I started this blog to explain my decision to leave the United States and to move to South Africa. Now it is time for me to say a fond farewell to Stellenbosch University, my academic home for these “fantastic five years.”
I want to thank the people who made it possible for me to come to Stellenbosch U. The South African Medical Research Council teamed with the Department of Science and Technology (now the Department of Science and Innovation) to contribute 60% of the funds required for my five year contract, and the Dean of the Faculty of Medicine and Health Sciences agreed to contribute the other 40%. Gerhard Walzl, now the head of the Department of Biomedical Sciences at the Faculty, marshalled these resources to make my coming possible. After I arrived, he had the challenges of managing me, too!
You might ask why this contract must come to an end. The reality is that money is very tight in South Africa. Business growth was barely keeping pace with population growth when I arrived, with continuing “load shedding” power cuts undermining the economy. In a recent audit of government spending, only 100 of 421 government bodies achieved “clean” audits; money that should have been invested in national infrastructure was spent in dubious ways. South Africa engaged in a largely successful response to COVID-19, but there’s no question that lockdowns had punitive effects on its economy. In academia, researchers who were able to cover much of their salaries through grants had far more job-security than those who were not (and I have definitely not prioritized grant writing while at Stellenbosch). The academic job market at the close of 2020 is a tough one.
I will write another post about my plans for 2021, but this post is intended to look back at my time with Stellenbosch. Is it all celebrations, or do I have regrets?
From Strength to Strength
Quality Colleagues
I have repeatedly been inspired by the researchers with whom I have worked at my three main universities. I would particularly single out the “SARChi” Research Chairs at Stellenbosch University, the University of Cape Town, and the University of the Western Cape. South Africa designed an incentive funding program to retain South Africans in-country who might otherwise have moved to nations with more developed economies. I haven’t met a “SARChi” whom I didn’t admire.
I would also say that the junior investigators at Stellenbosch and elsewhere are a strong group, too. At UWC I would highlight Bronwyn Kirby and Ashwil Klein; Dr. Kirby “rolled out the red carpet” for me to teach essentially whatever topics I would like, while Dr. Klein always has a new idea for building the use of mass spectrometry at his institution. I will really miss the Immunology crew and the crop of up-and-coming post-docs in Human Genetics and TB Genomics. The wealth of skill in my colleagues throughout the Cape Town metro was always a source of inspiration for me.
Teaching the World
Upon arrival in Cape Town, I was unsure who my students would be. I knew that coursework figured heavily in the “B.Sc. Honours” year, but M.Sc. and Ph.D. students did not typically attend classes. For someone who loves being in front of a class room, it was hard to hear that I would have just a few lectures each year. That said, I’ve offered a variety of courses to all comers, from the week of bioinformatics each year in honours to a once-a-week program to teach the Python programming language. When my program officer with the SA Medical Research Council told me she wanted me teaching as broadly as possible, though, I began talking with postgraduate programs at UWC and (Stellenbosch rival) University of Cape Town about teaching opportunities. UWC, as I mentioned above, has had an endless appetite for classes; in 2019 and 2020, I was teaching a week of bioinformatics, three lectures for sequencing informatics in their Next-Generation Sequencing module, two or three lectures in the Proteomics module, and almost all of the Clinical Biomarkers module! While working with Nelson Soares at UCT (he has since moved to the University of Sharjah in the UAE) I enjoyed our monthly “big show” for the community proteomics meetings, and I gave occasional lectures to their honours program, too.
One of the happy accidents of such broad teaching was that I was able to record instructional videos of almost all of these classes. Last year I assembled an index to the YouTube videos and slide PDFs that regularly draws more page views than all my other blog entries put together. I have been grateful to present workshops in other African countries from this exposure. So far I have taught in Ghana, Malawi, and Namibia, but I fervently hope to arrange workshops in Ethiopia, Mozambique, Botswana, or… well, practically anywhere!
This section would not be complete without my praising the students who have chosen my lab for their B.Sc. Honours, M.Sc., or Ph.D. programs. Again, while some of these postgraduate students were at Stellenbosch U, I also served as co-supervisor to students at other universities, even a pair of M.Sc. students at the U of Malawi College of Medicine in Blantyre! Just like the best students I knew back in the States, these postgraduates frequently pushed me to learn new techniques and application areas; to give one example, a 2020 UWC B.Sc. Honours student wanted to work in GI disease, so we framed a challenging project in celiac disease, a first time for me as well. She did an amazing job with it! Just a couple weeks ago, I attended the Ph.D. graudation ceremony for Marina Kriek, a researcher who joined my team after working in industry. I am very grateful for the chance to work with such talented individuals.
Linking South Africa into Global Networks of Molecular Biology
South Africa is a very cosmopolitan place, with postgraduates frequently accepting jobs in Europe or America. Many of the professors who rise to high leadership positions have experience working at institutions in the Global North. My experience with global mass spectrometry, however, had left me something of a blind spot for proteomics research within South Africa. I would highlight two different projects during my time with Stellenbosch that I hope will increase the awareness of what South Africa has to offer on the global stage. After living in South Africa for two years, I had gotten to know researchers at mass spectrometry laboratories across the country. At the invitation of Ron Orlando, a team of us crafted a manuscript describing the types of challenges associated with establishing mass spectrometry facilities in the developing world. Writing a paper with colleagues from six different institutions was challenging, but I was delighted with the result. Our product was later selected as the paper of the year for the Journal of Biomolecular Techniques (the journal of the ABRF)!
In 2019, we were able to make another stride forward into the international community when the Human Proteomics Organization (HUPO) Proteomics Standards Initiative (PSI) held its annual workshop in Cape Town. At first, I was unsure how many of my colleagues would make the trip to the southern tip of Africa, but our attendance was really solid, and many South African graduate students got to network with leaders in the field of proteome informatics. Since this was the first science meeting I had ever organized, I was thrilled with the result.
Emerging Research Interests
Scientists, like all people, can fall into a rut if undisturbed. I have spent the great majority of my career publishing on the identification of peptides, proteins, and post-translational modifications from tandem mass spectrometry data. It’s been a lovely “rut!” Coming to South Africa, however, meant that I would need to broaden my thinking to handle a broader array of bioinformatic and biostatistical challenges. Could I help people accustomed to manual interrogation of flow cytometry data begin using more automated techniques for gating? Could I automate recognizing DNA sequence variants through high-resolution melt curves? While I made some starts in these two directions, the challenge that has been consuming most of my concentration recently has been this: how can we conduct “functional genomics” (transcriptomics or proteomics) in non-model organisms without well-established genome annotations? After substantial work in Salvia hispanica (chia), Crocuta crocuta (spotted hyena), and Hermetia illucens (black soldier fly), I finally feel I have enough answers to pen manuscripts. I have enjoyed asking myself again just what I find interesting!
Pangs of Remorse
Just as there are no perfect people, there are no perfect jobs! I have plenty of reasons to have enjoyed the last five years, and I hope I’ve been able to convey that above. I have, however, experienced a couple of sticky points that have bedeviled me.
Shaken to the Core
Because my professorship was primarily funded from external sources, I was named as a “Research Chair in Proteomics” for Stellenbosch University. I interpreted that title as making me responsible for seeing proteomics technologies deployed as adeptly and as broadly as possible. I sought to establish a solid relationship with the Central Analytical Facilities, which operated the Proteomics Laboratory of the Mass Spectrometry Unit at the Faculty of Medicine and Health Sciences. Seeing that the Proteomics Lab relied on several external USB hard drives as backups, I built a file server for their exclusive use from one of the heavy servers I had brought with me from the States. I offered my services to help researchers who had produced data in the Proteomics Lab get the most information possible from those experiments. For those first few months, I felt we were well-positioned to see real growth in mass spec-based proteomics.
I had become aware, though, of some challenges that caused some potential mass spectrometry users to walk away from the Proteomics Lab after initial pilot experiments. These challenges were not unusual ones for core facilities. They related to reproducibility and comparability, prices for services, experimental sensitivity, etc. I briefly spoke with the head of Central Analytical Facilities at an impromptu meeting, and he recommended that I put my suggestions for how CAF Proteomics could be improved in writing. Halfway into 2016, I wrote a four-page letter detailing ways that my division could work with the Proteomics Lab to improve “takeup” of proteomics at our university. Well, my relationship with CAF immediately cratered. To give a very concrete example, my Proteomics Laboratory key was reclaimed the very next day. I was the Research Chair for Proteomics, but after the mid-point of 2016, my ability to work with the Proteomics Laboratory at my own campus was at an end. I never really recovered from this loss.
No Job is Finished…
Something I hadn’t truly appreciated about my previous institution (an excellent university in the state of Tennessee) was the degree of staff support we enjoyed. As an assistant professor there, I and a handful of other professors were supported by an administrative assistant. When I wanted to write a grant, our department had its own grant coordinator. Even as a new assistant professor, I had my own individual office, with space adjoining it for my lab team. It is important to understand that a grant awarded to a professor is split into “direct costs” (monies to fund the research directly) and “indirect costs” (monies to keep the lights on). At my former institution, an NIH grant of a million dollars would be accompanied by indirect costs of $600,000, reflecting an “facility and administrative rate” of 60%.
NIH grants are frequently won by professors at Stellenbosch University, but their “facility and administrative rate” is locked at 8% because we are not an American university. As a consequence, departments at Stellenbosch are much less able to support a large number administrative staff. A large load then falls on individual staffers for handling issues such as travel reimbursement and shared equipment loan (such as the tabletop projector for the seminar room). I would particularly like to mention Trudy Snyders, the senior secretary for our division, who demonstrated great patience with me on many occasions. The Faculty of Medicine and Health Sciences does have a Research Grants Management office, but a substantial amount of grant proposal help within our division came from the generosity of Helena Kuivaniemi, a professor with unflagging energy. Until the final year of my contract with Stellenbosch, our division occupied two floors of the aging physiology and anatomy (Fisan) building, with space at such a premium that even some SARChi Chairs were sharing a room with other lab heads. At the conclusion of 2020, I was able to see my division happily taking up residence in the new Biomedical Research Institute, a huge upgrade in its infrastructure.
All in all…
I was very lucky to have these five years with Stellenbosch as a time to reinvent myself. Living in these beautiful surroundings, working with people I admire, allowing me to tinker with new possible directions for my research was a genuine gift. Some cynics back in 2015 told me I would regret moving myself across the Atlantic, but I wouldn’t give up this time for anything. Stellenbosch has made its mark on me.
Picking Up The Tabb 
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