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endgame.tex
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endgame.tex
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\title{Putting Dental Calculus Under the Microscope}
\author{Bjørn Peare Bartholdy}
\date{}
\begin{document}
%% Mandatory proefschrift page for Leiden PhD dissertations %%
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\Huge\textbf{Putting Dental Calculus Under the Microscope}\par
\vspace{\baselineskip}
\huge\textit{}\par
\vfill % this space will be whatever is left on the page
\Large{Proefschrift}\par
\vspace{\baselineskip}
\linespread{1.3}
\large{ter verkrijging van \\
de graad van Doctor aan de Universiteit Leiden, \\
op gezag van Rector Magnificus prof.dr.ir. H. Bijl, \\
volgens besluit van het College voor Promoties \\
te verdedigen op Donderdag 30 Mei 2024 \\
klokke 11.15 uur \\[1.5cm]
door} \\[1.5cm]
\Large{Bjørn Peare Bartholdy}\par
\end{center}
%% End: Proefschrift %%
%% Promotor and committee page %%
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\noindent\begin{tabular}{p{8em} l}
\large
\textbf{Promotor} & \large Dr.~Amanda G. Henry \\
\rule{0pt}{4ex}\large\textbf{Second} \\ \large\textbf{Promotor} & \large Prof.dr.
Annelou van Gijn \\
\large
\rule{0pt}{8ex}\textbf{Committee} & \rule{0pt}{4ex}\large Prof.dr.
Patrick Degryse
\\[0.2mm]
& \indent\textit{Leiden University} \\[0.2mm]
& \indent\textit{Katholieke Universiteit
Leuven} \\ & \rule{0pt}{4ex}\large Prof.dr. Matthew James Collins
\\[0.2mm]
& \indent\textit{University of Copenhagen} \\[0.2mm]
& \indent\textit{University of
Cambridge} \\ & \rule{0pt}{4ex}\large Dr.~Alison Crowther
\\[0.2mm]
& \indent\textit{University of
Queensland} \\ & \rule{0pt}{4ex}\large Prof.dr. Carla Lancelotti
\\[0.2mm]
& \indent\textit{Universitat Pompeu Fabra and
ICREA} \\ & \rule{0pt}{4ex}\large Dr.~Christina Warinner
\\[0.2mm]
& \indent\textit{Max Planck Institute for Evolutionary
Anthropology} \\[0.2mm]
& \indent\textit{Harvard University} \\
\end{tabular}
\begingroup
\hspace{0.000001cm}
\vfill
\begin{flushleft}
\line(1,0){225} \\ %%%% Change colour of line to match chapters %%%%
\textbf{Cover:} Design by Krijn Boom and image by Petra
Korlevic \\[0.4cm]
\textbf{Funding:} This research has received funding from the European
Research Council under the European Union's Horizon 2020 research and
innovation program, grant agreement number STG--677576
(``HARVEST''). \\[0.4cm]
\textbf{Print version:} \href{https://doi.org/10.5281/zenodo.11077009}{2024.04.1} \\[0.4cm]
\textbf{Printed by:} Gildeprint \\[0.4cm]
\end{flushleft}
\endgroup
%% End: promotor and committee page %%
\frontmatter
%%%\maketitle
%
\clearpage
\thispagestyle{empty}
\vspace*{\fill}
\vspace*{3cm}
\hfill\textit{En bar røv at trutte i}
\par
\hfill\vspace*{4cm} Jan Bartholdy
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\chapter*{Preface}
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This is not a traditional dissertation, which was a conscious choice on
my part. First of all, it's not very common for a dissertation in my
faculty to have a preface, which is why I have prefaced this preface
with an explanation for why I need a preface. This mainly explains
decisions regarding the format and style of my dissertation rather than
the scientific content, which is why you won't see the phrase `dental
calculus' here. Oh, shoot\ldots{}
Feel free to jump directly to \href{01-intro.qmd}{Chapter 1} if you
don't want to read this.
When I started my PhD research I had no intentions of shaking things up.
I was going to put my head down and do my research, publish my articles
in traditional journal venues, create a traditional article-based
dissertation, and finish in the allotted four years. Six years later,
and I accomplished\ldots{} well, none of the above. Along the way I got
a look behind the curtain of academic publishing. I didn't like what I
saw. Not even a little bit. This was fueled by an introduction to Open
Science. Science in the context of Open Science just made sense to me.
This caused some delays as I dove head first into an Open Science rabbit
hole. Also, covid. At first I vowed (to myself and those around me who
would listen) never to publish any of my papers in Evilseer. Then, I
took it a step further and vowed the same for more major publishers,
including Springer and Wiley. Why do we pay publishers to take our
copyright, publish our research, then pay extra so we're allowed read
it? You may not be paying out of pocket, but your library is likely
covering those costs with expensive subscriptions. I'm sure they would
much rather use that money on more useful stuff. All this to say, you
won't find any of my PhD papers in the traditional journals. I wanted to
try different platforms, like preprint servers and PCI\_Archaeology.
Around the beginning of my PhD research I was also introduced to R
statistical software. I can no longer remember how this came about, but
after many months of rage-quitting and returning to SPSS, vowing never
to open R again, I started to see the value of using scripting languages
(and free, open-source software) for statistical analysis. It turns out
when you have a document outlining every step you made in the analysis,
it's easy to reproduce; both by yourself and others. Who knew? No need
for the same `point and click' all over again. I used R Markdown for
most of my output, website, presentations, articles, etc. Then I took it
a step further and started writing my dissertation in R Markdown (and
eventually Quarto). My dissertation was now fully reproducible, and
could be rendered in different formats with little change to the
documents with the actual content. One of these formats was HTML. I
could turn my dissertation into a website. That was pretty cool. I could
have a dynamic, outward-facing dissertation easily modified when needed.
This series of events led me to publishing my dissertation online,
before it was completed, as a way to show the progress to the world. Of
course most of the world didn't actually care, but a few people thought
it was a pretty cool idea; and, more importantly, it made the writing
part enjoyable. Or at least as enjoyable as something that's not very
enjoyable in the first place. It definitely motivated me to make
continuous progress. The (theoretically) wide availability of my
dissertation made me start thinking about accessibility. This means
increasing the readability and legibility of the dissertation, not only
with the formatting, but with the language used. This doesn't
necessarily mean that it can be easily picked up by someone with limited
knowledge of the field. Writing `academically' is not just exclusionary
to members of the public, but also to those for whom English does not
come naturally. Plus, I've found it to be a tedious read, even as a
native English speaker. In my experience, writing more accessibly also
requires a deeper understanding of the subject matter.
Open Science is a priority in all of my work and will be reflected in
this dissertation; sometimes directly, sometimes indirectly. Admittedly
this is occasionally taken to an extreme: A fully reproducible
dissertation, publishing everything before it's actually done, and
avoiding traditional journals. Ultimately I was just fed up with the
status quo. We as researchers need to do better. Contributing to
knowledge requires more than having a paper accepted in a `prestigious'
journal. We need to ask ourselves why we are doing science, and for whom
we are doing it.
\phantomsection\label{acknowledgements}
\bookmarksetup{startatroot}
\chapter*{Acknowledgements}
\addcontentsline{toc}{chapter}{Acknowledgements}
\markboth{Acknowledgements}{Acknowledgements}
Where to begin? So many people helped shape this thesis, and therefore I
do not take full responsibility for the quality (or lack thereof) of
this work.
First of all, my understanding supervisor, Dr.~Amanda Henry, who waited
patiently through delays caused by covid and two kids. Not to mention
supporting all my non-traditional ventures in the name of Open Science
and accessibility. prof. dr. Annelou van Gijn for providing feedback on
experiment design and dissertation drafts.
Dr.~Shira Gur-Arieh for endless encouragement and moral support, as well
as FTIR analysis on the model calculus. Dr.~James Fellows Yates and
Dr.~Zandra Fagernäs were always able to reignite my excitement for the
project when I occasionally felt it slipping away. Their enthusiasm was
always appreciated. James was also an important contributor to the main
biofilm model paper, as I struggled to implement the EAGER pipeline, not
to mention an inspiration on how to PhDad.
Dr.~Ben Marwick and Dr.~Esther Plomp, whose passion and commitment to
Open Science inspired me to make all of my work as open and transparent
as possible. This also likely contributed to some of the delays; so,
thanks for that.
My colleagues at TU Delft (Yasemin and the Data Steward team,
especially) who were very encouraging about finishing my dissertation
while working a part-time job. Some Figures were created on Biorender
using the TU Delft institutional subscription.
Anouk, Marie, Supriya, and Nina for having the patience to be friends
with a PhD student with two small children. Femke and Maia for being
great and motivating office mates.
Of course, I have to acknowledge my family for their moral support, and
since they are the most likely to read this. Liam and Oliver, for making
everything a bit more of a challenge.
Finally, my dad. An unlimited source of support and guidance through the
whole process. I couldn't have done it without you. I only wish you
could have been here to see me finish it.
\phantomsection\label{open-science-statement}
\bookmarksetup{startatroot}
\chapter*{Open Science Statement}
\addcontentsline{toc}{chapter}{Open Science Statement}
\markboth{Open Science Statement}{Open Science Statement}
All materials and data, including the source code for the dissertation
itself, are made available to the best of my ability. All articles in
association with the dissertation are/will be Open Access.
All outputs can be found, either directly or indirectly, on the Open
Science Framework (\href{https://doi.org/10.17605/OSF.IO/3YX8M}{DOI:
10.17605/OSF.IO/3YX8M}).
\begin{center}
\includegraphics[width=1.04167in,height=\textheight]{figures/osf-qr.png}
\end{center}
\bookmarksetup{startatroot}
\chapter{Introduction}\label{chap-intro}
Dental calculus is becoming a popular substance in research on the
behaviour and biology of people in the past. You may also know it as
tartar or mineralised plaque. In other languages the word is often
related to ``tooth stones''. In fact, calculus is itself latin for
`pebble'. This was originally used as a term for mathematical
calculations using counting stones, and only later used to describe
various calcifications in the human body
(\url{https://www.etymonline.com/word/calculus}). This can be the cause
of some confusion, as calculus is also a branch of mathematics. If you
see the term `calculus' in this dissertation, you can safely assume that
I'm referring to stuff that grows on your teeth and for which you
receive lectures from your dentist, and not the topic you dreaded in
high school.
I will briefly describe the formation of dental calculus here, but for a
more thorough review of the entire process I refer you to
\hyperref[chap-background]{Chapter 2}. Dental calculus is formed from
dental plaque, a substance that grows on your teeth and consists mainly
of bacteria and a surrounding structure called the extracellular matrix.
When the local environment within and around the plaque reaches a
favourable alkaline pH, both the extracellular matrix and bacteria
within will calcify (\citeproc{ref-jinSupragingivalCalculus2002}{Jin \&
Yip, 2002}; \citeproc{ref-whiteDentalCalculus1997}{D. J. White, 1997}).
The alkaline pH causes minerals (especially calcium and phosphate) from
saliva to enter the plaque, causing the extracellular matrix and
eventually also the bacteria to harden, resulting in a concrete-like
deposit on the surface of the teeth. The process repeats itself when new
bacteria colonise the surface of the newly formed dental calculus,
creating a layered structure, though somewhat disorganised
(\citeproc{ref-akcaliDentalCalculus2018}{Akcalı \& Lang, 2018};
\citeproc{ref-jepsenCalculusRemoval2011}{Jepsen et al., 2011}). Dental
plaque can accumulate more easily on teeth (and dental calculus) because
they are a hard, non-shedding surface. Most of the surfaces in our mouth
are covered by a layer of cells called the oral epithelium. These cells
are continuously renewed as new cells are formed and dead cells fall off
(\citeproc{ref-squierOralMucosa1998}{Squier \& Finkelstein, 1998}). This
constant turnover means that it is difficult for bacteria to build the
communities they require for producing biofilms. Enamel, the white
substance that covers the crown of your teeth, behaves differently. It
stops growing when the tooth has fully formed. After that, there is no
renewal. This allows bacteria to continue to grow and develop
communities if there is no intervention from you (or your dentist).
Dental plaque can trap a variety of different microparticles, including
bacteria, human proteins, and small debris from the food we eat
(\citeproc{ref-delafuenteDNAHuman2013}{De La Fuente et al., 2013};
\citeproc{ref-hendyProteomicCalculus2018}{Hendy et al., 2018};
\citeproc{ref-henryCalculusSyria2008}{Henry \& Piperno, 2008}). When the
plaque mineralises, it can preserve these microparticles over long
periods of time, even after the person whose teeth provided a home for
the calculus has died. Also, the main crystal structures in calculus
strongly bind DNA, making calculus a fantastic source of ancient DNA
(aDNA) from the mouth (\citeproc{ref-warinnerNewEra2015}{Warinner et
al., 2015}). Another advantage of dental calculus is that it represents
a more recent and direct source of diet than teeth or other bones. While
bones and teeth can take years to remodel and incorporate a dietary
signal, calculus forms on a much smaller timescale and is in direct
contact with the dietary material. Calculus can form within weeks at any
point during an individual's life and may, therefore, indicate a recent
and direct consumption of food, while bone can take years to show a
(indirect) dietary signal, following food molecules entering the
bloodstream, and finally entering the bone from there. Further, enamel
stops forming after the crown of the last tooth has developed---third
molars, or 'wisdom teeth---at around 16 years of age, and the turnover
of dentin is very limited
(\citeproc{ref-hillsonDentalAnthropology1996}{Hillson, 1996}). These
properties are probably why archaeologists have become increasingly
interested in dental calculus.
\section{Dental calculus in archaeology}\label{intro-arch}
The main archaeological interest in dental calculus is to explore
research questions involving diet and the evolution of the oral biome
and oral health. To this end, it can contribute a surprising amount for
such a small, seemingly insignificant material. This relates to its
ability to retain and preserve a wide variety of different materials,
from the food we eat to the bacteria that make their home in our mouths
(\citeproc{ref-adlerSequencingAncient2013}{Adler et al., 2013};
\citeproc{ref-yatesOralMicrobiome2021}{Fellows Yates et al., 2021};
\citeproc{ref-henryCalculusSyria2008}{Henry \& Piperno, 2008};
\citeproc{ref-warinnerPathogensHost2014}{Warinner, Rodrigues, et al.,
2014}; \citeproc{ref-warinnerEvidenceMilk2014}{Warinner, Hendy, et al.,
2014}). The goal of current studies targeting archaeological dental
calculus have not changed much since the early uses of dental calculus
in archaeological research, but the methods certainly have, allowing us
to unearth information that was previously not considered possible. By
my count, archaeological dental calculus has now been subject to various
forms of microscopy (\citeproc{ref-charlierSEMCalculus2010}{Charlier et
al., 2010}; \citeproc{ref-middletonOpalPhytoliths1994}{Middleton \&
Rovner, 1994}; \citeproc{ref-powerSynchrotronRadiationbased2022}{Robert
C. Power et al., 2022}); extractions of biomolecules including DNA,
proteins, and metabolites
(\citeproc{ref-adlerSequencingAncient2013}{Adler et al., 2013};
\citeproc{ref-warinnerEvidenceMilk2014}{Warinner, Hendy, et al., 2014});
and stable isotope analyses.
\begin{figure}
\centering{
\includegraphics{01-intro_files/figure-pdf/fig-plot-and-wordclouds-1.pdf}
}
\caption{\label{fig-plot-and-wordclouds}Plot of the number of articles
per year in bioarchaeology and clinical dentistry with the term `dental
calculus' in the title.}
\end{figure}%
Perhaps the most common use of dental calculus is to recreate the diet
of past people and populations (Figure~\ref{fig-plot-and-wordclouds}B).
One of the ways to do this is by dissolving the calculus in a weak acid
or decalcifant, or mechanically breaking it up. This process releases
any fragments of plants that were trapped within the calculus and can be
identified, for example with a microscope. The tricky part is not
destroying the plant fragments when releasing them from the calculus. As
far as I can tell, the first attempt at this was the extraction of
phytoliths (silicified plant remains) from the teeth of cows, sheep, and
horses (\citeproc{ref-armitageExtractionIdentification1975}{Armitage,
1975}). This was a somewhat isolated use-case, and the method didn't
really catch on until the 1990s
(\citeproc{ref-ciochonOpalPhytoliths1990}{Ciochon et al., 1990};
Middleton 1990, in \citeproc{ref-middletonOpalPhytoliths1994}{Middleton
\& Rovner, 1994}). The first extractions from human teeth followed
shortly (\citeproc{ref-foxPhytolithCalculus1996}{Fox et al., 1996}), and
there are now studies using plant microremains (especially starch
granules and phytoliths) from dental calculus to infer diet in past
peoples from across the world, including Pacific Islands
(\citeproc{ref-dudgeonDietGeography2014}{Dudgeon \& Tromp, 2014}), China
(\citeproc{ref-chenStarchGrains2021}{Chen et al., 2021}), Europe
(\citeproc{ref-fiorinCombiningDental2021}{Fiorin et al., 2021}), and
more (\citeproc{ref-buckleyDentalCalculus2014}{Buckley et al., 2014};
\citeproc{ref-henryCalculusSyria2008}{Henry \& Piperno, 2008};
\citeproc{ref-mickleburghNewInsights2012}{Mickleburgh \& Pagán-Jiménez,
2012}). The durable nature of dental calculus also means that
microremains within it can survive for millennia, allowing us to look at
the diets of early humans and other hominins
(\citeproc{ref-buckleyDentalCalculus2014}{Buckley et al., 2014};
\citeproc{ref-chenStarchGrains2021}{Chen et al., 2021};
\citeproc{ref-hardyStarchGranules2009}{Hardy et al., 2009};
\citeproc{ref-hardyNeanderthalMedics2012}{Hardy et al., 2012};
\citeproc{ref-henryDietAustralopithecus2012}{Henry et al., 2012},
\citeproc{ref-henryNeanderthalCalculus2014}{2014};
\citeproc{ref-henryCalculusSyria2008}{Henry \& Piperno, 2008};
\citeproc{ref-pipernoStarchGrains2008}{Piperno \& Dillehay, 2008}).
That bacteria can become trapped within calculus has been known to
archaeologists for a while
(\citeproc{ref-brothwellDiggingBones1981}{Brothwell, 1981}, ;
\citeproc{ref-vandermeerschMiddlePaleolithic1994}{Vandermeersch et al.,
1994}), but it wasn't used in archaeological research until DNA
extraction started to become more accessible
(\citeproc{ref-delafuenteDNAHuman2013}{De La Fuente et al., 2013}).
Dental calculus then became part of the third scientific revolution in
archaeology. The early studies focused on oral health in the past
(\citeproc{ref-adlerSequencingAncient2013}{Adler et al., 2013};
\citeproc{ref-delafuenteDNAHuman2013}{De La Fuente et al., 2013};
\citeproc{ref-warinnerPathogensHost2014}{Warinner, Rodrigues, et al.,
2014}). Bacteria have shorter lifespans than humans which makes them
useful when studying the evolution of bacteria in the human mouth
(\citeproc{ref-delafuenteDNAHuman2013}{De La Fuente et al., 2013};
\citeproc{ref-yatesOralMicrobiome2021}{Fellows Yates et al., 2021}).
Diet has also been a focus of paleogenetic research. This has mainly
been addressed by considering how long-term changes in the patterns of
bacteria within the mouths of our ancestors have changed that could be
related to changes in diet. Just like we adapt to deal with various
diseases, climates, etc., we also adapt to changes in our diet
(\citeproc{ref-adlerSequencingAncient2013}{Adler et al., 2013};
\citeproc{ref-yatesOralMicrobiome2021}{Fellows Yates et al., 2021}).
Directly identifying genetic markers of plants and animals within dental
calculus is difficult, but not impossible (see Warinner, Hendy, et al.
(\citeproc{ref-warinnerEvidenceMilk2014}{2014})). Most of the DNA within
dental calculus will be oral bacteria, and this will overwhelm the small
signal from plant DNA, which makes species identifications problematic
(\citeproc{ref-fagernasMicrobialBiogeography2022}{Fagernäs et al.,
2022}). A newer field of biomolecular archaeology, paleoproteomics, may
be able to address this issue by targeting plant proteins, along with a
range of other dietary protein sources. Hendy and coauthors were able to
identify a number of these in dental calculus, as well as proteins from
cereals, and milk proteins from different sources
(\citeproc{ref-hendyProteomicCalculus2018}{Hendy et al., 2018}). Dental
calculus has also become a target for extracting other biomolecules that
may be related to diet, such as alkaloids, fatty acids, and
carbohydrates
(\citeproc{ref-gismondiMultidisciplinaryApproach2020}{Gismondi et al.,
2020}; \citeproc{ref-velskoDentalCalculus2017}{Velsko et al., 2017}).
The methods used for this have also proven to be useful in detecting
compounds that are related to other activities and ceremonies, such as
nicotine (\citeproc{ref-eerkensDentalCalculus2018}{Eerkens et al.,
2018}), and may provide some evidence of medicinal practices
(\citeproc{ref-gismondiMultidisciplinaryApproach2020}{Gismondi et al.,
2020}).
To a lesser extent, the presence and amount of dental calculus on teeth
has been used as an indicator of dental health
(\citeproc{ref-drewettExcavationOval1975}{Drewett, 1975};
\citeproc{ref-lieverseDentalHealth2007}{Lieverse et al., 2007};
\citeproc{ref-sagneStudiesPeriodontal1977}{Sagne \& Olsson, 1977};
\citeproc{ref-zhangDentalDisease1982}{Zhang, 1982}). Pilloud \& Fancher
(\citeproc{ref-pilloudOutliningDefinition2019}{2019}) explored the terms
associated with a number publications on dental or oral health, dental
calculus came up as one of them; albeit not the most common, which was
(unsurprisingly) dental caries (Figure~\ref{fig-dental-terms}).
To a lesser, lesser extent, it has also provided some interesting
insights on non-dietary activities, such as occupations and smoking
habits. In a rare find, blue particles were detected in the dental
calculus of a Medieval German woman. These blue particles originated
from lapis lazuli, an exotic stone often ground into pigments and used
to illuminate manuscripts (\citeproc{ref-radiniMedievalWomen2019}{Radini
et al., 2019}). Nicotine was detected in dental calculus of
pre-colonisation individuals from California using Ultra-Performance
Liquid Chromatography Mass Spectrometry (UPLC-MS), showing direct
consumption of tobacco and providing more detailed insights on the
demographics of consumption in a way that no other human-adjacent
archaeological materials can.
\begin{figure}
\centering{
\includegraphics{figures/wordcloud.png}
}
\caption{\label{fig-dental-terms}Word cloud of most common dental terms
in articles. Figure is from Pilloud \& Fancher
(\citeproc{ref-pilloudOutliningDefinition2019}{2019}), Figure 1.}
\end{figure}%
It wasn't always appreciated for the wealth of information hidden within
its hardened shell. Until roughly 20 years ago, archaeologists who
encountered calculus had limited use for this material. Some researchers
quantified it using a simple four-stage scoring method that was
developed for recording deposits on archaeological dental calculus
(\citeproc{ref-brothwellDiggingBones1981}{Brothwell, 1981}), similar to
a common clinical scoring system
(\citeproc{ref-greeneSimplifiedOral1964}{J. G. Greene \& Vermillion,
1964}). The four-stage system is probably still the most widely used
among archaeologists. More detailed methods are also available
(\citeproc{ref-dobneyMethodEvaluating1987}{Dobney \& Brothwell, 1987};
\citeproc{ref-greeneQuantifyingCalculus2005}{T. R. Greene et al.,
2005}), but the original method is generally preferred for its
simplicity. Unfortunately, knowing the size of a calculus deposit is not
as valuable as being able to analyse the deposit itself, and the
deposits were often removed because they obscured tooth and root
morphology (\citeproc{ref-scottBriefHistory2015}{Scott, 2015}). This had
made a lot of people very angry and been widely regarded as a bad move
(\citeproc{ref-adamsRestaurantEnd2002}{Adams, 2002, p. 1}). Hindsight
being what it is, it's hard to blame anyone. A lot of dental research
mainly focuses on the prevention and removal of dental calculus.
The wide range of applications for dental calculus that we know about
today, and the fact that it's pretty much ubiquitous in the past thanks
to poor oral hygiene, makes it a really exciting target for future (and
current) paleodietary research. That being said, the study of dental
calculus doesn't seem to fit into any predefined areas of study within
(and beyond) archaeology. Most researchers seem to see it as a means to
the information contained within, rather than being worth studying in
its own right. This can be problematic. Other than what we can see with
our current methods, what do we really know about dental calculus and
how its growth and structure affect the reliability of these methods and
potentially distort our interpretations of the past?
\section{What is dental calculus?}\label{intro-what}
To answer these questions, we must first answer a single, surprisingly
difficult question: What is dental calculus? I'm not referring to its
formation or composition, which I briefly described
\hyperref[chap-intro]{above}. How do we categorise it? Is it a dental
disease? An oral health condition? A byproduct of oral conditions? We
start by exploring various definitions of oral health. Definitions in an
introduction are a little cliché and tedious, but often necessary. Since
oral health is a complex topic, definitions of oral health are often
purposefully (and confusingly) broad, and they extend beyond physical
well-being and into the realms of emotional and social comfort. The
World Dental Federation (FDI) defines oral health as the ability to
perform mouth- and face-related functions with confidence and without
pain (including smiling, speaking, eating, etc.)
(\citeproc{ref-fdiOralHealth}{{``{FDI}'s Definition of Oral Health
\textbar{} {FDI},''} n.d.})
(\url{https://www.fdiworlddental.org/fdis-definition-oral-health}). Both
the World Health Organisation (WHO) and FDI take a similar approach to
defining oral conditions, giving a list of conditions that cause
discomfort, pain, disfigurement, or death. The list includes the dental
conditions tooth decay (caries), gum disease (periodontal disease), and
dental trauma, but not dental calculus
(\citeproc{ref-whoOralHealth}{{``Oral Health,''} n.d.})
(\url{https://www.who.int/news-room/fact-sheets/detail/oral-health}).
While these are not likely to cause death, they are often the source of
physical and emotional discomfort, and may cause further health
complications if they are not dealt with in a timely fashion.
Dental calculus and dental plaque are not considered oral conditions
according to WHO. In fact, dental plaque is part of the normal
functioning of our oral biome
(\citeproc{ref-marshDentalPlaque2006}{Marsh, 2006}). When plaque reaches
a certain level of acidity over a prolonged period of time, the normal
functioning of the bacteria within the plaque may shift towards a
disease-causing function. The biofilm will cause the surface of the
enamel to demineralise, eventually resulting in a cavity (or caries).
Dental caries are unequivocally considered a dental disease. If,
instead, the biofilm calcifies, dental calculus is the result. Its
status in oral health is questionable.
Dental calculus is not known to be painful, nor does it affect the
ability to perform the functions listed above. However, with continued
accumulation, it may affect the confidence of the person performing
these tasks (\citeproc{ref-collinsHomelessDental2007}{Collins \&
Freeman, 2007}), and in extreme cases it can affect function
(\citeproc{ref-balajiUnusualPresentation2019}{Balaji et al., 2019}).
Most of the virulence and disease-causing potential is lost when the
bacteria within dental plaque calcify
(\citeproc{ref-akcaliDentalCalculus2018}{Akcalı \& Lang, 2018}). It has
been shown to contain pockets of living bacteria that can be detrimental
to oral and dental health
(\citeproc{ref-tanCalculusUltrastructure2004}{Tan, Gillam, et al.,
2004}; \citeproc{ref-tanBacterialViability2004}{Tan, Mordan, et al.,
2004}). The rough, porous surface of dental calculus is also a great
place for bacteria to attach more easily and develop a new layer of
plaque on the surface of the calculus. This is likely why there is often
a correlation (NOT causation) between dental calculus and periodontitis,
especially subgingival calculus
(\citeproc{ref-jepsenCalculusRemoval2011}{Jepsen et al., 2011};
\citeproc{ref-whiteDentalCalculus1997}{D. J. White, 1997}). Since it
seems to fulfill some of the criteria of an oral condition, it should be
considered as such, at least under the definitions provided by WHO and
FDI. Whether or not dental calculus can be considered an oral disease is
more questionable. While it does grow on the surface of teeth, it
doesn't seem to affect the underlying enamel. And while there is a
relationship with periodontal disease (which has been defined as a
dental disease), the nature of this relationship is still under debate,
with calculus likely being a secondary contributor
(\citeproc{ref-jepsenCalculusRemoval2011}{Jepsen et al., 2011}). As
such, we can probably limit the definition to an oral condition and not
necessarily a dental disease
(\citeproc{ref-pilloudOutliningDefinition2019}{Pilloud \& Fancher,
2019}). In fact, dental calculus is quite hard, so a layer of dental
calculus on a tooth can actually protect it from wearing down (although
there are better options).
\section{The study of dental calculus}\label{intro-study}
It seems that the researchers who are studying dental calculus approach
it from a wide range of different fields and backgrounds, including
genetics, proteomics, botany, and (bio)archaeology. The paleogeneticists
mine it for the wealth of information it contains on oral health and
disease in the past (\citeproc{ref-yatesOralMicrobiome2021}{Fellows
Yates et al., 2021}; \citeproc{ref-warinnerPathogensHost2014}{Warinner,
Rodrigues, et al., 2014}). Paleodiet researchers extract microremains
and residues from food (\citeproc{ref-henryCalculusSyria2008}{Henry \&
Piperno, 2008}; \citeproc{ref-mickleburghNewInsights2012}{Mickleburgh \&
Pagán-Jiménez, 2012}) to infer dietary practices. Bioarchaeologists use
its presence and amount to broadly infer diet, and dental and overall
health in a given population
(\citeproc{ref-belcastroContinuityDiscontinuity2007}{Belcastro et al.,
2007}; \citeproc{ref-lieverseDentalHealth2007}{Lieverse et al., 2007};
\citeproc{ref-novakDentalHealth2015}{Novak, 2015};
\citeproc{ref-slausDentalHealth2011}{Šlaus et al., 2011};
\citeproc{ref-yaussyCalculusSurvivorship2019}{Yaussy \& DeWitte, 2019}).
This leaves research output from studies of calculus scattered across
multiple venues, with no clear gathering point. I think it's fair to say
that dental calculus should be included in discussions of pathological
oral conditions, even if its role is secondary. But who is currently
studying dental calculus as a substance in its own right? And why do we
need to learn more about it if we're just interested in what's inside?
Related discussions have started to take place in recent years
(\citeproc{ref-bucchiComparisonsMethods2019}{Bucchi et al., 2019};
\citeproc{ref-radiniDirtyTeeth2022}{Radini \& Nikita, 2022};
\citeproc{ref-wrightAdvancingRefining2021}{Wright et al., 2021}).
The lack of a specific field of study for dental calculus to belong may
be related to how it's taught to students (and if it's taught at all).
Textbooks from the more established fields in bioarchaeology are
probably a good indicator of the teaching curricula, which also impacts
research focus. The most popular osteoarchaeology textbooks only briefly
mention dental calculus as more of a footnote than anything else. A
couple of lines describing what it is (usually `mineralised plaque') and
that it can contain food debris and bacteria T. D. White et al.
(\citeproc{ref-whiteHumanOsteology2011}{2011}). They're not wrong.
Diseases that manifest themselves in the skeleton as lesions on the
bones have a very clear home in paleopathology. No one questions whether
or not the degeneration of vertebrae from tuberculosis should be
included in the paleopathology textbooks (at least not as far as I'm
aware).
These textbooks often include chapters on dental disease, where more
detailed descriptions of dental calculus are usually found (e.g.
\citeproc{ref-robertsDentalDisease2007}{Roberts \& Manchester, 2007};
\citeproc{ref-waldronPalaeopathology2020}{Waldron, 2020}). Dental
caries, calculus' more famous sibling, will often get a few pages. In
some cases, dental calculus may even be hidden within a section on
periodontal disease or plaque
(\citeproc{ref-aufderheidePaleopathology1998}{Aufderheide et al., 1998};
e.g. \citeproc{ref-ortnerIdentificationPathological2003}{Ortner, 2003}).
The focus of these (sub)sections is varied, with some simply describing
what it is, and others giving brief discussion on the relationship
between calculus and periodontal disease. A more detailed section was
dedicated to dental calculus in \emph{Ortner's Identification of
Pathological Conditions in Human Skeletal Remains}, with a detailed
description of formation, structure, and application in (biomolecular)
archaeology (\citeproc{ref-kinastonOrtnerDentition2019}{Kinaston et al.,
2019}). The description extends well beyond any (paleo)pathological
significance of dental calculus. Can we fault the authors/editors for
not giving it more attention? After all, it's not a dental disease, and
its relationship with other dental diseases is unclear. What is clear,
is that it has implications for oral health, and, for that very reason,
could be addressed more extensively in paleopathology; certainly in the
textbooks that include dental disease.
On the surface, dental anthropology seems like a more suitable home for
the study of dental calculus. However, it's not included in \emph{A
Companion to Dental Anthropology}, an otherwise great resource on
studying archaeological teeth. The editors briefly acknowledge the
valuable information gained from calculus and that it holds a lot of
potential; but that's it (\citeproc{ref-scottBriefHistory2015}{Scott,
2015}). Other notable absences include textbooks such as \emph{Technique
and Application in Dental Anthropology} and \emph{New Direction in
Dental Anthropology}
(\citeproc{ref-townsendDentalAnthropology2012}{Townsend et al., 2012}),
both of which dedicate considerable attention to dental caries.
Hillson's \emph{Dental Anthropology}, a book that I consider to be the
`bible' for dental anthropology, has a section on dental calculus in the
Dental Disease chapter. It covers a basic description, the composition,
microscopic structure, methods used for recording archaeological
calculus, and the distribution in the dentition (i.e.~which teeth are
more prone to calculus buildup)
(\citeproc{ref-hillsonDentalAnthropology1996}{Hillson, 1996}).
Considering these are entire books devoted to the dentition, it seems
odd that there is often only a few paragraphs (if that) on dental
calculus. Granted, the only function teeth serve in the growth of dental
calculus is as a suitable surface on which to attach; though the role of
substratum is an important role, as dental calculus is seemingly unable
to form on other surfaces in the oral cavity.
Since the use of dental calculus in biomolecular archaeology is
relatively new, there are fewer available textbooks, and it rarely has a
dedicated course. The most common place to find descriptions of dental
calculus is, therefore, journal articles. There will be a short
paragraph on dental calculus formation (and sometimes composition) in
the introduction section. These are quite variable and are often limited
by the word count of the journal. Despite this, the descriptions will
often be as long, if not longer, than the sections in textbooks devoted
to dental calculus (\citeproc{ref-velskoMicrobialDifferences2019}{Velsko
et al., 2019}). The focus of these paragraphs are generally the same.
They describe the formation and mineral composition of dental calculus,
and provide some examples of how dental calculus has been used in
related studies (not unlike the beginning of this chapter). The
contribution of dental calculus to archaeology has been significant, so
it is likely to receive more and more attention going forward. In fact,
an entire chapter was recently devoted to dental calculus in the second
edition of \emph{Handbook of Archaeological Sciences}
(\citeproc{ref-fagernasDentalCalculus2023}{Fagernäs \& Warinner, 2023}).
Take that, dental caries!
\section{The challenges of studying dental
calculus}\label{the-challenges-of-studying-dental-calculus}
What we know about dental calculus and the influence of diet was
reviewed in an article aimed at (bio)archaeologists. The overall
conclusion reached in the article: it's still pretty unclear
(\citeproc{ref-lieverseDietAetiology1999}{Lieverse, 1999}). Now, 20-some
years later, there has been limited progress on this point. High-protein
diets are linked to an increase of urea, which is linked to an increase