Sifting Through the Sediments: Parasite Eggs from Night Soil Contexts

While the last thing that most people would want to get in the mail is night soil, I'm one of those people who excitedly awaits for jars of this stuff to arrive. (Because one: Such material is super cool and because two: "most people" are boring.) In my last two posts, I discussed how we look for parasites in the context of mummified tissues and desiccated feces. Today, I'm going to introduce you to another great source of literal pay-dirt for archaeoparasitologists.

Night Soil Sediments from the Past

A nightman's calling card from the 1800s.

For those who haven't been introduced to the phrase "night soil", I'm referring to dirt that has human fecal components. The term originated from the olden days when people would shovel human waste out of cesspools and outhouses during the night and later usually sell the excrement to farmers as a fertilizer. Many of these people employed as "nightmen" or "night soil men" were not allowed to work during the day and made up a portion of the lowest of low classes in most places. This was early human waste management in Europe, Africa, and Asia long before modern standards of disposal.

As you've probably already figured out, there were lots of problems with sanitation in the past. Before modern indoor plumbing, people found a variety of ways to store their steaming piles of...stuff...before nightmen could come and haul it away. Some were indoor chambers for relieving oneself. This included things like chamber pots or water closets (the early ancestor to modern flushing toilets). Others were outdoor pit latrines such as the outhouse, the privy, the dunny, the biffy, or the long-drop.

As excrement, other waste materials, and soil fill these types of features, evidence of parasites is preserved in a stratigraphic way (with the oldest layers at the bottom and the youngest layers at the top). Archaeologist excavate these types of features along with middens (trash heaps), cisterns, and other collections of human waste from sites all over the world. These sediments are collected with provenience information carefully recorded and dates associated with other things recovered from the same layer.

Analyzing Latrine Sediments
Once these sediments make their way to people like me, they are examined using a sequential analysis model (or at least they should be) to gather all of the information that can possibly come from such material. To process this type of material, first we treat sediments with hydrochloric acid to react with any microfossil-binding calcium carbonate that might be present. Next, we use distilled water to screen heavy sediments and separate macrofossils (big pieces of plants, minerals, bones, insect remains, etc.) from microfossils (parasite eggs, starch granules, pollen, etc.) using the swirl technique. The macrofossils are dried and examined via a stereoscopic microscope. The microfossils are examined via light microscopy and exposed to further processing as needed.

SEM of Lycopodium spores.

Depending on the nature of the samples, we may need to use dangerous chemicals like hydrofluoric acid (for dissolving silicates) or zinc bromide (for heavy density flotation). We are very careful when using such things as they can be harmful if precautions aren't taken to protect ourselves. For example, we wear eye protection all the time...especially when we use zinc bromide because it attacks the optic nerve if splashed in your eye and can blind you. We also have lots of special safety protocols when we work with hydrofluoric acid as it can stop your heart if enough gets on your skin and you aren't treated quickly. Rule #1: Never do it alone, just in case. I'll be using this acid later this week for some sediments from Iowa. There will be two other people in the lab...one working on mites, and one hanging around in case I have any problems.

We also treat sediments with Lycopodium spore tablets just like we treat coprolites and mummy intestines. By adding a known amount of these spores as markers, we are able to quantify our microfossils and make sense of their presence in our samples. We use a microfossil concentration formula to determine the number of microfossils per unit (weight or volume) of sediment.

Taphonomic Issues
Like other kinds of archaeological materials, we must always consider the state of preservation for our samples. The addition of chemicals to break down excrement is something to be aware of in samples from certain places and time periods. As I learned from a recent set of historic samples from Missouri, the microfossils found in cisterns are fewer in number and much more degraded than those found in privies from the same time period.

We also must consider how often the sediments were exposed to abiotic agents of change, like wind and water. A series of wetting and drying episodes can degrade things as hardy as sporopollenin-laden pine tree pollen grains over time, leaving no evidence of anything that was once there. Biotic agents, like coprophagus (poop-eating) fungi, bacteria, and animals, can also affect what we find in latrine sediments.

From Privies to Parasites
Without going into too much detail about the types of microfossils found in latrine sediments, I thought I'd let all of you parasitophiles see some of the groovy parasite eggs that have been found from these contexts.

Parasite eggs recovered
from cemetery sediments.

Unfertilized  egg of
Ascaris lumbricoides

Molecular techniques have also been used on sediments to search for evidence of parasites that don't leave visible traces of themselves. Enzyme-linked immunosorbent assays (ELISAs) have been applied to samples in order to detect a number of protozoan parasites such as Giardia sp., and Entamoeba histolytica. 

Example ELISA plate.
Yellow wells = positive samples.

The Moral of the Story
Like mummies and coprolites, sifting through latrine sediments elicits reactions of both disgust and amazement from those following your work. The data that can be gathered from such studies are immense in volume and intensity. I have conducted a number of contract archaeology jobs that involved the analysis of latrine sediments, so I can literally call these types of material "pay-dirt" from both a scientific and from an economic standpoint. It is sad that so few researchers understand the importance and potential of examining latrine sediments, but at the same time this allows those of us who do see the value in these studies to work without a lot of interference. As always, these kinds of studies provide the best means of understanding what past people were eating and what exactly were eating them.

The Copious Little Coprolite: A Tale of Underrated Informants

As you may or may not already know, a great deal of my dissertation work focuses on the analysis of desiccated human feces (i.e. "coprolites"). These remains can come from archaeological sites such as caves and trash middens, or from direct human contexts such as mummified intestines or even burials in some special cases (e.g. Nivelles). Coprolites most often form in arid environments, preserving within them a vast amount of information about their depositors' diets, medicinal plant usage, and pathogens.  By analyzing these tiny cornucopias of data, we are able to learn not only what people were eating and what was eating them, but also to use these data to elucidate patterns of human behavior as our ancestors interacted with the world around them. Today, we are going to pay homage to something that doesn't often get the recognition that it deserves...the copious little coprolite.

A coprolite from Hinds Cave, Texas.

A Brief History of Coprolite Analysis
The word "coprolite" began as a descriptor of mineralized dinosaur feces used for the first time by a paleontologist named William Buckland in 1829. By the 1960s, the term had been applied to other fecal forms preserved via desiccation in addition to mineralization and was being used to describe fecal materials from archaeological contexts  in addition to paleontological contexts. There have been three distinct phases in this history of coprolite analysis stretching from 1829 up to the present.

The first phase (1829-1960) began with the birth of the term "coprolite". The value of human coprolites was not recognized until 1896, when a botanist named John William Harshberger suggested that looking at seeds in coprolites could reveal information about ancient diets. The early 1900s that followed Harshberger's suggestion saw researchers examining coprolites for other plant remains, like leaves and twigs, in addition to faunal remains, such as the tiny bones found in fecal deposits from a wide range of archaeological contexts. By the 1950s, people began looking more at the neat stuff in human coprolites. They started looking at hair and feathers as well as shell fragments and insect remains. Today, the study of "macrofossils" (macroscopic plant and animal tissues found in coprolites) is a crucial element of coprolite analysis.

Eventually, people began seeking smaller sources of evidence that today we call "microfossils" (things like pollen, starch granules, and our beloved parasite eggs). The first evidence of parasitism in the prehistoric New World came from whipworm (Trichuris trichiura) eggs found in an Incan mummy in 1954. This began the transition of coprolite analysis into the second phase (1960-1970). This phase saw the development of specialized techniques for examining microfossils and laid the foundations for later expansion.

The superstar researcher of the second phase was indisputably a man by the name of Eric Callen. Callen is known to many as the first true coprolite specialist. He completed three major analyses of coprolites recovered from New World archaeological sites and was working on a fourth when he died tragically in 1970. Despite being ridiculed by colleagues for his interest in coprolites (which were regarded as useless by researchers of that time), Callen persevered to become a legend in a now much more respected field. He developed methods for rehydration (a crucial first step in analyzing coprolites) and standardized other techniques for evaluating fecal deposits.

Various pollen grains

A wealth of other researchers also worked on coprolites during this second phase. It was during this era that pollen analysis was integrated into coprolite analysis. These early studies yielded incredible insights into the diets, medicinal plant usage, and even seasonal site occupations of prehistoric peoples of the New World. This era also saw the flickering of parasite studies that would ignite the third phase.


The current phase of coprolite analysis began in 1970. This phase has been characterized by both refined methods of analysis and by the expanse of these analyses into more interdisciplinary realms. Coprolite analysis grew to be applied in a broader sense to archaeological questions beyond the direct discoveries of dietary remains and evidence of diseases in antiquity. Techniques for quantifying macrofossils were developed over the course of a decade. Macrofossil identification techniques were also becoming more sophisticated and researchers began comparing coprolite data from various archaeological sites to one another. Pollen analyses also became more refined as methods for quantification and interpretation were tested and standardized. The study of phytoliths, fungal spores, and starch granules also became integrated into coprolite analysis. This allowed for more rigorous and fruitful assessments of nutrition through time and space.

A variety of phytoliths from the Tangue site in China.
{A–c = rice bulliform; d–g = rice double peaked; h, i = phytoliths from broomcorn millet husk;
j = long saddle; k = scutiform-bulliform from reed; l = common bulliform; m = Cyperus type;
n = trapeziform sinuate (tooth type); o = woody phytolith}

Which brings us up to the birth and subsequent growth of the field of archaeoparasitology. With foci in Brazil, Canada, Chile, England, Germany, Peru, and the United States, analyzing coprolites for evidence of parasitism grew exponentially. From the late 1970s right up through the early 1990s, methods for extracting and quantifying parasite eggs were developed. From the refinement of these methods came the ability of researchers to begin examining epidemiology of the past through the lens of parasitism. The following decades would usher in the integration of molecular techniques for finding evidence of parasitism that could not be seen with the naked eye. Studies using PCR and ELISA would revolutionize coprolite analyses to give researchers an even broader perspective of epidemiology in antiquity.

What's in a Coprolite and What Can They Teach Us?
As you likely gathered from the above, coprolites can treasure troves of taxonomic data. Breaking these into discrete components is how researchers conduct analysis, but only by re-combining dataset after discrete analyses are we able to get the full story that coprolites are trying to tell us. Reinhard and Bryant (1992) broke coprolites into their components in the following way:

1) Biological (Bacteria, Viruses, Fungi, Parasites, Insects, Pollen, Phytoliths, Macrobotanicals, and Macrofaunal Remains)

2) Mineral and Chemical (Sand, Grit, and Flakes, Charcot-Leyden Crystals, and Chemical Components)

All of these different elements that can be recovered from coprolites give dimension to the overall analysis. Taking in discrete datasets examining coprolites for a variety of components and synthesizing the information leads to the emergence of the bigger picture. By finding the eggs of fish tapeworms and tiny fish vertebrae in a land-locked population's coprolites, we can begin to understand prehistoric patterns of trade between this population an a coastal population. By finding the minuscule bones of rodents in the coprolites of cave dwellers, we can begin to picture the resource utilizations and ecological displacements that contributed to the origins of now-established zoonotic diseases among human populations today.

It is obvious, though not always intuitive for some, that diet and disease are intrinsically linked. This is true for the modern world as it was true for populations of the past. Understanding the nature of the diet-disease relationship comes to light by combining the data one can gather from coprolites. These little packets of poop are warehouses of information for understanding such relationships. They not only provide direct evidence (e.g. parasite eggs or pollen grains) but also proxy evidence (e.g. neotropical parasites found in pre-clovis coprolites from the pacific northwest point towards coastal human migration patterns into the new world).

Coprolite analysis is a vital aspect of archaeoparasitology, but also reaches far into other disciplines. Such studies are important for dietary reconstructions, understanding the interactions of people and their environments, and inferring aspects of early human behaviors. Advances in the areas of medicine, food technology, and environmental adaptation can be reflected by the composition of macrofossils and microfossils present in coprolites.

Today, coprolite analyses are being used to examine the origins of many diseases that plague modern societies. Diseases as different in their etiologies as Chagas' disease (caused by a parasitic protozoan) and diabetes (a metabolic disorder). Tracing the origins of such diseases is no small or simple task, but can be done through the analysis of the copious little coprolites that await researchers interesting in unveiling their stories.

The Moral of the Story
I could go on with a long, eloquent speech doting on the awesomeness of coprolite analysis and droning on about how excited I am about my own dissertation work with these remains, but I think by now you've probably read enough to wet your appetite for exploring coprolite analyses on your own. (Or, at least I hope I've so piqued your interest.) Instead, I will leave you with a somewhat crude, but appropriate message: Don't let anyone give you sh*t for liking coprolites. Seriously, people are quick to put down great work that originates from looking at things that some deem as "gross". (This is typically due to their own ignorance as to the significance of said work.) As a parasitophile, you are probably no stranger to the disgusted reactions of people who don't understand the value of parasitiology. But we don't do it for them, now do we? We do it for us. We do it to better understand the intricacies of the world around us. We do it because our passion knows no bounds. As a coffee cup that sits in an unnamed parasitology lab states: Don't let the bastards get you down!

Show Me the Mummy!: A Journey into the World of Mummy Studies

This week I embarked upon my first collaborations with an amazing person that I met my very first semester here. She was an undergraduate back in those days, but she has since grown into working on a graduate degree through a dental program and...oh yeah, she's a Fulbright scholar. ;) She spent a year in Chile examining the hair (which, apparently wasn't always attached to the head) of mummies. I am honored to be joining the effort to get a few papers out from the data that she collected before she made her way back here for dental school. Until these data are published, I can't really say too much about what we are doing, but meeting with her earlier this week got me to thinking that I should do a blogpost on mummy studies.

So here I am...finally getting back into that series that I wanted to start back in October, when things got crazy. I hope y'all enjoy this journey into the exciting and totally underrated world of mummy studies.

Mummies Across Time and Space

Xin Zhui, a.k.a. "The Diva Mummy"

As soon as you read the word "mummy", I'm sure your first thought was "EGYPT!"...or at least that word was in whatever your first thought was. Yes, there are some awesome mummies in Egypt and those are the mummies that have garnered the post popularity in global media. However, there are LOTS of other places in the world that can boast of their own mummies. There are mummies in Asia...that's right, Japan, Korea, Mongolia, China all have mummies. In fact, one of the most well-preserved mummies ever discovered was the body of a noble woman named Xin Zhui who died in 163 BCE. She lived a lavish lifestyle, but died of a heart attack around the age of 50. The care taken to preserve her body along with all of the artifacts found over 2,000 years after she was entombed have earned her the nickname "The Diva Mummy". Her body was so perfectly preserved that when researchers examined the body, they commented that it was almost like doing an autopsy of a recently deceased person. Her limbs were flexible and her organs were remarkably in-tact. Mummy researchers learned a lot about the health of this person, including that she harbored tapeworms! (Yay parasites!)

Mummies have also been found in other parts of the world like Europe and South America. I've done a little bit of work with European mummies (from Lithuania and from Italy) that were much younger (1700s and forward) than the Egyptian mummies or most of the mummies from Asia. The previously mentioned work with the Chilean mummies will be the first work I'll have ever done with South American mummies. The Chinchorro mummies, found in present day Chile and Peru, are the oldest artificially mummified human remains in the world. You heard that right. The oldest of these mummies predates the oldest Egyptian mummies by about 4,000 years!

Now, I could easily spend hours talking to you about the differences in mummies across the world because they are just so diverse and fascinating, but this is a blog post...despite my propensity to sometimes get a little long-winded. Suffice it to say that mummies can (and are) found in a variety of places on this planet and that they range in age from around 7,000 BC to much more modern mummies who died in say, the early 1900s (AD).

Types of Mummies
There are several ways that would could split up mummies by "type", but I'm just going to break it into two broad categories for today's purposes. First, you could have a "prepared", "artificial", or "anthropogenic" mummy. These terms all refer to bodies that did not undergo natural mummification as a product of the corpse's depositional environment. These mummies were instead created by intentional preparation of the bodies. Most people think of these kinds of mummies when they picture mummies. Long before embalming, mummification was common practice for dealing with the remains of the deceased in certain parts of the world. Most people think of Egypt, with their whole wrapping, organs in jars, and pulling the brain out through the nose things, but the way that various cultures prepared mummies are as unique as the cultures themselves. Often times, the bodies were eviscerated and packed with plant material like straw to help maintain the shape of the now hollowed out body. There were frequently local (or sometimes imported) oils, vinegars, and herbs used on the bodies. Bodies were typically tightly wrapped in linen or other textiles and placed in a well-ventilated area to allow for drying. Some bodies were later placed into coffins, sarcophagi, or even glass viewing cases.

Ötzi the Iceman

However, there's more than one way to make a mummy. Some of the most famous mummies in the world are the bodies of people who were mummified unintentionally as a product of the environment in which they died. These of most frequently referred to as "spontaneous" mummies. Arid environments are particularly good for naturally drying out the body. Thus we have some excellent mummies found in desert regions, like the Chinchorro mummies found in South America's Atacama desert that I mentioned earlier. Mummies can also be found in arid environments that are cold, like the mummy known famously as Ötzi the Iceman. This mummy was discovered by some Germans hiking in the Alps. The hikers thought they had stumbled upon the body of another hiker who had had an accident, but it turns out that the body was 5,000 years old. Political issues arose when Italy and Austria both tried to claim the body, but in the end it was determined to have been on Italian soil.

Head of the Tollund Man

Bodies can also be preserved by the environments peat bogs. When a person's body is left in a peat bog, the bones tend to dissolve because of the acidity of the bog itself (remember that bones have lots of calcium phosphate, which is basic in nature). However, the acidity of bogs along with having little to no oxygen, and lower ambient temperatures creates an amazing preservation environment for human skin. The skin preserves extremely well, though it does get crazy dark in color making them appear almost like statues in the photographs that I've seen. These conditions include highly acidic water, low temperature, and a lack of oxygen, and combine to preserve but severely tan their skin. While the skin is well-preserved, the bones are generally not, due to the acid in the peat having dissolved the calcium phosphate of bone. The Tollund Man is one of the most famous bog bodies, belonging to a man who was hanged sometime between 375-210 BCE.

As a fun side note, mummies don't have to be humans. (But you've probably heard of how the Egyptians mummified cats...because you're a smart one!) Egyptians also mummified dogs...and lots of them. I read a neat study a while back that looked at the ectoparasites on Egyptian dog mummies. I did a post about it, and later a presentation at a parasite seminar. (You can read it here, but please keep in mind that I wrote it a few years ago and I've learned a lot more about taphonomy and parasitology since then.) Egyptians also commonly mummified pet monkeys, gazelles, mongooses, and a variety of birds. Aside from pets, Egyptians mummified other animals, including crocodiles, baboons, fish, snakes, and even bulls, for religious purposes. I haven't really heard of any other cultures that mummified animals, but I wouldn't be the least bit surprised if such cultures existed.

Mummy Studies
The field of mummy studies is an ever-growing one. As we become more technologically advanced, we are given the opportunity to really examine mummies to help us answer questions about life in the past. Mummy studies give us insights into the worlds of people who lived long ago. By analyzing mummies, we are able to understand when these people died and often times under what circumstances. We learn about their diets, medical practices, and funerary rituals. We learn about their societies and are able to tell their long-since forgotten stories.

Mummy studies brings together researchers from all kinds of educational backgrounds. The expertise of archaeologists, anthropologists, radiologists, epidemiologists, forensic scientists, palynologists, medical historians, and, of course, archaeoparasitologists, are brought together to put together the stories of these mummies. The patterns of culture, diet, and disease begin to emerge as mummies reveal their secrets to these researchers.

If any of you are interested in mummy studies, I'd like to inform you of a mummy field school that is currently in the making to begin in the summer of 2016. The course will consist of 15 days in Italy studying the mummies of the region. You'll actually get to do hands-on analyses of some of these mummies as class projects after you learn from experts all about how such analyses are conducted! There's even a possibility that yours truly will be there as either faculty or staff...but let's not get too far ahead of ourselves! (Dissertation OP.)

Mummies and Archaeoparasitology
Many of you may have gotten this far asking the question, "So, when do we get to learn more about parasites?!?!" Okay, okay...let's get to the parasites! Like other areas of mummy studies, the recovery of parasite data is largely dependent on the preservation environment and on the available technology of the people studying mummy parasitism. The analysis of mummified remains can (and has) revealed evidence of ectoparasites (as you already know from talking about the ticks and hippoboscids found on the mummies of dogs from Egypt), helminths (i.e. "worms"), and even protozoans. Yes, there's a little something for every kind of parasitophiliac when it comes to mummy studies!

Lice from a pre-columbian, Chilean mummy.
Click here for a link to the paper.

One of the coolest things about ectoparasites is that they tend to preserve well since we are typically referring to arthropods like ticks, fleas, and lice when we use the term "ectoparasite". In terms of human mummies, lice are the paydirt of ectoparasite-related archaeoparasitology. Lice can not only be found in their adult states on mummies, but also exist in the form of nits and nymphs. For those who don't know, "nits" are cases that house developing lice and are cemented onto the shafts of hair in an infested person. These nits, both with and without nymphs inside of them, can be found on the hairs of mummies. Counting the number of these nits on a small section of hair can allow for quantified comparative data across various analyses of head lice and their mummified hosts. Currently, I'm involved in the preparation of a paper or two that will look at the lice of mummies from the Atacama desert of South America. I'll be sure to post all about it when this paper (or papers) is (are) published. Be on the lookout! ;)

Stole this one from my major professor's Facebook page.
It's an adult louse from a South American mummy!

Most of the studies published with regard to archaeoparasitology of mummies focus on the discovery of parasitic helminths. In fact, the first archaeoparasitological study ever published (Ruffer in 1910) described the discovery of calcified Schistosoma sp. eggs in the kidneys of two 12th dynasty Egyptian mummies. Since those days, mummies from around the world have  revealed evidence of infections with roundworms (Ascaris lumbricoides, Strongyloides stercoralis, Trichostrongylus sp., Trichuris trichiura, etc.), tapeworms (most often Taenia sp.), and flukes (Clonorchis sinensis, Dicrocoelium dendriticum, Gymnophalloides seoi, Metagonimus yokogawai, Schistosoma sp., etc.).

Paragonimus westermani eggs from
the liver of a female, Korean mummy.
Click here for a link to the paper.

My personal experience with mummies is limited, but growing with every passing semester. I've seen Ascaris lumbricoides and Trichuris trichiura eggs in a mummy from Lithuania and Clonorchis sinensis eggs from a Korean mummy. I've also analyzed mummies from other places and not found any parasite eggs. I'm hoping to expand this in the future as I become more involved with mummy studies.

Another aspect of studying mummy parasites is to look for things that can't actually be seen with our human eyes. I'm talking of course about protozoan parasites (one of my favorite groups of parasitic organisms!). Because these are delicate, single-celled organisms, they don't preserve in the way that helminth eggs preserve. Instead of leaving behind a physical form that can be found with the aid of a microscope, these parasites leave behind molecular traces that can be detected with the use of serological test kits, such as enzyme-linked immunosorbent assays (ELISA), or through the use of DNA detection techniques, such as polymerase chain reaction (PCR). These techniques have been most frequently utilized to identify parasites in archaeological materials such as coprolites and latrine sediments, but they have also been applied to mummy studies. For example, researchers have revealed that ancient peoples were infected with malaria (caused by Plasmodium sp.) by analyzing bone, muscles, and skin.

The conclusion of this section brings us back to the infinite awesomeness that will be the mummy field school mentioned earlier. Students will be working on independent research projects with the mummies. Some of those students will be looking specifically at the parasites that infected these individuals in life. It will be fascinating to see what new information will come from the systematic examination of these individuals over time.

The Moral of the Story
The world of mummy studies is a complex, interdisciplinary area with lots of discoveries just waiting to emerge from hard work of enthusiastic researchers. What we can learn from the past through archaeological material is always a puzzle, but mummies give us the unique ability to equate data with a particular individual rather than guessing at how many people are represented by a group of coprolites or a gram of latrine sediments. Understanding the diets, medical advancements, seasonality of death, and of course the diseases of mummies allows us to paint an epidemiological picture of past societies one person at a time. As I grow to be a more competent archaeoparasitologist, I can only hope that my path will cross with more and more of these astoundingly interesting individuals and the parasites that they hold on or within them.

The Nivelles Story: My Second Peer-Reviewed Paper Makes JAS

I get it. I kind of dropped the ball for, oh, three months. I can't even guarantee that I'm officially picking it back up again today. Last semester was insanely busy and went by before I could blink. I'm happy to report that other than being crazy it went really well for me. I published a book, got a paper out (for which I was lead author), passed my comprehensive exams, and lined up a ton (technical term) of new projects for the Spring. This semester doesn't look like it will be any slower (which isn't a bad thing), so I will try my best to keep up with posts, but please forgive me if I again drop the ball. (I promise to pick it up again when I get the chance!)

Today, I'm going to talk to you a little bit about my latest publication, which was published this month. This paper was quite a doozy! ("Doozy" is defined by Merriam-Webster as: "something that is unusually good, bad, big, severe, etc."... this paper was unusually good, bad, big, and a whole host of other words.)

My involvement with this paper began long after the analyses were complete. The story begins back in 2011, long before I made my way up to Nebraska. Dr. Karl Reinhard's Archaeoparasitology class began analyzing coproites excavated from skeletonized remains resting in Nivelles, Belgium. The coprolites were many, but hailed from only three individuals. These individuals had lived in this part of Europe during the Medieval period, a time notoriously ridden with filth and disease. As one would expect, these individuals were found to have been hosts to parasitic worms, namely Trichuris trichiura (the human whipworm) and Ascaris lumbricoides (the human mawworm or "giant intestinal roundworm"). European archaeoparasitology is known to yield evidence of such worms in great abundance, especially if you go back in time when our understanding of disease was dominated by miasmatism (the belief that diseases were caused by smells and "bad air" rather that pathogens as we know them to be caused by today).

Finding these individuals to be infected with worms was interesting and important, but it was the infections of a particular individual (from Burial 122) that made this study phenomenal. That individual was an elderly woman. Bone pathology reports tell us that she had no teeth and was suffering from arthritis. The coprolites taken from her remains were abnormally large in size and were much more numerous than would typically be found in such contexts. The coprolites were also backed up beyond her sacral region and into her lumbar region. This indicated that she likely suffered from a bowel obstruction or some other issue that led to constipation. This poor woman probably suffered greatly in her final days.

Examination of her coprolites revealed an abnormal amount of wheat glume in her feces. The fiber rife within her could have contributed to the obstruction, but why would she have been eating it in the first place? And why so much of it? As it turns out, this was a way that Medieval doctors sometimes treated people who were burdened by intestinal worms...and this lady had a major problem with worms.

Figure. 9. Average number of eggs per gram as represented by all three burial sites. 

Gray bars represent Trichuris trichiura while black bars represent Ascaris lumbricoides.

[From Racz et al., 2015]

As you can see from the histogram above, this woman suffered from two different types of worms AND suffered an EXTREMELY heavy infection with whipworms. Keep in mind that the above represents average eggs per gram of feces. That's a LOT of freaking whipworm eggs to find in one person. Let's not forget she also had mawworm eggs alongside those whipworm eggs. Here's a table from the paper that will (or at least should) blow your mind.

[From Racz et al., 2015]

Having so many worms in any one of these coprolite is staggering, but remember that all 8 of these coprolites were inside ONE person! If you add up the "eggs per coprolite" values, you get over 200,000 mawworm eggs and over 1.5 million whipworm eggs...again, all inside of the same person. (Seriously, just let that sink in for a moment.) A whipworm infection this bad has never been reported in anyone. This discovery brings our understanding of Medieval filth and disease to a whole new level. 

Additionally, a female whipworm can only lay about 30K-60K eggs a day (depending on your information source). Though we don't know how long these eggs were sitting inside of this severely constipated woman, we do know that she had to have more than a single worm laying eggs. Having a heavy load of whipworms can cause people to have problems like prolapsed rectum and compromised peristaltic activity of the intestines. (Which translates to: your rectum falls out of your butt and your intestines can't push poo out of you anymore because the muscles aren't working right.) The paper concludes that the extreme parasitism was likely affiliated with the cause of death for this woman.

The paper also discussed the importance of looking at parasite egg taphonomy (how things deteriorate or decay over time) and the co-infection of two worm species as it relates to other aspects of European archaeoparasitology.

I officially joined the Nivelles team as a co-author in my second year, though I had heard all about it in my first semester. You see, the manuscript was pieced together from the term projects of four students and introductory material from colleagues in Europe. The lead author had been working on trying to bring everyone's work together, but it still didn't read like it was written by one person. At the suggestion of my major professor, I worked with the lead author to cut, re-write, and otherwise clean up the manuscript so that it was publishable. This took up much more of my time than I had anticipated, but it was worth it once we finally got it submission-ready. In February, 2014, I took the position of corresponding author and pulled the manuscript through the submission process. We submitted to the Journal of Archaeological Science, and we received excellent reviews. After lots and lots of editing, we finally sent back the final proofs in October, 2014. Our paper was set to be published online in November and in print the following January. That's right, from submitting the first time to print publication was almost a full year. (This doesn't even include the time spent editing prior to submission.)

The Moral of the Story

Despite all the headaches, this was such an amazing project to be a part of, even in the later stages. The author line can boast of researchers spanning four countries on three different continents. It involved an undergraduate, two master's students, two PhD students, and senior researchers from multiple universities. It was a really cool thing to be involved in, and I'm very thankful to have been brought on to help. 

We even got some media attention for the work! Check out the article about it here!

Finally, as might become tradition for parasite papers that I publish, here is a title shot for your viewing pleasure. :)

A Journey into the World of Paleoparasitology: Learning New Things from Old Stuff

Given my research interests, this type of post is LONG overdue. I've decided that I need to do a series of posts about the field of paleoparasitology. Today, I'm going to start with some basic introductory stuff to prepare you for the next few weeks. So, pull up a chair, pour yourself a nice cup of hot tea, and prepare to be amazed by the work of researchers exploring a lost world of parasites.

Introductions

First things first. Let's talk terminology...after all, without understanding the proper technobabble one can't hold a conversation about a given subject. We'll start with an easy one:

Paleoparasitology--This word refers to a subfield of Paleontology that focuses on parasitic organisms of the past and on the relationships of parasites, vectors, and hosts in the past. Goncalves et al. (2003) stated, "Paleoparasitology is the study of parasites in archaeological material." Indeed, the majority of paleoparasitological studies have derived from the use of ancient materials most often obtained via excavation. The word is sometimes used in reference to any such materials, but in 1992 Dr. Karl J. Reinhard (my major professor) called for this term to refer solely to studies of "non-human, paleontological materials". In the same paper, he suggested that the term "archaeoparasitology" be used to describe the analysis of materials from human contexts for evidence of parasitism. 

Ascaris lumbricoides egg
from a Lithuanian mummy.

This brings us to Archaeoparasitology, which you now know refers to the
study of parasites from ancient materials of strictly human origin (e.g. coprolites, latrine sediments, and mummy intestines). This field is specific,
but highly interdisciplinary at the same time. The researchers within this field come from diverse backgrounds as organismal biologists, epidemiologists, ecologists, archaeologists, anthropologists, and paleopathologists, just to name a few. Many of the methods utilized in this field are borrowed from techniques used in other fields, such as veterinary parasitology or palynology.

While we are on the subject: Coprolites, if you don't already know, are desiccated feces.

Also, palynology refers to the study of "palynomorphs", which are tiny things found in air, water, or sediments including things like dinocysts, spores, or the little guys I like known as pollen. This field grew out of geology and is important for lots of reasons, but we will focus on the use of pollen as it relates to diet and environment so that we can tie it in with our understanding of parasitism in antiquity.

A Brief History of Paleoparasitology

The history of this field could fill a week's worth of lectures in a formal class setting (possibly more depending on the professor). I won't go through all of the details, but here's a few of the highlights in a timeline format:

Sir Marc Armand Ruffer, the first person to
describe parasite eggs from archaeological contexts.

~1910--Sir Marc Armand Ruffer publishes his findings of Schistosoma haematobium eggs (that's one of the three species of blood flukes that infect humans) in mummified kidneys from Egyptians dating to the 20th Dynasty (1250-1100 BC). This is the first time anyone had reported parasites from mummies, or any type of archaeological material for that matter.

~1921--Samuel T. Darling published a paper discussing the origins of South American hookworm infections among indigenous peoples based on assumptions regarding prehistoric human migrations.

~1925--Ernest T. Seton publishes On the Study of Scatology in the Journal of Mammology, which was important for demonstrating how fecal shape and content could be used to identify what order of mammal had deposited the material.

~1944--Lothar Szidat reported finding eggs from two geohelminth species (Trichuris trichiura a.k.a. the human whipworm and Ascaris lumbricoides a.k.a. "mawworms") in bog bodies from Prussia.

~1947--Van Cleave and Ross published an important methological paper describing the use of trisodium phospate for the rehydration of coprolites. The use of trisodium phosphate has now been applied to the rehydration of mummified tissues as well.

~1955--E.L. Taylor publishes his discovery of parasitic helminths recovered from a medieval cesspit. He was the first person to examine cesspits from this time period. Many others have followed in his footsteps to give us an exciting look into medieval parasitism.

~1955 & 1960--In two separate publications, Eric Callen and Thomas Cameron improved rehydration techniques. The 1960 article is one of the most frequently cited paleoparasitological papers.

The 1960s and 1970s saw an explosion of highly influential articles published in the field. The time period from 1910 up to the 1970s is often referred to as the "Exploratory Phase" of archaeoparasitology. This phase was followed by the "Population Phase" of the late 1970s through the late 1980s and by the "Synthesis Phase" in during which archaeology fused with parasitological theories. We will talk more about the predominant theoretical constructs of the field in a later post.

An example of an ELISA
(enzyme-linked immunosorbent assay)
used to detect parasite antigens.

The Synthesis Phase of archaeoparasitology was characterized by the integration of methodologies from other disciplines into the field. These borrowed techniques were adapted, reviewed, and refined throughout the 1980s and 1990s to establish methodological standards for studying parasitism via archaeological materials. Sadly, many of these standards have been lost in the influx of poorly-trained new-comers to the field and the well-established and painstakingly tested techniques can be found perverted in contemporary journal articles. Evolution of methods will be the subject of a future post.

With new technological advances in other fields came the application of new techniques in the field of paleoparasitology. The use of molecular techniques stretching from the 1990s onward has opened the door to paleoserology and the study of ancient DNA for looking at parasitism in the past. These topics will also be covered by a future post within this series.

The Big Questions of the Field
Every field has "big questions" associated with it, and paleoparasitology is no different. However, these questions are far broader and vary in their importance based on which researcher you are talking to.

The co-evolution of hosts and parasites is one region with lots of big questions. How long have humans been associated with parasite x? Did dinosaurs have parasites that evolved to parasitize modern archosaurians? Have modern advancements in helminth removal led to over-active immune systems leading to autoimmune diseases?

Tying into co-evolution questions are ecological questions, such as how host associations led to zoonotic infections in the past. ("Zoonosis" refers to a disease passed from animals to humans, e.g. rabies.) How long ago did Toxoplasma gondii establish itself in human populations?

Ecological questions involving humans, in turn, lead to behavioral and cultural questions. How did living in rockshelters and eating woodrats pull humans into the transmission cycle of Trypanosoma cruzi? How did domestication lead to human acquisition of new parasites? How did the diets of early people affect parasitism among populations? How did the lifestyles of hunter-gatherers as compared to agriculturalist predispose these groups to different types of parasites (and vice versa)?

Further branching off of these kinds of questions are questions of what parasitism can tell us about past societies. Was population x dealing with a sanitation crisis? How could a culture living far inland be infected with a parasite associated with marine fish? If parasite x requires conditions a, b, and c, how could population y have ever traveled using route z?

Questions regarding how parasitic infections were recognized, diagnosed, treated, spread, and otherwise dealt with during a variety of time periods at numerous geographic locations are the heart of paleoparasitology. Additional questions about human cultures, societal structures, subsistence patterns, migrational patterns, and trading routes can also be raised when dealing with parasite data.

The Moral of the Story

The field of paleoparasitology has a long and colorful past painted by the adroit work of observant naturalists and archaeologists. As we will learn over the course of the next several weeks, this field is interesting for both what has been discovered and for what is yet to be discovered. I suppose this could be said for any area of science, but it is especially exciting, for me at least, to add a time component to the research of parasitism. The big questions that come up within this field are as diverse as the researchers attempting to address them. The window of the past brings forth a better understanding of things as they were so that we can more efficiently address the nature of things as they are. I hope that over the next several weeks you will join me on this journey into the world of paleoparasitology.

Further Readings

If you are interested in the field of paleoparasitology or any subdiscipline thereof, I would encourage you to purchase this book. It is the best compilation of work in this area. In fact, it won one of Brazil's most natural sciences book awards, the Prêmio Jabuti, or "Tortoise Award." (Which you can learn more about here if you are interested. Also, here is a link to a news release about the book and about the Science Without Borders grant related to the collaborative work of the editors.) I'll be using my copy of this book as a reference for the series of posts relating to this field. (Also, the timeline stemmed from a much more detailed and informative timeline found in the first chapter of this book.)

Additionally, here's a great article published in the special edition 100th volume of the Journal of Parasitology that relates to paleoparasitology. It's a must-read for anyone interested!

Also, here are the citations mentioned in the post above:

Gonçalves, M.L.C., A. Araújo, and L.F. Ferreira (2003) Human intestinal parasites in the past: New findings and a review. Memórias do Instituto Oswaldo Cruz 98(Suppl 1):103-118.

Reinhard, K.J. (1992) Parasitology as an interpretive tool in archaeology. American Antiquity 57(2):231-245.

Officially an Author (Part II): Announcing My First Scientific Publication

Hey all! Well, it finally happened. After years as a graduate student, I have finally acquired my first piece of "academic currency". I thought it would be good to tell you guys a little bit more about it in this post and then give you a small preview of some other papers that I have in the works. Happy reading! :)

In February of this year, our lab received samples from mummies interred beneath the Dominican Church of the Holy Spirit in Vilinus, Lithuania. These samples represented intestinal, abdominal, and rectal contents from a handful of individual mummies. We analyzed these samples in search of parasites, starches, and pollen grains. The analysis was conducted by myself, my major professor, and a UCARE student whom we lovingly referred to as our "under-grunt". (UCARE is a program through our university that sponsors undergraduate research. It stands for "Undergraduate Creative Activities and Research Experiences".)

By the end of the month, we had not only finished the parasite analysis (the pollen analysis extended for another month or so), but I had also prepared a manuscript for publication regarding our parasite findings. Basically, we had found that one of the ten samples analyzed contained the eggs of both Ascaris lumbricoides (human mawworm) and Trichuris trichiura (human whipworm). These findings were exciting (aside from the fact that we found parasite eggs, which is always a cool thing) because this represented the first report of parasitic geohelminths in mummies from this area dating to this time period (18th-19th century). We also found lots of really cool mites along with their eggs, and we were able to discuss differential preservation of parasite eggs within mummy contexts because we found underdeveloped T. trichiura eggs. The discovery of these underdeveloped eggs coupled with encountering these eggs in groups of 2, 3, or in one case 9, led us to conclude that we had rehydrated material that had once had a female T. trichiura embedded within it. As the gravid (i.e. full of eggs) female decomposed, the eggs preserved inside of the mummy, but were never able to embryonate. This discovery highlights a problem that one only encounters when dealing with mummies as archaeoparasitological analysis of coprolites (desiccated feces) or latrine/privy/sewer/water closet sediments will only yield eggs that are more developmentally advanced because they were passed by the female and subsequently by the depositor of the feces. Hence, people who study mummy parasites must be able to recognize parasite eggs that are underdeveloped in addition to recognizing their fully-developed counterparts.

We sent this paper to our co-authors in Lithuania and everyone gave the manuscript the green light for submission. We chose to submit our paper to the International Journal for Paleopathology (henceforth known as "IJPP"). Before March had even rolled around we were anxiously awaiting reviewer comments. I'll spare you the details of the reviewer comments (both the constructive ones and the ones that merely demonstrated the reviewer's complete lack of familiarity with basic archaeoparasitological methodologies and concepts). The take-home here is that I got my baptism under fire as an author undergoing the peer-review process.

This may have been my first paper, but I wasn't completely naive when it came to the process. I had been told (or more precisely "warned") about how one could receive scathing reviews or about how reviewers weren't always well-suited to critique the work that they were reading. I was prepared to have a thick skin and to take every comment as a device for perfecting our paper. I was prepared to make both minor and major changes and to accept the criticism from people I assumed to be much more experienced than myself. What I was not prepared for were the asinine comments that served no purpose other than to point out "errors" that didn't really exist. I quickly learned that some of the reviewers could in no way be classified as my "peers", much less as experts in the field if they didn't understand some of the most fundamental concepts of the discipline. It was an odd experience, to say the least.

To balance out the oddness, we did have some really great comments from reviewers as well. We were asked to revise and resubmit. (Which is what every author wants to hear!) We made the changes. The paper went from a case study to a brief communication and we dropped all of the information about the mites. (Something for another paper someday.) We re-submitted and after a few weeks, the paper came back with additional reviewer comments and we were asked to make more dramatic changes and to resubmit again. We made said changes, shifting the focus of the article more toward the taphonomic aspects of the paper. We again, resubmitted. We were met with an additional request to revise and resubmit. By the end of it all, we had a very different looking manuscript than we had begun with, but we had a great article that was about to be published, which made all of the hassle worthwhile.

After editorial corrections and approving galley proofs, it finally happened. In August, a whole half of a year after the initial submission, I saw my name as first author on my first ever peer-reviewed scientific article. My first piece of primary literature will forever be cited as "Morrow et al., 2014". That's a good feeling!

The Moral of the Story
Sometime, it's okay to be a "late bloomer" as a scientist. I may not have had a publication as an undergraduate or even as a master's student, but my first one really was special. My first one taught me the skill of navigating the submission process as I was the corresponding author in charge of submission and communication with my co-authors. It taught me the importance of diplomacy and collaboration as I was in charge of coordinating revision efforts. It taught me patience, that the review process takes time whether you spend weeks or years preparing a manuscript. Most importantly, it taught me to handle idiotic comments in tactful, diplomatic language without buckling to the whims of reviewers who are blatantly incorrect in their assertions. (And, of course, it taught me to take constructive criticism...providing that it is, in fact, constructive...and use it as the wet stone to sharpen the blade of an incredible manuscript.) I'm so thankful that this particular experience was my first experience with peer-reviewed publication as bonafide scientist. Here's to many more in my future!

The article can be found online in all of it's full-color glory here if you are interested.

Ha! You thought I forgot about your sneak previews, didn't you! Fear not, faithful readers, for I shall never let you down! I can't disclose much until things actually get published, but here's a few topics covered by some of my "works in progress". In no particular order:

-Lack of parasites from embalming jars containing the remains of members of a very prominent Italian family. [Submitted.]

-Parasites from coprolites out of Medieval burials. [Just resubmitted this one for publication on Friday!

-Insects from an Italian mummy who is now a saint...making the insect remains "holy relics". (True story.) [In revision with co-authors.]

-Pollen/Dietary analysis of Lithuanian mummies. [Working on a manuscript.]

-Parasites from 1,200-1,400 year-old coprolites sealed beneath an adobe floor in a cave in Mexico. [Funding pending.]

-New methods for recovering parasite information from previously un-utilized source materials. [Funding pending.]

-Analyses of mites from European mummies. [Analysis ongoing.]

-Analysis of sediments from a sod house wall. [Analysis scheduled for later this semester.]

-Pollen and possible parasite analysis from a 8,000-9,000 year old Brazilian burial site. [Analysis scheduled for the Spring.]

-An assessment of the efficiency of flotation for pollen recovery out of karstic soils. [Analysis scheduled for the Spring.]

-A comparative review of archaeoparasitiological methods in contemporary literature. [Ongoing work on a manuscript.]

-Lice collected from a pre-clovis cave. [Waiting for samples.]