Archive | October, 2012

Keep on Diggin’

20 Oct

Horror of horrors, the original British version of the Time Team television show has been axed.  Cue plenty of ‘buried’ jokes by the media.  The show has been cancelled after a solid 20 years of bringing archaeological excavations and investigations to the public.  The show will continue with a new already filmed series which will be shown in 2013, but it has not been recommissioned for any other series after that, although one-off specials may be shown after this time.  There have been several well publicized problems during the latter series of Time Team, with a lack of focus on the archaeology itself and problems with presenters helping to drive the viewers away.  Although many professional archaeologists may gripe about Time Team and it’s misrepresentations about the archaeological sector, there is no doubt that it helped popularize archaeology and heritage on a large scale to a wide audience.  Fear not though restless viewer, although Time Team may have gone the way of Extreme Archaeology, the ever present Tim Taylor is currently devising new historical programs as we speak.  His statement regarding Time Team’s demise can be read here, whilst Francis Pryor’s can be read here.        

Meanwhile I recently took part in an archaeological dig as part of the Heritage Lottery FundedLimestone Landscapes Partnership‘.  The large scale project is based on the Magnesian Limestone plateau that runs from near the Tyne down to the Tees, and from the coast to central Durham, in north eastern England.  The aims are to help conserve and record the landscapes, wildlife, and rich heritage of the Magnesian Limestone whilst ‘enabling communities to learn about, enjoy and celebrate their local area’ .  I may be biased but this is an area of intense beauty, where the harsh realities of man’s industrial strength is matched only by the savage beauty of nature herself.

There are a wide range of projects available as a part of the program, and Community Archaeology is one such aspect of this.  Carried out under the direction of the Durham University Archaeological Services and volunteer members from the Architectural and Archaeology Society of Durham and Northumberland, the two week dig at Great Chilton seeks to investigate an Iron Age enclosure site.  Previous geophysical survey results had shown possible roundhouses, gullies and one or two boundary ditches; in other words a typical north eastern Iron Age settlement!

Approaching the Iron Age site at Great Chilton, with the rolling hills of County Durham in the background.

As I’ve stated before on this blog, I can’t contain my joy at being back out on site, even if it was just for the day.  Unfortunately for yours truly, the site is difficult to get to if you do not drive (although I am rectifying that situation), and as such I will not be able to attend the 2nd week of the excavation next week.  Walking across the field, with the short stubs of wheat being crushed underfoot, felt wonderful as the view of the spoil heaps loomed into view.  The sun managed to break through the morning mist as the day was set to be spent close to mother earth.  My task for the day was to excavate and help define a part of the ditch surrounding one of the Iron Age roundhouses in the first trench.  Although nothing of note was recorded it was a joy to be able to get stuck into the sandy soil and to take in the fresh October air.

Can you spot the Iron Age round house? 50%  sampling method of the outside ditch, where at meter intervals 1x1m square patches were uncovered and excavated down to define said ditch.

Community archaeology is on something of a high note at the moment as various projects around the country are including the local and not-so-local volunteers, whilst many archaeological units are including the local populace with engaging in the local heritage scenes.  I firmly believe that without volunteers archaeology would, in some respects, grind to a halt.  At Great Chilton I was re-united with a fellow digger who I had first met some time ago, on a similar Iron Age/Romano-British site in my hometown, and with who I have visited a few other sites since.  As the familiar clink of the WHS 4 inch pointing trowels filled the air I thought that this would probably be the last dig of the season, before the snows of winter appear.  Although I haven’t dug much this year I have felt grateful for the opportunities when I have had the opportunity to do so, and had once again enjoyed joining the extended family of archaeologists that toil away at sites throughout the country.

The next blog entry will concern the human foot as the final part of the skeletal anatomy that will be covered for the Skeletal Series entries.

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Guest Post: ‘Welcome to Commercial Archaeology: A Biased Introduction’ by Charles Hay

14 Oct

Charles A. Hay is currently aiming towards his next big adventure.  Prior to this he has worked as a field archaeologist throughout England for units such as Wessex Archaeology, Cambridge Archaeological Unit and the University of Sheffield.  He also holds an MA in Archaeology from the latter.  His writings, including investigations of philosophy and original short stories, can be found at his Human Friendly site alongside his numerous drawings, musings and photographs.  If you find him in a pub, he will be having a pint of Pendle or a good scotch.  If it is a working day, then a black coffee will do instead!  Charles has previously written for These Bones of Mine with a guest post titled Glass & Metal.

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A few weeks ago (sorry for the delay Dave), I was asked to write about commercial archaeology, the ups and downs, what it involves, how it is as a living, how to get in et cetera. The past fortnight (in fact, I suspect significantly longer, sorry again Dave) I’ve been attempting to come up with something both encouraging and suitably warning, equally weighted, inspirational; a one-stop advice sheet.

So, interestingly enough, that version ended up reading like bullshitty gumph.

Instead, I’ve decided to take a much more straightforward approach. Instead of advertising, I’m going for the storytelling approach.

Listen.

I’m not really, really sure how I managed to gain (relatively) stable employment in commercial archaeology. I am prone to telling the same stories repeatedly so anyone who knows me knows the story. I graduated back in 2007 with an English & History degree and the dawning realisation that English & History aren’t quite the career kickstarter subjects I imagined them to be as an eighteen year old. I therefore did what any self-respecting English & History graduate does: I worked in NHS administration for two years.

After several moments of epiphany along the lines of you should become a cartoonist and you should start wearing checked shirts, I finally had one that actually coalesced into something tangible. It was preceded by that most dangerous of decisions, to consult one’s inner child. Now this inner child had been yelling at me for a while for various reasons. I didn’t draw as many trains as was my habit as a five year old. I seldom watched marathons of Thunderbirds and Stingray anymore. I never got around to being a guy who dug old shit up.

The University of Sheffield let me onto their Archaeology MA course and the rest, as they say, is history.  Actually I’m guessing you probably want a little more than that.

Ok so after spending a semester feeling like a certifiable moron, I finally started to gain traction in the subject. Having zero idea what I would write for a PhD (or more accurately, several ideas too vague, wishy-washy and error fuelled to acknowledge in public), I started to lean toward the idea of commercial. I decided to go for the fieldwork based final project instead of a dissertation.

If you are currently thinking, “Charlie, most of your life decisions seem to be completely ad hoc and impulsive with no thought to real consequence”, yeah, I really can’t disagree.

Anyway, my plan for the fieldwork assignment was to use it to mine for references, tip-offs, advice, and alliances. I genuinely suspect it was, with regards to commercial archaeology, the best decision I made. It may well have been the most well thought through too. More or less everyone who supervised me on that first dig have turned out not only to be good, persisting (and persistent, helpfully in my times of grumpitude) friends, they turned out to be wonderfully, mind-bogglingly useful too. The Laurens, Lettys and Chrisses of this world are exactly the sort you need to be meeting to get positive and get a grip with a new career and I had the good luck to meet them all at once.

Due to a tip-off and a good word from Letty and a timely email, more or less immediately after my fieldwork assignment finished, I sadly left Sheffield behind with no idea when, or if, I would be back (as it happened, I was back the following March; not quite the epic absence I had envisaged). I left for my new job, a two month contract with Cambridge Archaeological Unit. The first day I turned up, I was so unbelievably nervous. My only experience so far had been volunteer digs over the summer so I felt as though I knew absolutely nothing. I wasn’t entirely incorrect. Looking back, if I’d known quite how much I was yet to learn at the point, I suspect I’d have been an order of magnitude more nervous.

The other point of aarrgh!! was meeting a whole bunch of new people. As is always the case when approaching a new group, they all seemed to know each other so well and so confidently that it seemed impossible for me to fit in. In this situation I tend to adopt the Cold Swimming Pool approach.

Dive in, make a splash, try not to look like too much of a twat.

Luckily, and I repeat this a lot, archaeologists are, on average (and also, in general; the majority are awesome, but there are some total chumps messing up the numbers) a friendly and inclusive bunch. It is true that I have never worked with any bunch of archaeologists with whom I felt lost or unwelcome. Within a couple of weeks I had been made to feel part of the pack and, by the time my contract was through, I was as sad to leave as I had been upon leaving paces I had lived for years.

It is interesting to ponder on exactly what about certain environments attract certain types of people. Archaeology certainly attracts the kind of philosophical, gregarious, intellectual, adventurous and pleasantly weird and nerdy people I have always gravitated to.

Perhaps it has to do with the human nature of archaeology. It is, after all, an attempt by us to contact, in the only way we have, those who ran before us. It is the inquisitive questioning of the long dead. This seems a little wishy-washy however, and would constitute a complete argument perhaps if you were drunk or if I were spectacularly attractive.

Let’s try another tac.

If I am being entirely honest, there is a great deal of lovable-misfittery in this business. Archaeology is not a vocational science. It is very much an interest settled upon as a result of a questing and wide-ranging personal curiosity about the universe and how what came to be came to be and why. It is for minds who ask, “how do things work, and why?” Curiosity and passion, perfectly suited for a subject which seems a hybrid offspring of science and art. As a result, you will rarely find an archaeologist completely focused on one subject of interest. Many are polymaths, and many harbour a huge array of hobbies and talents. I have learnt and worked with ex-teachers, ex-astrophysicists, people who understand the inside of cars (apparently not magic, who knew?) and people who, like myself, dream of careers in writing, directly passing excitement about the universe on to others, whilst perhaps becoming spectacularly rich and marrying some kind of unbelievably attractive actress maybe.

Hmm, that was quite a tangent. Let’s talk about lessons learnt.

Here’s something for you. Something I cannot overstate. Commercial archaeology is absolutely, completely and utterly balls knackering at points. Be prepared to spend your evenings, especially in the first months, absolutely dog-tired. Hoofing out enormous lumps of dirt is, to the surprise of precisely no-one, exhausting. Doubly so, as not only do these holes have to be dug comprehensively and quickly, they also have to be neat. You’ll get used to it. Or your arms will fall off. Either way, you’ll adjust.

This will, in time, come naturally, and some actually come to love it, but be prepared. On the plus side, it keeps you pretty trim and, with practice, you’ll get better and end up less destroyed without you really noticing the chance.

Another shock to the system: the weather. Earth’s atmosphere is a highly volatile jerk playing entirely by it’s own capricious rules. Own protective gear. I learned this the hard way at my job in Cambridge during the winter of 2010-2011. The local fire services were chiseling cats out of trees, we were all blinking in triple time to avoid eyeball freeze-over and I was out digging sans thermals. The back of my left leg split in the cold. Believe me when I tell you, that hurt. Own protective gear. Many units will give you waterproofs and boots and whatnot, but they most probably won’t give you thermals, knee-pads et cetera.

The biggest warning I can give here though, and one I would be irresponsible is this: If you are not ok with genuinely struggling for work in the first few years, forget it. I’m a happy archaeologist now, but holy hell I would not want to relive my first year attempting to get my foot in the door. There’s not a particularly chirpy or amusing way to put this: intermittent unemployment sucks on a profound and affecting way. Getting one or two month contracts after being on the dole for months is actually financially worse than being on the dole. That first month with no financial support makes you feel scuzzy and poor, on account of the poverty and general scuzzoscity that will bring to your life.

I searched far and wide for jobs during my wilderness months. I rang commercial companies over and over, generally making a nuisance of myself (incidentally, this strategy did work; ring up, be friendly, be enthusiastic, and make them remember your name, for god’s sake – a life lesson not constrained to archaeology). I also looked at office jobs, factory jobs, pizza guy jobs… The day I got an email from the university last summer asking me to assist in supervising one of their summer fieldschools (actually the same one which I had taken the previous year), I had been on a trial-run day working in a kitchen. I had spent the morning “bearding” mussels. I am deeply afraid of mussels. I still considered that job, due to needing to continue existence.

Now this period did end. I did manage to climb back on board and I suspect the waters in which I felt I had been drowning were not nearly so deep and tempestuous as I felt at the time, but I can unreservedly tell you this: If you are not willing to deal with that, find something more sensible to do. I battled through because I have an unusually loud and pushy inner child and because the archaeological community was one I simply was not willing to leave behind. The job’s a fun ride too.

So there you have it. I hope that steps a reasonably useful line between positivity and adequate warning. It is a fun job. The people are very awesome. Sometimes you’ll get very wet and muddy and grumpy and once my beard got full of snow but that’s not all of the time.

With regards to actually getting a job, I’ll summarise with these top tips which I also regard as being useful for life in general.

1. Get experience. Especially over summers, there are volunteer digs going on all over the place. If you’ve got money to burn (or use constructively, some might say), you can go and volunteer abroad, find awesome things and get a sweet tan to boot.

2. Make friends. With everyone. In the world. Or alternatively and more practically, work on your communication. Be outgoing or at least polite and friendly. Never be afraid to ask questions, especially questions you think are stupid. If you think they’re stupid now, the outcome of not knowing the answer will look a whole heap more stupid.

3. Connected to the previous point, make contacts. A lot of the time this will occur naturally through making friends with everyone in the world, but sometimes it takes further effort. Steel up and ring companies directly. Send them an email. Send them a cv. Smoke signal them. Everything. If you send an email into the ether and don’t get a reply, it’s because someone louder, more enthusiastic, possibly more obnoxious (eg. me) is holding their attention.

4. Grow an enormous pair of testicles or ovaries, because the path in is winding and treacherous; more than once you will have to consider hunting local cats to survive.

I hope this has been of some use to some people somewhere. I may have just been gassing on for several thousand words (it’s been known). Any further advice required can be acquired at the Red Deer pub on Friday evenings. My standard rate is a pint per aphorism, with a decline in quality directly proportional to amount of advice given.

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These Bones of Mine Note:

If you are an archaeologist and ever find yourself lost in South Yorkshire, I highly recommend the Red Deer pub, located in the delightful city of Sheffield, as a place to recuperate and recover.  You are bound to bump into a few archaeologists there…

Infectious Disease Part 2: Malaria and Associated Anaemic Conditions

5 Oct

This second post, and the first part, deal with biomolecular approaches and research studies in detecting  the presence of infectious diseases in human bone from archaeological material.  The recent coming of age of biomolecular techniques, as applied to archaeological material, has provided a rich and complex source of information in helping to uncover how infectious diseases spread in the historic and prehistoric past.  The second post, here, describes recent research focused on Malaria and associated anaemic conditions, including Sickle Cell Anaemia and Thalassaemia.  The first post can be found here.

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It has long been realised that malaria can only be recognised in skeletal remains via indirect evidence of presentation of the following pathological lesions- porotic hyperostosis, cribra orbitalia and marrow hypertrophy- which are taken as evidence of the presence of anaemia, the main contributor of mortality in malarial victims (Roberts & Manchester 2010).  However there is no pathognomonic bone lesion for either Plasmodium vivax or P. falciparum, the main human species of malaria causing Plasmodium genus  (Gowland & Western 2012: 303, Roberts & Manchester 2010: 233), and the above skeletal lesions have varying aetiologies including anaemia, osteitis, parasitic infection, and other interrelated deficiency diseases which are still not clearly understood (Gowland & Western 2012: 302).  To securely diagnose malaria in skeletal material, DNA identification of the Plasmodium genus must take place, and even then current Polymerase Chain Reaction (PRC) tests ‘do not appear to be able to amplify routinely the DNA of malaria pathogens from ancient bones’ (Gowland & Western 2012: 302).

Recent immunological techniques to identify antigens have also been used to isolate and identify P. falciparum, although false positives can occur as a result of contamination or diagenetic factors(Gowland & Western 2012: 302).  Gowland & Western (2012) have recently proposed a spatial epidemiological model for malarial spread in Anglo-Saxon England, which highlights the re-surging interest in malaria in the modern context as well as one affecting a past population.  This holistic approach used GIS data with diagnosed porotic hyperostosis in skeletal remains, mosquito (Anopheles atroparvus) habitat information and historical data in presenting a locality data set for malaria infected individuals (Gowland & Western 2010: 304-305).  The modelling of palaeopathological, climatic, and historical data, provides new information on disease range, mechanism of transmission, and infection localities.  However, there are also complicating factors in assessing and diagnosing malaria from other diseases, as noted below (Roberts & Manchester 2010: 234).

Particularly important are two inherited haemolytic anaemia’s, thalassaemia and sickle-cell anaemia, who are characterised by abnormal haemoglobin and increased destruction of red blood cells (Jurmain et al. 2011: 312, Roberts & Manchester 2010: 232).  Thalassaemia is a genetically determined disorder which is caused by a ‘problem of haemoglobin synthesis’ (Roberts & Manchester 2010: 233).  This results in failure or depression of synthesis of the chain, this leads to pale cells with low hemoglobin content which are then rapidly destroyed once formed.  There are three grades of the disease, minor, intermediate and major, the last of which includes severe anemia and possible bone changes; the range of the disease is typically centered in the Mediterranean, Middle East and Far East (Roberts & Manchester 2010: 233).  The importance is that it is seen as an adaptive response to malaria infection through the development of this heritable disease; that the high red blood cell turnover stalls and negates any effect of malarial infection.  Archaeological evidences comes from Greek, Turkish and Cypriot populations deriving from marshy contexts, which are ideal breeding grounds for mosquitoes, the prime vector for malaria (Roberts & Manchester 2010: 233).

Sickle-cell anaemia occurs as a result of the deformation and destruction of red blood cells which leads to over enlargement of bony centres (centered on the skull, pelvis, vertebrae) and over-activity of marrow production as the body produces more red blood cells (Waldron 2009).  This inheritable disease range is mainly located in Central and Eastern African populations who have high rates of the disease, but also affects Indian, Middle Eastern, and Southern European populations (Roberts & Manchester 2010: 234).  Jurmain et al. (2011: 312) remark that the sickle-cell allele hasn’t always been effective in malarial negation in human populations, and primarily came to prominence during the advent of agriculture, and in particular during the last 2000 years in Africa.  The origin of the mutation of the allele responsible, HB5 in haemoglobin, has been dated to 2100 to 1250 years ago in African populations (Jurmain et al. 2011: 312).  Although malaria infection has only relatively recently affected human populations, it has become a powerful selective force that still affects large portions of the world’s population today.

In conclusion, biomolecular approaches to archaeological and osteological remains are vital in unraveling past populations and the natural world (Jurmain et al. 2011).  The interactions between wild and domesticated animals, humans, insects and the environment are a prerequisite for understanding the mode of transmission and virulence of infectious diseases (Barnes et al. 2011, Gowland & Western 2012, Jurmain et. al 2011).  Yet, we must take into consideration the difficulties in understanding infectious disease; examples of the osteological paradox are ever present, understanding the aetiology of bone changes, and the context of genetic differences between populations must be noted whilst PCR amplification, aDNA detection and genome explorations methods must be continually improved for clearer results (Li et al. 2011, Schurch et al. 2011, Spigelman et al. 2012, Tran et al. 2011); this approach must be multidisciplinary in understanding past and present populations (Jurmain et al. 2011, Roberts & Manchester 2010, Waldron 2009).

The modern world has changed, and the boundaries that once protected various human populations has changed dramatically with cheap air travel and vast population movement; this is unprecedented in both history and prehistory, and in population density and scale, but also at the genetic level in human genetic variation (Hawks et al. 2007, Jurmain et al. 2011: 311).  The eradication of smallpox, the Bill and Melinda Gates foundation in fighting malaria, and the ongoing WHO (World Health Organisation) case against polio (Branswell 2012: 50) are strong examples of what can be achieved worldwide.  By building a past population profile of the effects of infectious disease, we are better prepared for the fight tomorrow.

Bibliography:

Barnes, I., Duda, A., Pybus, O. G. & Thomas, M. G. 2011. Ancient Urbanization Predicts Genetic Resistance to Tuberculosis. Evolution. 65 (3): 842-848.

Branswell, H. 2012. Polio’s Last Act. Scientific American. 306 (4): 50-55.

Gowland, R. L., & Western, A. G. 2012. Morbidity in the Marshes: Using Spatial Epidemiology to Investigate Skeletal Evidence for Malaria in Anglo-Saxon England (AD 410- 1050). American Journal of Physical Anthropology. 147: 301-311.

Hawks, J., Wang, E. T., Cochran, G. M., Harpending, H. C. & Moyzis, R. K. 2007. Recent Acceleration of Human Adaptive Evolution. Proceedings of the National Academy of Sciences. 104 (52): 20753-20758.

Jurmain, R., Kilgore, L. & Trevathan, W. 2011. The Essentials of Physical Anthropology, International Edition. Belmont: Wadsworth.

Li, Y., Carroll, D. S., Gardner, S. N., Walsh, M. C., Vitalis, E. A. & Damon, I. K. 2007. On the Origin of Smallpox: Correlating Variola Phylogenics with Historical Smallpox Record. Proceedings of the National Academy of Science. 104 (40): 15787-15792.

Roberts, C. & Manchester, K. 2010. The Archaeology of Disease. Stroud: The History Press.

Schurch, A. C., Kremer, K., Kiers, A., Daviena, O., Boeree, M. J., Siezen, R. J., Smith, N. H., & Soolingen, D. V. 2010. The Tempo and Mode of Molecular Evolution of Mycobacterium Tuberculosis at Patient-to-Patient Scale. Infection, Genetics and Evolution. 10 (1): 108-114.

Spigelman, M., Shin, D. H., & Gal, G. K. B. 2012. The Promise, the Problems and the Future of DNA Analysis in Palaeopathology Studies. In Grauer, A. L. (ed). A Companion to Palaeopathology. Chichester: Blackwell Publishing Ltd.  pp.133-151.

Tran, T., Aboudharam, G., Raoult, D., & Drancourt, M. 2011. Beyond Ancient Microbial DNA: Nonnucleotidic Biomolecules for Palaeomicrobiology. BioTechniques. 50: 370-380.

Waldron, T. 2009. Palaeopathology. Cambridge: Cambridge University Press.

Infectious Disease Part 1: Treponemal Disease & Smallpox

5 Oct

The following two posts deal with biomolecular approaches and research studies in detecting the presence of infectious diseases in human bone from archaeological material.  The recent coming of age of biomolecular techniques, as applied to archaeological material, has provided a rich and complex source of information in helping to uncover how infectious diseases spread in the historic and prehistoric past.  Whilst it has help clear some mysteries up, it has unleashed others.  The first post, here, describes recent research focused on Treponemal diseases (including Yaws, Syphilis and Pinta) and Smallpox.  The second post can be found here.

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Treponemal Diseases

Roberts & Manchester (2010: 216) note that infectious diseases are ‘not solely microbiological entities but are a composite reflection of individual immunity, social, environmental, and biological interaction’.  The study of treponemal disease, in particular, is fraught with controversy and stigma, both in the modern and historical contexts (Lucas de Melo et al. 2010: 1, Roberts 2000), and in the nature of its spread and transmission.  However the combination of molecular pathology, phylogenetics, and palaeopathological studies, are helping to produce a clearer genetic origin of the disease and the impacts that this disease had, and continues to have, on the world at large (Hunnius et al. 2007: 2092).  Typically the bacterial diseases of the genus Treponema are split into different forms; pinta (T. carateum), yaws (T. pallidum subspecies pertenue), endemic syphilis (T. pallidum subspecies edemicum) and venereal/congenital syphilis (T. pallidum subspecies pallidum) (Table 1; Lucas de Melo et al. 2010: 2).  The four forms were, until recently, indistinguishable in physical and laboratory characteristics (Roberts & Manchester 2010: 207), whilst the pinta strand does not affect bone (Waldron 2009: 103).  DNA analysis of the bacteria of venereal syphilis has shown a difference between it and the non-venereal types; although it is noted that there is no change in the clinical presentation of the disease (Roberts & Manchester 2010: 207).

Table 1. Geographic location, transmission and whether bone is affected for treponemal disease (after Waldron 2009: 103).

Yaws was likely the first disease to emerge, probably from an ape relative in Central Africa, whilst the endemic form of syphilis derived from an ancestral form in the Middle East and the Balkans at a later date, whilst T. pallidum was the last to emerge, probably from a New World progenitor, although the issue is still highly contentious (Roberts & Manchester 2010: 212, Waldron 2009: 105).  Gaining virulence at a dramatic rate in the 15th and 16th centuries AD in Europe, venereal syphilis affected a large section of the population due to its mode of transmission.  It should be noted, however, that bone changes in syphilis are rare in the early stages but common in the tertiary stage of the disease (Roberts & Manchester 2010).  It has also been noted that there could be a back and forth transmission, from one treponemal disease to another, within intra-population groups changing from one environment to another; that ultimately it’s possible that each social group, or population, has its own treponemal disease suited to its ‘geographic and climatic home and its stage of cultural development’ (Roberts & Manchester 2010: 213).

However, this infectious disease, in its venereal form, is particularly hard to locate and identify in archaeological populations; the limitations of biomolecular palaeopathology have become clear (Bouwman & Brown 2005: 711, Hunnius et al. 2007, Lucas de Melo et al. 2010: 10).  Bouwman & Brown’s (2005) experiment, and Hunnius et al. (2007) subsequent paper, have highlighted the difficulties in amplifying T. pallidum subspecies T. pallidum, even in highly suspected bone samples.  Bouwman & Brown (2005: 711) tested 9 treponemal samples using the Polymerase Chain Reaction (PCR) tests, optimized to highlight ancient treponemal DNA.  This resulted in poor amplification of  treponemal ancient DNA (aDNA) from human bone, even with bone of varying origins (geographic, social and climatic samples).  3 outcomes where postulated; the bones were either not suitable for aDNA retrieval, treponemal aDNA was present but the PCR was not sensitive enough to be pick it up, or there was no treponemal DNA in the bones (Bouwman & Brown 2005: 711-712).  Subsequent investigations and phylogenetic approaches have highlighted that the disease invades different parts of the body at impressive rates, but in the later stages of the disease, the organism’s DNA is not present in the actual bone itself, just at the stage when an osteologist can identify it macroscopically (Hunnius et al 2007: 2098).  Phylogenetic evidence supports evidence of variations in the virulence of syphilis, and the support of a more distant origin, possibly around 16,500 to 5000 years ago, but where exactly remains unsolved (Lucas de Melo et al. 2010: 2).  Interestingly, in the early 20th century P. Vivax (the main causer of malaria) was used as a treatment for patients with neurosyphilis in a procedure by the physician Julius Wagner-Jauregg; it was injected as a form of pyrotherapy to introduce high fevers to combat the late stage syphilitic disease by killing the causative bacteria (Wagner-Jauregg 1931).

Smallpox

The Smallpox virus is particularly devastating and disfiguring disease, but thankfully no longer an active infection in the modern world (Manchester & Roberts 2010: 180).  Although kept only in laboratory samples now, there is an ongoing concern regarding whether it could be a danger to modern archaeologists dealing with infected material (Waldron 2009: 110).  The disease, once contracted, either leads to recovery with lifelong immunity or death.  The severe form is called variola major and is documented in the Old World with a 30% death rate once contracted, whilst its less virulent form, named variola or alastrim minor, is found in Central America and has a mortality rate of 1% (Hogan & Harchelroad 2005, Li et al. 2007: 15788).  Smallpox, the strictly human variola virus pathogen, is found in literature and documentary records during the last 2000 years (Larsen 1997), yet an osteological signature is not present or identifiable in infected individuals (Waldron 2009: 110).  Therefore to find out the origins of the disease, Li et al. (2007) used correlated variola phylogenetics with historical smallpox records to map the evolution, origin and transportation of smallpox between human populations.

Li et al. (2007: 15787) state that no credible descriptions of the variola virus have been found on the American continent or sub-Saharan Africa before the advent of westward European exploration in the 15th century AD; suggesting that with European exploration and expansion came the virulent waves of smallpox that helped to decimate the existing Native American populations, who previously had no contact or natural immunization with such a highly virulent disease.  It is worth noting here the disease has been used in warfare as a chemical weapon surprisingly early.  During the 18th century American colonial wars between the French, British and the Native Americans, the British forces stationed in America actively infected items of clothing that were given to the Native population to help aid the spread of the disease among the Native Americans , who at that time were largely allied to the French.  This weakened the Native American population dramatically during the various colonial wars and subsequent colonial expansion westward; it’s estimated nearly half of the American Native population died from smallpox alone and its naturally rapid commutable spread of smallpox through human populations (Hogan & Harchelroad 2005).

Li et al. (2007: 15787) note that there are ambiguous gaps in the evolution of smallpox disease itself however.  Li et al. (2007) initiated a systematic analysis of the concatenated Single Nucleotide Polymorphisms (SNP’s) from the genome sequences of 47 variola major isolates from a broad geographic distribution to investigate its origins.  Variola major has a slowly evolving DNA genome, which means a robust phylogeny of the disease is possible (Hogan & Harchelroad 2005).

Firstly, the results showed that the origin of variola was likely to have diverged from an ancestral African rodent–borne variola like virus, either around 16,000 or 68,000 thousand years ago dependent on which historical records are used to calibrate the molecular clock (East Asian or African) (Li et al. 2007: 15791).  Taterapox virus is associated with terrestrial rodents in West Africa, and provides a close relationship with the variola virus.  It is entirely possible that variola derived from an enzootic pathogen of African rodents, and subsequently spread from Africa outwards (Li et al. 2007: 15792).  Secondly, evidence points towards two primary clades of the variola virus, both from the same source as above, but each represent a different severity and virulence of the variola virus.

The first primary clade is represented by the Asian variola major strains, which are the more clinically severe form of smallpox;  the molecular study of its natural ‘clock’ suggests it spread from Asia either 400 or 1600 years ago (Li et al. 2007: 15788).  Included in this first primary clade is the subclade of the African minor variation of the main Asian variola major disease.  The second primary clade compromises two subclades, of which are the South American alastrim minor and the West African isolates (Li et al. 2007: 15788).  This clade had a remarkably lower fatality rate in comparison to the above clade.  The importance of phylogeny analysis is that it highlights areas of disease prevalence and virulence that can be missed, or indeed entirely absent, from the osteological and archaeological record (Brown & Brown 2011).

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