Last month, I completed teaching a graduate course for the tenth time. After several years (in the early 1990’s) of thinking about launching a new alternate-year seminar course and then planning it, I began teaching PATH 480 in the fall of 1994. The original name of the course, maintained through the first seven times I taught it, was: “Immunology, Evolution and Logic.” Beginning in 2009, another faculty member, Derek Abbott, joined me in teaching the course, and the title was revised to: “Logical Dissection of Biomedical Investigations.” In my portion of the course, I retained an emphasis on the relevance of logic and evolutionary principles to thinking about immune recognition and immune functioning more generally. I focused class sessions on concepts and underlying assumptions critical to experimental investigations as well as on experimental design and data interpretation in articles reporting studies pertaining to immune recognition. Dr. Abbott has focused his portion of the course on the practical cognitive skills involved in reviewing papers and grant proposals pertaining primarily to innate immune signaling.
While the central focus of the class, or my portion of the class beginning in 2009, was on original articles pertinent to immune recognition, readings on logic and evolution were also included, especially in the earlier portion of the semester. My educational goals were both to have the students gain in understanding of how antibodies, T-cell receptors, and class I and class II major histocompatibility complex (MHC) molecules recognize the molecules they interact with (i.e., antigens) and to foster critical and independent thinking. Derek and I expected his sessions, focused on critically analyzing manuscripts describing experimental studies and grant proposals, to effectively complement my somewhat more abstract sessions.
The papers for the first session of the class have always included the original post-quantum physics elaboration of the notion that biomolecular recognition necessarily requires complementarity between receptor and ligand (Pauling and Delbrück, 1940). Although Pauling and Delbrück include no data in their report, it is useful for prompting students to consider the origins of a notion they may never have really thought much about. A second paper that I have generally included for the first session contains one of the earliest enunciations of a thoroughly evolutionary perspective on the humoral immune response (Talmage, 1959; http://evmedreview.com/?p=724). This paper, by David Talmage, was certainly one of the first to develop in detail the implications of a scheme for antibody production based on variation and selection of what we now call B-cell clones for the antigen recognition properties of the antibodies they make. A couple years earlier (1957), in a review on a range of immunological topics for the Annual Review of Medicine, Talmage (an M.D.) had briefly outlined the set of ideas about antibody production that with roughly contemporaneous and independent elaboration (Burnet, 1957 and 1959) became known as the clonal selection theory, arguably “pre-dawn” Darwinian medicine for those who date the dawn to 1991.
The first or second session would also include a portion of an introductory chapter from a book on mathematical logic (DeLong, 1970) and commentary pertaining to evolution, which in the last edition of the course was an article by Kevin Padian (2008) on the key conceptual advances made by Charles Darwin. These readings facilitate my efforts to have the students think more explicitly about their scientific reasoning processes than may normally be the case and to introduce key evolutionary concepts and perspectives that serve to ground the students in standard modes of evolutionary thinking.
Next we review a couple of seminal articles that provided key insights into the primary and tertiary structures of antibody variable (V) domains. Historically first is a paper on antibody primary structure focused on the organization of immunoglobulin V domains into framework and hypervariable regions, in which most of the amino acids that directly contact the antigen are found (Wu and Kabat, 1970). The other seminal article provided the first-ever three-dimensional structure of a protein antigen-antibody complex (Amit et al., 1986). Key insights in these papers are related back to points made in the earlier and previously discussed papers by, respectively, Pauling and Delbrück and David Talmage as well as the readings on logic and evolution. The next readings in this most recent version of the course pertaining to logic and evolution were another portion from DeLong (1970) and an article by Ernst Mayr on key features of Darwin’s thought (2000).
Classes over the next several weeks focus on how our ideas on the structural features of protein-antigen-antibody complexes changed over time, thermodynamic perspectives on these same interactions, and potential differences between viewpoints emphasizing structural versus thermodynamic aspects (Bhat et al., 1990; Bhat et al., 1994; Lawrence and Colman, 1993; Hawkins et al., 1993; Patten et al., 1996). The latter two papers demonstrate, counter-intuitively for some, that starting with an antibody exhibiting significant affinity for a particular protein antigen, most mutations in the genes encoding the antibody V domains that increase affinity of the antibody for the antigen occur at positions of amino acids that do not contact the antigen.
This year, I was able to include a fascinating recent study from Nussenzweig and colleagues (Klein et al., 2013; http://evmedreview.com/?p=1863) in which the authors demonstrate that key heavy chain V domain mutations in potent and broadly neutralizing antibodies occur in substantial numbers of framework residues. The conventional wisdom has been that most affinity-influencing mutations occur in the hypervariable regions, not the framework regions. So, with sufficiently intense selection pressure and of sufficient duration, our inductively-generated expectations can be utterly confounded. These sorts of immunological phenomena are currently fully comprehensible only within a framework of evolutionary change in populations of B lymphocytes.
The final weeks of the class have varied more than the earlier weeks. For the 2013 edition we finished up by discussing recognition of antigen by conventional T-cells (i.e., T cells expressing alpha/beta antigen-specific receptors), which actually means recognition of complexes of either self class I or class II MHC antigens noncovalently associated with peptides (Zinkernagel and Doherty, 1974; Allen et al., 1987; Threlkeld et al., 1997). In the context of full-fledged immune responses to, for example, pathogens, these peptide fragments are derived from pathogen-encoded proteins. Why T cells recognize antigen in this way that seems significantly more complex than how antibodies recognize antigen is, again, most comprehensible from a vantage point informed by evolution-related concepts and principles.
Zinkernagel (an M.D.) and Doherty (a V.M.D, Ph.D.), received the 1996 Nobel Prize for Physiology or Medicine in part because their findings, that supported the “MHC-restriction” of antigen recognition by T cells, provided a plausible evolution-based explanation for the vast polymorphism of the MHC genes in mammals. Their ideas were also applied to formulating evolution-based explanations for the newly discovered tendency (Schlosstein et al., 1973; Brewerton et al., 1973) for particular HLA alleles to be associated with particular autoimmune diseases, another example of Darwinian medicine more than 25 years ago.
The last classes, in some years were devoted to discussing other papers relating to T-cell receptor recognition of peptide-MHC complexes or to MHC-peptide interactions themselves (Madden et al., 1993; Garboczi et al., 1996). Alternatively, in some years we focused on broader questions, such as what the immune system recognizes in a general sense (Matzinger, 2002; Medzhitov, 2002; Vance, 2000). Does it respond primarily to non-self, a notion popularized by Burnet in the formulation that the immune system distinguishes self from non-self, or does it respond primarily to “dangerous” substances, a notion popularized by Matzinger? Answering such a question necessarily involves evolutionary considerations.
The mechanics of the course have evolved through the years. Classes are a mixture of my providing background information about the articles and Socratic questioning of the students. I try to get the students to commit to positions and express their inevitable disagreements, with me or with one another, on the assumption that more learning occurs when one is invested, even if only temporarily, in a line of thought.
At the start of the course I have the students fill out what I refer to as the Preliminary Knowledge Survey, which asks a variety of basic questions relating to immunology, evolution, and logic so that I know where the students are starting and they have a baseline to which they can compare their knowledge and understanding at the end of the course. So, as the course comes to a close, I distribute the Preliminary Knowledge Survey Revisited, asking the same questions and the initial Survey.
Some years ago, I began providing questions with each set of assigned articles to guide the students’ reading. In order to provide the students with a record of our class discussions (in addition to the articles themselves) to which they can later refer to revisit significant insights and to rekindle particular connections between ideas derived from evolution or logic and immunological phenomena, I also provide summaries of the class sessions as best as I can re-create them after the fact. After the last class session, Derek and I also provide a couple pages of what we call “take-home” lessons. Finally, we give the students a reasonably detailed survey to obtain feedback on the substance, organization, and administration of the course.
Although I have kept track of all of the students who have taken PATH 480 since 1994, I have not had the time and resources to pursue long-term follow-up to assess how the course has affected the students’ scientific thinking or practice. While I would like to have such follow-up, I do not imagine that it would be easy to isolate the effects solely attributable to PATH 480.
I have also considered creating an online version of the course that would be a continuing educational experience either for course alumni or for anyone interested. Such an initiative in lifelong learning I would like to call a modest online continuing course, or MOCC, which could be taken in part as a comment on the at times hyperbolic promotion associated with the recent trend for offering massive open online courses, or MOOCs by both universities and for-profit enterprises.
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