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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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

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

​​This paper [1] covers an interesting topic in that it presents through ethnography an insight into a traditional method of food production which is gradually declining in use. In addition to preserving traditional knowledge, the ethnographic study of grinding stones has the potential for showing how similar tools may have been used by people in the past, particularly from the same geographic region.

[1] Thongdok Norbu J., Nimasow Gibji, Nimasow Oyi D. (2021) Ran-thok and Ling-chhom: indigenous grinding stones of Shertukpen tribes of Arunachal Pradesh, India. Zenodo, 5118675, ver. 4 peer-reviewed and recommended by PCI Archaeo. doi: https://doi.org/10.5281/zenodo.5118675

Tektites, a naturally occurring glass produced by major cosmic impacts and ejected at long distances, are known from five impacts worldwide [1]. The presence of this impact-generated glass, which can be dated in the same way as a volcanic rock, has been used to date archaeological sites in several regions of the world. This paper by Marwick and colleagues [2] reviews and adds new data on the use and misuse of this specific material as a chronological marker in Australia, East and Southeast Asia, where an impact dated to 0.78 Ma created and widely distributed tektites. This material, found in archaeological excavations in China, Laos, Thaïland, Australia, Borneo, and Vietnam, has been used to date layers containing lithic artifacts, sometimes creating a strong debate about the antiquity of the occupation and lithic production in certain regions.

The review of existing data shows that geomorphological data and stratigraphic integrity can be questioned at many sites that have yielded tektites. The new data provided by this paper for five archaeological sites located in Vietnam confirm that many deposits containing tektites are indeed lag deposits and that these artifacts, thus in secondary position, cannot be considered to date the layer. This study also emphasizes the general lack of other dating methods that would allow comparison with the tektite age. In the Vietnamese archaeological sites presented here, discrepancies between methods, and the presence of historical artifacts, confirm that the layers do not share similar age with the cosmic impact that created the tektites.

Based on this review and these new results, and following previous propositions [3], Marwick and colleagues conclude that, if tektites can be used as chronological markers, one has to prove that they are in situ. They propose that geomorphological assessment of the archaeological layer as primary deposit must first be attained, in addition to several parameters of the tektites themselves (shape, size distribution, chemical composition). Large error can be made by using only tektites to date an archaeological layer, and this material should not be used solely due to risks of high overestimation of the age of the archaeological production. 

[1] Rochette, P., Beck, P., Bizzarro, M., Braucher, R., Cornec, J., Debaille, V., Devouard, B., Gattacceca, J., Jourdan, F., Moustard, F., Moynier, F., Nomade, S., Reynard, B. (2021). Impact glasses from Belize represent tektites from the Pleistocene Pantasma impact crater in Nicaragua. Communications Earth & Environment, 2(1), 1–8, https://doi.org/10.1038/s43247-021-00155-1

[2] Marwick, B., Son, P. T., Brewer, R., Wang, L.-Y. (2022). Tektite geoarchaeology in mainland Southeast Asia. SocArXiv, 93fpa, ver. 6 peer-reviewed and recommended by PCI Archaeology, https://doi.org/10.31235/osf.io/93fpa.

[3] Tada, T., Tada, R., Chansom, P., Songtham, W., Carling, P. A., Tajika, E. (2020). In Situ Occurrence of Muong Nong-Type Australasian Tektite Fragments from the Quaternary Deposits near Huai Om, Northeastern Thailand. Progress in Earth and Planetary Science 7(1), 1–15, https://doi.org/10.1186/s40645-020-00378-4