Quantitative reasoning given uncertainty is precisely the kind of approach necessary to understand how complex systems work.
In the late afternoon on February 10, 2020, the Center for Microbial Dynamics and Infection held a rapid response Coronavirus forum, featuring three short talks on what was then an unfolding epidemic that appeared to be focused almost entirely in Asia. The Suddath Room was packed by a standing room only crowd (a scene that would not be possible today). Although two of the speakers were from Georgia Tech – myself and Phil Santangelo from BME – the forum’s first speaker was Trevor Bedford from the Fred Hutch Institute, and with good reason.
Dr. Bedford is one of the co-developers of nextstrain.org, a site dedicated to real-time tracking of pathogen evolution. Dr. Bedford had been one of the earliest to sound the alarm on the potential consequences of a cluster of viral pneumonia cases in Wuhan China. His group along with collaborators takes a ‘phylogenetic’ approach to analyzing viral sequence data, i.e., striving to understand the relationship amongst viruses in an evolutionary sense, while linking geography and dynamics to understand origins, transmission, and change.
This work is rigorous and timely, particularly given that it strives to break through usual academic time-scales. The work of nextstrain – and of clinical labs, public health experts, and quantitative modeling groups around the world – have moved the speed at which a virus sample is extracted, sequenced, analyzed, and even contextualized with analytics and situation reports from months to days. This speed means that quantitative studies of viral dynamics have rapidly moved beyond retrospective analyses of outbreaks-past and assessments of outbreaks to come into direct engagement with outbreaks as they unfold.
This integration of biological principles, large-scale data, and computational modeling is a hallmark of what makes nextstrain so powerful. It’s also the kind of work that modelers from within and outside traditional public health fields – both here at Georgia Tech, at nearby institutions like GSU and UGA, and across the US and globally – have been doing since early 2020. Quantitative reasoning given uncertainty is precisely the kind of approach necessary to try and understand how complex systems work and in many cases – including epidemics, climate, cardiac dynamics, and cancer – to try and change outcomes. This type of quantitative reasoning given uncertainty is also a hallmark of QBioS training.
In these past few months, multiple QBioS students have been involved in responding to COVID-19, primarily by applying their modeling skill sets to the problem of understanding what kind of trajectory might unfold in the absence of interventions and how strategic interventions – from social distancing to leveraging serological testing – might control the pandemic. Beyond research, the first year QBioS cohort organized a virtual May workshop focused on ‘hands-on’ modeling of epidemics; attended by more than 50 students, scientists, and faculty from Georgia Tech, local institutions (including Spelman College), and internationally. The workshop helped provide the foundational context for developing epidemic models of the kind used as part of ongoing decision making at local and national levels. But even for those students not directly involved in COVID-19 response, there are lessons to be learned on the value of moving research from the laboratory, field, computer, or chalkboard to serve the public good.
The QBioS program remains a science program. The mission of QBioS is to train students to identify fundamental principles that underlie the structure, dynamics, and function of living systems at scales spanning molecules, cells, tissue, populations, and ecosystems. This focus on basic science reflects a viewpoint that fundamental principles are of intrinsic value – and that advances in principles can become a gateway for action-taking (whether developing a drug, device, algorithm, or even a public health policy). In doing so, an emphasis on discovering principles of living systems must remain at the forefront of our mission. These principles are of deep value and represent far more than simply the grist that serves technological change.
The COVID-19 pandemic has transformed the world in which we live and will continue to do so for the foreseeable future. For far too many, COVID-19 has meant severe illness for them or for a loved one, leading to over 100,000 reported fatalities in the United States alone – and even this number is almost certainly an under-estimate of the true impact. Yet, without early viral alert systems – of the kind developed by Trevor Bedford at Fred Hutch – without epidemic models – of the kind developed by researchers right here at Georgia Tech – and without a deep understanding of principles of immunology – of the kind being worked on by GT colleague Phil Santangelo and many others across the globe – we simply won’t have the same chance to develop interventions, policies, therapeutics, and technologies necessary to find a way forward.
This next year will be different in many ways. Like you, I am eager to return to normal, but aware that normalcy is a far way off. QBioS will continue to adapt, grow, and evolve. As Director, I am grateful to have the chance to learn more about topics far from my own expertise, and to see QBioS students make deep contributions to problems related to cardiac dynamics, the evolution of multi-cellularity, understanding of locomotion, microbial interactions and (of course) viral dynamics. This Spring was to have marked the start of a new QBioS tradition: a 4th year seminar series, organized and delivered by QBioS students on these topics and more. We managed to start the series, but with COVID-19, the tradition will have to wait for the Fall. I look forward to being there.
As many of you know, I had originally intended to spend next year at the Institute of Biology at the Ecole Normale Superieure in Paris. These plans, like many, have also been affected by COVID-19. Hence, I will remain at Georgia Tech this coming academic year, but the plans to expand the leadership team will move forward. Beginning in July 2020, it is my distinct pleasure to welcome Will Ratcliff as Co-Director and JC Gumbart as Associate Director. Together, our expanded leadership team will enable us to launch new programs, develop new partnerships, and support the lifecycle of QBioS students from recruitment, matriculation, and (soon) to graduation and career development.
This has been a longer Director’s “note” than usual. It’s also been a longer, and more complicated year. We will continue to share news and information of relevance to the QBioS community – whether COVID-19 related or not – as plans for the 2020-2021 year unfold. Our expanded leadership team is committed to keeping you informed and to supporting QBioS students in their paths to scientific discovery, professional development, and service to the larger community.
I wish all of you well in these challenging times and hope to see you, even at a distance, in the weeks and months to come.