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Databse Fun: Of Databases, Statistics and Isotopes

25 Nov

I know what you are thinking – what sort of misspelled title is that for a blog post? The answer is below dear reader (1)!

Databases are, in my humble opinion, awful, tedious and time consuming beasts to create and are often best tackled head on armed only with a black coffee for sustenance as you try to accurately type a mind-numbing amount of data into an excel spreadsheet at 2am in the university library.  (That may just be my experience though!).  The beauty of a completed database, however, cannot be overestimated.  This is where you get to test out hypotheses based on the data that you have selected and gathered for your research question, where all of the core information lies and where the data can be repeatedly and demonstratively tested again and again.  A completed and ordered database is a thing of beauty and, when looked at 6am in the morning after a tiring night of inputting data, a thing of magnificence!

But let’s start at the beginning.  I recently had cause to look again at the database I had made for my MSc dissertation and, as I scrolled across and down the excel spreadsheet, I could just about remember the hours I had spent producing the spreadsheet, justifying the column titles and entering the data itself.  My data set included strontium isotopic results gathered from 422 individuals across 9 different sites from the Neolithic Linearbandkeramik (LBK, roughly 5500BC to 4800BC) culture of Central Europe, with my sample ranging geographically from the modern countries of Austria, Czech Republic and Germany. The data set used for my study was carefully culled from a literature review and a close reading of a number of journal articles that were available at that time (mid 2012).

My aim was to investigate statistically the claim of patrilocality in the LBK culture as proposed by Bentley et al. (2012) by investigating the specific sex and age differences within the profile group by using strontium isotopes as proxies.  Strontium isotopes samples (specifically 87Sr/86Sr) are often taken from both human and animal skeletal remains (primarily from teeth, specifically the 1st, 2nd and 3rd molars as they reflect Sr values throughout the life of an individual) as it survives well in archaeological contexts and is an informative approach to investigate mobility and local/non-local status of individuals.  Strontium values reflect geochemical signatures in the dietary component of the individuals, which comes from the soils and the underlying geological landscape that the individual lived on.  There are issues with this method (2) (see also this blog’s comments section).  Strontium isotopic investigations in archaeology are often studied in conjunction with oxygen isotopes (18O/16O) sampled from tooth enamel as well (specifically the 2nd molar) which represents water drank in life, but, frustratingly, this has not been the case in the LBK literature.

I knew that I wanted to statistically test the data set using SPSS 19, the standard statistical program widely used in the social sciences, but I first needed to tabulate and code the data so it would be useful when it came to testing the data.  As the study also included comparisons of the funerary grave goods and a basic demographic investigation of each site coding the entries (1=male, 2=female or 1=present 2=absent) allowed for comparisons to be made in the SPSS program and for statistical tests to be carried out.  The strontium itself was, as expected, non-parametric, which meant that the data adhered to no specific characteristic structure or parameter.

nonparamet

The normality test, using the Kolmogorov-Smirnov and Shapiro-Wilk statistical tests, indicates that the strontium data used for this study of the 422 individuals was not distributed normally (the P-value, nominally a significance value, is 0.000 for these tests). This means that tests such Spearman’s Rho correlation (quantity between variation), Mann-Whitney U (2 independent variables) and Kruskal-Wallis (3 or more independent variables) are the most appropriate statistical tests to perform on this data set (Bryman & Cramer 2011: 245).

When building the database I also wanted any relevant information and references easy to hand so I included the skeletal number (as given in the articles), site name, period, sex, sex code, isotope source, body position, funerary artefacts found and reference etc for each individual used in the study (see below).

MScdatabase

A screen shot of the database used in my MSc dissertation displaying the revelent information of the 422 individuals from the LBK sites used in the study. The data was entered in a Excel spreadsheet before being transferred to SPSS for statistical investigation. Click to enlarge.

The data was carefully added over a number of days once I had gathered all the required journal articles discussing the sites I had chosen  The sites themselves were largely located in southern Germany, with the 9 sites nicely split into three time periods throughout the chronology of the LBK period.  Perhaps somewhat hastily I added this to the database and assigned the values of the individuals with a Early, Middle and Late ranking for their respective site.

MScdatabase22

Towards the bottom of the database used for the study. Here we can see the references cited for each site used in the study and the specific coding for funerary items (the two columns before reference column on the right hand side, where 1 depicts present and 0 absent).

During the construction of this database I did encounter problems as I had not built such a large database before, indeed the only time I had really used a database properly was for my undergraduate dissertation some years previous whilst using ArcGIS.  The problems this time included whether I was actually coding the funerary items the right way round or not, reading back through the database and correcting any errors in typing (especially for the strontium values) and making sure I correctly identifying the individuals used in their respective articles.  There are some things inherent in archaeology that cannot be solved.  This includes lacking contextual data or written site reports (which may or may not exist hidden in regional archaeological unit headquarters, not known or available to the public or indexed on any site).

Of course there were problems with my approach, which I expounded on in fuller detail in the thesis itself.  This did include problems interpreting the strontium results and distinguishing between local and non-local individuals at the site when there is no reference data to compare it to and debating my own statistical approach.  Still, as frustrating as building the database was, I did enjoy carrying out my own investigation of it immensely.  On rainy days I often think that my dataset could do with a second look at and investigation, perhaps I could change this approach or that, use this statistical method instead and isolate that clump of individuals etc.

It may be a pipe dream for the moment (I lack a working SPSS program for one!) but this is as much of a key part of archaeology and archaeological research as digging in the mud is.  Research is what drives archaeology and human osteology forward, from new scientific techniques to reviewing old data and finding new patterns.  The past is always present in new technology, you just have to drive it forward sometimes.

I will be introducing the Neolithic LBK culture in further detail in an upcoming post and discussing the merits of my thesis in further detail in another post.  For now I hope you have enjoyed this brief delve into what was the core of that research, the database itself.

Notes:

(1.) This post was named in honour of a spelling mistake I made in the contents pages of my MSc thesis, spotted only when I proudly showed a friend a copy of the thesis a few weeks after the hand in date.  This, of course, led to gales of laughter from both of us (and to my internal cringing) as my poor editing skills came to light and it still remains a favoured joke to this day.

(2.) A few problems have become apparent with the strontium isotope technique, as with any mature and widespread application of a scientific technique, and it is worth mentioning them here (Bentley et al. 2004: 366).

Firstly is the issue of what a local and non-local signature mean for the prehistoric individual, as technically the 87Sr/86Sr ratio reflects diet over a period of time, and said food could have come from non-local sources.  However, this could be a distinct benefit, as it may be possible to identify individuals whose subsistence activity took place over a diverse range of territories (Bentley et al. 2004: 366, Price et al. 2002: 131).  Secondly, diagenesis affects anything buried and groundwater strontium has a tendency to penetrate the skeleton after burial (Bentley et al. 2004: 366).  In this study only enamel from the permanent dentition (1st or 2nd molars) is used, as this mitigates the effects of diagenesis because enamel is a strong biological material containing large mineral crystals, rendering it much less porous than bone and it is highly resistant to biochemical alteration (Killgrove 2010, Richards et al. 2008).  The third issue concerns the environmental heterogeneity of the strontium isotope signatures, which as Bentley (et al 2004: 366) points out ‘vary in different minerals of a single rock, in the leaves, stems and roots of a plant, or in water sources such as streams and precipitation’.  The measurement of small herbivore bones, or snail shells, at the locality of the archaeological site, preferably from the same chronological age, can obtain a remarkably consistent 87Sr/86Sr ratio, which is representative of the local catchment area (Bentley et al. 2004: 366).  The use of strontium ratio is however just one tool among many that is used to shed light on our ancestors; it should always be used in combination with other techniques of investigation to elucidate the full range of potential data present of archaeological sites and materials (Montgomery 2010, Richards et al. 2001, Van Klinken et al. 2000).

Bibliography:

Bentley, R. A., Price, T. D. & Stephan, E. 2004. Determining the ‘local’ 87Sr/88Sr Range for Archaeological Skeletons: A Case Study from Neolithic Europe. Journal of Archaeological Science. 32 (4): 365-375.

Bentley, R. A., Bickle, P., Fibiger, L., Nowell, G. M., Dale C. W., Hedges, R. E. M., Hamiliton,. J., Wahl, J., Francken, M., Grupe, G., Lenneis, E., Teschler-Nicola, M., Arbogast, R-M., Hofmann, D. & Whittle, A. 2012. Community Differentiation and Kinship Among Europe’s First Farmers. Proceedings of the National Academy of Sciences Early Edition. doi:10.1073/pnas.1113710109. 1-5.

Bryman, A. & Cramer, D. 2011. Quantitative Data Analysis with IBM SPSS 17, 18 & 19: A Guide for Social Scientists. London: Psychology Press.

Killgrove, K. 2010. Migration and Mobility in Imperial Rome. PhD Thesis. University of North Carolina. (Open Access).

Montgomery, J. 2010. Passports from the Past: Investigating Human Dispersals Using Strontium Isotope Analysis of Tooth Enamel. Annals of Human Biology. 37: 325–346. (Open Access).

Price, T. D., Burton, J. H. & Bentley, R. A. 2002. The Characterisation of Biologically Available Strontium Isotope Ratios for the Study of Prehistoric Migration. Archaeometry. 44 (1): 117-135.

Richards, M.P., Fuller, B,. T. & Hedges, R. E. M. 2001. Sulphur Isotopic Variation in Ancient Bone Collagen from Europe: Implications for Human Palaeodiet, Residence Mobility, Modern Pollutant Studies. Earth and Planetary Science Letters. 191 (3-4): 185-190.

Richards, M. P., Montgomery, J., Nehlich, O. & Grimes, V. 2008. Isotopic Analysis of Humans and Animals from Vedrovice. Anthropologie. XLVI (2-3): 185-194.

Van Klinken, G., Richards, M. and Hedges, R. 2000. An Overview of Causes for Stable Isotopic Variations in Past European Human Populations: Environmental, Ecophysiological, and Cultural Effects. In S. Ambrose and M. Katzenberg (eds). Biogeochemical Approaches to Palaeodietary Analysis. New York: Kluwer Academic. pp. 39-63.

Neolithic Craftsmanship In Central Europe

22 Jan

A recent paper by Tegel et al. (2012) demonstrates the intricate wood crafting abilities of the Neolithic Linearbandkeramik culture, known as the LBK, in the construction of water wells from planks of wood dated from 5500 BC to 5098 BC.  From the analysis of four wooden wells, and a total of 151 oak timbers from the wells, the precise history of their construction can be confirmed.  This is exciting news as it is firsthand evidence from a range of LBK sites of the carpentry skills, as practiced by the builders, that were apparent during the culture’s existence.  The LBK are typically known as one of the first major European cultures that helped spread agriculture via a number of different mechanisms (Bogaard et al. 2011), and are noted for their use of  cemeteries (Zvelebil & Pettit 2012), differential deposits of shoe last adzes in graves, and uniformity of small settlements and clustered long houses throughout Central Europe, although tantalizingly little remains of their famous long houses.

Bentley et al. (2012) have recently delved into extensive strontium isotope testing of cemetery populations and have released a slew of papers suggesting that, due to different ratios in the presence of male and female adult individuals, the LBK culture practiced patrilocality, i.e. that women moved around to other sites to start families or join different villages, whilst the fathers and sons largely stayed within their birthplace landscape.  Although it should be noted that there are some regional differences, with certain populations practicing transhumance with cattle, possibly moving with them throughout a varied landscape (Rasteiro et al. 2012).  Furtheer to this, there has been little coverage or investigation of infant or juvenile remains in the LBK culture, and this is a research bias that is similar to the under-consideration of of such populations in the wider Neolithic archaeological record (Lillie 2008).

journal.pone.0051374.g004

A detail from some from some of the water wells excavated from sites in Eastern Germany that were used in the dendro-chronological analysis and reconstruction (Tegel et al. 2012: 2). The majority of the wells were block lifted from their Neolithic period excavation sites and micro-excavated in wet lab conditions to allow preservation, greater photographic resolution, laser recording and stratigraphic recording. A reconstruction of their wooden joints was possible, because of this technique and the care taken to preserve the wood in-situ.

Article Abstract:

“The European Neolithization ~6000−4000 BC represents a pivotal change in human history when farming spread and the mobile style of life of the hunter-foragers was superseded by the agrarian culture. Permanent settlement structures and agricultural production systems required fundamental innovations in technology, subsistence, and resource utilization. Motivation, course, and timing of this transformation, however, remain debatable. Here we present annually resolved and absolutely dated dendroarchaeological information from four wooden water wells of the early Neolithic period that were excavated in Eastern Germany. A total of 151 oak timbers preserved in a waterlogged environment were dated between 5469 and 5098 BC and reveal unexpectedly refined carpentry skills. The recently discovered water wells enable for the first time a detailed insight into the earliest wood architecture and display the technological capabilities of humans ~7000 years ago. The timbered well constructions made of old oak trees feature an unopened tree-ring archive from which annually resolved and absolutely dated environmental data can be culled. Our results question the principle of continuous evolutionary development in prehistoric technology, and contradict the common belief that metal was necessary for complex timber constructions. Early Neolithic craftsmanship now suggests that the first farmers were also the first carpenters.”

Read more here.

Below are further sources to delve into the intriguing LBK culture.

Bibliography and Further Sources:

Bentley, R. A., Bickle, P., Fibiger, L., Nowell, G. M., Dale C. W., Hedges, R. E. M., Hamiliton,. J., Wahl, J., Francken, M., Grupe, G., Lenneis, E., Teschler-Nicola, M., Arbogast, R-M., Hofmann, D. & Whittle, A. 2012. Community Differentiation and Kinship Among Europe’s First Farmers. Proceedings of the National Academy of Sciences Early Edition. doi:10.1073/pnas.1113710109. 1-5.

Bogaard, A., Krause, R. & Strien, H.-C. 2011. Towards a Social Geography of Cultivation and Plant Use in an early Farming Community: Vaihingen an der Enz, South-West Germany. Antiquity. 85: 395-416.

Bramanti, B., Thomas, M. G., Haak, W., Unterlaender, M., Jores, P., Tambets, K., Antanaitis-Jacobs, I., Haidle, M. N., Jankauskas, R., Kind, C.-J., Lueth, F., Terberger, T., Hiller, J., Matsumura, S., Forster, P & Burger, J. 2009. Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe’s First Farmers. Science. 326 (5949): 137-140.

Lillie, M. C. 2008. Suffer the Children: ‘Visualising’ Children in the Archaeological Record. In: C. Barcvarov (ed.) Babies Reborn: Infant/Child Burials in Pre- and Protohistory. Conference Proceedings, UISPP, Lisbon. BAR International Series. 1832. Oxford: Archaeopress. pp. 33-43.

Rasteiro, R., Bouttier, P., Sousa, C. C & Chikhi. 2012. Investigating Sex-biased Migration During the Neolithic Transition in Europe, Using an Explicit Spatial Simulation Framework. Proceedings of the Royal Society B Biological Sciences. Doi:10.1098/rspb.2011.2323 accessed on the 20th of May 2012.

Tegel W., Elburg R., Hakelberg D., Stäuble H. & Büntgen U. 2012. Early Neolithic Water Wells Reveal the World’s Oldest Wood ArchitecturePLoS ONE. (12): 1-8. e51374. doi:10.1371/journal.pone.0051374

Vanmontfort, B. 2008. Forager-Farmer Connections in an ‘Unoccupied’ Land: First Contact on the Western Edge of LBKTerritory. Journal of Anthropological Archaeology. 27 (2): 149-160.

Zvelebil, M. & Pettitt, P. 2012.  Biosocial Archaeology of the Early Neolithic: Synthetic Analyses of a Human Skeletal Population from the LBK Cemetery of Vedrovice, Czech Republic. Journal of Archaeological Science. In Press.

MSc Abstractions

15 Sep

I am home and I am broke, but I’m thankful my dissertation has been handed in on time!  Whilst it is a sweet relief that it is over, I am not altogether happy with that particular body of work.  I probably shouldn’t, but it’s quite possible I’ll review it and apply a few new tests on the LBK dataset I used just to settle some nagging thoughts.

The abstract for my MSc dissertation is as follows:

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Local and non-local individuals have long been a source of interest in the consideration of the spread of Early Neolithic farming societies in Europe.  This study investigates the strontium isotope signatures of 422 individuals from 9 Linearbandkeramik sites spread across their chronological range, with a focus on SW Germany.  The sites used in this study include: Vedrovice, Neider-Morlen, Vaihingen, Aiterhofen, Schwetzingen, Kleinhadersdorf, Nitra, Talheim and Stuttgart-Mühlhausen.  A variety of sites are represented, including critically important early sites (Vedrovice, Neider-Morlen), sustained cemetery sites (Aiterhofen, Nitra) and a massacre site (Talheim).  Using a battery of statistical tests, this study investigates the differences in the strontium isotopic data (87Sr/86Sr) between males, females and juveniles.   This is carried out at broad levels of the data profile, period profile and site profile, coupled with other variables such as funerary artefacts and age categories, in the light of recent literature categorising the LBK society as patrilocal in nature.   The results indicate no statistical significance between the categories; however a review of the literature indicates that the most appropriate tests have not been applied.  A discussion of the recent literature indicates that the theory of the practice of patrilocality in the LBK culture can be upheld, whilst this study introduces some interesting variable behaviour in the LBK culture.

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Now that I’ve finished the dissertation,  my own blog posts should hopefully become more regular in number.  Whilst researching and thinking about my thesis topic, I have mulled over various osteological and archaeological thoughts.  In due course these should turn into posts, with future topics likely to include the role of disability and individuals in prehistory, and a brief discussion on the role and theory of pain in palaeopathological case studies.  And I will, of course, finish the Skeletal Series.

In the meantime enjoy some Leonard Cohen…

Another Quick (Neolithic) Update….

7 Jun

I haven’t updated as much as I would have liked recently for a variety of reasons, mainly due to a recent glut of essays, but I’d thought I’d add this quickly.

In my About page, I mention that two of my primary interests within archaeology are the Mesolithic and proceeding Neolithic periods, yet I’ve not wrote much about them on this blog.  However this will change (eventually), but as I have now attended the frankly excellent First Farmers conference at the University of Cardiff (see my post here about it), I’d thought I’d report that there has been some further developments concerning the main thrust of the conference.  The Linearbandkeramik culture, Central Europe’s first Neolithic Farmers (5500BC to around 4800BC), were the main topic of the talks and presentations given in Cardiff, and a recent paper by some of the organisers and presenters at the conference (Bentley et al 2012-see link below), have published the preliminary results from a large isotopic research project as a part of this.

The article is well worth a read, and concerns patterns of patrilocality, kinship and status based on the migration of female and male adults from the LBK culture, gathered from the archaeological evidence and the use of strontium isotopes gathered from human remains.  I want to draw your attention to two recently written blog entries concerning the paper.  Firstly we have Katy Meyers post at her blog ‘Bones Don’t Lie’ here, and her entry dated to the 1st of June entitled ‘The Earliest Evidence of Status Differentiation’.  Secondly, we have Rosamary Joyce’s blog, ‘Ancient Bodies, Ancient Lives‘, and her entry concerning the article which is entitled ‘Men, Women and Neolithic Equality‘.

Both of these blog entries take two different approaches in evaluating the article, and it is interesting to note both pick up on different themes.  Katy’ post deals with the interesting revelations of social status and differentiation as taken from the archaeological artefacts (mainly shoe last adzes), and evidence of adult female migration. The paper by Bentley et al (2012) makes note that it was possible that farmed land was passed down via adult males from the same family, and suggest differential land use, as  practiced by the LBK.  Joyce’s article makes the point that there are several sites and individuals that do not fit the overall model that the authors propose, alongside comments of how anthropological thought is always processed through a prism of its own history.

Perhaps a salient point to consider is a remark made by Dr Guido Brandt at the Cardiff conference in the consideration of the fact that we can always do with more bioarchaeological samples, including both human and animal bone, to gather a bigger data set as archaeological possible.  We must also always define isotopic parameters, from the geology, geography,  foods used and procured, and human and faunal data.  A point was made at the conference that over 6000 LBK sites have so far been uncovered and identified in Central European countries.  The questions remains the same; how many samples do we need to gather a representative?  And at what scale do we define patterns of migration?

I will no doubt come to know the LBK culture and the use of stable isotopes in migration patterns well as I have chosen this area for my dissertation topic….

Source:

Bentley, R., Bickle, P., Fibiger, L., Nowell, G., Dale, C., Hedges, R., Hamilton, J., Wahl, J., Francken, M., Grupe, G., Lenneis, E., Teschler-Nicola, M., Arbogast, R., Hofmann, D. & Whittle, A. 2012. Community Differentiation and Kinship Among Europe’s First Farmers. Proceedings of the National Academy of Sciences Early Edition. 1-5. DOI: 10.1073/pnas.1113710109