Cahokia: America’s first city

[Thank you all for returning to my blog after a two month hiatus!  The exceptionally busy time is past, and I can resume writing.  I’ve missed sharing these with you!]

Because I grew up in Kansas City, Missouri, driving back and forth across I-70 has always seemed like a birthright.  When I attended the 2017 ASMS conference in Indianapolis, driving there from my parents’ home in KC seemed an obvious choice.  On my way back to KC, though, I stopped at Cahokia Mounds State Historic Site.  A comment from my brother had jogged my memory of Guns, Germs, and Steel, a core text of human anthropology.  The Mississippian cultural tradition, to which Cahokia belongs, could have been one of the original “Cradles of Civilization,” and I wanted to see it first hand.

At first glance, Cahokia is visually marked by the massive Monks Mound (with a base covering 14 acres / 57,000 m²) and many nearby mounds.  What makes this site significant?  Cahokia represents the first urban settlement within the borders of the United States.  Researchers have estimated that its population approached 20,000 citizens at its peak, between 1050 and 1100 A.D.  This development was possible because of plant domestication along the Mississippi River, starting as early as 3000 B.C. with squash, sunflower, and marsh elder.  The rise of Cahokia, however, probably coincides strongly with the arrival of corn, domesticated in central America.  Farming made city development possible, since adequate food supply allows diversification of labor into different functional roles.  I borrowed my title for this post, by the way, from William Iseminger’s book detailing decades of archaeological research at Cahokia.

I have mentioned several World Heritage Sites in my travels, such as the Great Wall of China, the Historic Center of Warsaw in Poland, or even the Cape Floral Region of South Africa.  The United States of America offers a total of 23 sites on the World Heritage list, and Cahokia Mounds was added to this list in 1982, putting it on a parallel with Mesa Verde or the Statue of Liberty!  It seems unfortunate, then, that Cahokia has never been granted National Historic Landmarks protection from the National Parks Service.  Instead, the State Historic Site has scraped together enough funds to acquire around half of the land originally covered by Cahokia; many of the original mounds of the city, in fact, have already been lost as farmers consolidated fields and as St. Louis expanded its reach.  The destruction of Powell Mound, the marker for the western boundary of Cahokia, illustrates the pressures on this site.

Walking around the site

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Monks Mound (Mound 38) is the tallest structure remaining at Cahokia.

If I may reverse the order of the walking tour, I would start at Monks Mound itself, “North America’s biggest prehistoric earthen structure.”  In some respects, the mound represents a high platform (~100 feet above ground level) built atop a lower platform (~35 feet above ground level).  The name comes from a group of Trappist monks who farmed atop the lower platform during 1809-1813.  One might naturally ask of the mounds “what’s in there?”  In fact, several of the mounds have flat tops, and that’s because they served as platforms for important buildings; one will not find buried treasure in this type of mound!  It is worth noting that the mound builders lacked some key tools, such as the wheel and axle.  All the clay and mud of this mound was taken from a nearby “borrow pit” by individuals with baskets or pots and then walked to the construction site.  Recent research suggests that Monks Mound was built within a span of 20 years!

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The view toward St. Louis from atop Monks Mound

The view from atop the mound is stellar.  The Mississippi River flood plain is vast and flat, so 100 feet of elevation is enough to see quite far.  In the picture above, you should be able to see the St. Louis Arch, at a distance of approximately ten miles.  This high elevation was home to a temple, courtyard, and high pole, with the temple measuring 104 by 48 feet.  The mound sends a clear statement about who ruled Cahokia, much as the massive construction of the Forbidden City sent that message in Beijing.

If Monks Mound represented Cahokia’s Capitol Hill, where was the city?  The large field in which I was standing for the first photo has been named as the Grand Plaza.  The 40 or 50 acres of ground are almost completely flat.  As our tour guide said, “Illinois is flat, but it’s not that flat.”  In fact, archaeologists have produced evidence that the Cahokians leveled the area by adding fill dirt of up to three feet across this large area, then added a sandy surface atop it.  The area likely played a fair number of community roles, not least of which was the field where athletes would try their hands at chunkey, a sport where players would compete to roll small stone discs onto the playing field and then launch a stick to land as close as possible to where the stone would stop its roll.

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The Twin Mounds appear to have served as a ceremonial center for funerary rites.

The Grand Plaza extended south to the Twin Mounds.  Mounds 59 and 60 are approximately half a kilometer away from Monks Mound, and they appear to have functioned as a “charnel house” or site for funerary rites.  Mound 60 was a platform mound, so it is likely to have had a structure constructed atop it.  Mound 59 is not a platform mound but rather a conical structure named “Round Top”– it appears to the right in the photo above.  When these conical mounds have been excavated at other sites, they frequently contain burials; respect for the dead is one of the reasons that Round Top has not been formally excavated.  Since much of this site was unprotected for years, though, Round Top was occasionally pilfered by the curious.  The link for Mound 59 relates a story from 1915 of boys who began digging for treasure in Round Top.  They found a skeleton with a copper serpent on its chest.  One of the boys claimed it as his own, and it has been lost to history.

Formal archaeology has continued at this site for decades, of course, and one of the most interesting stories has come from Mound 72.  To an untrained eye, the mound appears quite small and dull.  Its unusual orientation and location away from others, however, drew attention from researchers beginning in 1967.  In total, the remains of 270 different people have been found in the mound.  Most of them appear to have been young women, killed ritually, but a group of 39 skeletons seem to represent individuals who died in violent chaos.  Their mass burial completely contrasts with the “beaded burial,” an individual lying atop twenty thousand beads made from shells imported from the Gulf of Mexico.  Certainly mound 72 demonstrates that residents of Cahokia were not held to be equal after death.

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The palisade wall stretched two miles, a thousand years ago!

Cahokia was protected from possible attack by a two-mile palisade.  This wall ran outside Monks Mound, around the Grand Plaza, and encompassed even the Twin Mounds.  Rather than building the wall of masonry, as practiced by the Chinese in constructing an early segment of the Great Wall, the Cahokians cut down young trees, stripped their branches, burned the ends to prevent decay, and buried the ends in a long trench.  Since the trees rotted with time, the wall needed frequent replacement.  This demand for timber was apparently a big driver in the deforestation of this area next to the Mississippi River.

Early civilizations sought to regularize the cultivation of crops, and the Cahokians constructed “Woodhenge” to show the changing seasons.  A circle of tall poles are found to the west of Monks Mound.  At the equinoxes, the sun rises directly behind Monks Mound from that vantage.  Archaeologists have found evidence for at least five different constructions of Woodhenge on this site, ranging up to 476 feet in diameter.  Today, Woodhenge is somewhat separated from the rest of the Cahokia site as the nearby town continues to develop.  The atmosphere of the calendar is diminished only a bit by the gas station across the street.

Cahokia in context

How did Cahokia rate in the world of 1000 A.D.?  As I mentioned above, Cahokia was missing some key resources.  The Americas lacked the invention of the wheel (as well as domesticated animals for pulling wagons), and Cahokia is prehistoric by definition since the population had not developed a written language.  Cahokia had very little ability to work with metals; most of its copper came from up north, and they lacked techniques to smelt it, for example, to produce bronze.  Once corn arrived at Cahokia, its cultivation swiftly exhausted the soil since beans were not available for crop rotation.  These are some pretty big barriers to the longevity of this city!

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Porcelain figurines from the Song Dynasty (National Museum of China)

By comparison, we might look at four cities that were the greatest successes of 1000 A.D: Córdoba, Baghdad, Constantinople, and Kaifeng.  Córdoba and Baghdad were enjoying the “Golden Age of Islam.”  Córdoba was the capital of its Caliphate under the Umayyad dynasty, and its population may have reached a half million inhabitants (about twenty-five Cahokias).  Baghdad, on the other hand, had already crested a million in population by this time under the Abbasids, who made it a renowned center of learning.  Byzantium had endured for almost a thousand years when it became Constantinople in 330 A.D., serving as the new capital for the Roman empire; by 1000 the city was experiencing the Macedonian Renaissance, with a population somewhere between that of Córdoba and Baghdad.  Kaifeng had been selected as a capital by the Song Dynasty of China when they came to power in 960.  The population of 400,000 struggled with typhus, but the armies this city controlled were sophisticated enough to use gunpowder in siege warfare!

Compare these major cities with Cahokia in the same era.  Its less diverse agriculture, limited availability of soft metal, and oral tradition without a written language forecast an unhappy fate when its descendants met those of the East.  In fact, one of the great mysteries for Cahokia is discerning which native American tribes are most related to the great Mississippian city!  By the time De Soto reached the Mississippi River in 1541, Cahokia had long since been abandoned.  A 2004 exhibit by the National Endowment for the Humanities attempted to show the richness of the culture that existed before contact with Europeans.  Tragically, that first contact led to plagues that ravaged the indigenous inhabitants of North America well before colonists began moving their boundaries westward.  To visit Cahokia, though, is to witness a high point of the culture of native America.

The photographs of a life in motion

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At last count, my trusty Canon EOS-M2 had produced 9099 images for me.

The last two months have been chockablock with professional and personal activities.  As a result, I have neglected my blog!  I know what my next post will address, and I have plenty left to say on other topics, too.  I will return to writing posts when I can sneak in some extra time (late June?).

In the meanwhile, I hope you will enjoy these albums of photographs that I took during the busy travels of 2016 and early 2017.  Looking back at that period, it is amazing to me that I traveled so much!

Inside South Africa

Date Blog Post Images
20161221 Table Mountain Google Photos
20161216 Cape Point Google Photos
20161213 Robben Island Google Photos
20160908 Kimberley Google Photos
20160702 Northern Cape Google Photos
20160319 Eastern Cape Google Photos
20160312 Cape Agulhas Google Photos

Outside South Africa

Date Blog Post Images
20170113 Prague Google Photos
20161019 Warsaw Google Photos
20161015 Berlin Google Photos
20160926 Shanghai Google Photos
20160917 Beijing Google Photos
20160611 London (no post) Google Photos
20160416 Ghent Google Photos

Teaching on the sly

When I first arrived at Stellenbosch University, I was a bit concerned.  I had thoroughly enjoyed organizing my own semester-long class in bioinformatics for M.Sc. and Ph.D. students at Vanderbilt University.  Under the “British System,” though, students encounter their final classes in the “Honours” year, crammed between the three-year Bachelor’s program and the two-year Master’s program.  Interestingly, a student may attend Honours at a different college than where he or she completed a bachelor’s degree, and the student may go to yet another university for a Master of Science after the Honours, so long as the training is judged to be relevant.

Overview of South African education program

This sequence describes the common route through South African education, from kindergarten to a terminal degree.

I would take a moment to explain a couple of important features here.  In South Africa, students are required to complete only the first nine grades, called “General Education and Training.”  In the United States, graduation from high school means that you have met your high school’s requirements for that goal (which in turn must meet state requirements).  In South Africa, however, high schools essentially serve to prepare students to take the “matric” exams, which are set (created) and marked (graded) nationally.  Matric successes or failures are what decide a student’s opportunities going forward.  I should also say that the chart above describes the academic track.  Many students take advantage of TVET (Technical and Vocational Education and Training) schools that lead to a certificate or diploma rather than a degree (these campuses have also experienced significant protests).  Each of these training types is considered in determining the SAQA level for a job candidate.

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The 2016 Honours class for the Division of Molecular Biology and Human Genetics

Students who come to Honours in the Division of Molecular Biology and Human Genetics (MBHG) may come from quite a variety of schools and backgrounds.  Like other divisions throughout Stellenbosch University and the University of Cape Town, we are trying to “transform,” or more faithfully represent the broader population of South Africa, and so we seek out candidates who may not have been able to afford the best schools for bachelor’s training.  Transformation is a hard task, and many universities are struggling [Note to self: read that overview chapter!].

My first exposure to teaching at Stellenbosch, then, was to create a bioinformatics “module” for our Honours students.  The group above got to serve as test subjects for my new curriculum, which spanned just four days in 2016.  Instead of 43 one-hour classes from my old Vanderbilt BMIF 310, I adjusted to four morning laboratories (each three hours) and four afternoon lectures (each two hours).  With so little time, I was obviously quite superficial in my coverage.  For 2017, though,  I will conduct a bioinformatics module that extends for eight days (during the first eight business days of May).  I am keeping the hands-on and lecture split the same as last year.  I think the doubling to eight days will be good for both the students and the professor!

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In this still from Useful Hour 3, Haiko, Michael, and I impersonate parts of a linked list.

Lecturing just eight days a year isn’t really satisfying my itch to teach, though.  This year I initiated a wildcat “course” of sorts.  The “Useful Hour” takes place each Wednesday at 1:30 PM.  Anyone on campus can attend, and we record videos each week for those who cannot.  The topics have generally been focused on computers, bioinformatics, or biostatistics, though in the coming week we will branch out into biochemistry, as well.  Since the Useful Hour covers so much terrain, I have tried to treat each segment as an independent story, with the topic for each Wednesday announced by my listserv on Monday.  It could be that the loose structure of the Useful Hour will cause its undoing, but for now I am really enjoying its playful vibe.

My work with the Blackburn Lab at the University of Cape Town on Tuesdays has led to another opportunity.  I have teamed up with Nelson Soares, a staff scientist, to create a monthly “Big Show” tutorial for the community of proteomics researchers throughout Cape Town.  Our recent program gave graduate students and post-docs the opportunity to present the essentials of protein identification and quantitation.  In April, we will look at the opportunities their acquisition of a SCIEX TripleTOF will confer on the group.  I appreciate that the students are also willing to listen to a lecture from me, from time to time!

The very latest teaching gig is one I hesitate to mention, since we are still formulating it.  In talking with more members of the Biotechnology Department at the University of the Western Cape, I’ve realized that they have a critical need for more biostatistics training.  I have never taught this subject formally, though I was part of the weekly “Omics” clinic for Biostatistics at Vanderbilt University for a few years.  Certainly one cannot function for long in genomics, transcriptomics, or proteomics without knowing something about biostatistics.  Teaching biostatistics formally is likely to teach me as much about the subject as the students who attend!  I hoped to use slides from Stellenbosch University for teaching weekly courses at UWC, but I could not get that use approved.  Instead, I have once again borrowed the expertise of my friend Xia Wang at the University of Cincinnati.  I am hopeful that I will be able to understand and use her didactic materials.  They’re written in the LaTeX math formatting language, so I will need to remind myself how to edit and export to a format I can display, like PDF. My last real experience with LaTeX was when I wrote my Ph.D. dissertation in 2003.

With students on three university campuses, I think I will finally feel like I have real some momentum in my teaching!

Bang for the buck: U.S. aid to South Africa

Out of $4 trillion dollars in the U.S. federal budget, how much is spent on foreign aid?  While most people in a recent poll thought it was around a quarter of the annual budget, the true answer is around one percent.  In this post, I want to explain two key programs that have impacted my new home country: PEPFAR and AGOA.  The United States plays a substantial role in making the future of South Africa brighter!

PEPFAR: Curtailing the epidemic of HIV/AIDS

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During the first eight years of the millennium, I rarely had anything positive to say about the President of the United States.  President George W. Bush, though, signed into law the “U.S. Leadership Against HIV/AIDS, Tuberculosis, and Malaria Act of 2003,” which transformed medical care in southern Africa.  His name is still respected in South Africa because of this law; it yielded the President’s Emergency Plan for AIDS Relief (PEPFAR).  This program has been renewed twice by bipartisan vote, in 2008 and 2014.  In the thirteenth year of the program, PEPFAR supported anti-retroviral treatment (ART) for 11.5 million people living with the Human Immunodeficiency Virus (HIV), with that number having climbed by 50% since 2014.  Some two million babies have been born without HIV from mothers who carry the virus.  This is an amazing accomplishment, and it couldn’t have come at a more critical time.

The HIV crisis in South Africa began as it did in the United States, with AIDS appearing in the community of gay men during the early 1980s.  Cases were documented in the heterosexual community in 1987.  By 1990, the crisis had begun to grow rapidly.  It is worth noting that South Africa was coping with tremendous changes during this period as the Apartheid government was compelled to cede power; Nelson Mandela was released from prison in February of 1990.  When he became President in 1994, however, the new government was unable to do much about the growing epidemic.  1996 was a watershed year for HIV as ART was announced, and the first drugs became publicly available (though expensive).  In 1999, Thabo Mbeki was elected President, and the public thought that HIV prevention and treatment might become a priority under his leadership.  His Presidential AIDS Advisory Panel, however, was dominated by HIV denialists / “AIDS dissidents” who claimed the virus had nothing to do with AIDS.  Not only were ART drugs not made available widely, but ART was withheld from pregnant women carrying the virus.  Nelson Mandela re-entered the debate in 2000 by a powerful closing speech at a Durban international conference on AIDS.  The topic became even more personal to him when his son died of AIDS in 2005.  Against this complex historical background, the prevalence of heterosexually transmitted HIV-AIDS was surging.  “By 1994, this had risen to 7.6%, and by 2005 was 30.2%, with an estimated 5.5 million of South Africa’s 47 million people infected.  An estimated 1000 new HIV infections and 900 AIDS deaths occurred each day” [Giliomee and Mbenga, p. 418].

PEPFAR has a tremendous role to play in today’s South Africa.  The program currently estimates that 7,000,000 people in the country are living with HIV, with approximately half protected by ART.  180,000 people die of AIDS each year in South Africa. “South Africa now has the largest number of patients on anti-retroviral drugs in the world, and South African life expectancy has increased by more than a decade.” [Bekker et al.]  Just imagine the impact if PEPFAR were no longer paying for HIV treatment!

Please be aware that there have been changes in the Trump Administration that suggest this program may be in trouble.  It is no exaggeration to say that real people will die without PEPFAR.

AGOA: “Trade, not Aid!”

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Debate may never end over the best way for wealthy nations to support the growth of poor nations.  When wealthy countries give food aid to poor nations, those efforts can undermine the economic growth of agriculture in those countries.  The African Growth and Opportunity Act (AGOA) was enacted in 2000, the last year of Bill Clinton’s presidency.  You may be thinking, “gosh, another economic treaty I need to know about!”  In fact, AGOA is not a treaty.  AGOA is a unilateral decision by the United States to drop taxes and quotas on imports of particular goods from countries in sub-Saharan Africa.  The program began by including 34 countries and soon expanded to 40.  After the first fifteen-year run of the program, the U.S. Congress decided to renew AGOA for an additional ten years in 2015.  Each year, the President decides exactly which countries will be extended these benefits.

The metrics for AGOA success paint a somewhat equivocal picture.  The 2016 biennial report shows $23.5 billion in exports from Sub-Saharan Africa in the year 2000.  This number grew to $86.1 billion in the year 2008 before falling back to $18.5 billion in 2015.  This might seem an abject failure, but much of the decline reflects reduced oil exports to the United States and the worldwide recession of 2009.  Most Sub-Saharan countries, of course, would like to export to the world’s biggest economy!  America, in turn, uses this desire to requiring development toward “a market-based economy; the rule of law, political pluralism, and the right to due process; the elimination of barriers to U.S. trade and investment; economic policies to reduce poverty; a system to combat corruption and bribery; and the protection of internationally recognized worker rights” [2016 biennial report, p. 8].  Essentially, the United States waives taxes on imports from countries that behave as the United States would like to see.

South Africa has had an interesting story within the framework of AGOA.  As the continent’s most advanced and diversified economy, South Africa was a bit of a question mark for inclusion in the 2015 renewal of the law.  Did it make sense to give these trade benefits to an economy that was already moving rapidly?  South Africa made itself a less attractive trade partner by raising trade barriers against American farmers exporting meat to South Africa, which caused them to violate the “elimination of barriers to U.S. trade” rule above.  At the start of 2016, the situation had deteriorated enough that Barack Obama suspended AGOA benefits for South Africa.  This action was enough to convince the foot-dragging South African government to drop its trade barriers, and so South Africa is once again an AGOA beneficiary in good standing.

What will happen to AGOA under the Trump Administration? Although President Trump has been ambivalent on the subject of free trade, he has not signaled that he will seek to end AGOA either by unlisting all participant countries or seeking the repeal of AGOA through the Congress.  Africans do not expect great things from President Trump, though.  His Tweets about South Africa have had a generally negative tone.

In the end, South Africa is proud of its ability to take care of its own problems.  If AGOA comes to an end, the country will lose one of its best customers for fruits and vegetables, and the automobile industry growing in the Eastern Cape would suffer.  The loss of PEPFAR, on the other hand, would devastate health care in South Africa.  The economy of South Africa is not strong enough to bear the cost of supporting ART on this scale.  The country already relies on the permissive, pro-public health intellectual property laws of India to have access to generic ART.  We can all hope that the PEPFAR and AGOA relationships between South Africa and the United States continue under President Trump!

An extraordinary journey in three universities

Last November, I received some very welcome news.  The Deputy Vice-Chancellor for Academics at the University of the Western Cape informed me that I had been named an Extraordinary Professor in the Department of Biotechnology!  My work within that department had been going well, when persistent student protests closed the university through the end of 2016.  This letter reflected the ongoing hope of Biotechnology that our collaboration would continue when the students returned to their studies.  Today I received my official badge, so I would like to write about the work that is developing at each of the three local universities at which I have an appointment.

I have written about my travels among the campuses in and around Cape Town.  I would stress that I spend most of my time at my home institution, the Tygerberg campus for Stellenbosch University.  Bioinformatics has seen considerable investment by the university.  The South African Tuberculosis Bioinformatics Initiative represents the concentration of bioinformatics investigators for our campus: Gerard C. Tromp, Gian van der Spuy, and me.  There are other data scientists, though!  The Centre for Evidence-based Healthcare, led by Taryn Young, offers statistical expertise.  Tonya Esterhuizen specializes in biostatistics.  As I will explain in a moment, I hope to work with them more in the days to come.  This year, my formal teaching duties at my home campus will double.  Don’t worry for me, though, since I will host the Honours students for the Division of Molecular Biology and Human Genetics for only eight days!  I am glad that bioinformatics will have the “standard” module length for our Honours program, equal to Immunology and several other subjects.  I have been supplementing my teaching through an informal “course,” called the “Useful Hour.”  I have begun teaching all comers about a range of subjects, from computers to programming and statistics.  I hope to pull in some philosophy of science soon, as well.  I have been filming these subjects as a bit of an experiment, and it has been handy for those who cannot attend.img_20170126_152122

Hugh Patterton, Gerard Tromp, and I coordinate our efforts near Simonsberg.

The Stellenbosch campus of Stellenbosch University has made strides in bioinformatics, as well.  Hugh Patterton, a professor in the Department of Biochemistry, has been named to lead bioinformatics efforts at this campus.  Naturally, our group (SATBBI) has been talking with Hugh about ways we can reinforce each other’s efforts.  Some of our consultations on the Stellenbosch campus have pointed in the direction of microbiome research, an area that is replete with bioinformatics challenges.  I look forward to seeing what emerges!

I am highlighting the University of the Western Cape in this post, of course!  In describing bioinformatics at the campus, I should start by mentioning the South African National Bioinformatics Institute (SANBI).  Alan Christoffels leads this group of investigators.  They’re an interesting group, with considerable success in capacity development within South Africa and across the continent.  My home on the campus, however, has been with the Department of Biotechnology.  In many respects, this reflects how I have spent my career.  I set the mold in graduate school, when I was a bioinformaticist surrounded by analytical chemists.  I like being close to the people who generate the data I work with!  In the Department of Biotechnology, I work most closely with the group of Ashwil Klein, the lecturer who heads the Proteomics Research and Service Unit.  They have primarily emphasized a gel-based workflow, meaning that they partially isolate proteins on a 2D gel before identifying the spot based on the peptide masses they observe on the Bruker Ultraflex TOF/TOF.  The group is actively moving toward additional instruments, though, and the acquisitions should greatly broaden their capabilities.  I enjoy the intellectual challenges their group produces, since the rules of the road are somewhat less established for agricultural proteomics.

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The new UWC Chemical Sciences and Biological Sciences Buildings rise above the Cape Flats Nature Reserve.

In attending the department’s recent strategic retreat, I was introduced among the researchers of UWC Biotechnology more broadly.  I was particularly glad to meet with Dr. Bronwyn Kirby, who heads the Next Generation Sequencing Facility.  We discussed the Honours course offered for the department (I taught bioinformatics for the proteomics module last year), and I believe I’ll get to add some bioinformatics for the sequencing module in 2017!  I was also delighted to meet the SARChI chair who heads the Institute for Microbial Biotechnology and Metagenomics (IMBM), Marla Trindade.  We spoke about what the students of the institute most needed, and establishing a structured curriculum for biostatistics seemed very high on the list.  I mentioned the biostatistics researchers at Stellenbosch above.  My hope is to be able to use much of the structure Stellenbosch has already built in its Biostatistics I and II classes as a model for teaching biostatistics at UWC Biotechnology.  It would be my first effort at teaching biostatistics formally; I hope that I have absorbed enough to be a good teacher for this subject!

I continue to spend my Tuesdays with the University of Cape Town medical school and to visit the Centre for Proteomics and Genomics, as well.  UCT named me an Honorary Professor in the Department of Integrative Biomedical Sciences halfway through 2016.  My interactions there have principally taken place within the Institute of Infectious Disease and Molecular Medicine (IDM), borrowing from the network of relationships that Jonathan Blackburn has established there.  I have worked with Nelson Soares, his Junior Research Fellow, to create monthly programs for the Cape Town community invested in proteomics.  This Tuesday, we started this series for 2017 with an introduction to the methods we use for identifying and quantifying proteins.  I was really pleased that Brandon Murugan, a senior graduate student in the Blackburn Lab, felt comfortable enough to present this material!

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I enjoyed my sundown cruise with the SATVI team in May of last year!

From the very beginning of my time in South Africa, I have been working with the South African Tuberculosis Vaccine Initiative (SATVI).  Recently they began having their research in progress meetings on Tuesday morning, allowing me to take part.  I really like the interaction.  They take my questions seriously, and I think we all learn from working together.  Certainly I would find great meaning in being part of a successful vaccine trial for this disease!

I have another group I must mention in describing bioinformatics across these three universities.  Nicola Mulder’s “CBIO” team has been an opening wedge in bioinformatics education for South Africa.  Their H3Africa BioNet courses have been used to supplement the content of B.Sc. education in places like the University of Limpopo.  It should be no surprise that many of the people I have mentioned in today’s post have collaborated in a manuscript describing the growth of bioinformatics in South Africa.  Our field is key to the future of public health and to the advances in biotechnology yet to come!

With the new year, a new office!

The Division of Molecular Biology and Human Genetics occupies the fourth floor of the FISAN building at the SUN Faculty of Medicine and Health Sciences.  As its research programs have become better funded, substantial numbers of clinical and research staff have been added to its roster.  One practical result of this addition was that I shared an office with three other researchers when I arrived in South Africa in late 2015.  With the start of 2017, however, our division has gained access to office space on the third floor.  I am happy to report that as of last week, I have a new solo office!

This move does not come without regrets, though.  I have become friends with the inhabitants of F416, and my new hallway currently seems quite lonely by comparison.  Sam Sampson is a group leader who came to SUN via the National Research Foundation “South African Research Chairs Initiative,” and she has impressed me with her concentration skills in our busy office.  I also appreciate her thoughtful gift of teaspoons when mine went missing!  I really value Kim Stanley’s friendship; she has been very tolerant of my practical jokes, and occasionally I catch a glimpse of her mischievous sense of humor.  She invests countless hours in the REDCap study databases that undergird much of the research for our division.  Nasiema Allie was the last of the four people in our office to arrive.  Her job is quite critical since she ensures that the BSL3 lab facilities for our division are as safe as they can be.  Why is that a big deal?  Our division emphasizes research in tuberculosis, and we culture Mycobacterium tuberculosis from patient samples.  Some of the strains we recover from patients are resistant to every drug available to treat this disease.  Let’s just say that I don’t store my lunch in the freezers lining the division’s hallways!

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Our freezers are equipped with wireless boxes that “phone home” if the temperature inside rises.

My new digs are on the wing extending east from the FISAN entrance.  To be on the third floor means I am several feet closer to the flock of chickens at ground level.  When I open the window (!) of my new office to feel a sweet afternoon breeze, I also get to hear the crowing of the roosters.  Last week we also had the questionable benefit of being closer to the smell of decomposition as cadavers were moved downstairs; FISAN is an Afrikaans abbreviation for “physiology and anatomy!”  That said, the third floor has great accommodations for the bioinformatics and biostatistics students we will be training in SATBBI.  The student chamber we have selected has abundant space, featuring bookshelves, a chalkboard, a bulletin board, and even a sink!  Right outside we have a smaller area we hope to position as a meeting room.

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We haven’t reached our final configuration for the desks in the bioinformatics student workspace.

This brings us to my office.  I was one of the first professors to pick out my new home, and I decided on one featuring a blue wall (rather than the beige featured throughout the complex), an intact chalkboard (rather than the removal scars from one that had been removed), and a ledge underneath its narrow window.  I discovered that the ledge was the perfect height for tucking a cabinet or drawer set from our old furniture upstairs.  They will match the desk that my graduate student and I hauled downstairs from my old office.  The ledge is sturdy enough that I can stand on it to raise my window, so I feel confident that it will house some plants for me soon!

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All I need now is a coffee table.

Moving my computers down was a bit more worrisome.  Happily, the LAN port (or “network point,” as they would say here) was already live, though it is a slower 100 Mbps rather than gigabit.  In any case, my Ubuntu Linux file server “Deep Thought” made the transition downstairs without a hiccup.  I recently brought my Intel Core i7 workstation “Alabaster” from home; it connects to the network wirelessly, so I can use a network wire to connect the two computers in my office directly.  Using a gigabit network port exclusively to communicate between the pair means I can use the RAID from Deep Thought almost as though it were a local hard drive in Alabaster.  This may be as good place as any to mention an act of generosity from Vanderbilt University.  When I decided to move my lab to South Africa, the Department of Biomedical Informatics allowed me to move almost all the computers associated with my laboratory to Stellenbosch University!  It made a real difference to my new division.

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What office is complete without a memento or ten?

I have assembled a collection of treasures on my desk that link me to my past.  Probably my oldest memento is a koosh ball that I acquired in high school.  I am very fond of my jar of marbles for my discussions in frequentist biostatistics; I bought these marbles when I was starting as a professor at Vanderbilt from the Moon Marble Company, near Kansas City.  My first Ph.D. graduate student bought me a jade pen holder that I use everyday.  My singing bowl from China gets a special place of prominence.  A small, red Buddha was a parting present from the Harkeys, close friends from Nashville.  An analog clock from Vanderbilt reminds me of my friend Bing Zhang, who headed to Houston around the time I moved to Cape Town.  I don’t remember where my Ganesh came from, but he has a reputation for finding the solutions to problems, so he definitely belongs on my desk!

My name placard has moved, I have given up my key to F416, and all my things have migrated downstairs.  Over the weekend, my lovely girlfriend bought me white and colored chalk for my new chalkboard!  Now it’s time for the science to flow from my desk once again.  Wish me luck!

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This hallway awaits the rest of its occupants!

 

Prague: off the beaten track in Vyšehrad

An index to the Prague series appears on the first post.

For my final full day in Prague, I opted for a hike to the top of Vyšehrad, a hill castle guarding the south river approach to Prague.  This area is considerably less visited by tourists than is true of the Old Town or the castle (Pražský hrad).  I was unsure what to expect, but I felt sure that my legs would appreciate one last stretch before the train and flight back home to South Africa!

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I loved these bright colors.

My stroll took me through some of the key historical buildings of the New Town.  I have already shared a photo of the New Town Hall, but I am sure I have not mentioned the delightful orange and white building next door to the Saint Stephen (Svatý Štěpán) church (built when New Town was new).  Just to the west, I encountered the large public park in front of New Town Hall.  I headed south to encounter the substantial Church of St. Ignatius (Kostel svatého Ignáce).  As I stepped into the vestibule, I encountered a homeless person, asking for change.  Since I had no Czech currency left other than some minor change, he was disappointed, and he responded with a phrase I recognized from reading spy novels (loosely translated “oh my god!”).  In the image below, I have shown the interior of St. Ignatius at the left.

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Two Prague churches: St. Igantius (left) and the Benedictine Emmaus Monastery (right)

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Who doesn’t need stillness from time to time?

It is plain that the church on the right places a much lower value on decoration!  As you might have anticipated from the photo caption, the next site I visited was the Emmaus Monastery.  I had not seen any tourist literature directing me to the place, but a helpful sign directed me to the entrance.  The friendly docent refused to let me pay the full adult admission and insisted on student admission instead (which was handy, since I only had a little pocket change).

I walked through the door into nearly total silence.  The square cloister was very peaceful, receiving only indirect light from the enclosed courtyard.  The pamphlet I had received at the entrance gave a helpful map explaining the art in each alcove.  The images were very old, dating from the creation of the abbey by Charles the IV in 1347, and the monastery had suffered bomb damage during World War II.  Restoration on the art has not yet returned its former glory.

I was strongly moved by the peace of the cloister.  After a quick look at the nave I included in the comparison above, I paused at the corner of the cloister for just a moment.  I sang a song for my friends back in Nashville.  The reverberations were very comforting.  I continued on to a small chapel that I had missed on my initial walk.  I was astonished to see the image of a spear head that I had last seen in Warsaw!  This chapel had once featured sacred relics believed to be from the Crucifixion, specifically nails from the cross and the spear that had pierced Jesus.  The art in this small chapel has been restored to a much greater extent than in the cloister outside.

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A refurbished chapel in the Emmaus Monastery

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This massive gateway dates from 1841.

Having spent some time with the transcendent, I was ready for a bit of a slog.  I trudged south along the evocatively named “Na Slupi” in the cold wind.  It seemed to be picking up speed, and a few snow flurries came my way.  I came to a rail underpass that was my route to the Vyšehrad access.  The roads led steeply uphill.  Soon I encountered the massive brick gate (cihelná brána) of the rooftop fortress.  I nearly fell on my backside trying to get a photo; once I stepped away from the roadbed, I was slipping and sliding on ice.

I should explain that Vyšehrad was prominent in the ancient history of Prague and regained standing in medieval times.  The castle atop Vyšehrad was the ducal seat of the Přemyslid dynasty during the 10th century, before Prague Castle was constructed on the opposite side of the Vltava River.  The area’s rebirth came about after the New Town extended to the south in the 1350s.  After the ancient fortress fell into ruin, a new Baroque fortress atop Vyšehrad was established after the Thirty Years’ War, in 1654.

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The church looks pretty great for being nearly a millennium old!

My first stop inside the walls was a visit to the Rotunda of St. Martin.  The rotunda represents an ancient type of church architecture that pre-dates Gothic cathedrals by half a millennium.  St. Martin was constructed during the reign of Vratislaus II, who died in 1092.  The building has been decommissioned and renovated a few times over.  Its walls still contain a Prussian cannon ball from 1757!

I wandered south to the most external gate of the walls, Tabor Gate, originally built in 1655.  The information center was closed when I walked past, and most signs that I observed were in Czech, so I felt somewhat unsure of what I was seeing.  As I followed the walk back north on a bluff to the east side of the Vltava River, though, I was treated to some really lovely views of today’s Prague.  I saw a private boat harbor to the east side of the river, and ice had covered the entirety of its surface.  Soon, though, I came across some ruins.

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Libušina lázeň was a medieval Gothic lookout tower.

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The St. Peter and Paul Basilica

Legends surround this place, as well.  After the warrior Čech settled in this area, his son Krok produced three daughters.  The youngest daughter, Libuše, was famed for her wisdom and prophecies.  She was selected as leader for the land, as a result (and gave her name to the tower shown above).  When people complained that a woman should not lead by herself, she prophesied that her white horse would lead her servants to Prince Přemyslid, who would become her husband.  Soon thereafter, the happy couple launched the first dynasty that ruled Bohemia from Prague.

Even before the creation of the New Town, a church had stood at the crest of Vyšehrad.  The 11th century church was remodeled in the second half of the 14th century and again at the end of the 19th.  St. Peter and Paul has been an important part of Prague history as the political leadership shifted between Vyšehrad and Prague Castle and as religious leadership has shifted among the three principal churches of the city (the others being St. Vitus and Our Lady before Týn).

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Final resting place of one of my favorite composers

The graveyard adjoining St. Peter and Paul came into vogue during the 19th century, and a quick walk through the grounds will show any number of beautiful memorials and tombs.  The classical composers Antonín Dvořák and Bedřich Smetana are both interred there, and I recognized Jan Neruda, a writer and poet, as well.  It seemed strange that this place at the edge of the city would have regained this prominence at such a late date.

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King Wenceslaus looks out on a magnificent view of his city.

I was glad, though, that I could finish my visit to Prague at Vyšehrad.  My final moments of tourism saw me slipping and sliding across the icy hill top.  At last I reached a lovely equestrian statue of St. Wenceslaus.  It dates from 1680, when it was crafted by Bendl for the Prague Horse Market.  This area was subsequently renamed “Wenceslaus Square;” the statue currently standing outside the National Museum was a later replacement.  I think that the dukes, kings, and emperors who have ruled Prague would be delighted if they could see it today.  I know I was!