Tag Archives: biography

ASMS 2018: Exhilarating and exhausting

The American Society of Mass Spectrometry annual conference represents my one sure visit to the United States each year.  What is it about this meeting that keeps bringing me back across the Atlantic Ocean?  What makes this gathering feel like an academic home?

Early Days

My first encounter with ASMS took place in 1998, when I attended the annual conference in Orlando.  During this and other early years of the conference, I made it my goal to eat only free food during the four days of the conference.  I remember ice cream breakfasts from a vendor at this first meeting!  Being notoriously frugal did my waistline no favors, but then I was skinny as a rail during graduate school.


Prof. Pevzner, from his early days as a Wild West sheriff

My Ph.D. project involved the creation of a automated sequence tag inference engine from low-resolution tandem mass spectra of peptides.  That meant I had one particular talk on my agenda for ASMS 1998.  I listened with rapt attention to talk WOF 3:10 given by Pavel Pevzner (then a scientist at Millennium Pharmaceuticals) describing his SHERENGA software: “Automated De Novo Peptide Sequencing.”  I remember introducing myself to him after his talk.  When I mentioned my project, I remember poking in that we were competitors!  I was a frightfully competitive guy back then.  I am grateful that Pavel let the comment pass; in the two decades since that meeting he and I have become friends.

I feel I must mention ASMS 2004, the year that John Yates, III won the Biemann Medal, which I consider to be mass spectrometry’s highest award.  The conference was held at Nashville, TN, which was lovely given that I was a post-doc at Oak Ridge National Laboratory, just four hours down the interstate.  I arrived at the conference to learn that Steve Gygi, a friend of mine from graduate school, had played an epic prank on John and me at one of the preliminary meetings.  A student of his had captured a video of John and me encouraging people to get out onto the dance floor at a Keystone Symposium.  Steve had used the video in a research talk to show that while John was an expert in biochemistry, analytical chemistry, and bioinformatics, he couldn’t dance!


…of which the less said, the better

Professional Integration

To attend a yearly conference is one thing, but becoming part of its organization is quite another.  After I joined the faculty of Vanderbilt University in 2005 as an assistant professor, I decided that ASMS was the organization that felt most like “home” to me, and I began paying my dues yearly rather than haphazardly on the years I planned to attend the conference.  I became familiar with a growing number of its luminaries, both through the senior scientists with whom I collaborated and through smaller meetings, such as the Association of Biomolecular Resource Facilities and the United States Human Proteomics Organization.  Happily, I gained a reputation as an energetic speaker who could make mass spectrometry informatics seem more approachable.

My three biggest public roles within ASMS have all been drawn from the field of mass spectrometry informatics.  I feel deeply honored to have twice selected the speakers to appear in panels on the informatics of identification.  My second big involvement was with the Bioinformatics Interest Group.  After the main panels on each full day of the conference, ASMS features workshops for interest groups, running from 5:45 to 7:00 PM.  Since the conference attendees tend to exhaustion after such busy days, the workshops function best when they feature passionate speakers that interact quite a lot with the audience.  I am certainly not ashamed to stand outside the meeting room, inviting absolute strangers to join our group!  I enjoyed my moments as Donahue, running between different members of the audience with the microphone.

My biggest engagement, however, has been a long-running ASMS short course.  In 2011, Alexey Nesvizhskii, Nuno Bandeira, and I offered “Bioinformatics for Protein Identification” for the first time.  In this two-day short course (on the Saturday and Sunday preceding the conference), we introduced the algorithms that enable protein identification for newcomers to proteomics.  Happily, the course drew a good response, and we have now run the short course for eight consecutive years!  It’s a lot of work, and it makes each ASMS visit six days rather than four, but I really draw a lot of satisfaction from working with the participants.


The 2018 class

ASMS 2018: San Diego

What made this year such a busy program?  I would start with the fact that I completed my Ph.D. at San Diego, and I had many friends to visit while there!  I was very grateful to visit with friends from the “Darkstar” science fiction, gaming, yoga, and movie-making club; I hadn’t seen many of them for fifteen years!  I was also happy to see Ben Winnick, a friend of mine since my undergraduate years at the University of Arkansas.  It’s humbling to think I have known him since 1997.  These social calls complemented the professional friendships I was able to renew at the conference.

Since John Yates has made his home in San Diego since 2000, I was also glad to attend the reunion dinner he organized on the Saturday before the conference.  I was sitting down to dinner with my extended family of 200 friends, a bit worn out from running the first day of our short course, when I learned that the first speaker for the event had dropped out due to illness.  I was soon penciled in to replace him!  I frantically scribbled some notes while eating so that I could share some of my favorite stories from the early Yates Lab.  I was glad I could make people laugh!

Although I was not part of this year’s bioinformatics interest group, I was included as a speaker for the Analytical Lab Managers Interest Group under Emily Chen and David Quilici at their Monday evening workshop.  I emphasized the methods core lab managers need to incorporate “Big Data” into their work, emphasizing data repository use and careful statistics.  I slumped into my hotel bed directly after this talk; I had been yammering about something or other almost continuously for three straight days.


Dave goes contrarian.

Wednesday put me right back on stage.  I was slated for a mock debate over at the Informatics Hub.  I was paired with my friend Juan Antonio Vizcaino (responsible for PRIDE repository); he would argue that Big Data was transforming proteomics, and I would argue that Big Data was creating more problems than it was worth!  It’s true that I have some doubts about the value of Big Data practices to date.  I hope my talk caused participants to think about good strategies for its incorporation.

Of course, the “work” that most conference attendees incur still awaited me.  I had submitted a poster reporting work I have conducted in agricultural proteomics with the University of the Western Cape.  We created an ortholog mapping table via BLAST that allowed us to determine which protein in sorghum mapped to which protein in maize.  We then used the mapping table to re-align our spectral count table so that the counts for each ortholog pair appeared on the same row.  This means our statistical model can look for differences between our “wet” and “dry” cohorts in both species, simultaneously!  I look forward to writing that paper.  My poster had been slated for Thursday, so I dutifully stood beside my A0 format poster throughout the morning and into the early afternoon.  I was glad to see that the poster hall was not completely deserted, even on the last day.

I am grateful to the people that launch the annual conference for ASMS each year.  It’s wonderful to gather with friends and see what each of us has created in the course of our work!


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

19941002-Lyon photo01

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.


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.


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!

With the new year, a new office!

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

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


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

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


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

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


All I need now is a coffee table.

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


What office is complete without a memento or ten?

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

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


This hallway awaits the rest of its occupants!


Making digital images from 35mm slides

As a young man, my father was quite the technologist.  He bought a reel-to-reel tape audio recorder during his service in the U.S. Army, and so I can hear the voices of my grandparents during a long road trip in the 1960s or my parents during their vacation to the South in 1971.  Dad acquired a super-eight film movie camera during that time as well, and he shot movies with it up to the time I was a child.  He even became a camera buff, shooting more than one thousand photographs that were developed as 35mm slides.  As a result, I can draw on an unparalleled archive of images from my family’s history.

As a technologist of a different sort, I have tried to bring this archive into the digital age.  During my college years, I was able to produce an 8mm video camera recording for much of Dad’s movie footage, and I digitized that footage through a miniDV video camera and Firewire cable in later years.  During my graduate school years, I digitized the audio from a few hours of reel-to-reel tape to produce audio CDs.  Oddly, producing high-resolution scans of the 35mm slides has posed the biggest challenge.  Today I can report that we have finally found a way to digitize those amazing boxes of slides!

When I was in graduate school at Seattle (1996-2000), I performed my first experiments with slide scanners.  My friend Elizabeth allowed me to use her HP Photosmart slide scanner, and the resulting images were okay, for the time.  I tried buying an inexpensive slide scanner from another company, and yet the product from the hours of time I invested in using it was fairly disappointing.  In recent years, I purchased a Canon CanoScan 8600F, a flatbed scanner with a lid that can backlight transparent sources.  The images from this flatbed have been pretty nice, since it can operate at 4800 dpi, but scanning even a single slide at this resolution takes a fair amount of time.  I’ve never managed to scan the whole collection with scanners.  I have also found that scanners do not cope very well with the range of brightness that we encountered with the slides; many dark slides simply produced poor quality images in any scanner.

In 1999, I discovered that Canon had produced the FP-100 slide adapter for my Hi-8 video camera, and I acquired one for the princely sum of $120.  Essentially, the FP-100 was a low-temperature lamp, a bracket through which one could move a slide holder (with some wiggle room for positioning), and a ring to attach to the front of the camera.  I was glad that the cool lamp was bright enough to illuminate the darkest images from the collection, since the video camera could adjust its iris to the content of the slide.  Because the video camera could only resolve 480 lines in each image, though, the video images we produced through it were not quite what I wanted.


The entire sandwich of equipment is unwieldy, but it works well enough!

In 2015, I found the missing ingredient.  My Canon EOS-M camera employs a prime (non-zoom) lens with an external fitting of 43 mm.  I asked my photographically talented friend Brad Melton for some assistance on how I would connect the 46 mm FP-100 to the prime lens, and he located a “stepup ring” for me.  Would a slide adapter intended for a video camera be usable with a modern mirrorless high-resolution still camera?  We quickly discovered that the camera was unable to focus on the slide images because the lens was too close to the CCD to focus on an image so near.  I compensated by adding a macro tube between the camera body and the lens.  The entire sandwich of equipment included these elements:

  1. Canon EOS-M2 mirrorless camera
  2. Meike MK-C-AF3B 10mm macro tube
  3. Canon EF-M 22mm f/2 STM prime lens
  4. HeavyStar Dedicated Metal Stepup Ring 43mm-46mm
  5. Canon FP-100 slide adapter.

I was reasonably pleased with the performance, on the whole, but there are certainly some drawbacks. The first is the problem of achieving good focus. Many of these slides now carry a fair amount of dust, and the camera was frequently inclined to auto-focus on the dust rather than the image. The second issue results from the image being so close to the lens; the edges of the slide are considerably farther from the lens than the center. Focusing on one part of the image generally meant that parts of the slide farthest from the focus point would be more than a little fuzzy. This photo gives an example of this behavior:


In the left snapshot, I have selected my mother’s face as the focus point. In the right, I have selected my grandmother’s instead.

I also encountered some degenerate behavior in the focus.  I would occasionally flip the selector over to use manual focus rather than automatic.  After cranking the focus ring all the way to one end of the dial, I would sometimes discover that the camera thought it was being operated by a madman and would force the focus back in the other direction.  When I tried switching to a different macro tube thickness, I was entirely unable to focus, so I simply felt grateful that I could get these images to focus at all!

In some cases, the slide scanner had dealt very poorly with slide images that were quite dark overall or that featured a significant contrast between light and dark portions of a frame.  Happily, the Canon EOS-M2 seemed to handle these contrasts better because it was storing brightness levels in the 14-bit depth afforded by the CR2 raw file format.


My older brother always wanted to play.

One of the most common claims about 35mm slides is that they are far more resilient to aging than are prints from the same negatives.  Did that hold up?  The image of my father on the mule at the top of this post dates from 1964, around fifty years before this blog post was written.  The hues may be somewhat less vibrant than they were originally, but I doubt very much that a print from 1964 would hold up as well.  In this case, I have cropped to approximately 40% of the original field of view.  The slide below this is from 1965, showing my mother during her graduation ceremony from Northeast Missouri State Teachers College.  Again, I have cropped to about 40% of the original slide (in part to strip away unfocused areas).


These slides enable me to see my parents in the primes of their lives!

Of course, capturing the original CR2 files for each of a thousand slides is just the beginning.  From here, I will need to export each to a TIFF file, crop the image to a new dimension, possibly apply a noise reduction filter, and export to JPG (the images I included here have not been gone through noise reduction, though I did scale down the resolution considerably from the 18 megapixel originals).  That step will take considerable time, but I believe the result will be a far more useful archive for our family history.

I hope that this post will contribute some ideas for how to get your family archives in a more manageable condition!


Our family

Six months in South Africa: looking back

On November 23rd of 2015, I stepped off a plane at Cape Town International Airport to begin living what I had been planning for the preceding eighteen months.  Now, six months after taking that flight, I want to take a moment to reflect on the journey so far.

I am living here, not just working here.

People are not merely units of production.  I could not do my job without bringing my humanity to it, and that humanity requires nurturing!  I frankly envy people who can bring their families along on an international adventure because they bring with them a support network.  Because I moved by myself, I needed to forge a support network for myself as a matter of top priority.  I was particularly fortunate for the friendship of Philomène and the Tromp family in those first few weeks; Gerard provided his guest room to acclimatize a bewildered American for two weeks, and he laid out a clear set of steps I needed to get my banking set up, acquire a cell phone, and otherwise get started here.  Philomène immediately acted like we had been best friends for years.  From those beginnings, I was able to build out my friend network at the university, make friends with neighbors and folks who helped me get my home together, and even join a choir.  For me, the ultimate statement of living here has taken place during the last several weeks; I’ve started a relationship with a wonderful woman who was born in Cape Town.  All of these connections have changed me from being an American looking nervously at the South Africans to an American who is at home in Cape Town.

Leaping hurdles creates an illusion of progress.

If you know me personally, you know that I am a “fixer.”  If I see a problem, I set out to fix it with little hesitation.  Moving to a new country surrounds one with innumerable challenges of this sort.  For the first few months, I frequently found myself out of energy because I had burned it all on the latest problem.  In particular, getting my home DSL network services in order was a huge time-sink, but the worst part of that mess was the feeling of bitterness and enmity that it engendered in me.  Life is certainly better when we have the leisure to be at rest.  I reached a place in the first months of this year when I was a bit of a nervous wreck from constantly going to battle.  I might have spared myself that degree of anxiety by remembering that it is unnecessary for everything to be perfect right away.  Stillness is not a skill I have mastered just yet!

Physical distance confers political distance.

I followed United States public policy debates like the paparazzi followed Princess Diana.  Being on the other side of the world, though, has drained some of the passion from that pursuit for me.  Apparently, the United States has been up in arms lately about which public restrooms should be allowable for people who are transgender.  Living in a country where public sewage issues are a matter of real public health concern, I feel somewhat mystified why anyone would try to argue against restroom access for anyone.  As Donald Trump nears nomination from the Republican Party, many friends in South Africa have asked me why Americans would find his candidacy appealing.  If I were still living in the United States, I know that I would already be in a high lather about the November election.  Instead, it all feels very far away, very remote from me.  Though I intend to vote in the general election, I know that I have been changed by the experience of living abroad.  I wonder how it will feel to visit the United States again.  Will I have become a stranger in my own country?

This was no mistake.

My brother was the first person to ask the question.  I had been in South Africa for approximately four months when he asked during a Skype call, “do you think you made a mistake in moving there?”  I had never thought to ask myself that question, so I did not really have an answer ready other than to say that I like it here.  To answer it more completely, I would go through this list:

  • Am I physically healthy here?  Well, I have lost ten pounds (I was at my highest weight ever when I moved to South Africa).  My skin is probably suffering a bit from the abundant sunlight.  I caught some sort of gastrointestinal nastiness that seems to go around South Africa in summer time.  Otherwise, I would say I have been pretty healthy.
  • Am I happy here?  In general, I would say yes.  South Africans have been incredibly welcoming, inviting me to their braais and generally being open toward me.  People who speak Afrikaans more comfortably are willing to switch to English when I am nearby.  I must balance the traffic situation against that, though.  It’s a rare ten minutes on the national roads in Cape Town when nothing has happened to alarm me.  Motorcycles blasting by on the line between lanes, minibus taxis turning left from the rightmost lane, drag racing, driving down the shoulder, you name it!  I saw greater chaos in some cities in India as a passenger.  I’d have to say this is the worst traffic I have ever personally navigated.
  • Do I feel fulfilled in my career here?  Yes, I believe I do.  Every workplace has its limitations, of course, and I’ve come against some obstacles here that truly vex me.  My colleagues, though, have shown themselves to be caring and open to what I have to say.  We do not have the facilities of the leading universities to which I am accustomed, but the minds at work here are exceptional.  I feel that I have skills to offer their projects that they really need and want.

I assembled my plan to move to South Africa with very limited experience of the country in person (just one week in late 2014).  I am relieved that what I expected to find here has mostly come to life.  I cannot feel that coming here was a mistake.  This adventure has made me feel very alive!

Communicating helps us feel our loads are shared by others.

I began this blog in January of 2015.  You might be surprised to learn that this is the 104th post that I have entered on the blog.  Since I average around 1000 words per post, my full blog is approximately the length of a novel!  It has served many purposes for me.  At first, I intended it as a way to explain to my friends why I felt a need for change in my career.  Eventually I thought that other people who were looking at an international move might find the process notes interesting.  Ever since I have arrived in Cape Town, though, I have used the blog as a compact way to let everyone know what was going on with me.  Throughout, I have always tried to write a new post within seven days of the prior one.  I know I have been letting that slip lately.

I want to take this opportunity to thank all of you for reading this blog so frequently.  There is no greater gift that you can give a writer than your attention as a reader.  More importantly, knowing that people were reading these posts made me feel connected at a time when I did not yet know enough people in Cape Town to be at home here.

Thank you, friends.



After six months’ effort, my house is sold!  It is hard to imagine anything else that would make this move feel more real.

This moment marks the first time in almost two decades that I have neither owned a home nor had one under contract.  I first bought a condo when I moved to Seattle for graduate school in 1996, and I had a contract on a new place when I moved to San Diego, to Oliver Springs (East Tennessee), and to Nashville.  By contrast, I won’t be able to make a bid on a place in Cape Town until I have a bank account in South Africa.  I cannot establish a bank account in South Africa until I am present in-country under a Temporary Residence Permit.  The TRP depends entirely upon the consulate general, at this point.

I have had one home base in each city I have inhabited since Seattle, with the exception of Nashville.  The reason is that I really hate moving!  I started out in an up-and-coming neighborhood within Nashville when I moved there in 2005.  I suffered a Christmas Eve daylight break-in, and shortly thereafter a gang of teenagers blew the side mirror off my car with fireworks while I was driving.  Then my car was keyed.  I decided to move out of that neighborhood.

When the financial markets tanked in 2008-2009, I felt the right moment had arrived to go house bargain shopping.  I fell in love with a residence that was in a more established neighborhood, a bit closer to campus. I loved its tower with two bay windows as well as the open flow throughout its downstairs for parties.  In July of 2009, I bought it.  Having always managed to sell my prior home without trouble, I was dismayed that my first Nashville home was so much trouble to sell.  It had been on the market for months, and then the 2010 Nashville floods dumped a bunch of water in the basement of the old house.  A family bought it in the aftermath of that storm.

The sale of my most recent home was pretty challenging.  The real estate market in Nashville is very hot!  As one moves into higher price regimes, though, the number of potential buyers drops off pretty rapidly.  I was very impressed by the team of realtors who helped me sell it.  We listed at a top-dollar price at first, and the initial rush of house visitors did not lead to a bid.  I was excited to get a contract in place to sell it, but it fell apart just as I left for Cuba because the roof had hail damage.  I replaced the roof, with help from my insurance, and happily a new contract emerged soon thereafter.

Now a new occupant will enjoy my pretty castle.  Farewell, house!  I loved your stately beauty!

Dave with his realtor, Megan

Dave with his realtor, Megan

Taking a farewell tour

If you knew you were leaving the nation where you were born, what would you do to say goodbye?  My road trip through New Mexico and Colorado was my first answer to that question.

When I was a child, my family annually launched itself on a two-week summer vacation.  My parents wanted us to see all of the United States and even a bit of Canada and Mexico.  Essentially, if we could drive there, we were going to try!  During those many trips, we visited all 48 of the contiguous United States.  We invested significant time in some states, like Colorado or California.  Other states we’ve only glimpsed, such as our small touch of southwestern Maine.  In other cases we essentially passed through cities (such as New York) that other families would have stayed in for many days.  As a result, I can hardly hear the name of a state without having some memory pop up from my experiences.  Of course, thirty years later, I’ve muddled many of these places together in my mind.

I began my farewell tour by driving west from Nashville to Albuquerque on I-40.  People say you can see nothing from the interstate, but my goal was to get out to the desert Southwest as quickly as I could.  My plan was pretty simple; getting to Albuquerque was essentially two full days of driving.  I would front-load the work so that the first day was the worst, leaving myself an easier job for day two.  The following day I could celebrate July Fourth with my friend from elementary school, Brad.

Those two long days of driving have already melded together in my thoughts.  Western Tennessee is hilly and heavily wooded, but once you reach Memphis, you’re in a flood plain.  Little Rock, Arkansas, always surprises me because you can drive entirely through the city without once getting a sense of where downtown is located.  Oklahoma had changed since last I had seen it.  I do not remember where the transition happened, but rather suddenly gentle hills and trees gave way to prairie, and massive wind turbines seemed to be everywhere.  My overnight stay in Weatherford, OK, was uneventful; the hotel was long past its prime, but it was clean, and I was safe.  Somehow I hadn’t realized that I would pass through Texas, but my brief stop in Amarillo was essentially all I remember.  Passing into New Mexico was a bit of a thrill as the car descended from the top of a massive plateau to the desert below.  Albuquerque itself welcomed me with sudden altitude and direction changes.  Since I am a fan of Douglas Adams, I was very happy to see the road sign that “Gusty Winds May Exist” along with its tattered windsock.  Shortly thereafter I was with my friend Brad and his wife Angela.

Mesa Verde National Park has remained very distinct in my memories.  When I was a child, the cliff dwellings seemed like something from another universe.  I remembered them as being thousands of years old, but they actually come from around the time of the European dark ages.  I tried to put it in context for myself by saying that Islam was experiencing a golden age under the Abbasid caliph when the ancestors of the Pueblo people first began farming the mesa top.  I had excellent travel companions.  Not only had Brad and Angela provided housing by towing their trailer to the park, but Angela had recommended we take the hike into Spruce Canyon.  It was a lovely meditative journey, with different flora at each step.  I won’t forget the company of my friends– or the gasping of my lungs as I tried hiking uphill in the lower oxygen of 7000 feet.  We were able to spend time at Spruce Tree House, Cliff Palace, and Balcony House before rains arrived in earnest.  It’s a magical place.

A view of Cliff Palace at Mesa Verde

A view of Cliff Palace at Mesa Verde

After the fun of time with friends, it was something of a shock to be alone again as I began my trip east.  U.S. highway 160 led through Durango to Pagosa Springs to Del Norte.  I was astonished by the beauty of this highway.  When I passed Chimney Rock it was quite obvious!  I arrived at Alamosa, CO, early enough that I could enjoy the town a bit.  The following morning I was delighted to return to the Great Sand Dunes National Park, another location that had haunted my memories from Colorado.  I hardly recognized the place.  I had previously visited in late summer, and early summer looked very different.  The creek was very wide, blocking an easy walk to the dune field, but hearing the water trickle and gurgle its way toward the marsh was very relaxing.  I surprised myself by resting on a sand bar rather than climbing up the dunes.  My epic bout with mosquitoes during a quick hike at the visitor’s center may have sapped my energy.  Soon, though, I was on my way to Colorado Springs.

The Great Sand Dunes, with a couple of deer in the foreground

The Great Sand Dunes, with a couple of deer in the foreground

Garden of the Gods is a very unusual city park.  I was happy to intercept my brother’s family, also on vacation, and we wandered around taking pictures of the kids scrambling on the rock formations.  I was delighted to learn that the name of the park stemmed from a conversation between two gentlemen: “This is the perfect place for a beer garden!”  “Yes, a beer garden for the gods!”  We enjoyed our stroll together, and soon I was headed north to overnight with my friends Chris and Meg, whom I’d originally met while living in San Diego.  Belatedly, I realized that saying farewell (for now) to old friends was emerging as a major theme for this vacation.

Dave at the Garden of the Gods

Dave at the Garden of the Gods

The next day mixed a greeting with a farewell.  I had a chance to see my friend Brian from elementary school as I passed through Shawnee, KS.  I enjoyed meeting and playing with his family.  It’s interesting to me that twenty years may have passed since my last seeing Brian, and yet his mannerisms fit exactly in that cubbyhole of my memory from high school.  Old friends travel with you, I think!

After an overnight with my parents, I drove hard for Nashville.  Despite a nasty lightning storm at Paducah, I was able to sleep in my own bed after more than a week of travel.  There is no delight to match it.  I am starting to say my farewells to the United States, and I am sure that there’s much more of that to follow!