​The paper “Percolation Package – From Script Sharing to Package Publication” by Sophie C. Schmidt and Simon Maddison (2023) describes the development of an R package designed to apply Percolation Analysis to archaeological spatial data. In an earlier publication, Maddison and Schmidt (2020) describe Percolation Analysis and provide case studies that demonstrate its usefulness at different spatial scales. In the current paper, the authors use their experience collaborating to develop the R package as part of a broader argument for the importance of code sharing to the research process. 

The paper begins by describing the development process of the R package, beginning with borrowing code from a geographer, refining it to fit archaeological case studies, and then collaborating to further refine and systematize the code into an R package that is more easily reusable by other researchers. As the review by Joe Roe noted, a strength of the paper is “presenting the development process as it actually happens rather than in an idealized form.” The authors also include a section about the lessons learned from their experience. 

Moving on from the anecdotal data of their own experience, the authors also explore code sharing practices in archaeology by briefly examining two datasets. One dataset comes from “open-archaeo” (https://open-archaeo.info/), an on-line list of open-source archaeological software maintained by Zack Batist. The other dataset includes articles published between 2018 and 2023 in the Journal of Computer Applications in Archaeology. Schmidt and Maddison find that these two datasets provide contrasting views of code sharing in archaeology: many of the resources in the open-archaeo list are housed on Github, lack persistent object identifiers, and many are not easily findable (other than through the open-archaeo list). Research software attached to the published articles, on the other hand, is more easily findable either as a supplement to the published article, or in a repository with a DOI.

The examination of code sharing in archaeology through these two datasets is preliminary and incomplete, but it does show that further research into archaeologists’ code-writing and code-sharing practices could be useful. Archaeologists often create software tools to facilitate their research, but how often?  How often is research software shared with published articles? How much attention is given to documentation or making the software usable for other researchers? What are best (or good) practices for sharing code to make it findable and usable? Schmidt and Maddison’s paper provides partial answers to these questions, but a more thorough study of code sharing in archaeology would be useful. Differences among journals in how often they publish articles with shared code, or the effects of age, gender, nationality, or context of employment on attitudes toward code sharing seem like obvious factors for a future study to consider.

Shared code that is easy to find and easy to use benefits the researchers who adopt code written by others, but code authors also have much to gain by sharing. Properly shared code becomes a citable research product, and the act of code sharing can lead to productive research collaborations, as Schmidt and Maddison describe from their own experience. The strength of this paper is the attention it brings to current code-sharing practices in archaeology. I hope the paper will also help improve code sharing in archaeology by inspiring more archaeologists to share their research code so other researchers can find and use (and cite) it. 

References

Maddison, M.S. and Schmidt, S.C. (2020). Percolation Analysis – Archaeological Applications at Widely Different Spatial Scales. Journal of Computer Applications in Archaeology, 3(1), p.269–287. https://doi.org/10.5334/jcaa.54 

Schmidt, S. C., and Maddison, M. S. (2023). Percolation Package - From script sharing to package publication, Zenodo, 7966497, ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7966497

The advent of biomolecular methods has certainly increased our overall comprehension of archaeological societies. One of the materials of choice to perform ancient DNA or proteomics analyses is dental calculus[1,2], a mineralised biofilm formed during the life of one individual. Research conducted in the past few decades has demonstrated the potential of dental calculus to retrieve information about past societies health[3–6], diet[7–11], and more recently, as a putative proxy for isotopic analyses[12]. 

Based on a proof-of-concept previously published by their team[13], Bartholdy and collaborators’ paper presents the identification of compounds and their secondary metabolites derived from consumed plants in individuals from a XIXth century rural Dutch archaeological deposit[14]. Sørensen indeed demonstrated that drug intake is recorded in dental calculus, which are mineralised biofilms that can encapsulate drug compounds long after the latter are no longer detectable in blood. The liquid-chromatography coupled to mass spectrometry (LC-MS/MS)-based method developed showed the potential for archaeological applications[13]. 

Bartholdy et al. utilised the developed LC-MS/MS method to 41 buried individuals, most of them bearing pipe notches on their teeth, from the cemetery of the 19th rural settlement of Middenbeemster, the Netherlands. Along with dental calculus sampling and analysis, they undertook the skeletal and dental examination of all of the specimens in order to assess sex, age-at-death, and pathology on the two tissues. The results obtained on the dental calculus of the sampled individuals show probable consumption of tea, coffee and tobacco indicated by the detection of the various plant compounds and associated metabolites (caffeine, nicotine and salicylic acid, amongst others). 

The authors were able to place their results in perspective and propose several interpretations concerning the ingestion of plant-derived products, their survival in dental calculus and the importance of their findings for our overall comprehension of health and habits of the XIXth c. Dutch population. The paper is well-written and accessible to a non-specialist audience, maximising the impact of their study. I personally really enjoyed handling this manuscript that is not only a good piece of scientific literature but also a pleasant read, the reason why I warmly recommend this paper to be accessible through PCI Archaeology.

References

1.      Fagernäs, Z. and Warinner, C. (2023) Dental Calculus. in Handbook of Archaeological Sciences 575–590. https://doi.org/10.1002/9781119592112.ch28

2.      Wright, S. L., Dobney, K. & Weyrich, L. S. (2021) Advancing and refining archaeological dental calculus research using multiomic frameworks. STAR: Science & Technology of Archaeological Research 7, 13–30. https://doi.org/10.1080/20548923.2021.1882122

3.      Fotakis, A. K. et al. (2020) Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 375, 20190584. https://doi.org/10.1098/rstb.2019.0584

4.      Warinner, C. et al. (2014) Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344. https://doi.org/10.1038/ng.2906

5.      Weyrich, L. S. et al. (2017) Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature 544, 357–361. https://doi.org/10.1038/nature21674

6.      Jersie-Christensen, R. R. et al. (2018) Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. Nat. Commun. 9, 4744. https://doi.org/10.1038/s41467-018-07148-3

7.      Hendy, J. et al. (2018) Proteomic evidence of dietary sources in ancient dental calculus. Proc. Biol. Sci. 285. https://doi.org/10.1098/rspb.2018.0977

8.      Wilkin, S. et al. (2020) Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years. Nat Ecol Evol 4, 346–355. https://doi.org/10.1038/s41559-020-1120-y

9.      Bleasdale, M. et al. (2021) Ancient proteins provide evidence of dairy consumption in eastern Africa. Nat. Commun. 12, 632. https://doi.org/10.1038/s41467-020-20682-3

10.   Warinner, C. et al. (2014) Direct evidence of milk consumption from ancient human dental calculus. Sci. Rep. 4, 7104. https://doi.org/10.1038/srep07104

11.   Buckley, S., Usai, D., Jakob, T., Radini, A. and Hardy, K. (2014) Dental Calculus Reveals Unique Insights into Food Items, Cooking and Plant Processing in Prehistoric Central Sudan. PLoS One 9, e100808. https://doi.org/10.1371/journal.pone.0100808

12.   Salazar-García, D. C., Warinner, C., Eerkens, J. W. and Henry, A. G. (2023) The Potential of Dental Calculus as a Novel Source of Biological Isotopic Data. in Exploring Human Behavior Through Isotope Analysis: Applications in Archaeological Research (eds. Beasley, M. M. & Somerville, A. D.) 125–152. https://doi.org/10.1007/978-3-031-32268-6_6

13.   Sørensen, L. K., Hasselstrøm, J. B., Larsen, L. S. and Bindslev, D. A. (2021) Entrapment of drugs in dental calculus - Detection validation based on test results from post-mortem investigations. Forensic Sci. Int. 319, 110647. https://doi.org/10.1016/j.forsciint.2020.110647

14.   Bartholdy, Bjørn Peare, Hasselstrøm, Jørgen B., Sørensen, Lambert K., Casna, Maia, Hoogland, Menno, Historisch Genootschap Beemster and Henry, Amanda G. (2023) Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population, Zenodo, 7649150, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7649150

This paper (2023) describes The Living Hill project dedicated to the archaeological park and fortress of Poggio Imperiale in Poggibonsi, Italy. The project is a collaboration between the Poggibonsi excavation and Entertainment Games App, Ltd. From the start, the project focused on the question of the intended audience rather than on the used technology. It was therefore planned to involve the audience in the creation of the game itself, which was not possible after all due to the covid pandemic. Nevertheless, the game aimed towards a visit experience as close as possible to reality to offer an educational tool through the video game, as it offers more periods than the medieval period showcased in the archaeological park itself.

The game mechanics differ from a walking simulator, or a virtual tour and the player is tasked with returning three lost objects in the virtual game. While the medieval level was based on a 3D scan of the archaeological park, the other two levels were reconstructed based on archaeological material. Currently, only a PC version is working, but the team works on a mobile version as well and teased the possibility that the source code will be made available open source. Lastly, the team also evaluated the game and its perception through surveys, interviews, and focus groups. Although the surveys were only based on 21 persons, the results came back positive overall.

The paper is well-written and follows a consistent structure. The authors clearly define the goals and setting of the project and how they developed and evaluated the game. Although it has be criticized that the game is not playable yet and the size of the questionnaire is too low, the authors clearly replied to the reviews and clarified the situation on both matters. They also attended to nearly all of the reviewers demands and answered them concisely in their response. In my personal opinion, I can fully recommend this paper for publication.

For future works, it is recommended that the authors enlarge their audience for the quesstionaire in order to get more representative results. It it also recommended to make the game available as soon as possible also outside of the archaeological park. I would also like to thank the reviewers for their concise and constructive criticism to this paper as well as for their time.

References

Mariotti, Samanta. (2023) Transforming the Archaeological Record Into a Digital Playground: a Methodological Analysis of The Living Hill Project, Zenodo, 8302563, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology https://doi.org/10.5281/zenodo.8302563

The 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.

The paper “Research workflows, paradata, and information visualisation: feedback on an exploratory integration of issues and practices - MEMORIA IS” (Dudek & Blaise, 2023) describes a prototype of an information system developed to improve the traceability, transmissibility and verifiability of archaeological research workflows. A key aspect of the work with MEMORIA is to make research documentation and the workflows underpinning the conducted research more approachable and understandable using a series of visual interfaces that allow users of the system to explore archaeological documentation, including metadata describing the data and paradata that describes its underlying processes. The work of Dudek and Blaise address one of the central barriers to reproducibility and transparency of research data and propose a set of both theoretically and practically well-founded tools and methods to solve this major problem. From the reported work on MEMORIA IS, information visualisation and the proposed tools emerge as an interesting and potentially powerful approach for a major push in improving the traceability, transmissibility and verifiability of research data through making research workflows easier to approach and understand.

In comparison to technical work relating to archaeological data management, this paper starts commendably with a careful explication of the conceptual and epistemic underpinnings of the MEMORIA IS both in documentation research, knowledge organisation and information visualisation literature. Rather than being developed on the basis of a set of opaque assumptions, the meticulous description of the MEMORIA IS and its theoretical and technical premises is exemplary in its transparence and richness and has potential for a long-term impact as a part of the body of literature relating to the development of archaeological documentation and documentation tools. While the text is sometimes fairly densely written, it is worth taking the effort to read it through. Another major strength of the paper is that it provides a rich set of examples of the workings of the prototype system that makes it possible to develop a comprehensive understanding of the proposed approaches and assess their validity.

As a whole, this paper and the reported work on MEMORIA IS forms a worthy addition to the literature on and practical work for developing critical infrastructures for data documentation, management and access in archaeology. Beyond archaeology and the specific context of the discussed work discussed this paper has obvious relevance to comparable work in other fields.

References