Tag Archives: international

Dar es Salaam: peaceful harbor, thriving city

An index to this series appears at the first post.

Just as we cannot tell the history of St. Petersburg without Peter the Great, to tell the history of Dar es Salaam without Majid bin Said, first Sultan of Zanzibar, would be impossible.  In 1862, Mzizima was a fishing village beside an extensive harbor, populated by Swahili who had moved down from Somalia and Zaramo inhabitants who had come from further inland.  By 1879, many partially-completed city blocks had been constructed along the waterfront to form the nucleus of Dar es Salaam, the “harbor of peace.”  What would inspire the Sultan to invest so heavily in constructing a city from scratch?

From village to city

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Sultan Majid bin Said, from the British Library

Zanzibar’s economy thrived on two sources: transit trade and plantation agriculture.  The area that became Dar es Salaam incorporated the largest natural harbor in close proximity to Zanzibar.  The Sultan saw that a well-developed port could further boost the flow of goods from Sub-Saharan Africa into Zanzibar.  As his reign progressed, the attractions of a second home away from the constant strain of the court at Zanzibar also became apparent.  Sultan Majid passed away in 1870, however, leaving the sultanate to his brother Barghash, who had contested Majid’s selection as Sultan.  The second Sultan of Zanzibar was much more interested in developing the infrastructure of Zanzibar than he was in building a city on the continental coast.  A French missionary visited the city site in 1886 and had this to say:

Situated on the shore of its harbour, like an Arab woman in rags in the home of her former husband, Dari Salama appears to mourn its isolation and poverty. To the left, the palace of Said Majid is still to be seen, half concealed by mass growth… (Brennan and Burton, pg. 18)

Because Natasha and I had found a hotel close to the ferry terminal, we were quite close to the oldest structures in Dar es Salaam.  The “Old Boma,” constructed in 1866-1867, stands just opposite the ferry terminal.  Many British colonies in Africa constructed bomas as a single building housing government offices and police startions.  The building currently houses an organization dedicated to architectural heritage.  When I see the walking tours they made available, I really wish we had signed up for one or more!  Sultan Majid’s palace has been demolished, but an ancillary structure, possibly built to house his harem, evolved in time to house the “White Fathers” organization in 1922.

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Atiman House may have begun life as a harem, but now it houses missionaries.

Rebirth at the close of the 19th century

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A mission stands near St. Joseph’s Catholic Cathedral.

These older buildings were subsequently joined by two substantial churches that were for years the tallest buildings in the city.  A building that was once a mission has been repurposed as some sort of government building.  Quite close by we found St. Joseph’s Cathedral.  The foundation stone was laid in 1898, and the construction was completed in 1902. Just a couple blocks away one finds a rather different kind of church.  German missionaries constructed a Lutheran church at roughly the same time… and they used a Bavarian Alpine style!  It’s quite a striking departure from the Catholic design.

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The Azania Front Church was constructed starting in 1898.

Carl Peters, violent colonizer

If the Sultan of Zanzibar had turned his back on Dar es Salaam, what led to this growth boom at the end of the nineteenth century?  At this point we must introduce Carl Peters, a German colony builder who was largely responsible for the creation of “German East Africa.”  Representing his “Society for German Colonization,” he toured what is now Tanzania through 1884 securing “treaties” with leaders throughout the region.  He returned to Germany to found the German East Africa Company. He attempted to convince an initially unwilling Otto von Bismarck to grant him an imperial charter to transform these pieces of paper into an actual German colony.

The influence of Carl Peters on German East Africa was highly aggressive, first in the sense that he single-mindedly pursued more “treaties:” “most of [the Society’s] funds were absorbed by financing treaty-gathering expeditions” (Perras p. 113).  In the second sense, Carl Peters actively advocated for the use of violence to maintain control of the local citizenry.  He was apparently fond of asking “Haven’t you shot a negro yet!?”  It was in connection with Carl Peters’ efforts to achieve leverage in this region that Emily Ruete (sister of Sultan Barghash) returned to Zanzibar with a German fleet.  Peters’ heavy-handed aggression led to a late 1880s rebellion against the German East Africa Company which was overcome through use of the German military.  After that involvement, it was clear that the colony would be officially supported, and an 1890 treaty swapped territories between British and German areas in East Africa to reduce the tension between the two (Perras p. 168).

In other words, the last decade of the nineteenth century brought the “Scramble for Africa” to what is now Tanzania.  What the Sultan of Zanzibar had started at Dar es Salaam would be expanded upon by the Germans.  The church buildings I showed above reflect this area passing from Sultanate to German control.  World War I, however, brought a substantial shift in power.  The Treaty of Versailles stripped Germany of its African colonies, and France and Great Britain were the recipients (apparently returning the inhabitants to self-rule wasn’t a popular idea– that would wait until the independence movements long after World War II).

Today’s Dar es Salaam

In 2009, the World Bank estimated the population of Dar es Salaam as 2.7 million.  Tanzania has become the second most populous country in East Africa (after Ethiopia) with 40.4 million people.  The city is the economic centre of the country, even if the capital is the much smaller Dodoma.  In 2012, Tanzania’s national bureau of statistics reported that Dar es Salaam had reached 4.4 million out of 45 million; people continue to migrate to the city from the countryside to find work.

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The Port Authority (left) and twin towers (right) dominate the area near the ferry port.

The Dar es Salaam skyline has been changing dramatically in recent years.  The Tanzania Ports Authority (2015) and PSPF Commercial Twin Towers (2014) are the only buildings in Tanzania to exceed 150 meters in height.  The PSPF is the Public Service Pensions Fund for the country, while the Tanzania Ports Authority is a parastatal organization to manage the busy port of Dar es Salaam.  These are just the most visible examples, though; the tallest seven buildings in Tanzania were all constructed since 2010, and all were in Dar es Salaam!

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Zanzibar: transiting Dar es Salaam

An index to this series appears at the first post.

Preparing for our trip to Zanzibar looked straightforward on its face: nail down some flights and ferries, pick some hotels, secure a visa, and acquire some cash.  The route through these obstacles, however, was more complex than we had appreciated.

The preparation

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Flight path

I had first realized Zanzibar might be a good destination when I learned that the discount Mango Airlines flew directly to Zanzibar from Johannesburg.  Once we tried to square their flight schedule with our availability (starting Dec. 29th), however, we ran into problems.  Mango flies between JNB and ZNZ just twice a week, on Tuesdays and Saturdays (both directions on both days).  Once we combined the cost of JE926 and JE927 with a flight from Cape Town to Johannesburg, we were looking at a higher cost.  Instead, we opted for a similar flight on South African Airways: SA322/SA188 on the way north, and SA187/SA377 on the way south.  This flight pair, however, landed us in Dar es Salaam, Tanzania, rather than Zanzibar itself.  We would need to take the ferry to and from the island.  We decided to face the challenge of ferry tickets on the day we needed them.

First Rule of Travel: school holidays are when everybody travels.

We picked hotels during November 24-27th via Booking.com.  Even though we made our reservations a month in advance, it still seemed that a lot of our options were already out of space.  We decided on the Iris Hotel in Dar es Salaam for our overnight to catch the ferry (it’s a short taxi ride from the ferry terminal).  Our longest stay would be seven nights at the Riverman Hotel, located next to the Anglican Cathedral to the east side of Stone Town in Zanzibar.  This hotel was a bit of a compromise because it was relatively inexpensive but required sharing bathrooms with other guests.  We would wrap up with three nights in the posh Harbour View Suites at Dar es Salaam.  I supplied my credit card for all three sites.  Almost done!

Second Rule of Travel: don’t leave the visa for the last minute.

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image by adlerweb

My American passport meant that I needed a visa (Natasha was home free as a South African).  I realized too late that Tanzania has established only a high commission in Pretoria, not a consulate down here in the Western Cape.  On December 15th, I printed copies of our hotels and flight itinerary, a one-page visa application, and proof of payment ($100: Americans are required to get the more expensive multiple entry visa).  Along with two passport photos, I couriered all of these materials with my passport to Pretoria.  Then I waited… too long, in fact!  When I phoned the consulate on December 22nd, I learned that they’d long since finished the visa but were waiting for me to arrange pickup.  I called the copy shop to set up the courier, but I received the distressing news that SWE courier service was on holiday break and would not resume service until January 6th!  I panicked but lined up FedEx Express to retrieve my passport on December 27th.  I was quite panicky until I was able to retrieve my passport from the FedEx offices at Cape Town’s airport on December 28th for my flight on December 29th.

Tanzania is certainly a tropical country, and that meant we needed to think about disease.  Yellow fever and malaria are both rather unpleasant conditions endemic to the area.  Both Natasha and I visited the travel clinic for inoculations against yellow fever (receiving little yellow cards to provide as evidence), and we received stern warnings about mosquitoes, pledging that we would use chemical deterrents and stay securely behind mosquito netting at night.  Those little yellow cards would be required by immigration officials along the way.

The arrival

Our flights on South African Airlines were completely fine.  We were surprised at the smallness of the jet that brought us here from Johannesburg (an Airbus A320?), but it was one of the gentlest landings I can remember. I am very grateful to have acquired my visa in advance of the trip; it would have been possible to have acquired it at the airport, but things felt a little chaotic down there, and they dealt only in cash. We tried first one line for immigration and then for another, but an American family produced a twenty-minute delay on the first line, and an American woman produced a ten-minute delay on the other. In the end, they processed me through the Tanzanian citizen line, while Natasha completed immigration on the first booth where we’d stood in line.

We were both a little concerned about acquiring cash. My efforts to get Tanzanian shillings or U.S. dollars in Cape Town had been foiled when my bank required far too much paperwork for practicality (passport, visa to remain in South Africa, work contract, travel itinerary). I had visited a foreign exchange business at the Tyger Valley Centre, and they reported that Tanzanian shillings were available nowhere within South Africa!

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This sign meant my Mastercard was about to yield some currency!

We tried two different ATMs at the Dar es Salaam airport. The first was an NBC bank kiosk, and it simply wouldn’t allow any of our cards to withdraw cash. The second was a green and white CRDB bank kiosk, and that worked much better. I withdrew 200,000 shillings (the equivalent of $90 USD), and Natasha pulled a smaller amount.  Travelers definitely need to have currency on hand; the economy in Tanzania runs on cash.

The taxi drivers were on us like flies. They were sad to see us wandering to the tourist information booth to acquire a map. A taxi driver got behind the counter to help us. When he expected payment for the tourist map, we turned away and pursued a taxi option from the flock. We negotiated a rate for a taxi to the Iris Hotel (the airport is some distance southwest of the city center) from dollars to shillings; they seemed satisfied with 75000 shillings ($34). Our driver led us to a vehicle that looked like a Toyota Prius V, though it did not seem to be a hybrid.

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Our route from the airport did not allow for much creativity.

The drive to town in the fading sunlight was not particularly remarkable. Hawkers can be found at any intersection, and the pedaled ice cream carts were a nice touch. The industrial district looked friendlier than similar districts in South Africa, in part because of better landscaping but also because there were no shacks. Once we hit downtown, the traffic was more stationary, and then we turned off the road to a pitted dirt track leading through a night market, and then we were at our hotel.

A member of the hotel staff at the Iris volunteered to walk Natasha and me over to a local restaurant.  She and I used the tried-and-true “point and nod” approach to pick some beef-and-vegetable mix and some rice.  We enjoyed it thoroughly, though the meat was a bit tough to chew.  I wonder if this could result from traditional slaughter methods rather than carefully regulated municipal abattoirs.

Our guide, by the way, put a new spin on a controversy that had consumed Natasha and me as we prepared for the trip.  Was it “tan ZANE ee ə,” or was it “tan zə NEE ə?”  Our guide, however, provided a rather different answer: “tan ZAHN yə!”  Consider our worlds rocked.

Moscow: One last bit of wandering

An index to this series is found on its first post.

November 2, 2017

The last day in any place is always bittersweet. I want to be home, but I don’t want to waste the opportunity of time in another place. My responsibilities in that place have ended, but my email threatens to enchain me as soon as I return home. Of course, the thought of my loved one at home makes me weak in the knees! I tried to be realistic with my plan for the last day, but reality had a few surprises in store for me.

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A view of “Moscow City” from my hotel room

Ditching the luggage

Saying farewell to the Korston Club Hotel was no challenge. I would not have to hold my breath to avoid the smell of smoke as I exited my non-smoking room. I would not have to endure more self-promotional posters on every surface. Most of all, I would not have to listen to more of their advertising jingles in the elevator. After a heavy breakfast at their buffet, I strapped together my 26 inch roller back, my backpack, and my laptop handbag and rolled across the street to the park. The weather had finally changed from drizzle to clear skies, but that also meant the temperature had dropped. I rolled down the paved road to the metro stop and bought metro tickets.

To start the day, I navigated to Paveletskaya, the train station in SE Moscow from which I would catch the Airport Express train to DME airport. I had realized only the night before that I was leaving through DME rather than SVO. I’m awfully glad that someone at the conference asked me to confirm the airport! Paveletskaya required me to switch between the red train and the circular brown route, and this time I was doing it with all my luggage in tow. I hit some runs of stairs that were less than pleasant, given all the gifts that now occupied my bag. In any case, I was at the train station pretty quickly (despite having gotten on the brown line in the wrong direction at first).

Obviously I didn’t want to tow all that freight throughout the day, so I found the luggage storage office. I panicked at first because I passed one that had obviously been out of operation for years. Once I reached the right place, though, I learned that I needed to show my passport and pay 270 RUB in cash to leave each bag. I swallowed my pride and shoved my laptop back into my backpack, surrendering only the roller bag. Now I was free for more ambitious navigation! I hopped the green line into the city center.

My plan: the Kremlin

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No, Marx has not been exiled from Moscow!

My goal was pretty straightforward. Since my flights to South Africa began near midnight, I had the entire day to play. I would enter the Kremlin to see the classic buildings inside! I popped out at the (Bolshoi) Theatre exit. I paid my respects at the statue of Marx in its square. As I walked past the State Historical Museum, I heard a loud voice advertising its neighbor, the 1812 War museum (when Alexander I faced down Napoleon’s troops). I continued with steadfast determination.

Next, I saw the line for Lenin’s tomb. It seemed I might get through in an hour or so. I passed onward to Red Square and gazed again at St. Basil’s Cathedral. Hadn’t I seen an entry to the Kremlin on this side? I could not see where I could enter.

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It is hard to photograph St. Basil’s without a mob of people!

In any case, I thought I should probably plan for lunch before going in so I would be fully fueled for exploration. I walked past the GUM mall again, this time to the block on its side away from Red Square. I saw a few churches, but it seemed I had moved substantially away from the tourists. I found a pleasant restaurant for lunch, and I lingered over a meal of eggplant casserole, flower tea, and bread. I have been re-reading the “His Dark Materials” trilogy from Philip Pullman, so I read for a little while. The restaurant played an album of covers by a band with a mellifluous tone. It was surprising to hear a soothing version of “Seven Nation Army” by the White Stripes. I wondered if I should tell the waiter of the time I was driving in a parking lot when Jack White jaywalked in front of me.

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Tomb of the Unknown Soldier

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My father in the late 1960s

Now fed, I was ready to enter the Kremlin! I entered a set of gardens on the northwest face of the fortifications. I paused respectfully at the Tomb of the Unknown Soldier. I looked at the soldiers standing guard and reflected that my father might have played some similar role during his time as an Honor Guardsman in the U.S. Army. I continued on my way, seeing raised places in the marble sidewall to represent particular cities in Russia that were home to particular struggles, such as Stalingrad. Of course, the names were written in Cyrillic lettering, challenging my ability to sound them out. After two weeks in Russia, I found it a lot easier to sound out many words, though some of the complex sounds stubbornly resisted my efforts to memorize them.

I reached the bridge for entry to the long axis of the Kremlin at last, but something was wrong. The staff entrance was live, but tourists could not enter. Instead, I saw a signpost indicating that the Kremlin was… CLOSED? I was uncertain whether the change reflected an ordinary Thursday or was due to preparations for the century anniversary of the October Revolution (which is in early November, by the modern calendar).

Well, figs!

Interlude: Dave attempts an alternative plan.

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This baptism from a millennium ago has had far-reaching consequences.

The sunlight was lovely, and even though the breeze was cool, I decided to continue to the massive statue of Vladimir I that I had seen from the far side of the road a few days ago. It did not disappoint at close range. It has very dramatic detail, and some trick with his eyes makes them seem to peer right at the observer. I was able to examine the panels of relief behind him, and I saw that his baptism as a Christian was certainly the aspect of his rule that the monument celebrated. I encountered an Indian tourist, and he and I took photos for each other. He mentioned that the museum of 1812 was pretty interesting. I looked to the south and saw the massive church with five golden spires at the side of the Moskva River, another tourist site I had considered for the afternoon. I turned my back and walked the length of the Kremlin back to the 1812 museum.

It was closed.

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Spoiler: Napoleon withdrew his troops at great cost!

In the absence of a plan, Dave improvises.

I wandered a bit in the area beyond the museum. I knew it was an area that offered interesting shopping, so I pushed into those neighborhoods. I asked a shopkeeper about bookstores in the area, and she pointed me up the road on the opposite side. I’d found her suggestion approximately a block and a half later. The shopkeeper greeted me by replying that she had no books in English. I pointed to one on the table and suggested that I’d enjoy taking a look. She shrugged. My interest in the shop grew as I realized she had large-scale posters from the Soviet era hanging around the upper shelves. I found books of smaller versions, but no poster tubes. Her shop seemed to have a fair number of history books, but of course they were in Russian. In the end, I found three books that I wanted, at “non-tourist” prices:

  • A book of fairy tales by Pushkin, one of Russia’s favorite authors
  • A book detailing the life of an American who served as a nurse in Siberia during the Russian Civil War
  • A book showing postcards from a variety of Russian cities in the nineteenth and twentieth centuries

As my brother might once have exclaimed, “SCORE!” I was ready to check out when the sales clerk uttered that word that brings so much terror to the visitor: “Rubles.” No, my credit card had no value. Happily, the nearest bank was within sight.

I realized on my jaunt to the bank that the neighboring shop was also a bookstore. I found the copy of Lonely Planet’s Russia for 1800 RUB (just over $30). That might have seemed a better deal before this trip. I considered getting their “Eyewitness Top 10” for Moscow (I liked the St. Petersburg one), but I was again out of cash. In any case, this shop had piles of English-language books, but they were almost all paperback. I moved on up the street.

Sharing Lubyanka with filmmakers

Just like that, my feet had returned me to Lubyanka Square. The memorial service was a memory. The center point of the service, a stone set in the square to remember victims of political executions during the Soviet Era, was surrounded by red flowers (chrysanthemums?) and bottled candles. I was reading its sign when a young Russian asked me if I could move to the side. He and his cinematographer were filming an older gentleman, relating his narrative about (one presumes) a friend or relative who died during the Soviet Era. I didn’t have anything in particular to do, so I sat at an out-of-sight park bench to watch their work.

It seems that the director was adopting a cue-and-response interview. Occasionally they would stop the older gentlemen, re-set to another camera angle, and then restart. The gentleman seemed to be willing to humor them, even shooting some “B-Roll” of his wandering in an arc around the stone monument. From time to time, the older gentleman or the producers would shoot an eye in my direction. Given the location (in front of the KGB building) and the presumed material, I realized they may be concerned that I was watching them for reasons other than my whimsical nature. While the cinematographer modified his equipment, I asked the director to capture a photo of me with the stone.

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This Solovetsky Stone is partner to the one I saw in St. Petersburg.

Starting my journey south

With that, I had no other plan but to return to the rail station, acquire an Airport Express ticket (500 RUB) and rescue my luggage. All of that went smoothly. The Airport Express run was really smooth, taking around 45 minutes from start to finish. The train dumped us essentially across the street from the airport terminal entrance, so the worst part was dealing with everybody’s desire to rush off the train at once!

Once at the airport, I had more than an hour before boarding passes would become available, so I ran for some dinner upstairs, then returned to the line for Emirates Air. I hadn’t checked in online from my hotel this morning, and I got a nasty surprise when I arrived at the desk. They could not immediately give me a seat assignment, and the flight was oversold! I waited two minutes in a bit of a sweat where the agent could see me. Happily, my suspense ended very rapidly and she handed me two boarding passes. I had what looked like a middle seat on the way to Dubai (the shorter flight), but I discovered that it was the emergency exit row, with nobody to my left! I was on the aisle for the long leg to Cape Town. After passing through immigration, baggage, and customs, I returned to the arms of Natasha.  That feeling spells “HOME” for me!

 

The birth of a new conference

An index to this series is found on its first post.

November 1, 2017

How does a new conference enter the academic calendar? I was encouraged by the example set by the Clinical Proteomics / Post-Genome Medicine meeting (ClinProt 2017), and I thought it might be useful to talk about some of the things that the group did really well, while relating a bit of what unfolded for me in my last day at the conference.

Logo_BGRS-shrinkFirst off, this is far from the first meeting to take place in Russia on the subject of human proteomics. The Russian Human Proteome Organization has been operating since 2002, and it sponsors two distinct meetings yearly. The main meeting takes place in the city of Kazan each October. Members who are particularly interested in bioinformatics may participate in an annual meeting at the city of Novosibirsk (Bioinformatics of Genome Regulation and Structure / Systems Biology). The RHUPO has also successfully organized a big event for the world HUPO; in 2009, Dr. Alexander Archakov hosted the third Human Proteome Project Workshop in Moscow!

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Human Proteome Project, Moscow (2009)

The ClinProt 2017 meeting seemed special in that it sought to foster connections among many different institutions within Russia; the program was salted with several investigators across Europe and the broader world, but the emphasis seemed to be on developing networks within the country, including multidisciplinary links. As I look across the eleven-member organizational team in the conference program, I see five different research institutions, all in Russia, represented by post-doctoral scientists. This team of junior researchers will all have valuable experience for the future, and senior scientists who attended the meetings will remember who they could rely upon when trying to solve a last-minute problem before a talk!

I would catalog several things, then, that the organizers did right:

Skin in the game
Because several institutions contributed organizers, more schools sent speakers, poster presenters, and trainees. In total, 350 people registered, and 274 attended. That’s pretty great for a first conference!
Personal touch
Several speakers mentioned that they had been recruited by an organizer who knew them from prior contact. Since professors frequently get spammed by for-profit conferences, these personal contacts made a difference in getting the names they wanted for the meeting agenda.
Detail focus
I heard several of the organizers quietly worrying about whether something was going to go just right. Throughout, it was clear that each person knew what his or her responsibility included. The team was definitely committed.
Industry works
I occasionally hear academics sneer at the inclusion of instrument and reagent vendors in speaker rosters, but their participation in a meeting adds more than just money. I was glad to see a representative from Helicon lecture on the value of CyTOF for cell counting applications, since I am mentoring a student working with such data.

I became aware that we had some special guests today as I lingered in the speaker ready room. Several people in suits made an appearance. I had a rapid conversation with Sergey Suchkov, an M.D. and Ph.D. who has a relentless energy about him. He has a strong interest in developing relationships among BRICS nations in the field of “precision medicine” (sometimes called “personalized medicine”), and he wanted to talk about some possibilities between South Africa and Russia in that space. We agreed to touch base this afternoon when he could introduce me to another M.D. Ph.D. friend of his who has become involved in genome bioinformatics. That meting put forward some interesting possibilities in tuberculosis, which has become problematic in the Russian prison system. I hope we will be able to define some projects we can pursue together in this space.

Right away, though, I had to leave our discussion to teach my afternoon workshop on performing post-hoc quality control assessment in large-scale proteome projects. I was very grateful that the conference organizers could add a link to their website so that participants could download the R statistical script and input files for the workshop directly from the link above. That way the conference attendees who needed to leave Moscow early can still get access to the tutorial.

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Image from my paper with Xia Wang introducing “IDFree” metrics

This was my first time to teach a workshop on quality control. My normal curriculum has emphasized protein identification or the recognition of post-translational modifications. Since I am now chairing the HUPO-PSI working group on quality control, though, it was a good time for me to put together some training materials in this space. I chose a highly visible data set, the 1425 LC-MS/MS experiments that the Vanderbilt team produced from colorectal cancer samples for the National Cancer Institute CPTAC program. The workshop would focus on recreating figures that Xia Wang at U-Cincinnati had scripted in the R statistical environment from tables of QC metrics that my team had generated.

I was really pleased with the dozen or so students who attended the workshop. Their questions were very good, and their understanding of the statistical concepts was at a very high level. To give one example, a student asked how differently the files would have spread in my plot of the first two principal components if we had used ordinary PCA rather than robust PCA. Another asked how hierarchical clustering would visualize these data in principal components space. These are not the questions one encounters with people who have never seen PCA before!

So color me impressed. This meeting ran like clockwork, and the students came ready to learn. The speaker list did not have some of the biggest names in world proteomics, but in fact I trusted what I was hearing more because it came from investigators who had worked at the bench more recently. I am of course grateful for the time I’ve been given to see Russia first-hand, but in the end I was brought here to teach and to learn. I enjoyed both missions!

 

Feeling very far from home

An index to this series is found on its first post.

October 31, 2017

I think professionals of all sorts are often surprised by the ways in which emotion can invade their work lives, and scientists are no exception. On October 31st, I found myself struggling to come to terms with being in Russia on a day when the first indictments were announced in response to the Russian government’s intervention in the most recent U.S. presidential election.

I have read before that jet lag is difficult to distinguish from a combination of exhaustion and dehydration. On Halloween I asked myself why I found it so hard to be productive at the ClinProt 2017 meeting. The answer, I think, was a combination of exhaustion and grief. The exhaustion is easy to explain. I left from South Africa on October 19th, so the 31st marked my twelfth consecutive day away from home. Even if much of my trip was vacation time, I tend to use a lot of energy on my vacation days!

Why would I be feeling grief, though? Some of it stemmed from the loneliness of being away from Natasha and my friends in Cape Town. I also felt a pang at spending the day in a place that doesn’t celebrate Halloween with the enthusiasm we do in the United States. The principal push, though, was a sense of loss from the unraveling of United States institutions.

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Public Domain image of Robert Mueller, III

Around twenty-four hours ago, Special Investigator Robert Mueller announced that George Papadopoulos, a foreign policy advisor to the Donald Trump presidential campaign, had admitted guilt in lying to the FBI. He had attempted to hide the fact that he made several attempts to connect the Trump campaign with his contacts in the Russian government. Two “bigger fish” in the campaign, Paul Manafort and Rick Gates, have been arrested and are now facing twelve charges ranging from conspiracy against the United States, money laundering (apparently attempting to hide the fact that they had been paid by the Russian government), failing to disclose the fact that they had been paid by foreign governments, and making false statements to law enforcement.

I think most of my readers have inferred that I disagree with almost all of President Donald Trump’s actions since taking office. I would really like to believe, however, that he thinks his actions are what the country actually needs. I once heard that Alberto Gonzales, previously the Attorney General under George W. Bush and now the Dean of Belmont University College of Law in Nashville, claimed that no President of the United States could ever take an action that he (or she) believed would hurt the country. To the contrary, it seems obvious to me that President Trump has behaved in ways that are already hurting the United States. Just the same, I have wished that President Trump believed his actions are justified and appropriate. The fact that two people so close to him face charges of conspiring against the United States erodes my hope that President Trump actually wants what is best for the United States.

Of course, we have known since January of 2017 that the United States intelligence community believes it has proof that Russia intervened in the U.S. presidential election. My sense of this claim is that it takes at least two forks: 1) The Russian government wanted U.S. citizens to feel less faith that its elections were fair, and 2) The Russian government wanted the undermine Hillary Clinton’s reputation to diminish her standing if she were able to win the election. When I was planning my trip to Russia, I had to ask whether I was willing to visit a country for which the government would attempt such an influence.

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An image for high school classmate Jason P. from “Rocky IV”

I decided that the people whom I would meet in Moscow had no part in such an attempt. I know that the scientists here already must deal with challenges in acquiring equipment because United States laws place special restrictions on exports to Russia. My goal in coming here is not so different than my goal in conducting research and mentoring in South Africa, really. I want to see the community of researchers throughout the world become more adept at retrieving information from their data, seeing that their clinical research aims are just as intended for the betterment of humanity as my own are.

1412867676245I have said before that I am a Global Citizen. For me, this means that where I see public health threats, I want to place my research efforts on the other pan of the scales. It means that the suffering of a person counts the same no matter the color of his or her skin, his or her gender, his or her religion (if any!), and his or her nationality. I believe that all the life of planet Earth is worth protecting. I sure hope that Earth’s governments will help rather than hinder that mission.

 

Clinical proteomics in Russia and my last pair of pants

An index to this series is found on its first post.

October 30, 2017

At last the first day of ClinProt 2017 had arrived! I set aside my now-muddy pairs of jeans in favor of my fresh and clean blue dress pants, laced up my shiny black shoes, and put on my enthusiastic green shirt. With a spot of breakfast downstairs (on my third morning eating there, I found that the milk jug was full for the first time!), I was ready to meet with the others for a shuttle van ride over to the conference.

Moscow traffic at 8:20 AM is a bit intense. The drivers here are a bit more careful of road laws than I have seen in other countries, but they still produce some pretty creative merges in their traffic jams. What would have been a few minutes on the subway was more like a half hour on the road, but my dress pants were still pristine when we arrived at the Congress Center at the I.M. Sechenov First Moscow State Medical University. The facility had a lovely central hall, with a graceful split staircase to the two main venues for our meeting. I hadn’t seen lecture halls in which an array of nine HDTVs replaced the more typical projector. It certainly produced a bright image, though the borders between screens were distracting.

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Why project when you can emit?

The Clinical Proteomics 2017 meeting was organized because a confluence of groups wanted to consolidate researchers in this country. EuPA, the European Proteomics Association, helps to integrate activities that span national proteomics societies. The Russian Human Proteomics Organization (RHUPO) sought to foster a sense of community among Russian research groups in this area. The Sechenov First Moscow State Medical University was happy to contribute a venue for the event, and many instrument, reagent, and other vendors agreed to take part, as well. I haven’t learned the total count of attendees yet, but I know that there are 87 research posters. For a first effort, I think it is clear that a great many things have gone well.

From the very first talk, it was apparent that Russian clinical proteomics researchers are grappling with challenges that became familiar to me as part of the National Cancer Institute (NCI) CPTAC program. Anna Kudryavtseva discussed her efforts to reconcile proteomics data with those that had been produced by NCI The Cancer Genome Atlas (TCGA), working in a particular sub-type of head and neck cancer. Prioritizing genes that were more frequent targets of mutation in tumors has value for understanding which proteins are most useful to monitor closely, for example. It was a great “plenary” (all attendees) talk to kick off these discussions.

As soon as we split to multiple sessions, I was on duty. I co-chaired the “Genomics and Beyond” panel with Sergey Moshkovskii. It was a bit odd to be fielding this panel while the Protein Informatics workshop was taking place in another room (that topic has been my bread and butter for two decades)! In this case, however, Sergey and I were not only chairing the session but also leading it with our two lectures, both in the field of proteogenomics.

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Photo credit: Olga Kiseleva

I defined the term by saying that we want to improve our interpretation of genomic data by integrating proteomics data, and we want to improve our interpretation of proteomics data by integrating genomic data (I was trying to be ecumenical). From there, I led the group through the new paper that I’ve published with Anzaan Dippenaar and Tiaan Heunis, in which we demonstrated our ability to recognize sequence variations and novel genes in Mycobacterium tuberculosis “bugs” that had been isolated from patient sputum in South Africa. Sergey followed up by finding evidence of RNA editing in fruit flies.

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Photo credit: Olga Kiseleva

The other speakers in the panel were also quite interesting. Matthias Schwab was visiting from Germany, and he educated the group on the current status of the field of pharmacogenomics. Vladimir Strelnikov, a geneticist, described the value of bisulfite sequencing for measuring DNA methylation in breast cancer. Sergey Radko outlined a SISCAPA-like strategy for using “aptamers” to enrich proteins prior to Selected Reaction Monitoring. Artem Muravev closed out the session to discuss the challenges of biobanking. This last talk was delivered in Russian, so I benefited quite a lot from real-time translation to English by Anastasia, one of two translators fielding our session (during my talk, she had been translating my words to Russian as I worked through my slides). Finally all the speakers came together for fifteen minutes of question and answer. I tweaked our pharmacogenomics speaker a little bit by saying that even if we had the complete sequences for every human on earth in our hands today, personalized medicine would not have arrived!

With the morning complete, everyone adjourned to a nearby restaurant. I was a little leery when I learned our destination was the Black Market, but I needn’t have worried; we wandered down the street to a lovely restaurant named “Black Market.” I had the Black Market Burger and felt thoroughly happy. I felt very grateful that the European Proteomics Association picked up the bill for that morning’s speakers!

Back in the conference, I enjoyed hearing my long-time friend David Goodlett discuss his long-term monitoring study of diabetes. He’s a careful guy, and it is good to see that he can make label-free proteomics sing in biofluids (a tough space to work), recognizing protein pairs for which expression can flag the onset of disease. It’s very reminiscent of the kind of study Stellenbosch University has produced in the space of tuberculosis. Our next speaker returned to the subject of biobanking, and he delivered his talk via Skype, not my favorite format. I am a big believer in contact with my audience.

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Did I mention it was my enthusiastic green shirt?

I threw all my remaining energy into the poster session. Interacting with researchers at the start of their careers is very rewarding, and people who stand beside their work without knowing whether or not anyone will take interest have a hard job. These students were even braver, since they were prepared to defend their work in English!

I started with a poster very near and dear to my heart. A.V. Mikurova was evaluating the different levels of sequence coverage achieved by database search (Mascot, X!Tandem) and de novo algorithms (PepNovo+, Novor, and PEAKS) when working with 27 LC-MS/MS experiments for a defined mixture of human proteins. We discussed the relative unresponsiveness of sequence coverage as a metric for performance evaluation and the challenge of ensuring the algorithms had comparable configuration. I asked S.E. Novikova about her choices of statistical model for a time-series measurement of proteomes in response to all-trans retinoic acid. I hope my statistics lectures online will be useful to her, though it sounds like she’s already on the right track. N.V. Kuznetsova taught me a few things I didn’t know about celiac disease! She had been evaluating the ability of Triticain-Α to degrade the most immunogenic peptide of gluten-family proteins. Finally, J. Bespyatykh was presenting a poster on the proteomics of Mycobacterium tuberculosis from a strain called Beijing B0/W148. Her work obviously had a strong relationship to what Tiaan and Anzaan had published with me, so we had a great conversation about the work. I hope we can help her find a sequence database that is a more ideal fit for her proteomes than the generic “H37Rv” protein database. I was really pleased to speak with so many students about their work at this meeting.

With that, I slumped onto a wall and didn’t move very much. The other conference attendees had flowed back into the conference room for an afternoon round of talks. I let my mind wander for a bit, though I did have some nice conversations with the vendors. Soon, though, I heard some odd noises echoing through the entry hallway. Was there a music practice room somewhere in the building? Was that a tuba?

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Dixieland music in Moscow! Photo credit: Olga Kiseleva

My questions were answered when I eventually joined everyone downstairs for a catered closing reception. The organizers had invited a Dixieland band to perform for our reception! The group was really solid. I particularly liked one of their trumpeters, since he had a smooth Chuck Mangione vibe going on. I kept recognizing songs only part of the way, since they were singing many of the lyrics in Russian! I finally got a solid hit on “Mack the Knife!” I sat up close to enjoy the show.

With the evening at an end, I declined invitations to go hit a bar and walked to the nearby Frunzenskaya subway station. Two stops later, I was in my neighborhood. I trudged up the paved driveway to the street with my hotel. As I awaited the green light at my last crosswalk before the hotel entrance, a car drove too close to the curb where I was waiting, and dirty rainwater soaked my last clean pair of pants.

 

Moscow: “Forgotten” monuments

An index to this series is found on its first post.

October 29, 2017

During the last day before our conference opened, I decided to go in search of monuments from the USSR, buried within today’s Russian Federation. The Moscow City Council decided in 1991 to move statues of Communist luminaries to the Muzeon Park of Arts. I wanted to see this collection in hopes of visiting a bête noir from my days of reading spy novels! I found more than I bargained for.

Reaching the Muzeon Park was not terribly difficult. The Red Line of the metro ran directly from my hotel to the “Park of Culture” stop. From there, I needed only to walk across the Moskva River bridge (a sales clerk got me pointed in the right direction). Two big attractions drew my eyes even while I was crossing the bridge. The first, a kilometer to my northeast, was a monumental statue larger than any I had ever seen; I’ll tell you more about that in a minute. The other was a massive Communist-era gateway to the south of the bridge on the eastern shore. It provided the entrance to Gorky Park, a massive Central Park including massive gardens and amusement rides for kids. My goal, however, was the set of gardens on the north side of the road, surrounding the Tretyakov Gallery on Krymsky Val.

I was glad to see that entry was entirely free. At first, I was concerned I had come to the wrong place. The statues that I saw at first met Communist ideals, but they weren’t figures I recognized. Once I reached the area to the northeast of the gallery, however, that changed in a hurry.

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Be cautious of true believers. Iron Felix

He was standing tall, high on his pedestal, looking just as I expected. Felix Dzerzhinsky was sculpted to look absolutely assured in his convictions, wearing a full-length trench coat that was modeled almost like a holy robe. For years after its creation in 1958, this statue stood in Lubyanka Square, here in Moscow, just yards away from the KGB headquarters. The statue is so famous that it received a name of its own, “Iron Felix!”

Why would this aristocratic ethnically Polish man, born in Belarus, be so commemorated? Dzerzhinsky created the Cheka, or Soviet secret police, in 1917, and he remained at their helm as they were renamed the GPU (state political directorate), until he experienced a fatal heart attack in 1926. During the Russian Civil War (1917-1922), he was responsible for the execution of tens of thousands without trial. His statue in front of KGB headquarters sent a clear message about the state’s willingness to use lethal force against its own citizens.

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“Uncle Joe”

“Felix” is not alone in this park, though. Josef Stalin appears there in a 1938 granite statue by S.D. Merkurov. His nose seems to have been chipped off in its relocation. I suppose that being a megamurderer will leave some hard feelings.

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V.I. Lenin, architect of the “Stronghold of Peace”

Of course Lenin has statues all over this part of the world. The “Young Lenin” statue from the 1970s seems the most charming, especially given its location next to “USSR, the Stronghold of Peace” in aluminum. Marx and Brezhnev are also nearby. I thought I might find Kalashnikov (rifles) or Mikoyan and Gurevich (MiG aircraft) in the garden as well, but I did not. I did, however, see Mikhail Frunze, a 1920s minister of defense for whom an academy for general staff officers was named.

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This monument to the Russian navy is not subtle.

The monument that towers above it all, however, is the almost otherworldly in its scale. To celebrate 300 years of the Russian Navy, a 98 meter statue of Peter the Great in steel, bronze, and copper was erected on the Moskva River. I was surprised to learn that it is only the eighth largest statue in the world (large Buddhas dominate that list). For comparison, the Statue of Liberty is 93 meters. It appears that Muscovites are less than satisfied with this monument, though. Remember that Peter the Great built St. Petersburg to be his capital rather than staying in Moscow!

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The artist and his work

I lingered in the park to peruse an open-air market of oil paintings. The artists were there to discuss their work, though many were not comfortable in English. I had a good conversation with a gentleman with leonine grey hair. We discussed different styles in which he had tried painting (small canvasses, rich in detail, larger formats in impressionism, etc). He had a lot of feelings about the architecture of St. Petersburg and that of Moscow. He showed me two paintings side-by-side to compare the styles. One of them really caught my eye, showing a nineteenth century view of a Moscow neighborhood with the sun angling low in the sky as people move cargo through the streets on sleds. It is captured in an impressionistic style on a 30x40cm canvas. We talked about the price, and I decided to purchase it, even though it was a bit costlier than I might have liked. My birthday is coming up. Natasha reminded me I’m allowed to bring home goodies for myself, as well!

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Federal Security Service headquarters

A misty drizzle had begun to fall, and I had to ask whether or not I had the energy for more touring. I opted to continue my journey up to the Lubyanka stop of the red subway line. When I exited the metro, I had a bit of an oppressive feeling. Some of it came from a memorial being held in Lubyanka Ploschad near another Solovetsky Stone like I had seen in St. Petersburg. In South Africa, memorial services can be rather raucous, and I wanted to stay clear of anything of the sort here. It was important, though, to see this square where Iron Felix had stood so long. It’s certainly not marked as a tourist attraction, but the old KGB headquarters is right there on the northeast side of the square, though now it serves at the offices for the “Federal Security Service.”

I walked past the building toward the theatre district. I found a cafe with the silly name “Му-Му” and a cartoonish cow out front (it’s pronounced “moo moo”). I ate chicken noodle soup, pork lasagna, fruit juice, and even a piece of carrot cake to shake off my doldrums!

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the famed Bolshoi

From there, I simply walked. I passed the famed Bolshoi Theatre, then walked the loop passing counter-clockwise around the Kremlin from there.

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Mikhail Lomonosov is like Ben Franklin, only Russian!

I spent a moment with the Mikhail Lomonosov monument in front of the old building for the Moscow State University. Having seen his likeness twice in both St. Petersburg and Moscow impressed me on his legacy here!

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He authored “The Idiot,” but he was far from being one himself!

I passed the Russian State Library, enjoying the statue of Dostoevsky but wishing the pigeon would nest somewhere else. I wondered why I had seen this author twice but hadn’t seen any sign of Tolstoy.

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Vladimir I (956-1015)

Near the south end of the Kremlin, I encountered the massive monument to Prince Vladimir, the ruler who brought Christianity to the Kievan Rus’. The people in the photo cannot even get their heads at the level of his toes!

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What a great spot for an “I’ve been to Moscow” shot!

I continued across the Moskva River, thinking that I would get a nice view of the entire Kremlin complex from there, and I was right! A bump-out on the bridge is perfectly positioned to showcase the Kremlin towers, the Cathedral of the Annunciation, and the State Kremlin Palace. After I photographed a family for their camera, they agreed to photograph me, and I am thrilled with the result.

Even though it was only three o’clock in the afternoon, I felt that I’d walked in drizzle quite long enough. Time for a nap at the hotel!

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