled “From paper to byte: An interim report on the digital transformation of two thing editions” submitted by Frederic Auth and colleagues discusses how those rich and often meticulously illustrated catalogues of particular find classes that exist in many corners of archaeology can be brought to the cutting edge of contemporary research through digitisation. 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, taxonomy, classification theory, and computational approaches in archaeology. Auth et al. (2023) begin with outlining the useful notion of the ‘thing-edition’ originally coined by Kerstin Hofmann in the context of her work with the many massive corpora of finds that have characterised, in particular, earlier archaeological knowledge production in Germany (Hofmann et al. 2019; Hofmann 2018). This work critically examines changing trends in the typological characterisation and recording of various find categories, their theoretical foundations or lack thereof and their legacy on contemporary practice. The present contribution focuses on what happens with such corpora when they are integrated into digitisation projects, specifically the efforts by the German Archaeological Institute (DAI), the so-called iDAI.world and in regard to two Roman-era material culture groups, the Corpus der römischen Funde im europäischen Barbaricum (Roman finds from beyond the empire’s borders in eight printed volumes covering thousands of finds of various categories), and the Conspectus Formarum Terrae Sigillatae Modo Confectae (Roman plain ware). Drawing on Bruno Latour’s (2005) actor-network theory (ANT), Auth et al. discuss and reflect on the challenges met and choices to be made when thing-editions are to be transformed into readily accessible data, that is as linked to open, usable data. The intellectual and infrastructural workload involved in such digitisation projects is not to be underestimated. Here, the contribution by Auth et al. excels in the manner that it does not present the finished product – the fully digitised corpora – but instead offers a glimpse ‘under the hood’ of the digitisation process as an interaction between analogue corpus, research team, and the technologies at hand. These aspects were rarely addressed in the literature, rooted in the 1970s early work (Borillo and Gardin 1974; Gaines 1981), on archaeological computerised databases, focused on technical dimensions (see Rösler 2016 for an exception). Their paper can so also be read in the broader context of heterogeneous computer-assisted knowledge ecologies and ‘mangles of practice’ (see Pickering and Guzik 2009) in which practitioners and technological structures respond to each other’s needs and attempt to cooperate in creative ways. As such, Auth et al.’s considerations not least offer valuable resources for Science and Technology Studies-inspired discussions on the cross-fertilization of archaeological theory, practice and currently emerging material and virtual research infrastructures and can be read in conjunction to Gavin Lucas’ (2022) paper on ‘machine epistemology’ due to appear in the same volume. Perhaps more importantly, however, the work by Auth and colleagues (2023) exemplifies the due diligence required in not merely turning a catalogue from paper to digital document but in transforming such catalogues into long-lasting and patently usable repositories of generations of scholars to come. Deploying the Latourian notions of trade-off and recursive reference, Auth et al. first examine the structure, strengths, and weakness of the two corpora before moving on to showing how the freshly digitised versions offer new and alternative ways of analysing the archaeological material at hand, notably through immediate visualisation opportunities, through ceramic form combinations, and relational network diagrams based on the data inherent in the respective thing-editions. Catalogues including basic descriptions and artefact illustrations exist for most if not all archaeological periods. They constitute an essential backbone of archaeological work as repeated access to primary material is impractical if not impossible. The catalogues addressed by Auth et al. themselves reflect major efforts on behalf of archaeological experts to arrive at clear and operational classifications in a pre-computerised era. The continued and expanded efforts by Auth and colleagues build on these works and clearly demonstrate the enormous analytical potential to make such data not merely more accessible but also more flexibly interoperable. Their paper will therefore be an important reference for future work with similar ambitions facing similar challenges. References Auth, Frederic, Katja Rösler, Wenke Domscheit, and Kerstin P. Hofmann. 2023. “From Paper to Byte: A Workshop Report on the Digital Transformation of Two Thing Editions.” Zenodo. https://doi.org/10.5281/zenodo.8214563 Borillo, Mario, and Jean-Claude Gardin. 1974. Les Banques de Données Archéologiques. Marseille: Éditions du CNRS. Gaines, Sylvia W., ed. 1981. Data Bank Applications in Archaeology. Tucson, AZ: University of Arizona Press. Hofmann, Kerstin P. 2018. “Dingidentitäten Und Objekttransformationen. Einige Überlegungen Zur Edition von Archäologischen Funden.” In Objektepistemologien. Zum Verhältnis von Dingen Und Wissen, edited by Markus Hilgert, Kerstin P. Hofmann, and Henrike Simon, 179–215. Berlin Studies of the Ancient World 59. Berlin: Edition Topoi. https://dx.doi.org/10.17171/3-59 Hofmann, Kerstin P., Susanne Grunwald, Franziska Lang, Ulrike Peter, Katja Rösler, Louise Rokohl, Stefan Schreiber, Karsten Tolle, and David Wigg-Wolf. 2019. “Ding-Editionen. Vom Archäologischen (Be-)Fund Übers Corpus Ins Netz.” E-Forschungsberichte des DAI 2019/2. E-Forschungsberichte Des DAI. Berlin: Deutsches Archäologisches Institut. https://publications.dainst.org/journals/efb/2236/6674 Latour, Bruno. 2005. Reassembling the Social: An Introduction to Actor-Network-Theory. Oxford: Oxford University Press. Lucas, Gavin. 2022. “Archaeology, Typology and Machine Epistemology.” Zenodo. https://doi.org/10.5281/zenodo.7622162 Pickering, Andrew, and Keith Guzik, eds. 2009. The Mangle in Practice: Science, Society, and Becoming. The Mangle in Practice. Science and Cultural Theory. Durham, NC: Duke University Press. Rösler, Katja. 2016. “Mit Den Dingen Rechnen: ‚Kulturen‘-Forschung Und Ihr Geselle Computer.” In Massendinghaltung in Der Archäologie. Der Material Turn Und Die Ur- Und Frühgeschichte, edited by Kerstin P. Hofmann, Thomas Meier, Doreen Mölders, and Stefan Schreiber, 93–110. Leiden: Sidestone Press. | From paper to byte: An interim report on the digital transformation of two thing editions | Auth. Frederic; Rösler, Katja; Domscheit, Wenke; Hofmann, Kerstin P. | <p>One specific form of publication for archaeological objects are catalogues, atlases and corpora. Kerstin Hofmann has introduced the term ‘Ding-Editionen’ (thing editions) for this category of publications that present their data in lists, short... | ![]() | Antiquity, Computational archaeology, Dating, Theoretical archaeology | Felix Riede | 2022-11-08 16:00:49 | View | |
21 Mar 2023
Automation and Novelty –Archaeocomputational Typo-Praxis in the Wake of the Third Science RevolutionRecommended by Shumon Tobias Hussain“Archaeology, Typology and Machine Epistemology” submitted by G. Lucas (1) offers a refreshing and welcome reflection on the role of computer-based practice, type-thinking and approaches to typology in the age of big data and the widely proclaimed ‘Third Science Revolution’ (2–4). At the annual meeting of the EAA in Maastricht in 2017, a special thematic block was dedicated to issues and opportunities linked to the Third Science Revolution in archaeology “because of [its] profound and wide ranging impact on practice and theory in archaeology for the years to come” (5). Even though the Third Science Revolution, as influentially outlined by Kristiansen in 2014 (2), has occasionally also been met with skepticism and critique as to its often implicit scientism and epistemological naivety (6–8), archaeology as a whole seems largely euphoric as to the promises of the advancing ‘revolution’. As Lucas perceptively points out, some even regard it as the long-awaited opportunity to finally fulfil the ambitions and goals of Anglophone processualism. The irony here, as Lucas rightly notes, is that early processualists initially foregrounded issues of theory and scientific epistemology, while much work conducted under the banner of the Third Science Revolution, especially within its computational branches, does not. Big data advocates have echoed Anderson’s much-cited “end of theory” (9) or at least emphatically called for an ‘empirization’ and ‘computationalization’ of theory, often under the banner of ‘data-driven archaeology’ (10), yet typically without much specification of what this is supposed to mean for archaeological theory and reflexivity. The latter is indeed often openly opposed by archaeological Third Science Revolution enthusiasts, arguably because it is viewed as part of the supposedly misguided ‘post-modernist’ project. Lucas makes an original meta-archaeological contribution here and attempts to center the epistemological, ontological and praxeological dimensions of what is actually – in situated archaeological praxis and knowledge-production – put at stake by the mobilization of computers, algorithms and artificial intelligence (AI), including its many but presently under-reflected implications for ordering practices such as typologization. Importantly, his perspective thereby explicitly and deliberately breaks with the ‘normative project’ in traditional philosophy of science, which sought to nail down a universal, prescriptive way of doing science and securing scientific knowledge. He instead focuses on the practical dimensions and consequences of computer-reliant archaeologies, what actually happens on the ground as researchers try to grapple with the digital and the artefactual and try to negotiate new insights and knowledge, including all of the involved messiness – thereby taking up the powerful impetus of the broader practice turn in interdisciplinary science studies and STS (Science and Technology Studies (11)) (12–14), which have recently also re-oriented archaeological self-observation, metatheory and epistemology (15). This perspective on the dawning big data age in archaeology and incurred changes in the status, nature and aims of type-thinking produces a number of important insights, which Lucas fruitfully discusses in relation to promises of ‘automation’ and ‘novelty’ as these feature centrally in the rhetorics and politics of the Third Science Revolution. With regard to automation, Lucas makes the important point that machine or computer work as championed by big data proponents cannot adequately be qualified or understood if we approach the issue from a purely time-saving perspective. The question we have to ask instead is what work do machines actually do and how do they change the dynamics of archaeological knowledge production in the process? In this optic, automation and acceleration achieved through computation appear to make most sense in the realm of the uncontroversial, in terms of “reproducing an accepted way of doing things” as Lucas says, and this is precisely what can be observed in archaeological practice as well. The ramifications of this at first sight innocent realization are far-reaching, however. If we accept the noncontroversial claim that automation partially bypasses the need for specialists through the reproduction of already “pre-determined outputs”, automated typologization would primarily be useful in dealing with and synthesizing larger amounts of information by sorting artefacts into already accepted types rather than create novel types or typologies. If we identity the big data promise at least in part with automation, even the detection of novel patterns in any archaeological dataset used to construct new types cannot escape the fact that this novelty is always already prefigured in the data structure devised. The success of ‘supervised learning’ in AI-based approaches illustrates this. Automation thus simply shifts the epistemological burden back to data selection and preparation but this is rarely realized, precisely because of the tacit requirement of broad non-contentiousness. Minimally, therefore, big data approaches ironically curtail their potential for novelty by adhering to conventional data treatment and input formats, rarely problematizing the issue of data construction and the contested status of (observational) data themselves. By contrast, they seek to shield themselves against such attempts and tend to retain a tacit universalism as to the nature of archaeological data. Only in this way is it possible to claim that such data have the capacity to “speak for themselves”. To use a concept borrowed from complexity theory, archaeological automation-based type-construction that relies on supposedly basal, incontrovertible data inputs can only ever hope to achieve ‘weak emergence’ (16) – ‘strong emergence’ and therefore true, radical novelty require substantial re-thinking of archaeological data and how to construct them. This is not merely a technical question as sometimes argued by computational archaeologies – for example with reference to specifically developed, automated object tracing procedures – as even such procedures cannot escape the fundamental question of typology: which kind of observations to draw on in order to explore what aspects of artefactual variability (and why). The focus on readily measurable features – classically dimensions of artefactual form – principally evades the key problem of typology and ironically also reduces the complexity of artefactual realities these approaches assert to take seriously. The rise of computational approaches to typology therefore reintroduces the problem of universalism and, as it currently stands, reduces the complexity of observational data potentially relevant for type-construction in order to enable to exploration of the complexity of pattern. It has often been noted that this larger configuration promotes ‘data fetishism’ and because of this alienates practitioners from the archaeological record itself – to speak with Marxist theory that Lucas briefly touches upon. We will briefly return to the notion of ‘distance’ below because it can be described as a symptomatic research-logical trope (and even a goal) in this context of inquiry. In total, then, the aspiration for novelty is ultimately difficult to uphold if computational archaeologies refuse to engage in fundamental epistemological and reflexive self-engagement. As Lucas poignantly observes, the most promising locus for novelty is currently probably not to be found in the capacity of the machines or algorithms themselves, but in the modes of collaboration that become possible with archaeological practitioners and specialists (and possibly diverse other groups of knowledge stakeholders). In other words, computers, supercomputers and AI technologies do not revolutionize our knowledge because of their superior computational and pattern-detection capacities – or because of some mysterious ‘superintelligence’ – but because of the specific ‘division of labour’ they afford and the cognitive challenge(s) they pose. Working with computers and AI also often requires to ask new questions or at least to adapt the questions we ask. This can already be seen on the ground, when we pay attention to how machine epistemologies are effectively harnessed in archaeological practice (and is somewhat ironic given that the promise of computational archaeology is often identified with its potential to finally resolve "long-standing (old) questions"). The Third Science Revolution likely prompts a consequential transformation in the structural and material conditions of the kinds of ‘distributed’ processes of knowledge production that STS have documented as characteristic for scientific discoveries and knowledge negotiations more generally (14, 17, 18). This ongoing transformation is thus expected not only to promote new specializations with regard to the utilization of the respective computing infrastructures emerging within big data ecologies but equally to provoke increasing demand for new ways of conceptualizing observations and to reformulate the theoretical needs and goals of typology in archaeology. The rediscovery of reflexivity as an epistemic virtue within big data debates would be an important step into this direction, as it would support the shared goal of achieving true epistemic novelty, which, as Lucas points out, is usually not more than an elusive self-declaration. Big data infrastructures require novel modes of human-machine synergy, which simply cannot be developed or cultivated in an atheoretical and/or epistemological disinterested space. Lucas’ exploration ultimately prompts us to ask big questions (again), and this is why this is an important contribution. The elephant in the room, of course, is the overly strong notion of objectivity on which much computational archaeology is arguably premised – linked to the vow to eventually construct ‘objective typologies’. This proclivity, however, re-tables all the problematic debates of the 1960s and – to speak with the powerful root metaphor of the machine fueling much of causal-mechanistic science (19, 20) – is bound to what A. Wylie (21) and others have called the ‘view from nowhere’. Objectivity, in this latter view, is defined by the absence of positionality and subjectivity – chiefly human subjectivity – and the promise of the machine, and by extension of computational archaeology, is to purify and thus to enhance processes of knowledge production by minimizing human interference as much as possible. The distancing of the human from actual processes of data processing and inference is viewed as positive and sometimes even as an explicit goal of scientific development. Interestingly, alienation from the archaeological record is framed as an epistemic virtue here, not as a burden, because close connection with (or even worse, immersion in) the intricacies of artefacts and archaeological contexts supposedly aggravates the problem of bias. The machine, in this optic, is framed as the gatekeeper to an observer-independent reality – which to the backdoor often not only re-introduces Platonian/Aristotelian pledges to a quasi-eternal fabric of reality that only needs to be “discovered” by applying the right (broadly nonhuman) means, it is also largely inconsistent with defendable and currently debated conceptions of scientific objectivity that do not fall prey to dogma. Furthermore, current discussions on the open AI ChatGPT have exposed the enormous and still under-reflected dangers of leaning into radical renderings of machine epistemology: precisely because of the principles of automation and the irreducible theory-ladenness of all data, ecologies such as ChatGPT tend to reinforce the tacit epistemological background structures on which they operate and in this way can become collaborators in the legitimization and justification of the status quo (which again counteracts the potential for novelty) – they reproduce supposedly established patterns of thought. This is why, among other things, machines and AI can quickly become perpetuators of parochial and neocolonial projects – their supposed authority creates a sense of impartiality that shields against any possible critique. With Lucas, we can thus perhaps cautiously say that what is required in computational archaeology is to defuse the authority of the machine in favour of a new community archaeology that includes machines as (fallible) co-workers. Radically put, computers and AI should be recognized as subjects themselves, and treated as such, with interesting perspectives on team science and collaborative practice.
Bibliography 1. Lucas, G. (2022). Archaeology, Typology and Machine Epistemology. https:/doi.org/10.5281/zenodo.7620824. 2. Kristiansen, K. (2014). Towards a New Paradigm? The Third Science Revolution and its Possible Consequences in Archaeology. Current Swedish Archaeology 22, 11–34. https://doi.org/10.37718/CSA.2014.01. 3. Kristiansen, K. (2022). Archaeology and the Genetic Revolution in European Prehistory. Elements in the Archaeology of Europe. https://doi.org/10.1017/9781009228701 4. Eisenhower, M. S. (1964). The Third Scientific Revolution. Science News 85, 322/332. https://www.sciencenews.org/archive/third-scientific-revolution. 5. The ‘Third Science Revolution’ in Archaeology. http://www.eaa2017maastricht.nl/theme4 (March 16, 2023). 6. Ribeiro, A. (2019). Science, Data, and Case-Studies under the Third Science Revolution: Some Theoretical Considerations. Current Swedish Archaeology 27, 115–132. https://doi.org/10.37718/CSA.2019.06 7. Samida, S. (2019). “Archaeology in times of scientific omnipresence” in Archaeology, History and Biosciences: Interdisciplinary Perspectives, pp. 9–22. https://doi.org/10.1515/9783110616651 8. Sørensen, T. F.. (2017). The Two Cultures and a World Apart: Archaeology and Science at a New Crossroads. Norwegian Archaeological Review 50, 101–115. https://doi.org/10.1080/00293652.2017.1367031 9. Anderson, C. (2008). The end of theory: The data deluge makes the scientific method obsolete. Wired. https://www.wired.com/2008/06/pb-theory/. 10. Gattiglia, G. (2015). Think big about data: Archaeology and the Big Data challenge. Archäologische Informationen 38, 113–124. https://doi.org/10.11588/ai.2015.1.26155 11. Hackett, E. J. (2008). The handbook of science and technology studies, Third edition, MIT Press/Society for the Social Studies of Science. 12. Ankeny, R., Chang, H., Boumans, M. and Boon, M. (2011). Introduction: philosophy of science in practice. Euro Jnl Phil Sci 1, 303. https://doi.org/10.1007/s13194-011-0036-4 13. Soler, L., Zwart, S., Lynch, M., Israel-Jost, V. (2014). Science after the Practice Turn in the Philosophy, History, and Social Studies of Science, Routledge. 14. Latour, B. and Woolgar, S. (1986). Laboratory life: the construction of scientific facts, Princeton University Press. 15. Chapman, R. and Wylie, A. (2016) Evidential reasoning in archaeology, Bloomsbury Academic. 16. Greve, J. and Schnabel, A. (2011). Emergenz: zur Analyse und Erklärung komplexer Strukturen, Suhrkamp. 17. Shapin, S., Schaffer, S. and Hobbes, T. (1985). Leviathan and the air-pump: Hobbes, Boyle, and the experimental life, including a translation of Thomas Hobbes, Dialogus physicus de natura aeris by Simon Schaffer, Princeton University Press. 18. Galison, P. L. and Stump, D. J. (1996).The Disunity of Science: Boundaries, Contexts, and Power, Stanford University Press. 19. Pepper, S. C. (1972). World hypotheses: a study in evidence, 7. print, University of California Press. 20. Hussain, S. T. (2019). The French-Anglophone divide in lithic research: A plea for pluralism in Palaeolithic Archaeology, Open Access Leiden Dissertations. https://hdl.handle.net/1887/69812 21. A. Wylie, A. (2015). “A plurality of pluralisms: Collaborative practice in archaeology” in Objectivity in Science, pp. 189-210, Springer. https://doi.org/10.1007/978-3-319-14349-1_10 | Archaeology, Typology and Machine Epistemology | Gavin Lucas | <p>In this paper, I will explore some of the implications of machine learning for archaeological method and theory. Against a back-drop of the rise of Big Data and the Third Science Revolution, what lessons can be drawn from the use of new digital... | Computational archaeology, Theoretical archaeology | Shumon Tobias Hussain | Anonymous, Rachel Crellin | 2022-10-31 15:25:38 | View | |
26 Oct 2022
![]() 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 https://doi.org/10.31235/osf.io/a5tgpUsing Cactus Thorns to Drill Quartz: A Proof of ConceptRecommended by Donatella Usai and Jonathan HannaQuartz 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. References:
| Technological analysis and experimental reproduction of the techniques of perforation of quartz beads from the Ceramic period in the Antilles | Madeleine 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, Traceology | Donatella Usai | 2022-09-06 14:01:51 | View | |
12 Dec 2022
![]() Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?Romain Cottereau, Katia Ortiz, Yann Locatelli, Alexandra Houssaye*, Thomas Cucchi* https://doi.org/10.1101/2022.08.22.504790Mobility in pigs: A microanatomical perspectiveRecommended by Nimrod MaromPig 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.
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, Zooarchaeology | Nimrod Marom | 2022-08-26 20:29:01 | View | |
01 Dec 2022
![]() Surface texture analysis in Toothfrax and MountainsMap® SSFA module: Different software packages, different results?Ivan CALANDRA, Konstantin BOB, Gildas MERCERON, François BLATEYRON, Andreas HILDEBRANDT, Ellen SCHULZ-KORNAS, Antoine SOURON, Daniela E. WINKLER https://doi.org/10.5281/zenodo.4671438An important comparison of software for Scale Sensitive Fractal Analysis : are ancient and new results compatible?Recommended by Alain QueffelecThe community of archaeologists, bioanthropologist and paleontologists relying on tools use-wear and dental microwear has grown in the recent years, mainly driven by the spread of confocal microscopes in the laboratories. If the diversity of microscopes is quite high, the main software used for 3D surface texture data analysis are mostly different versions of the same Mountains Map core. In addition to this software, since the beginning of 3D surface texture analysis in dental microwear, surface sensitive fractal analysis (SSFA) initially developed for industrial research (Brown & Savary, 1991) have been performed in our disciplines with the Sfrax/Toothfrax software for two decades (Ungar et al., 2003). This software being discontinued, these calculations have been integrated to the new versions of Mountains Map, with multi-core computing, full integration in the software and an update of the calculation itself. New research based on these standard parameters of surface texture analysis will be, from now on, mainly calculated with this new add-on of Mountains Map, and will be directly compared with the important literature based on the previous software. The question addressed by Calandra et al. (2022), gathering several prominent researchers in this domain including the Mountains Map developer F. Blateyron, is key for the future research: can we directly compare SSFA results from both software? Thanks to a Bayesian approach to this question, and comparing results calculated with both software on three different datasets (two on dental microwear, one on lithic raw materials), the authors show that the two software gives statistically different results for all surface texture parameters tested in the paper. Nevertheless, applying the new calculation to the datasets, they also show that the results published in original studies with these datasets would have been similar. Authors also claim that in the future, researchers will need to re-calculate the fractal parameters of previously published 3D surfaces and cannot simply integrate ancient and new data together. We also want to emphasize the openness of the work published here. All datasets have been published online and will be probably very useful for future methodological works. Authors also published their code for statistical comparison of datasets, and proposed a fully reproducible article that allowed the reviewers to check the content of the paper, which can also make this article of high interest for student training. This article is therefore a very important methodological work for the community, as noted by all three reviewers. It will certainly support the current transition between the two software packages and it is necessary that all surface texture specialists take these results and the recommendation of authors into account: calculate again data from ancient measurements, and share the 3D surface measurements on open access repositories to secure their access in the future. References Brown CA, and Savary G (1991) Describing ground surface texture using contact profilometry and fractal analysis. Wear, 141, 211–226. https://doi.org/10.1016/0043-1648(91)90269-Z Calandra I, Bob K, Merceron G, Blateyron F, Hildebrandt A, Schulz-Kornas E, Souron A, and Winkler DE (2022) Surface texture analysis in Toothfrax and MountainsMap® SSFA module: Different software packages, different results? Zenodo, 7219877, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7219877 Ungar PS, Brown CA, Bergstrom TS, and Walker A (2003) Quantification of dental microwear by tandem scanning confocal microscopy and scale-sensitive fractal analyses. Scanning: The Journal of Scanning Microscopies, 25, 185–193. https://doi.org/10.1002/sca.4950250405 | Surface texture analysis in Toothfrax and MountainsMap® SSFA module: Different software packages, different results? | Ivan CALANDRA, Konstantin BOB, Gildas MERCERON, François BLATEYRON, Andreas HILDEBRANDT, Ellen SCHULZ-KORNAS, Antoine SOURON, Daniela E. WINKLER | <p>The scale-sensitive fractal analysis (SSFA) of dental microwear textures is traditionally performed using the software Toothfrax. SSFA has been recently integrated to the software MountainsMap® as an optional module. Meanwhile, Toothfrax suppor... | ![]() | Computational archaeology, Palaeontology, Traceology | Alain Queffelec | Anonymous, John Charles Willman, Antony Borel | 2022-07-07 09:58:50 | View |
21 Nov 2022
![]() Removing Barriers to Reproducible Research in ArchaeologyEmma Karoune and Esther Plomp https://doi.org/10.5281/zenodo.7320029Three levels of reproducible workflow remove barriers for archaeologists and increase accessibilityRecommended by Ben MarwickOver 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, 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
| Removing Barriers to Reproducible Research in Archaeology | Emma 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 archaeology | Ben Marwick | 2022-06-07 10:02:46 | View | |
20 Jul 2022
![]() Faunal remains from the Upper Paleolithic site of Nahal Rahaf 2 in the southern Judean Desert, IsraelNimrod Marom, Dariya Lokshin Gnezdilov, Roee Shafir, Omry Barzilai, Maayan Shemer https://doi.org/10.1101/2022.05.17.492258New zooarchaeological data from the Upper Palaeolithic site of Nahal Rahaf 2, IsraelRecommended by Ruth BlascoThe Levantine Corridor is considered a crossing point to Eurasia and one of the main areas for detecting population flows (and their associated cultural and economic changes) during the Pleistocene. This area could have been closed during the most arid periods, giving rise to processes of population isolation between Africa and Eurasia and intermittent contact between Eurasian human communities [1,2]. Zooarchaeological studies of the early Upper Palaeolithic assemblages constitute an important source of knowledge about human subsistence, making them central to the debate on modern behaviour. The Early Upper Palaeolithic sequence in the Levant includes two cultural entities – the Early Ahmarian and the Levantine Aurignacian. This latter is dated to 39-33 ka and is considered a local adaptation of the European Aurignacian techno-complex. In this work, the authors present a zooarchaeological study of the Nahal Rahaf 2 (ca. 35 ka) archaeological site in the southern Judean Desert in Israel [3]. Zooarchaeological data from the early Upper Paleolithic desert regions of the southern Levant are not common due to preservation problems of non-lithic finds. In the case of Nahal Rahaf 2, recent excavation seasons brought to light a stratigraphical sequence composed of very well-preserved archaeological surfaces attributed to the 'Arkov-Divshon' cultural entity, which is associated with the Levantine Aurignacian. This study shows age-specific caprine (Capra cf. Capra ibex) hunting on prime adults and a generalized procurement of gazelles (Gazella cf. Gazella gazella), which seem to have been selectively transported to the site and processed for within-bone nutrients. An interesting point to note is that the proportion of goats increases along the stratigraphic sequence, which suggests to the authors a specialization in the economy over time that is inversely related to the occupational intensity of use of the site. It is also noteworthy that the materials represent a large sample compared to previous studies from the Upper Paleolithic of the Judean Desert and Negev. In summary, this manuscript contributes significantly to the study of both the palaeoenvironment and human subsistence strategies in the Upper Palaeolithic and provides another important reference point for evaluating human hunting adaptations in the arid regions of the southern Levant. References [1] Bermúdez de Castro, J.-L., Martinon-Torres, M. (2013). A new model for the evolution of the human pleistocene populations of Europe. Quaternary Int. 295, 102-112. https://doi.org/10.1016/j.quaint.2012.02.036 [2] Bar-Yosef, O., Belfer-Cohen, A. (2010). The Levantine Upper Palaeolithic and Epipalaeolithic. In Garcea, E.A.A. (Ed), South-Eastern Mediterranean Peoples Between 130,000 and 10,000 Years Ago. Oxbow Books, pp. 144-167. [3] Marom, N., Gnezdilov, D. L., Shafir, R., Barzilai, O. and Shemer, M. (2022). Faunal remains from the Upper Paleolithic site of Nahal Rahaf 2 in the southern Judean Desert, Israel. BioRxiv, 2022.05.17.492258, ver. 4 peer-reviewed and recommended by Peer community in Archaeology. https://www.biorxiv.org/content/10.1101/2022.05.17.492258v4 | Faunal remains from the Upper Paleolithic site of Nahal Rahaf 2 in the southern Judean Desert, Israel | Nimrod Marom, Dariya Lokshin Gnezdilov, Roee Shafir, Omry Barzilai, Maayan Shemer | <p>Nahal Rahaf 2 (NR2) is an Early Upper Paleolithic (ca. 35 kya) rock shelter in the southern Judean Desert in Israel. Two excavation seasons in 2019 and 2020 revealed a stratigraphical sequence composed of intact archaeological surfaces attribut... | ![]() | Upper Palaeolithic, Zooarchaeology | Ruth Blasco | Joana Gabucio | 2022-05-19 06:16:47 | View |
26 Sep 2022
![]() The management of symbolic raw materials in the Late Upper Paleolithic of South-Western France: a shell ornaments perspectiveSolange Rigaud, John O’Hara, Laurent Charles, Elena Man-Estier, Patrick Paillet https://doi.org/10.31235/osf.io/z7pqgCaching up with the study of the procurement of symbolic raw materials in the Upper PalaeolithicRecommended by Beatrice Demarchi based on reviews by Begoña Soler Mayor , Catherine Dupont and Lawrence StrausThe manuscript "The management of symbolic raw materials in the Late Upper Paleolithic of South-Western France: a shell ornaments perspective" by Solange Rigaud and colleagues (Rigaud et al. 2022) is a perfect demonstration that appropriate scientific methodologies can be used effectively in order to enhance the historical value of findings from “old” collections, despite the lack of secure stratigraphic and contextual data. The shell assemblage (n = 377) investigated here (from Rochereil, Dordogne) had been excavated during the first half of the 20th century (Jude 1960) and reported in 1993 (Taborin 1993), but only this recent analysis revealed that it was composed of largely unmodified mollusc shells, most of allochthonous origin. Rigaud et al. interpret this finding as the raw materials used to produce personal ornaments. This is especially significant, because the focus of research has been on the manufacture, use and exchange of personal ornaments in prehistory, much less so on the procurement of the raw materials. As such, the manuscript adds substantially to the growing literature on Magdalenian social networks. The authors carried out detailed taxonomic analysis based on morphological and morphometric characteristics and identified at least nine different species, including Dentalium sp., Ocenebra erinaceus, Tritia reticulata and T. gibbosula, as well as some bivalve specimens (Mytilus, Glycymeris, Spondylus, Pecten). Most of the species are commonly found in personal ornament assemblages from the Magdalenian, reflecting intentional selection (also shown by the size sorting of some of the taxa), and cultural continuity. However, microscopic examinations revealed securely-identified anthropogenic modifications on a very limited number of specimens: one Glycymeris valve (used as an ochre container), one Cardiidae valve (presence of a groove), one perforated Tritia gibbosula and two perforated Tritia reticulata bearing striations. The authors interpret this combination of anthropogenic vs natural “signals” as signifying that the assemblage represents raw material selected and stored for further processing. Assessing the provenance and age of the shells is therefore paramount: the shells found at Rochereil belong to species that can be found on both the Atlantic and Mediterranean coasts. Assuming that molluscan taxa distribution in the past is comparable to that for the present day, this implies the exploitation of two catchment areas and long-distance transportation to the site: taking sea-level changes into account, during the Magdalenian the Mediterranean used to lie at a distance of 350 km from Rochereil, and the Atlantic was not significantly closer (~200 km). Importantly, exploitation of fossil shells cannot be discounted on the basis of the data presented here; direct dating of some of the specimens (e.g. by radiocarbon, or amino acid racemisation geochronology) would be beneficial to clarify this issue and in general to improve chronological control on the accumulation of shells. Nonetheless, the authors argue that the closest fossil deposits also lie more than 200 km away from the site, thus the material is allochthonous in origin. In synthesis, the Rochereil assemblage represents an important step towards a better understanding of the procurement chain and of the production of ornaments during the European Upper Palaeolithic. References Jude, P. E. (1960). La grotte de Rocherreil: station magdalénienne et azilienne, Masson. Rigaud, S., O'Hara, J., Charles, L., Man-Estier, E. and Paillet, P. (2022) The management of symbolic raw materials in the Late Upper Paleolithic of South-Western France: a shell ornaments perspective. SocArXiv, z7pqg, ver. 4 peer-reviewed and recommended by Peer community in Archaeology. https://doi.org/10.31235/osf.io/z7pqg Taborin, Y. (1993). La parure en coquillage au Paléolithique, CNRS éditions. | The management of symbolic raw materials in the Late Upper Paleolithic of South-Western France: a shell ornaments perspective | Solange Rigaud, John O’Hara, Laurent Charles, Elena Man-Estier, Patrick Paillet | <p>Personal ornaments manufactured on marine and fossil shell are a significant element of Upper Palaeolithic symbolic material culture, and are often found at considerable distances from Pleistocene coastlines or relevant fossil deposits. Here, w... | ![]() | Europe, Symbolic behaviours, Upper Palaeolithic | Beatrice Demarchi | 2022-04-23 19:20:02 | View | |
30 Sep 2022
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 https://doi.org/10.1101/2022.03.13.483627Assessing glutamine deamination in ancient parchment samplesRecommended by Beatrice Demarchi based on reviews by Maria Codlin and 3 anonymous reviewersData 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 data | Bharath 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, Zooarchaeology | Beatrice Demarchi | 2022-03-22 12:54:10 | View |
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