Author Archives: dtabb1973

The trail of three dreamers: the Inanda Heritage Route

August 7, 2017

Why would Nelson Mandela cast his first vote in an Indian township in the homelands of the Zulu when he came from the Xhosa people?  Today’s adventure in Durban took me some distance from the standard tourist fare. Instead, I was able to learn a little bit about the lives of three men who began bending the arc of South African history toward justice: Mohandas K. Gandhi, Isaiah Shembe, and John L. Dube.

My destination was the Inanda Heritage Route.  From the information I could find online, it was apparent that I would be heading well off the beaten path for this adventure.  I was able to navigate the construction site at the entrance from the M41 to the N2.  The red earth of Durban was very apparent!  I traveled south to the R102 and headed away from downtown; very shortly I was on the M25, traveling into townships and industrial areas.  The M25 was tarred, which gave me some confidence.  I grinned when I passed a garbage dumpster that was literally on fire; I hear the phrase “dumpster fire” frequently in relation to the news, and here was the real deal!  Every kilometer or so I saw a series of blue and white flags celebrating the people whose former homes I would visit today.  Soon I turned onto a small dirt road, flanked by shacks, that led up a short hill to my first site for the day.  An attendant waved me into the parking lot for Phoenix Settlement.

Mohandas K. Gandhi

While people associate Gandhi with India casting off English rule, few realize that the first two decades of his career in social justice took place in South Africa. When Gandhi arrived in South Africa in 1893, he was really struggling to get his law career into motion. After he was thrown off a train in Pietermaritzburg for trying to use his first-class train ticket, his consciousness that racial discrimination must be countered began to grow. He read Tolstoy, Ruskin, and Thoreau avidly.

IMG_9907In 1904, Gandhi decided to create the Phoenix Settlement on 100 acres of land to the northwest of Durban. He named his house “Sarvodaya,” meaning “progress of all.” Life for the community that grew there was very spartan; Gandhi held that human work should always target needs rather than desires (a theme John Ruskin popularized in Unto This Last). He began to spin his own thread to weave homespun clothing.

IMG_9919His wife and children moved to join him, as did activists from throughout South Africa. Gandhi began a newspaper, entitled the Indian Opinion, and published it from the Phoenix Settlement. He continued to live in South Africa until 1914.

In the closing days of the Apartheid government, different ethnic groups were deliberately played against each other. During 1985, the Inanda area, adjoining the Phoenix Settlement, erupted in riots. Much of the Phoenix Settlement, including Sarvodaya, was burned to the ground. After 1994, however, the democratic government recreated the main buildings of Phoenix from historic photographs. Today, the former printing press serves as a computer skills training laboratory for the surrounding community under the Gandhi Development Trust, charging only R20 ZAR (less than $2 USD) for ten hours of training in Microsoft Word!

I enjoyed my time at Phoenix.  The site acts as a guidepost to other historical sites linked to the Inanda community, with a museum featuring information about all three people I highlight in this post.  I had the place to myself for a bit, but then two busloads of students from New Hampshire arrived at the site.  They had come to Durban on a church mission trip.

Isaiah M. Shembe

Born in the 1870s to a Zulu family, Isaiah Shembe experienced a powerful vision while a young man, and he became part of the Wesleyan Church and then the Baptist Church. He became an evangelist, and his interaction with Nkabinde, a formerly Lutheran prophet, led him to create a healing ministry in 1910. Just a year later, he created the iBandla amaNazaretha (Nazareth Baptist Church), and he transformed a farm within walking distance of Gandhi’s Phoenix Settlement into the holy city of Ekuphakameni.

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The replica staff was not bolted down. I am a rebel.

Shembe’s church has continued to grow in membership since his death in 1935, now incorporating millions of followers. Much of its appeal comes from his syncretic abilities, transforming the Zulu art of praise poetry into a powerful set of hymns. His hymnal, primarily composed between 1910 and 1940, may have been the first book ever published in the Zulu language. Today, one may see the “Nazaretha” described as an “African Initiated Church,” reflecting that its practices were defined by Africans for Africans. In 1976, the church suffered a schism, resulting in a new settlement being created a short drive to the west in Ebuhleni.

I was curious to learn more about the Nazaretha, but their towns were not set up as museums or monuments.  I would have needed to set up prior arrangements with a tour guide to visit those locations.  Instead I followed the buses of students from Gandhi’s site back to the tar road, through a couple of turns, and then hopped off the M25 onto a dirt track.  It jolted upwards to a ridge featuring the Ohlange Library and the Ohlange High School.  We had arrived at the Ohlange Institute!

John L. Dube

Born in 1871 to Christian converts at the Inanda Mission Station, John Dube was destined to become the first president of the African National Congress. As a boy, John Dube got into a fight at school, and American missionary William Wilcox was asked to have a word with him. Their relationship grew over time, and when Wilcox returned to the United States, John Dube came along, becoming a student at Oberlin College in Ohio. His collaboration with Wilcox continued, though, and Dube began raising funds for a school in South Africa by giving talks on a tour through several states, and he authored a book on the challenges of being caught between the traditional values of his home and the structures of the Western world. He alternated between South Africa and the United States between 1892 and 1900, gaining an ordination as priest by the Congregational Church and forming a relationship with Booker T. Washington, who impressed upon Dube the importance of career training for empowering young people with self-reliance.

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This, the oldest extant building of the Ohlange Institute, is barely mentioned on-site.

John Dube began making his mark on South Africa in 1900, when he founded the Zulu Christian Industrial Institute, renamed a year later to the Ohlange Institute. His chosen site was, again, within walking distance of the Phoenix Settlement and of the Shembe town of Ekuphakameni. It ranked as the first educational institution with a black director in South Africa. Its initial enrollment of 63 students soon bloomed to more than 100; by 1917, women were also allowed to enroll. In 1903, Dube created a Zulu-language newspaper Ilanga Lase Natal (the Natal Sun). His message of “Honour the man who works” and scornful “demise of the idler” began reaching a wider community. The school’s finances had become threatened enough by 1924 that Dube allowed the school to become part of the “Department of Native Education” (note that while the Nationalists did not bring “Apartheid” to the government until 1948, the earlier government under Smuts had plenty of racial limits in place).

Dube’s enduring relationship with the American religious community put him in a difficult position. He was committed to non-violence, and the 1906 Bambatha Rebellion put him on the opposite side of the Zulu chiefs. Nonetheless, his prominence in fostering the growth of the Zulu community positioned him well for the 1912 convocation of educated South African elites to establish the South African Native National Congress, renamed in 1923 to become the African National Congress.

IMG_9955When Nelson Mandela cast his ballot in 1994 at the John L. Dube building of the Ohlange Institute, he walked to the memorial monument at Dube’s grave and said, “I have come to report, Mr. President, that South Africa is now free.” He explained his decision to come to this site with these words:

I voted at Ohlange High School in Inanda, a green and hilly township just north of Durban, for it was there that John Dube, the first president of the ANC, was buried… When I walked to the voting station, my mind dwelt on the heroes who had fallen so that I might be where I was that day, the men and women who had made the ultimate sacrifice for a cause that was now finally succeeding… I did not go into that voting station alone on 27th April; I was casting my vote with all of them.

During my time at the Ohlange Institute, the students of the high school on the site showed a lot of curiosity about their visitors.  One boy asked to have his picture taken with me.  A group of girls were giggling behind me, and when I turned around to say hello, one said, “you are handsome!”  We all laughed.

Mzinyathi Falls

With these three giants in my mind, I was ready for a moment apart from the world. I should be clear that the two sites I had visited (Phoenix Settlement and Ohlange Institute) were quite close to the M25 highway that burrows into the heart of this principally Indian township. Both sites had security gates and personnel guarding entry, and I could walk around each with a sense of security. The dirt roads connecting the sites to the highway were somewhat worrisome, with shacks or cinderblock houses beside them. My next destination was at least a kilometer off the M25, though, and I was unsure what I would find.

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This mix of formal and informal buildings appears just above the falls.

Just navigating to the turnoff for Mzinyathi Falls was a bit shocking. On that route, the M25 juts north from a traffic circle that doubles as a public square / taxi minibus rank, and I missed my turn on the first attempt. I was soon back on course, driving past “tuck shops” built from shipping containers. When I saw the turn for the Falls, my face fell. The route south was just a dirt road of one lane. The Litchi-Car bounced and jostled merrily along, and soon the endless rows of shacks and cinderblock houses gave way to a ravine on the left side. No sign indicated that I had reached the falls, though, and I bounced on another quarter mile before turning around for fear that my car couldn’t navigate back up the slope.

When my eyes landed on the falls, though, I felt it was all worth it. Ironically, they were easier to see on the way back to the highway! I fell into conversation with Nehemiah, a Zambian who had come to South Africa to work in a friend’s shop (it didn’t turn out well). We stood at a half wall on the edge of the ravine, and I shot photos and videos of the cascade.

When one has been in a dry country for a while, the sound of water becomes a little magical, really. It does not surprise me that these falls are considered a holy place for baptisms by the followers of Isaiah Shembe.  I loved the rainbow reflecting off the water vapor at the bottom. Perhaps South Africa has “moved on” from being the Rainbow Nation, but I still take comfort in my belief that the leaders of tomorrow still feel inspired by luminaries like Gandhi, Shembe, and Dube.

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On foot in Durban

August 6, 2017

My plan to visit museums today ran afoul of a simple scheduling problem: it’s Sunday. I reassembled my plans last night so that I would spend today visiting the center of Durban, taking in its beaches and historic center. Why not take advantage of the fact that the business commuters are staying away today?

I decided to drive my rental car to Mini Town, which sits at the northern end of Durban’s Golden Mile. I parked near some sports fields in an area used for overflow event parking at the Olive Convention Center. To be able to park in downtown for a full day with no charge was an unexpected bonus! I walked a couple of blocks and found myself right at the entrance to Mini Town.

On the Beach

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The electric train has passed the trestle bridge at Mini Town.

I don’t really have much to say about Mini Town as an attraction. I thought that it would contain models of famous buildings throughout the world or even throughout South Africa. Instead, the great majority of its models are small buildings carrying logos and advertisements for local businesses. A few were rather nicer, such as the Durban City Hall and a couple of Muslim shrines. If you are a fan of model railroads, you might enjoy the site, because it is encircled by a track. At one point, it crosses a bridge over water, and the bridge has a central section that raises in order to allow a tall ship through the channel. With that said, Mini Town was mostly a bust.

I turned my face to the south and began a long trek down the beach. Durban’s beaches are quite lovely. They’re wide and sandy, just like the ones I enjoyed in San Diego, and the water of the Indian Ocean is a lot warmer than what one would experience in Cape Town! The beaches are lined with massive hotels, such as the Southern Sun.

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A park sandwiched between the beach and hotel

One of the hotels had constructed a lovely park on the beach, featuring fountains and flowers. It looked like an excellent place for a picnic, but it was still only 10:30 in the morning.

I had not walked very far when I realized that I had made a serious mistake in omitting my hiking hat from my packing list. Even though we are in winter, Durban’s sun was making my head hurt. I pulled off the beach trail and found a flea market full of sales booths. Durban has long been home to a substantial number of people descended from the people of India; they were recruited to South Africa to support the sugar-growing agriculture of the area. Today, Durban has the highest concentration of Indian inhabitants outside India! Surrounded by booths of sellers, I was struck by the change in ethnic makeup. At Parow Centre in Cape Town, I would be surrounded by people from the Cape Coloured population (48.8% of the Western Cape population in the 2011 census), but in Durban, the Indian population is ascendant (7.4% of the KwaZulu-Natal population in the 2011 census).

I found a seller who had some buffalo leather caps for sale. It reminded me of one I’d purchased years ago near London (that I never get to wear in Cape Town’s climate). The listed price wasn’t too bad, just R150 ZAR, but I asked him if there were a Sunday morning discount. He suggested that R130 ZAR would be the Sunday price, and I took it. I think a $10 USD hat that keeps the sunburn away from my scalp is a bargain!

Down the beach I trod, watching people playing on the sand and hawkers trying to draw interest to their wares. A fair number of them were selling Zulu art, either the furry headdress of a warrior or colorful bead-work for earrings or chokers. Of course, one cannot really stop to look, because the moment he or she does, a crowd of salesmen will begin calling! A very persistent leather belt salesmen required direct communication before he went away.

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Panorama produced through Microsoft Image Composite Editor

The beach has several piers pointing into deeper water. I walked out to the end of one to watch surfers attempt to ride the waves. On the whole, though, I did not see many people enjoying the waters. I am sure it would be quite different had I been visiting in summer on a school holiday!

uShaka Marine World

As I crossed into the southernmost beaches, the area became less inviting. It was clear that many of the people around me had slept outside last night, and the buildings were not in great repair, either. I kept my head up until I passed that zone.

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I believe this is a restaurant!

At last, I found myself in the area of uShaka Marine World, a water park offering the “highest water slide in the Southern Hemisphere” along with Africa’s largest aquarium. I had considered spending some time in there, but I’d left my swimsuit in the car. I still enjoyed the fact that some of their attractions had been built inside a ship hull!

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Lentil “Bunny Chow” at Nadia’s Curry Cafe

Instead, I visited its restaurants at Village Walk! Three years ago, researchers from K-RITH (now AHRI) had taken me to the Moyo Restaurant, where I had been wowed by a troupe of traditional dancers. I think that would be the first time I’d seen Zulu warrior dancing. This time, though, I opted for its next door neighbor, Nadia’s Curry Cafe. For my lunch, I ordered a “bunny chow,” that Durban-most of Indian cuisine! The restaurant cut an unsliced loaf of bread in half, and then they made a hollow inside it by pulling out a plug of bread. They poured my lentil curry into the hollow and added a salad on the side. It was delicious!

After lunch, I wandered through the uShaka shopping mall where I had bought my niece and nephews some beaded Christmas ornaments back in 2014. I was happy to see a team from the Department of Science and Technology running a table for National Science Week at the aquarium.

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Farewell to the amusement park!

As I left Marine World, I was a bit unsure of my course. I felt that it was important for me to try to see the historic center of the city, but I had already walked some distance that day. Resting my feet over lunch, though, seemed to have restored them. I decided to strike out to the west toward the City Hall.

Don’t look like a tourist on foot in downtown Durban.

I would not recommend the walk to City Hall from the beach for most tourists. My walk North along Mahatma Gandhi showed me many building in poor repair. Several churches along my route were ending Sunday services, and I took a look inside St. Peter’s Catholic Church for a moment. As I continued my walk, I felt pretty out-of-place, and the ever-present taxi shuttle buses didn’t help my mood. I turned left on Margaret Mncadi and saw more of the same disrepair. A tourist map I acquired on the beach showed a “Revolving Restaurant” overlooking the enclosed harbor. I looked up at it from below, and I am not sure I would want to depend on its structural integrity. In any case, it was closed on Sundays. I turned up Samora Machel to reach the City Hall, and I was pleased to see buildings from an earlier era had been preserved properly.

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A shady verandah at the Old Court House!

I started on the grounds of the Old Court House Museum (closed on Sunday). The style of the yellow and white building seemed to fit this area like an old shoe. The covered walkway around the building would have been a great relief from the relentless sun.

I was walking toward the city hall itself when a security guard stopped me and said I had to stay outside the parking area since it was closed for Sundays. I crossed the street into the Medwood Gardens and snapped a couple of photos of the massive building, trying to find the right moment to snap the photo so passing cars wouldn’t appear!

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Find the right place to photograph the entire massive structure would be a challenge!

I continued to Church street and found another informal market in progress there, but a substantial number of panhandlers were nearby. I pulled my camera from my bag for a moment to capture the Post Office, and immediately people began approaching me for money.

I turned my heel on the area and struck a brisk pace back toward the beach along Dr. AB Xuma. I did see some much newer buildings that were clearly getting much more attention than the run-down district through which I’d approached city hall. The Inkosi Albert Luthuli International Convention Centre was massive and gleaming! I wondered just when the building would end as I turned the corner to follow Stalwart Simelani North.  Eventually I reached the M4 on foot, and soon I was reunited with the Litchi-car.

I returned to my hotel for a lovely, lingering nap.

From the Beach to Bloem!

August 5, 2017

There are only so many places one can conveniently drive from Cape Town. The drive from Cape Town to Johannesburg, for example, would take thirteen and a half hours, by the book. My desire to see the eastern half of the country motivated me to plan a week-long road trip; I would fly to Durban to kick off the trip and fly home from Bloemfontein at the end!

20170817-Road-MapMy trip plan began in Durban, the third-largest city in South Africa (after Cape Town). I hoped to take in some of its tourist sites as well as learn a bit more about Gandhi‘s life in South Africa. From there I would drive inland to Pietermaritzburg, a smaller city founded by Voortrekkers. The next two stops were considerably less urban! My visits to Monk’s Cowl and Golden Gate Highlands National Park would let me see some of the most glorious mountain scenery in the country. While surrounded by South Africa, I would leave it by visiting the nation of Lesotho while staying in the nation’s capital, Maseru. Finally, I would visit the judicial capital of South Africa, Bloemfontein. I hope that this map makes the plan of this trip easier to follow!

My experiences with South African Airways has mostly been positive, but I decided to return to a non-governmental airline for this trip. I first flew with Mango Airlines in November, 2014, during my initial trip to the country. Coincidentally, my new trip would recapitulate that first flight as I hopped from CPT to King Shaka International in Durban. I flew on a Saturday afternoon, and Natasha was very kind to drive me to the airport through traffic crowded with sports fans on their way to Newlands Stadium.

The flight was quite uneventful. Mango used a Boeing 737-800, the same kind of plane one frequently sees with Southwest Airlines in the United States. The seats were plain, though reasonably comfortable. I believe South African airlines are less prone to packing passengers in like sardines than we frequently see in the States. Only two hours were required to go from coast to coast across South Africa.

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The Litchi-Car

Perhaps not many people know this about me, but I enjoy driving quite a bit less than others. I feel okay when I am in my own car, but driving a friend’s car or a rental car is distinctly uncomfortable. For this trip, I had rented a car with Tempest Car Hire, which has an agreement with Mango Airlines. Despite the fact that most of my drive would be uphill, I opted for the least expensive cars they rented. When I arrived at the Tempest office at King Shaka International, however, a problem arose. Their records showed that I would drop the car off at Bloemfontein, so that was fine, but they looked at me quite blankly when I asked them to confirm that I could drive into Lesotho (apparently the border guards check to see if rental cars have written permission for crossing the border). At first, the administrators simply said no, but I asked them to reconsider since my entering Swaziland (another small, landlocked nation in the northeast of South Africa) was perfectly fine with their policies. A telephone call later, the staff handed me my letter within the rental contract. I wandered out to the car to see my chariot for nine days!

I know it’s quite silly, but I tend to give my cars a name. Strawberry, for example, has been a very reliable ride for me since I found her in December of 2015. To stay with the same theme, I decided that the pretty white Kia Picanto from Tempest would be called “Litchi.” Her first gear made me stall out on my first few tries to start from a stop, but soon I felt that I was learning her rhythms. I started my running battle with the car’s turn signals (here called an “indicator”), though; the headlights and indicators are reversed on Litchi versus what I have become accustomed to in Strawberry.

I had a small city map of Durban, but I did not have a map to get me to my hotel, the Road Lodge Umhlanga Ridge. I had some misgivings about staying in Durban proper; it’s a huge city, and it has a bit of a reputation as a rougher place (this may be entirely unfair, since Cape Town is now the ninth most dangerous city in the world by murder rates). As a result, I set up my room in Umhlanga, a northern suburb of Durban that has a growing economy and a legendary beach.

Alone in the dark without a map in a foggy rental car

20170817-Bad-NavigationMy drive to Umhlanga was my worst navigation experience in years. I entered the N2 southbound without a problem, and I made it through the toll plaza without stalling out the engine (the fee was just five and a half Rand, or about $0.41 USD). My attempt to improvise by hopping onto the M4 coastal highway ran into a snag when I got mixed up on the interchange and found myself heading back toward the airport on the N2! I was able to reverse course at the next exit, but the sinking sun cooled everything down, and condensation started to collect inside the windscreen. I dropped a window.

I still had the “M4” in my mind when the exit for the M41 in Umhlanga came up, and I careened southward on the N2, still looking for the right road. There were no nearby exits, though, and soon I was cresting a rise to the north of Durban. A moment of magic happened that jolted me right back into my memories of Durban in 2014; as I continued south down the hill I just mounted, I saw the first valley that is home to Durban. From a dark landscape all around me, I was suddenly surrounded by streetlights in every direction. It’s a very impressive way to first experience the city.

At long last another exit appeared, this time for the KwaMashu highway. I mostly knew the name of this road from Rob Byrne‘s traffic news on SAFM; during rush hour this road is frequently quite busy! I decided to take the exit and head east on the R102 (into Durban North). The road curved to the south, though, and soon I was almost to Durban itself. I took another road east to the coastal highway, and I was soon on the M12, headed north to Umhlanga.

In fact, I reached Umhlanga before I knew it! I drove through the lovely Umhlanga Ridge, a wealthy business district crammed with new buildings, and I turned east on the M41 at a traffic circle, which headed me away from Umhlanga Ridge, right back toward Durban. I had returned to the M4 along the coast before I was able to exit and beg a security guard for help. I was, by that time, very close, and Google Maps on my Android phone was able to get me the last mile. In the future, I will try to spend more time with that option first. (I’ve had no Internet at home for the last two days before my trip. Thanks, Telkom!)

At any rate, I was able to reach my hotel before seven P.M. I had to take a couple of tries at parking near it. My hotel is jammed between a NetCare hospital and the massive Gateway Theatre of Shopping. I was arriving just in time for dinner on Saturday night, and the roads were as crowded as you might expect. After looping through the hospital and mall areas a few times, I was able to maneuver into the mall parking lot, and a few minutes of stalking exiting shoppers finally acquired a “rock star” parking spot, just thirty feet from the hotel door.

I was at my “home” for the next three nights! After checking into my room, I trudged over to the mall to enjoy some pesto fettuccine for dinner. The evening would be a good one, despite my having driven roughly five times as far as necessary to get to my hotel!

What protein database is best for tuberculosis?

As many of you know, I have specialized in the field of proteomics, the study of complex mixtures of proteins that may be characteristic of a disease state, development stage, tissue type, etc.  Here in South Africa, my application focus has shifted from colon cancer to tuberculosis.  As a newcomer to this field, I’ve been curious to know whether the field of tuberculosis has good information resources to leverage in its fight against the disease.

The key resource any proteomics group can leverage is the sequence database, specifically the list of all protein sequences encoded by the genome in question.  The human genome incorporates around 20,310 protein-coding genes (reduced from estimates of 26,588 from the 2001 publication), but those genes code for upwards of 70,000 distinct proteins through alternative splicing. Bacteria are able to get by with far smaller numbers of genes.  E. coli, for example, functions with only 4309 proteins.  The organism that infects humans and other animals to produce tuberculosis is named Mycobacterium tuberculosis.  If we were to rely upon the excellent UniProt database, from which I quoted E. coli protein-coding gene counts, we would probably conclude that M. tuberculosis relies upon even fewer genes: only 3993 (3997 proteins)!

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UniProt is an excellent all-around resource for proteomics, but researchers in a particular field usually gravitate to a data resource that is particular to their organism.  People who work with C. elegans for developmental studies, for example, use WormBase.  People who study genetics with D. melanogaster would use FlyBase.  People in tuberculosis have frequently turned to TubercuList for its annotation of the M.tb genome (comprising 4031 proteins).  This database, however, has not been updated since March of 2013 (available from the “What’s New” page).  Can it still be considered current, four years later?

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e-ensembl

As a recent import from clinical proteogenomics, my first impulse is still to run to the genome-derived sequence databases of NCBI, particularly its RefSeq collection.  I found a NCBI genome for M. tuberculosis there, with a  last modification date from May 21, 2016 and indicating its annotation was based upon “ASM19595v2,” a particular assembly of the sequencing data.  This was echoed when I ran to Ensembl, another site most commonly used for eukaryotic species (such as humans) rather than prokaryotic organisms (such as bacteria).  Their Ensembl tuberculosis proteome was built upon the same assembly as was the one from NCBI.

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As a former post-doc from Oak Ridge National Laboratory, I am always likely to think of the Department of Energy’s Joint Genome Institute.  The DOE sequences “bugs” (slang for bacteria) like nobody’s business.  Invariably, I find that I can retrieve a complete proteome for a rare bacterium at JGI which is represented by only a handful of proteins in UniProt!  This makes JGI a great resource for people who work in “microbiome” projects, where samples contain proteins from an unknown number of micro-organisms.  In any case, they had many genomes that had been sequenced for tuberculosis (using the Genome Portal, I enumerated projects for Taxonomy ID 1773).  I settled for two that were in finished state, one by Manoj Pillay that appeared to serve as the reference genome and another by Cole that appeared to be an orthogonal attempt to re-annotate the genome from fresh sequencing experiments.

The easiest way to compare the six databases I had accumulated for M. tuberculosis is to enumerate the sequences in each database.  The FASTA file format is very simple; if you can count the number of lines in the file that start with ‘>’, you know how many different sequences there are!  I used the GNU tool “grep” to count them:

grep -c "^>" *.fasta
  • TubercuList: 4031 proteins
  • NCBI GCF: 3906 proteins
  • DOE JGI Cole: 4076 proteins
  • DOE JGI Pillay: 4048 proteins
  • Ensembl: 4018 proteins
  • UniProt: 3997 proteins

So far, one could certainly be excused for thinking that these databases are very nearly identical.  Of course, databases may contain very similar numbers of sequences without containing the same sequences.  One might count how many sequences are duplicated among these databases, but identity is too tough a criterion (sequences can be similar without being identical).  For example, database A may contain a long protein for gene 1 while database B contains just part of that long protein sequence for gene 1.  Database A may be constructed from one gene assembly while Database B is constructed from an altogether different gene assembly, meaning that small genetic variations may lead to small proteomic variations.

pgec20header20final20editI opted to use OrthoVenn, a rather powerful tool for analyzing these sequence database similarities.  The tool was published in 2015.  Almost immediately, I ran into a vexing problem.  The Venn diagram created by the software left out TubercuList!  I was delighted to get a rapid response from Yi Wang, the author of the tool (through funding of the United States Department of Agriculture’s Agricultural Research Service).  The tool could not process TubercuList because it contained disallowed characters in its sequence!  I followed his tip to sniff the file very closely.  I found that both sequence entries and accession numbers contained characters they should not.  Specifically, I found these interloping characters:

+ * ' #
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OrthoVenn Venn chart

Scrubbing those bonus characters from the database allowed the OrthoVenn software to run perfectly.  Before we leave the subject, I would comment that these characters would cause problems for almost any program designed to read FASTA databases; in some cases, for example, the protein containing one of those characters might be prevented from being identified because of these inclusions!  My read is that they were introduced by manual typing errors; they are not frequent, and they appeared at a variety of locations.  Let’s remember that they have been in place for four years, with no subsequent database release!

Most people are accustomed to seeing Venn diagrams that incorporate two or three circles.  In this case I compelled the software to compare six different sets.  The bars shown at the bottom of the image show the numbers of clusters in each database; note that these differ from the number of sequences reported in my bullet list above because OrthoVenn recognizes that sequences within a single database may be highly redundant of each other!  (If sequences were completely identical, they could be screened out by the Proteomic Analysis Workbench from OHSU.)  Looking back at the six-pointed star drawn by the software, we might conclude that the overlap is nearly perfect among these databases.  We see four clusters specific to the JGI Pillay database, and 131 clusters specific to some sub-population of the databases, but the great bulk of clusters (3667) are apparently shared among all six databases!

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The Edwards visualization from OrthoVenn

Oh, how much difference a visualization makes!  Shifting the visualization to “Edwards‘ Venn” alters the picture considerably.  Now we see that the star version hides the labels for some combinations of database.  We see that 3667 clusters are indeed shared among all six databases.  After that, we can descend in counts to 131 clusters found in the Pillay and Cole databases from JGI; does this reflect a difference in how JGI runs its assemblies?  Next we step to 106 clusters found in UniProt, Ensembl, Tuberculist, and NCBI GCF, but neither of the JGI databases.  The next sets down represent 70 clusters found in all but NCBI GCF or 25 clusters found in all but the two JGI databases and NCBI GCF.

I interpret this set of intersections to say that tuberculosis researchers are faced with a bit of a dilemma.  If they use a JGI database, they’ll miss the 106 clusters in all the other databases.  If they use Ensembl or TubercuList, they will include those 106 but lose the 131 clusters specific to the JGI databases.  Helpfully, OrthoVenn shows explicitly which sequences map to which clusters.  Remember that when I downloaded the Ensembl and NCBI databases, I saw that they were both based upon a single genome assembly called ASM19595v2.  Did they contain exactly the same genes?  No!  Ensembl contained two fairly big sets of genes that NCBI omitted, including 70 and 25 protein clusters, respectively.  NCBI contains another 11 protein clusters that were omitted from Ensembl.  Just because two databases stem from the same assembly does not imply that they have identical content.

For my part, I may use some non-quantitative means to decide upon a database.  I do not like making manual edits to a database since then others need to know exactly which edits I’ve made to reproduce my work.  That takes away TubercuList.  Next, I feel strongly that the FASTA database should contain useful text descriptions for each accession.  Take a look at the lack of information TubercuList provides for its first protein:

Rv0001_dnaA

That’s right.  Nothing!  The Joint Genome Institute databases are quite similar in omitting the description lines. Compare that to what we see in the NCBI and UniProt databases:

NP_214515.1 chromosomal replication initiator protein DnaA [Mycobacterium tuberculosis H37Rv]
sp|P9WNW3|DNAA_MYCTU Chromosomal replication initiator protein DnaA OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) GN=dnaA PE=1 SV=1

That’s much more informative. We’ve got missing data here, too, though. Tuberculosis researchers have grown accustomed to their “Rv numbers” to describe their most familiar genes/proteins, but NCBI and UniProt leave those numbers out of well-characterized genes; the Rv numbers still appear for less well-characterized proteins, such as hypothetical proteins. By comparison, Ensembl includes textual descriptions as well as Rv numbers in a machine-parseable format for every entry:

CCP42723 pep chromosome:ASM19595v2:Chromosome:1:1524:1 gene:Rv0001 transcript:CCP42723 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:dnaA description:Chromosomal replication initiator protein DnaA

On this basis, I believe Ensembl may be the best option for tuberculosis researchers. It is kept up-to-date while TubercuList is not, and it allows researchers to refer back to the old Rv number system in each description.

I hope that this view “under the hood” has helped you understand a bit more of the kind of question that occasionally bedevils a bioinformaticist!

Are you ready to start a molecular biology M.Sc.?

Professors receive a lot of requests from international students for admission to post-graduate training.  In South Africa, that training could be for “Honours” (a one-year course), an “M.Sc.” (a two-year Master’s program), or a “Ph.D.” (typically three years, post Master’s).  For students changing from one country to another, however, the question of “equivalencies” is key.  Could a four-year B.Sc. (Bachelor’s of Science) from Egypt, for example, be treated as the same thing as a three year B.Sc. followed by one year of Honours in South Africa?  This post gives an example of the questions I asked as I recently tried to determine the right level of admissions for an international student.

The international office for my university had declared that a student’s four-year degree was certainly equivalent to a three-year B.Sc. in South Africa, but it left to the department’s discretion whether or not Honours training was required before a M.Sc.  To support the department’s decision, I decided to build an interview from questions that would delineate the limits of the candidate’s knowledge.  I used the roster of topics for the Division of Molecular Biology and Human Genetics 2017 Honours as a guide.  I used the number of didactic training days for each topic as a weight:

Field Duration
Molecular Biology 8 days
Mycobacteriology 7 days
Biostatistics 12 days
Bioinformatics 8 days
Immunology 8 days
Cell Biology 8 days
Scientific Communication 2 days

I also gave some consideration to the M.Sc. project the student would pursue in my laboratory.  In this case, the work related to the reproducibility of mass spectrometry experiments.  After pondering before my word processor, I selected these questions for the candidate’s interview:

# Field Question
1 Cell Biology What biological processes are described by the Central Dogma of molecular biology? Walk us through each.
2 Biochemistry What do we describe with Michaelis-Menten kinetics?
3 Computer Science How does iteration differ from recursion?
4 Analytical Chemistry By what property does a mass spectrometer separate ions?
5 Medicine In HIV treatment, what is the purpose of a “protease inhibitor?”
6 Biostatistics What role does the “null hypothesis” play in Student’s t-test?
7 Medicine What type of pathogen causes tuberculosis?
8 Genetics What is the purpose of a plasmid vector in cloning? What features do such vectors commonly contain?
9 Cell Biology What cellular process includes prophase, metaphase, anaphase, and telophase?
10 Mathematics The log ratio (base 2) between two numbers is 3. What is the linear ratio?
11 Immunology What is an antibody, and what is its relationship to an antigen? What are the major families of antibodies?
12 Computer Science What is the purpose of an Application Programming Interface (API) or “library?”
13 Biochemistry What do we describe as the secondary structure of a protein?
14 Genetics Of what components are nucleic acids constructed?
15 Biostatistics What is a Coefficient of Variation?
16 Mathematics If I divide the circumference of a circle by its diameter, what value do I get?
17 Immunology What type of immune cell is the primary factory for antibodies?

The interview, conducted via Skype, lasted approximately an hour. As I asked each question, I gave the question orally and pasted the text of that question into the chat session. Remember that as an American, I have a “foreign” accent for the English-speaking population of Africa! I did not want that to be a factor in the candidate’s performance. I was grateful that our division’s Honours program coordinator, Dr. Jennifer Jackson, accompanied me during the interview, both to monitor that the candidate was treated fairly and to ask follow-up questions of her own.

Why did it take an hour to answer these questions? As is customary in post-graduate education, each answer opened the door to a series of other questions. A student may give an answer that covers only part of the question, and the follow-up will poke into the omitted area to see if it is an area of weakness, almost like a dentist with an explorer goes after a darkened area of a tooth to see if it represents dental decay!

Another factor that I want to measure for students is the degree of integration that they have achieved in their educations. To recognize that a word has been mentioned in class is not sufficient; I need to see that students understand how key concepts relate to each other. This synthesis is sometimes hard to evaluate, but it’s important. A student who doesn’t understand how a concept integrates with others will not be able to apply the principle or recognize when it should come into play.

Before the readers of this blog begin showering me with applications, I need to emphasize that the questions I framed for this particular interview are not the questions I would ask of another candidate. The ones above were chosen to reflect the background of the candidate, the diploma program to which he or she had applied, and the nature of the project I had in mind.

I hope that this post will help you decide whether or not you are ready to plunge into post-graduate education!

Young David steps out of his comfort zone

Sometimes, a look through the scrapbook can be a very humbling experience.  I resolved this month to finish a project I launched in 1994.  At last I am publishing the journal I recorded during my first trip to Europe!  For the first time, I am bringing together the forty-two journal entries, my photographs, and the video camera footage that I recorded during my clockwise circuit around the continent.  Before you jump right into the journal, though, could I ask you to read a few thoughts?

More time has passed since I wrote that journal (23 years) than I had lived at that point (I was 20 years old).  The experiences of the last two decades have certainly left their mark.  Since that time, I’ve graduated from two degree programs; I’ve filled my passport with stamps; I’ve built my career in academia; I’ve achieved some level of comfort in finance; I’ve married and divorced.  All of these changes make it hard to recognize the person who wrote those entries as the same person writing this blog!

Setting the scene

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I’m sitting by “Le Crayon,” the tower of Credit Lyonnais.

The David who wrote this journal was experiencing profound discomfort.  As a fellow in the University of Arkansas Sturgis Fellows program, I was strongly pushed to spend at least a semester of my junior year abroad.  My undergraduate advisor, Doug Rhoads arranged for me to visit the laboratories of Jean-Jacques Madjar at the University of Lyons, where Thierry Masse mentored my project.  The fact is that I did not enjoy “wet bench” research, and I was becoming concerned that my Biology degree could equip me for a career I did not want!  To complicate the matter further, we never formalized my visa to work in the laboratory for a year-long stretch, and so I needed to leave France well before even a semester had passed.  Scheduling this journey through many countries was my fall-back plan, and my mother was working with the University of Arkansas to get a formal plan in place for the spring of 1995.  In short, I felt that I was failing in this first real test of applying my academic skills.

If you mainly know me as a globe-trotter who uprooted his career and moved to South Africa, you might be surprised to know that as a young man I disliked travel, and I feared change.  Ask the members of Yates Lab how huge a step it seemed to me to move from Seattle, Washington to San Diego, California in the year 2000.  I spent six months poring over maps and dawdling over last details in Seattle.  To go back further in time, I was always the first member of the family to feel it was time for us to return to Kansas City when our family took long road trips in the summer time.  If you read the journal, you will see a David feeling perpetually out of place and coping badly with exhaustion and self-induced malnutrition because I wasn’t willing to spend enough money on food.

The most redundant feature of the journal is that the 20-year-old me was completely agog at the young women I encountered on my travels.  Although a disproportionate number of my friends since elementary school have been female, I must say that I was essentially undateable until my mid-twenties.  I would summarize by saying that I routinely put women on a pedestal and couldn’t see myself as desirable.  This aspect of the journal is high on my list of cringe-inducers.

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I had already given up cursive in college.

What should we call the nexus of judgmental, puritanical, dismissive, and obsessed with money?  I am reminded in this journal that the person I am today was distilled from common mud.  Today I am not immune from these traits, but I do try to improve myself with time.  I have been tagged with the label “stubborn” more times than I would like to admit, but I hope that I can manage open-mindedness and respect for others at least from time to time.  In particular, I struggled to read the passages I wrote about the Turks in Budapest or the drive-by racism I dumped on Latin culture.  At least I realized that smug American chest-thumping was not preferable.  My memories of myself from that time have been substantially white-washed, but my text makes it clear I had a long way to go.  In my memories of that time, I mostly remember that the international relations scholar from Turkey taught me that a bishop or a castle is generally more reliable than a knight in the chess end-game.

From 1994 to now

Travel in Europe today is considerably simpler than it was in 1994.  Moving from country to country is considerably easier because of the Schengen agreement that eliminates customs at borders between countries and the Economic and Monetary Union that makes the Euro the only currency you need for much of the continent.  The traveler’s checks that fueled my travel are not needed in Europe; instead, you feed your bank card into an ATM, and out pops money.  My single telephone call home from Vienna would be likely replaced today by Skype; I could use my phone or computer in the WiFi of any hostel to chat right away with folks at home.

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My account book, in many currencies

I wrote my journal narrative in a spiral-bound notebook, and I kept strict accounts of every franc, Deutschmark, schilling, crown, etc. in a separate small notebook, both of which I acquired while living in Lyon.  I was very fond of Pilot rolling ball pens at the time, and so each page is filled with cramped blue writing.

While my parents used 35mm slide cameras to capture my early years, I carried a 126 film cartridge camera made by Vivitar with me to Europe.  As you will see, many of the images I mention never made it to print when I developed those films, and the term “focus” does not really apply.  In three cases, I used Microsoft’s Image Composite Editor to stitch together multiple photos into a single panorama.

19940618 Lyon cathedrals photo06

The two most visible cathedrals of Lyon, France

Computer video has come quite some distance since 1994.  I originally recorded the video on an analog Sharp “Video8” camera.  When I subsequently upgraded to a miniDV camera, I was able to transfer the video from the old camera to a new one via an S-video cable; this process recorded the video in a digital format on the new tape.  I was able to transfer that digital video without loss to a desktop computer with a FireWire card.  To deinterlace and compress the section of video I’ve posted to YouTube, I used the “yadif” filter of FFMPEG:

ffmpeg.exe -ss 00:00:09 -i input.avi -vf yadif -t 00:45:05 -c:v libx264 -preset slow output.mov

With those comments in place, I hope you enjoy reading the journal, a project 23 years in the making!

Johnny Clegg: the Spirit of the Great Heart

I would not have expected that a man born in the United Kingdom would be able to teach me about being South African, but Johnny Clegg is no ordinary man.  Last night, he kicked off his “Final Journey” tour in Cape Town, and Natasha and I eagerly acquired tickets to be part of the event.  In a sprawling three hour concert, Johnny Clegg demonstrated the depth he achieved in nearly four decades of musical performance.

johnny-clegg-valenciennes-davidata-14_07_2009In the zodiac of musical performance, I would place Johnny Clegg in a constellation with Peter Gabriel, Paul Simon, and Cat Stevens (now Yusuf Islam).  Peter Gabriel and Clegg performed duets as part of the “46664” concert series against HIV/AIDS.  Paul Simon, of course, produced the amazing “Graceland” through his connection with South Africa, braving significant controversy to do so.  Yusuf Islam incorporated a Zulu-language chorus made famous by Clegg into his recent song, “Angel of War.”  Clegg may not have the same recognition as these artists in the United States, but in other parts of the world his star has shone more brightly.

Johnny Clegg was nicknamed the “White Zulu” for his love of the Zulu language, culture, and dance.  His mother (born in Zimbabwe) moved their family to South Africa when he was seven years old, and his South African step-father (a crime reporter) introduced him to the townships.  Johnny was taught to play guitar by the housekeeper of his neighbor, and his skills soon introduced him to Sipho Mchunu, an innovator of Zulu guitar.  When the two began performing together in the 1970s, they could only play informal venues due to Apartheid-era restrictions intended explicitly to keep people of different races estranged from each other.

A feature of Johnny Clegg’s career that fascinates me, in particular, was that he abandoned an academic career in order to pursue his musical career.  Earning his BA and Honours in Social Anthropology at U. Witwatersrand, he became a lecturer on Zulu music and dance.  When the popularity of his music with Mchunu produced the opportunity to tour, he took a sabbatical, thinking that he would be back in academia within a year.  Instead he launched on an altogether different trajectory.  He did not lose his love for anthropology, however.  In 2010, he presented a thirteen-part television series with the South African Broadcasting Corporation to explore the connection between the landscape and culture of the country.  This week I borrowed a copy of the DVDs for this series from the Stellenbosch University Library.  I can hardly wait!

The Concert

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Even a bioinformaticist can take a selfie!

Natasha and I arrived at the GrandWest Casino for his concert with approximately fifteen minutes remaining before the concert, merging with a heavy flow of traffic into the parking area.  I had driven past the Casino before but had never been inside.  It is quite the place!  Besides containing a full-size cinema and some of the largest fast-foot franchises I have seen for several restaurants, its Grand Arena can seat 5,000 people.  Of course, it also features a hotel and the casino itself.  We navigated through dense crowds of pedestrians past many young people with trays of goodies for sale.  I decided to purchase a memento from the “official merchandise” table.  For R200 ($15), I acquired a DVD of Johnny Clegg’s favorite Zulu street guitar songs and two CDs full of music.

I was not sure what to expect from an opening act described as “Indie Dark Pop,” but Tailor was pretty entertaining! Natasha and I kept changing our minds about whether she was American or Australian.  When Johnny Clegg’s band took the stage, though, everyone sat forward on their seats.  Since almost every song he sings includes Zulu lyrics, one might have expected an audience that reflects South Africa’s racial diversity.  With tickets starting at R325 ($25), though, the audience was almost entirely white.  Their incomprehension of the Zulu phrases in songs and spoken word was pretty apparent (I was in the same boat).

This concert was structured autobiographically, reflecting that this is Johnny Clegg’s final tour.  He was diagnosed with pancreatic cancer in 2015, which his doctors treated successfully with chemotherapy.  The singer will retire from public life after this tour (and one last album, currently being mixed).  As one might have expected from his reputation as a lively performer, though, Johnny Clegg seemed driven by a restless energy.  When he spun tales from his past between musical numbers, he paced back and forth like a beast in a cage.  His footwork while dancing showed no sign of tiredness, with only a fifteen minute break mid-concert to rest!  When the concert featured pantsula dance or traditional Zulu war dance, however, most of the performance was carried by young people (who had serious skills, by the way).  Johnny Clegg did provide a powerful demonstration that he can still do the moves of the war dance, however, and the crowd roared with approval.

The appeal

What is it about Johnny Clegg that has drawn my attention so strongly during my nineteen months in South Africa?  I would have to start with the shared outsider identity.  It matters to me that South Africa could embrace someone born elsewhere.  I take real delight in what I find in this country, and I want to know that others could see me as part of South Africa’s story, too.  Being “the American” has a limited shelf-life; I want to be seen for what I can contribute instead!

As I listened to Johnny Clegg’s words from the stage last night, he solidified some other reasons I had been drawn to his music.  In introducing “Kilimanjaro,” he talked about the importance of keeping a long perspective, even as the world is convulsed with a self-destructive phase.  The strongest resonance I felt, though, was reserved for “Great Heart.”  As long-time readers will remember, I grappled with language to voice why I needed to move to South Africa.  May I borrow some words from Mr. Clegg?

I’m searching for the spirit of the great heart
To hold and stand me by
I’m searching for the spirit of the great heart
Under African sky
I’m searching for the spirit of the great heart
I see the fire in your eyes
I’m searching for the spirit of the great heart
That beats my name inside
Sometimes I feel that you really know me
Sometimes there’s much you can show me

By coming to South Africa, I have discovered even more than I sought in coming here.  To be part of this country’s struggle touches something vital within me.  I appreciate Johnny Clegg for singing that truth!